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• Published: 24 September 2021

On the past, present, and future of in vivo science

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A guide to open science practices for animal research

Contributed equally to this work with: Kai Diederich, Kathrin Schmitt

Affiliation German Federal Institute for Risk Assessment, German Centre for the Protection of Laboratory Animals (Bf3R), Berlin, Germany

* E-mail: [email protected]

• Kai Diederich, 
• Kathrin Schmitt, 
• Philipp Schwedhelm, 
• Bettina Bert, 
• Céline Heinl

Published: September 15, 2022

• https://doi.org/10.1371/journal.pbio.3001810
• Reader Comments

Translational biomedical research relies on animal experiments and provides the underlying proof of practice for clinical trials, which places an increased duty of care on translational researchers to derive the maximum possible output from every experiment performed. The implementation of open science practices has the potential to initiate a change in research culture that could improve the transparency and quality of translational research in general, as well as increasing the audience and scientific reach of published research. However, open science has become a buzzword in the scientific community that can often miss mark when it comes to practical implementation. In this Essay, we provide a guide to open science practices that can be applied throughout the research process, from study design, through data collection and analysis, to publication and dissemination, to help scientists improve the transparency and quality of their work. As open science practices continue to evolve, we also provide an online toolbox of resources that we will update continually.

Citation: Diederich K, Schmitt K, Schwedhelm P, Bert B, Heinl C (2022) A guide to open science practices for animal research. PLoS Biol 20(9): e3001810. https://doi.org/10.1371/journal.pbio.3001810

Copyright: © 2022 Diederich et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: The authors received no specific funding for this work.

Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: All authors are employed at the German Federal Institute for Risk Assessment and part of the German Centre for the Protection of Laboratory Animals (Bf3R) which developed and hosts animalstudyregistry.org , a preregistration platform for animal studies and animaltestinfo.de, a database for non-technical project summaries (NTS) of approved animal study protocols within Germany.

Abbreviations: CC, Creative Commons; CIRS-LAS, critical incident reporting system in laboratory animal science; COVID-19, Coronavirus Disease 2019; DOAJ, Directory of Open Access Journals; DOI, digital object identifier; EDA, Experimental Design Assistant; ELN, electronic laboratory notebook; EU, European Union; IMSR, International Mouse Strain Resource; JISC, Joint Information Systems Committee; LIMS, laboratory information management system; MGI, Mouse Genome Informatics; NC3Rs, National Centre for the Replacement, Refinement and Reduction of Animals in Research; NTS, non-technical summary; RRID, Research Resource Identifier

Introduction

Over the past decade, the quality of published scientific literature has been repeatedly called into question by the failure of large replication studies or meta-analyses to demonstrate sufficient translation from experimental research into clinical successes [ 1 – 5 ]. At the same time, the open science movement has gained more and more advocates across various research areas. By sharing all of the information collected during the research process with colleagues and with the public, scientists can improve collaborations within their field and increase the reproducibility and trustworthiness of their work [ 6 ]. Thus, the International Reproducibility Networks have called for more open research [ 7 ].

However, open science practices have not been adopted to the same degree in all research areas. In psychology, which was strongly affected by the so-called reproducibility crisis, the open science movement initiated real practical changes leading to a broad implementation of practices such as preregistration or sharing of data and material [ 8 – 10 ]. By contrast, biomedical research is still lagging behind. Open science might be of high value for research in general, but in translational biomedical research, it is an ethical obligation. It is the responsibility of the scientist to transparently share all data collected to ensure that clinical research can adequately evaluate the risks and benefits of a potential treatment. When Russell and Burch published “The Principles of Humane Experimental Technique” in 1959, scientists started to implement their 3Rs principle to answer the ethical dilemma of animal welfare in the face of scientific progress [ 11 ]. By replacing animal experiments wherever possible, reducing the number of animals to a strict minimum, and refining the procedures where animals have still to be used, this ethical dilemma was addressed. However, in recent years, whether the 3Rs principle is sufficient to fully address ethical concerns about animal experiments has been questioned [ 12 ].

Most people tolerate the use of animals for scientific purposes only under the basic assumption that the knowledge gained will advance research in crucial areas. This implies that performed experiments are reported in a way that enables peers to benefit from the collected data. However, recent studies suggest that a large proportion of animal experiments are never actually published. For example, scientists working within the European Union (EU) have to write an animal study protocol for approval by the competent authorities of the respective country before performing an animal experiment [ 13 ]. In these protocols, scientists have to describe the planned study and justify every animal required for the project. By searching for publications resulting from approved animal study protocols from 2 German University Medical Centers, Wieschowski and colleagues found that only 53% of approved protocols led to a publication after 6 years [ 14 ]. Using a similar approach, Van der Naald and colleagues determined a publication rate of 60% at the Utrecht Medical Center [ 15 ]. In a follow-up survey, the respective researchers named so-called “negative” or null-hypothesis results as the main cause for not publishing outcomes [ 15 ]. The current scientific system is shaped by publishers, funders, and institutions and motivates scientists to publish novel, surprising, and positive results, revealing one of the many structural problems that the numerous efforts towards open science initiatives are targeting. Non-publication not only strongly contradicts ethical values, but also it compromises the quality of published literature by leading to overestimation of effect sizes [ 16 , 17 ]. Furthermore, publications of animal studies too often show poor reporting that strongly impairs the reproducibility, validity, and usefulness of the results [ 18 ]. Unfortunately, the idea that negative or equivocal findings can also contribute to the gain of scientific knowledge is frequently neglected.

So far, the scientific community using animals has shown limited resonance to the open science movement. Due to the strong controversy surrounding animal experiments, scientists have been reluctant to share information on the topic. Additionally, translational research is highly competitive and researchers tend to be secretive about their ideas until they are ready for publication or patent [ 19 , 20 ]. However, this missing openness could also point to a lack of knowledge and training on the many open science options that are available and suitable for animal research. Researchers have to be convinced of the benefits of open science practices, not only for science in general, but also for the individual researcher and each single animal. Yet, the key players in the research system are already starting to value open science practices. An increasing number of journals request open sharing of data, funders pay for open access publications and institutions consider open science practices in hiring decisions. Open science practices can improve the quality of work by enabling valuable scientific input from peers at the early stages of research projects. Furthermore, the extended communication that open science practices offer can draw attention to research and help to expand networks of collaborators and lead to new project opportunities or follow-up positions. Thus, open science practices can be a driver for careers in academia, particularly those of early career researchers.

Beyond these personal benefits, improving transparency in translational biomedical research can boost scientific progress in general. By bringing to light all the recorded research outputs that until now have remained hidden, the publication bias and the overestimation of effect sizes can be reduced [ 17 ]. Large-scale sharing of data can help to synthesize research outputs in preclinical research that will enable better decision-making for clinical research. Disclosing the whole research process will help to uncover systematic problems and support scientists in thoroughly planning their studies. In the long run, we predict that the implementation of open science practices will lead to the use of fewer animals in unintentionally repeated experiments that previously showed unreported negative results or in the establishment of methods by avoiding experimental dead ends that are often not published. More collaborations and sharing of materials and methods can further reduce the number of animal experiments used for the implementation of new techniques.

Open science can and should be implemented at each step of the research process ( Fig 1 ). A vast number of tools are already provided that were either directly conceptualized for animal research or can be adapted easily. In this Essay, we provide an overview of open science tools that improve transparency, reliability, and animal welfare in translational in vivo biomedical research by supporting scientists to clearly communicate their research and by supporting collaborative working. Table 1 lists the most prominent open science tools we discuss, together with their respective links. We have structured this Essay to guide you through which tools can be used at each stage of the research process, from planning and conducting experiments, through to analyzing data and communicating the results. However, many of these tools can be used at many different steps. Table 1 has been deposited on Zenodo and will be updated continuously [ 21 ].

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Application of open science practices at each step of the research process can maximize the impact of performed animal experiments. The implementation of these practices will lead to less time pressure at the end of a project. Due to the connection of most of these open science practices, spending more time in the planning phase and during the conduction of experiments will save time during the data analysis and publication of the study. Indeed, consulting reporting guidelines early on, preregistering a statistical plan, and writing down crucial experimental details in an electronic lab notebook, will strongly accelerate the writing of a manuscript. If protocols or even electronic lab notebooks were made public, just citing these would simplify the writing of publications. Similarly, if a data management plan is well designed before starting data collection, analyzing, and depositing data in a public repository, as is increasingly required, will be fast. NTS, non-technical summary.

https://doi.org/10.1371/journal.pbio.3001810.g001

https://doi.org/10.1371/journal.pbio.3001810.t001

Planning the study

Transparent practices can be adopted at every stage of the research process. However, to ensure full effectivity, it is highly recommended to engage in detailed planning before the start of the experiment. This can prevent valuable time from being lost at the end of the study due to careless decisions being made at the beginning. Clarifying data management at the start of a project can help avoiding filing chaos that can be very time consuming to untangle. Keeping clear track of a project and study design will also help if new colleagues are included later on in the project or if entire project parts are handed over. In addition, all texts written on the rationale and hypothesis of the study or method descriptions, or design schemes created during the planning phase can be used in the final publications ( Fig 1 ). Similarly, information required for preregistration of animal studies or for reporting according to the ARRIVE guidelines are an extension of the details required for ethical approval [ 22 , 23 ]. Thus, the time burden within the planning phase is often overestimated. Furthermore, the thorough planning of experiments can avoid the unnecessary use of animals by preventing wrong avenues from being pursued.

Implementing open scientific practices at the beginning of a project does not mean that the idea and study plan must be shared immediately, but rather is critical for making the entire workflow transparent at the end of the project. However, optional early sharing of information can enable peers to give feedback on the study plan. Studies potentially benefit more from this a priori input than they would from the classical a posteriori peer-review process.

Most people perceive guidelines as advice that instructs on how to do something. However, it is sometimes useful to consider the term in its original meaning; “the line that guides us”. In this sense, following guidelines is not simply fulfilling a duty, but is a process that can help to design a sound research study and, as such, guidelines should be consulted at the planning stage of a project. The PREPARE guidelines are a list of important points that should be thought-out before starting a study involving animal experiments in order to reduce the waste of animals, promote alternatives, and increase the reproducibility of research and testing [ 24 ]. The PREPARE checklist helps to thoroughly plan a study and focuses on improving the communication and collaboration between all involved participants of the study (i.e., animal caretakers and scientists). Indeed, open science begins with the communication within a research facility. It is currently available in 33 languages and the responsible team from Norecopa, Norway’s 3R-center, takes requests for translations into further languages.

The UK Reproducibility Network has also published several guiding documents (primers) on important topics for open and reproducible science. These address issues such as data sharing [ 25 ], open access [ 26 ], open code and software [ 27 ], and preprints [ 28 ], as well as preregistration and registered reports [ 27 ]. Consultation of these primers is not only helpful in the relevant phases of the experiment but is also encouraged in the planning phase.

Although the ARRIVE guidelines are primarily a reporting guideline specifically designed for preparing a publication containing animal data, they can also support researchers when planning their experiments [ 22 , 23 ]. Going through the ARRIVE website, researchers will find tools and explanations that can support them in planning their experiments [ 29 ]. Consulting the ARRIVE checklist at the beginning of a project can help in deciding what details need to be documented during conduction of the experiments. This is particularly advisable, given that compliance to ARRIVE is still poor [ 18 ].

Experimental design

To maximize the validity of performed experiments and the knowledge gained, designing the study well is crucial. It is important that the chosen animal species reflects the investigated disease well and that basic characteristics of the animal, such as sex or age, are considered carefully [ 30 ]. The Canadian Institutes of Health Research provides a collection of resources on the integration of sex and gender in biomedical research with animals, including tips and tools for researchers and reviewers [ 31 ]. Additionally, it is advisable to avoid unnecessary standardization of biological and environmental factors that can reduce the external validity of results [ 32 ]. Meticulous statistical planning can further optimize the use of animals. Free to use online tools for calculating sample sizes such as G*Power or the inVivo software package for R can further support animal researchers in designing their statistical plan [ 33 , 34 ]. Randomization for the allocation of groups can be supported with specific tools for scientists like Research Randomizer, but also by simple online random number generators [ 35 ]. Furthermore, it might be advisable when designing the study to incorporate pathological analyses into the experimental plan. Optimal planning of tissue collection, performance of pathological procedures according to accepted best practices, and use of optimal pathological analysis and reporting methods can add some extra knowledge that would otherwise be lost. This can improve the reproducibility and quality of translational biomedicine, especially, but not exclusively, in animal studies with morphological endpoints. In all animal studies, unexpected deaths in experimental animals can occur and be the cause of lost data or missed opportunities to identify health problems [ 36 , 37 ].

To support researchers in designing their animal research, the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) has also developed the Experimental Design Assistant (EDA) [ 38 , 39 ]. This online tool helps researchers to better structure in vivo research by creating detailed schemes of the study design. It provides feedback on the entered design, drawing researcher’s attention to crucial decisions in the project. The resulting schemes can be used to transparently share the study design by uploading it into a study preregistration, enclosing it in a grant application, or submitting it with a final manuscript. The EDA can be used for different study designs in diverse scenarios and helps to communicate researcher plans to others [ 40 ]. The EDA might be particularly of interest to clarify very complex study designs involving multiple experimental groups. Working with the EDA might appear rather complex in the beginning, but the NC3R provides regular webinars that can help to answer any questions that arise.

Preregistration

Preregistration is an effective tool to improve the quality and transparency of research. To preregister their work, scientists must determine crucial details of the study before starting any experiment. Changes occurring during a study can be outlined at the end. A preregistered study plan should include at least the hypothesis and determine all the parameters that are known in advance. A description of the planned study design and statistical analysis will enable reviewers and peers to better retrace the workflow. It can prevent the intentional use of the flexibility of analysis to reach p -values under a certain significance level (e.g., p-hacking or HARKing (Hypothesizing After Results are Known)). With preregistration, scientists can also claim their idea at an early stage of their research with a citable individual identifier that labels the idea as their own. Some open preregistration platforms also provide a digital object identifier (DOI), which makes the registered study citable. Three public registries actively encourage the preregistration of animal studies conducted around the world: OSF registry, preclinicaltrials.eu, and animalstudyregistry.org [ 41 – 45 ]. Scientists can choose the registry according to their needs. Preregistering a study in a public registry supports scientists in planning their study and later to critically reevaluate their own work and assess its limitations and potentials.

As an alternative to public registries, researchers can also submit their study plan to one of hundreds of journals already publishing registered reports, including many journals open to animal research [ 8 ]. A submitted registered report passes 2 steps of peer review. In the first step, reviewers comment on the idea and the study design. After an “in-principle-acceptance,” researchers can conduct their study as planned. If the authors conduct the experiments as described in the accepted study protocol, the journal will publish the final study regardless of the outcome. This might be an attractive option, especially for early career researchers, as a manuscript is published at the beginning of a project with the guarantee of a future final publication.

The benefits of preregistration can already be observed in clinical research, where registration has been mandatory for most trials for more than 20 years. Preregistration in clinical research has helped to make known what has been tested and not just what worked and was published, and the implementation of trial registration has strongly reduced the number of publications reporting significant treatment effects [ 46 ]. In animal research, with its unrealistically high percentage of positive results, preregistration seems to be particularly worthwhile.

Research data management

To get the most out of performed animal experiments, effective sharing of data at the end of the study is essential. Sharing research data optimally is complex and needs to be prepared in advance. Thus, data management can be seen as one part of planning a study thoroughly. Many funders have recognized the value of the original research data and request a data management plan from applicants in advance [ 25 , 47 ]. Various freely available tools such as DMPTool or DMPonline already exist to design a research data management plan that complies to the requirements of different funders [ 48 , 49 ]. The data management plan defines the types of data collected and describes the handling and names responsible persons throughout the data lifecycle. This includes collecting the data, analyzing, archiving, and sharing it. Finally, a data management plan enables long-term access and the possibility for reuse by peers. Developing such a plan, whether it is required by funders or not, will later simplify the application of the FAIR data principle (see section on the FAIR data principle). The Longwood Medical Area Research Data Management Working Group from the Harvard Medical School developed a checklist to assist researchers in optimally managing their data throughout the data lifecycle [ 50 ]. Similarly, the Joint Information Systems Committee (JISC) provides a great research data management toolkit including a checklist for researchers planning their project [ 51 ]. Consulting this checklist in the planning phase of a project can prevent common errors in research data management.

Non-technical project summary

One instrument specifically conceived to create transparency on animal research for the general public is the so-called non-technical project summary (NTS). All animal protocols approved within the EU must be accompanied by these comprehensible summaries. NTSs are intended to inform the public about ongoing animal experiments. They are anonymous and include information on the objectives and potential benefits of the project, the expected harm, the number of animals, the species, and a statement of compliance with the requirements of the 3Rs principle. However, beyond simply informing the public, NTSs can also be used for meta-research to help identify new research areas with an increased need for new 3R technologies [ 52 , 53 ]. NTSs become an excellent tool to appropriately communicate the scientific value of the approved protocol and for meta-scientists to generate added value by systematically analyzing theses summaries if they fulfill a minimum quality threshold [ 54 , 55 ]. In 2021, the EU launched the ALURES platform ( Table 1 ), where NTSs from all member states are published together, opening the opportunities for EU-wide meta-research. NTSs are, in contrast to other open science practices, mandatory in the EU. However, instead of thinking of them as an annoying duty, it might be worth thoroughly drafting the NTS to support the goals of more transparency towards the public, enabling an open dialogue and reducing extreme opinions.

Conducting the experiments

Once the experiments begin, documentation of all necessary details is essential to ensure the transparency of the workflow. This includes methodological details that are crucial for replicating experiments, but also failed attempts that could help peers to avoid experiments that do not work in the future. All information should be stored in such a way that it can be found easily and shared later. In this area, many new tools have emerged in recent years ( Table 1 ). These tools will not only make research transparent for colleagues, but also help to keep track of one’s own research and improve internal collaboration.

Electronic laboratory notebooks

Electronic laboratory notebooks (ELNs) are an important pillar of research data management and open science. ELNs facilitate the structured and harmonized documentation of the data generation workflow, ensure data integrity, and keep track of all modifications made to the original data based on an audit trail option. Moreover, ELNs simplify the sharing of data and support collaborations within and outside the research group. Methodological details and research data become searchable and traceable. There is an extensive amount of literature providing advice on the selection and the implementation process of an ELN depending on the specific needs and research area and its discussion would be beyond the scope of this Essay [ 56 – 58 ]. Some ELNs are connected to a laboratory information management system (LIMS) that provides an animal module supporting the tracking of animal details [ 59 ]. But as research involving animals is highly heterogeneous, this might not be the only decision point and we cannot recommend a specific ELN that is suitable for all animal research.

ELNs are already established in the pharmaceutical industry and their use is on the rise among academics as well. However, due to concerns around costs for licenses, data security, and loss of flexibility, many research institutions still fear the expenses that the introduction of such a system would incur [ 56 ]. Nevertheless, an increasing number of academic institutions are implementing ELNs and appreciating the associated benefits [ 60 ]. If your institution already has an ELN, it might be easiest to just use the option available in the research environment. If not, the Harvard Medical School provides an extensive and updated overview of various features of different ELNs that can support scientists in choosing the appropriate one for their research [ 61 ]. There are many commercial ELN products, which may be preferred when the administrative workload should be outsourced to a large extent. However, open-source products such as eLabFTW or open BIS provide a greater opportunity for customization to meet specific needs of individual research institutions [ 62 – 64 ]. A huge number of options are available depending on the resources and the features required. Some scientists might prefer generic note taking tools such as Evernote or just a simple Word document that offers infinite flexibility, but specific ELNs can further support good record keeping practice by providing immutability, automated backups, standardized methods, and protocols to follow. Clearly defining the specific requirements expected might help to choose an adequate system that would improve the quality of the record compared to classical paper laboratory notebooks.

Sharing protocols

Adequate sharing of methods in translational biomedical sciences is key to reproducibility. Several repositories exist that simplify the publication and exchange of protocols. Writing down methods at the end of the project bears the risk that crucial details might be missing [ 65 ]. On protocols.io, scientists can note all methodological details of a procedure, complete them with uploaded documents, and keep them for personal use or share them with collaborators [ 66 ]. Authors can also decide at any point in time to make their protocol public. Protocols published on protocols.io receive a DOI and become citable; they can be commented on by peers and adapted according to the needs of the individual researcher. Protocol.io files from established protocols can also be submitted together with some context and sample datasets to PLOS ONE , where it can be peer-reviewed and potentially published [ 67 , 68 ]. Depending on the affiliation of the researchers to academia or industry and on an internal or public sharing of files, protocols.io can be free of charge or come with costs. Other journals also encourage their authors to deposit their protocols in a freely accessible repository, such as protocol exchange from Nature portfolio [ 69 ]. Another option might be to separately submit a protocol that was validated by its use in an already published research article to an online and peer-reviewed journal specific for research protocols, such as Bio-Protocol. A multitude of journals, including eLife and Science already collaborate with Bio-Protocol and recommend authors to publish the method in Bio-Protocol [ 70 ]. Bio-Protocol has no submission fees and is freely available to all readers. Both protocols.io and Bio-Protocol allow the illustration of complex scientific methods by uploading videos to published protocols. In addition, protocols can be deposited in a general research repository such as the Open Science Framework (OSF repository) and referenced in appropriate publications.

Sharing critical incidents

Sharing critical or even adverse events that occur in the context of animal experimentation can help other scientists to avoid committing the same mistakes. The system of sharing critical incidents is already established in clinical practice and helps to improve medical care [ 71 , 72 ]. The online platform critical incident reporting system in laboratory animal science (CIRS-LAS) represents the first preclinical equivalent to these clinical systems [ 73 ]. With this web-based tool, critical incidents in animal research can be reported anonymously without registration. An expert panel helps to analyze the incident to encourage an open dialogue. Critical incident reporting is still very marginal in animal research and performed procedures are very variable. These factors make a systemic analysis and a targeted search of incidence difficult. However, it may be of special interest for methods that are broadly used in animal research such as anesthesia. Indeed, a broad feed of this system with data on errors occurring in standard procedures today could help avoid critical incidences in the future and refine animal experiments.

Sharing animals, organs, and tissue

When we think about open science, sharing results and data are often in focus. However, sharing material is also part of a collaborative and open research culture that could help to greatly reduce the number of experimental animals used. When an animal is killed to obtain specific tissue or organs, the remainder is mostly discarded. This may constitute a wasteful practice, as surplus tissue can be used by other researchers for different analyses. More animals are currently killed as surplus than are used in experiments, demonstrating the potential for sharing these animals [ 74 , 75 ].

Sharing information on generated surplus is therefore not only economical, but also an effective way to reduce the number of animals used for scientific purposes. The open-source software Anishare is a straightforward way for breeders of genetically modified lines to promote their surplus offspring or organs within an institution [ 76 ]. The database AniMatch ( Table 1 ) connects scientists within Europe who are offering tissue or organs with scientists seeking this material. Scientists already sharing animal organs can support this process by describing it in publications and making peers aware of this possibility [ 77 ]. Specialized research communities also allow sharing of animal tissue or animal-derived products worldwide that are typically used in these fields on a collaborative basis via the SEARCH-framework [ 78 , 79 ]. Depositing transgenic mice lines into one of several repositories for mouse strains can help to further minimize efforts in producing new transgenic lines and most importantly reduce the number of surplus animals by supporting the cryoconservation of mouse lines. The International Mouse Strain Resource (IMSR) can be used to help find an adequate repository or to help scientists seeking a specific transgenic line find a match [ 80 ].

Analyzing the data

Animal researchers have to handle increasingly complex data. Imaging, electrophysiological recording, or automated behavioral tracking, for example, produce huge datasets. Data can be shared as raw numerical output but also as images, videos, sounds, or other forms from which raw numerical data can be generated. As the heterogeneity and the complexity of research data increases, infinite possibilities for analysis emerge. Transparently reporting how the data were processed will enable peers to better interpret reported results. To get the most out of performed animal experiments, it is crucial to allow other scientists to replicate the analysis and adapt it to their research questions. It is therefore highly recommended to use formats and tools during the analysis that allow a straightforward exchange of code and data later on.

Transparent coding

The use of non-transparent analysis codes have led to a lack of reproducibility of results [ 81 ]. Sharing code is essential for complex analysis and enables other researchers to reproduce results and perform follow-up studies, and citable code gives credit for the development of new algorithms ( Table 1 ). Jupyter Notebooks are a convenient way to share data science pipelines that may use a variety of coding languages, including like Python, R or Matlab, and also share the results of analyses in the form of tables, diagrams, images, and videos. Notebooks contain source code and can be published or collaboratively shared on platforms like GitHub or GitLab, where version control of source code is implemented. The data-archiving tool Zenodo can be used to archive a repository on GitHub and create a DOI for the archive. Thereby contents become citable. Using free and open-source programming language like R or Python will increase the number of potential researchers that can work with the published code. Best practice for research software is to publish the source code with a license that allows modification and redistribution.

Choice of data visualization

Choosing the right format for the visualization of data can increase its accessibility to a broad scientific audience and enable peers to better judge the validity of the results. Studies based on animal research often work with very small sample sizes. Visualizing these data in histograms may lead to an overestimation of the outcomes. Choosing the right dot plots that makes all recorded points visible and at the same time focusses on the summary instead of the individual points can further improve the intuitive understanding of a result. If the sample size is too low, it might not be meaningful to visualize error bars. A variety of freely available tools already exists that can support scientists in creating the most appropriate graphs for their data [ 82 ]. In particular, when representing microscopy results or heat maps, it should be kept in mind that a large part of the population cannot perceive the classical red and green representation [ 83 ]. Opting for the color-blind safe color maps and checking images with free tools such as color oracle ( Table 1 ) can increase the accessibility of graphs. Multiple journals have already addressed flaws in data visualization and have introduced new policies that will accelerate the uptake of transparent representation of results.

Publication of all study outcomes

Open science practices have received much attention in the past few years when it comes to publication of the results. However, it is important to emphasize that although open science tools have their greatest impact at the end of the project, good study preparation and sharing of the study plan and data early on can greatly increase the transparency at the end.

The FAIR data principle

To maximize the impact and outcome of a study, and to make the best long-term use of data generated through animal experiments, researchers should publish all data collected during their research according to the FAIR data principle. That means the data should be findable, accessible, interoperable, and reusable. The FAIR principle is thus an extension of open access publishing. Data should not only be published without paywalls or other access restrictions, but also in such a manner that they can be reused and further processed by others. For this, legal as well as technical requirements must be met by the data. To achieve this, the GoFAIR initiative has developed a set of principles that should be taken into account as early as at the data collection stage [ 49 , 84 ]. In addition to extensively described and machine-readable metadata, these principles include, for example, the application of globally persistent identifiers, the use of open file formats, and standardized communication protocols to ensure that humans and machines can easily download the data. A well-chosen repository to upload the data is then just the final step to publish FAIR data.

FAIR data can strongly increase the knowledge gained from performed animal experiments. Thus, the same data can be analyzed by different researchers and could be combined to obtain larger sample sizes, as already occurs in the neuroimaging community, which works with comparable datasets [ 85 ]. Furthermore, the sharing of data enables other researchers to analyze published datasets and estimate measurement reliabilities to optimize their own data collection [ 86 , 87 ]. This will help to improve the translation from animal research into clinics and simultaneously reduce the number of animal experiment in future.

Reporting guidelines

In preclinical research, the ARRIVE guidelines are the current state of the art when it comes to reporting data based on animal experiments [ 22 , 23 ]. The ARRIVE guidelines have been endorsed by more than 1,000 journals who ask that scientists comply with them when reporting their outcomes. Since the ARRIVE guidelines have not had the expected impact on the transparency of reporting in animal research publications, a more rigorous update has been developed to facilitate their application in practice (ARRIVE 2.0 [ 23 ]). We believe that the ARRIVE guidelines can be more effective if they are implemented at a very early stage of the project (see section on guidelines). Some more specialized reporting guidelines have also emerged for individual research fields that rely on animal studies, such as endodontology [ 88 ]. The equator network collects all guidelines and makes them easily findable with their search tool on their website ( Table 1 ). MERIDIAN also offers a 1-stop shop for all reporting guidelines involving the use of animals across all research sectors [ 89 ]. It is thus worth checking for new reporting guidelines before preparing a manuscript to maximize the transparency of described experiments.

Identifiers

Persistent identifiers for published work, authors, or resources are key for making public data findable by search engines and are thus a prerequisite for compliance to FAIR data principles. The most common identifier for publications will be a DOI, which makes the work citable. A DOI is a globally unique string assigned by the International DOI Foundation to identify content permanently and provide a persistent link to its location on the Internet. An ORCID ID is used as a personal persistent identifier and is recommendable to unmistakably identify an author ( Table 1 ). This will avoid confusions between authors with the same name or in the case of name changes or changes of affiliation. Research Resource Identifiers (RRID) are unique ID numbers that help to transparently report research resources. RRID also apply to animals to clearly identify the species used. RRID help avoid confusion between different names or changing names of genetic lines and, importantly, make them machine findable. The RRID Portal helps scientists find a specific RRID or create one if necessary ( Table 1 ). In the context of genetically altered animal lines, correct naming is key. The Mouse Genome Informatics (MGI) Database is the authoritative source of official names for mouse genes, alleles, and strains ([ 90 ]).

Preprint publication

Preprints have undergone unprecedented success, particularly during the height of the Coronavirus Disease 2019 (COVID-19) pandemic when the need for rapid dissemination of scientific knowledge was critical. The publication process for scientific manuscripts in peer-reviewed journals usually requires a considerable amount of time, ranging from a few months to several years, mainly due to the lengthy review process and inefficient editorial procedures [ 91 , 92 ]. Preprints typically precede formal publication in scientific journals and, thus, do not go through a peer review process, thus, facilitating the prompt open dissemination of important scientific findings within the scientific community. However, submitted papers are usually screened and checked for plagiarism. Preprints are assigned a DOI so they can be cited. Once a preprint is published in a journal, its status is automatically updated on the preprint server. The preprint is linked to the publication via CrossRef and mentioned accordingly on the website of the respective preprint platform.

After initial skepticism, most publishers now allow papers to be posted on preprint servers prior to submission. An increasing number of journals even allow direct submission of a preprint to their peer review process. The US National Institutes of Health and the Wellcome Trust, among other funders, also encourage prepublication and permit researchers to cite preprints in their grant applications. There are now numerous preprint repositories for different scientific disciplines. BioASAP provides a searchable database for preprint servers that can help in identifying the one that best matches an individual’s needs [ 93 ]. The most popular repository for animal research is bioRxiv, which is hosted by the Cold Spring Harbor Laboratory ( Table 1 ).

The early exchange of scientific results is particularly important for animal research. This acceleration of the publication process can help other scientists to adapt their research or could even prevent animal experiments if other scientists become aware that an experiment has already been done before starting their own. In addition, preprints can help to increase the visibility of research. Journal articles that have a corresponding preprint publication have higher citation and Altmetric counts than articles without preprint [ 94 ]. In addition, the publication of preprints can help to combat publication bias, which represents a major problem in animal research [ 16 ]. Since journals and readers prioritize cutting-edge studies with positive results over inconclusive or negative results, researchers are reluctant to invest time and money in a manuscript that is unlikely to be accepted in a high-impact journal.

In addition to the option of publishing as preprint, other alternative publication formats have recently been introduced to facilitate the publication of research results that are hard to publish in traditional peer-reviewed journals. These include micro publications, data repositories, data journals, publication platforms, and journals that focus on negative or inconclusive results. The tool fiddle can support scientists in choosing the right publication format [ 95 , 96 ].

Open access publication

Publishing open access is one of the most established open science strategies. In contrast to the FAIR data principle, the term open access publication refers usually to the publication of a manuscript on a platform that is accessible free of charge—in translational biomedical research, this is mostly in the form of a scientific journal article. Originally, publications accessible free of charge were the answer to the paywalls established by renowned publishing houses, which led to social inequalities within and outside the research system. In translational biomedical research, the ethical aspect of urgently needed transparency is another argument in favor of open access publication, as these studies will not only be findable, but also internationally readable.

There are different ways of open access publishing; the 2 main routes are gold open access and green open access. Numerous journals offer now gold open access. It refers to the immediate and fully accessible publication of an article. The Directory of Open Access Journals (DOAJ) provides a complete and updated list for high-quality, open access, and peer-reviewed journals [ 97 ]. Charité–Universitätsmedizin Berlin offers a specific tool for biomedical open access journals that supports animal researchers to choose an appropriate journal [ 49 ]. In addition, the Sherpa Romeo platform is a straightforward way to identify publisher open access policies on a journal-by-journal basis, including information on preprints, but also on licensing of articles [ 51 ]. Hybrid open access refers to openly accessible articles in otherwise paywalled journals. By contrast, green open access refers to the publication of a manuscript or article in a repository that is mostly operated by institutions and/or universities. The publication can be exclusively on the repository or in combination with a publisher. In the quality-assured, global Directory of Open Access Repositories (openDOAR), scientists can find thousands of indexed open access repositories [ 49 ]. The publisher often sets an embargo during which the authors cannot make the publication available in the repository, which can restrict the combined model. It is worth mentioning that gold open access is usually more expensive for the authors, as they have to pay an article processing charge. However, the article’s outreach is usually much higher than the outreach of an article in a repository or available exclusively as subscription content [ 98 ]. Diamond open access refers to publications and publication platforms that can be read free of charge by anyone interested and for which no costs are incurred by the authors either. It is the simplest and fairest form of open access for all parties involved, as no one is prevented from participating in scientific discourse by payment barriers. For now, it is not as widespread as the other forms because publishers have to find alternative sources of revenue to cover their costs.

As social media and the researcher’s individual public outreach are becoming increasingly important, it should be remembered that the accessibility of a publication should not be confused with the licensing under which the publication is made available. In order to be able to share and reuse one’s own work in the future, we recommend looking for journals that allow publications under the Creative Commons licenses CC BY or CC BY-NC. This also allows the immediate combination of gold and green open access.

Creative commons licenses

Attributing Creative Commons (CC) licenses to scientific content can make research broadly available and clearly specifies the terms and conditions under which people can reuse and redistribute the intellectual property, namely publications and data, while giving the credit to whom it deserves [ 49 ]. As the laws on copyright vary from country to country and law texts are difficult to understand for outsiders, the CC licenses are designed to be easily understandable and are available in 41 languages. This way, users can easily avoid accidental misuse. The CC initiative developed a tool that enables researchers to find the license that best fits their interests [ 49 ]. Since the licenses are based on a modular concept ranging from relatively unrestricted licenses (CC BY, free to use, credit must be given) to more restricted licenses (CC BY-NC-ND, only free to share for non-commercial purposes, credit must be given), one can find an appropriate license even for the most sensitive content. Publishing under an open CC license will not only make the publication easy to access but can also help to increase its reach. It can stimulate other researchers and the interested public to share this article within their network and to make the best future use of it. Bear in mind that datasets published independently from an article may receive a different CC license. In terms of intellectual property, data are not protected in the same way as articles, which is why the CC initiative in the United Kingdom recommends publishing them under a CC0 (“no rights reserved”) license or the Public Domain Mark. This gives everybody the right to use the data freely. In an animal ethics sense, this is especially important in order to get the most out of data derived from animal experiments.

Data and code repositories

Sharing research data is essential to ensure reproducibility and to facilitate scientific progress. This is particularly true in animal research and the scientific community increasingly recognizes the value of sharing research data. However, even though there is increasing support for the sharing of data, researchers still perceive barriers when it comes to doing so in practice [ 99 – 101 ]. Many universities and research institutions have established research data repositories that provide continuous access to datasets in a trusted environment. Many of these data repositories are tied to specific research areas, geographic regions, or scientific institutions. Due to the growing number and overall heterogeneity of these repositories, it can be difficult for researchers, funding agencies, publishers, and academic institutions to identify appropriate repositories for storing and searching research data.

Recently, several web-based tools have been developed to help in the selection of a suitable repository. One example is Re3data, a global registry of research data repositories that includes repositories from various scientific disciplines. The extensive database can be searched by country, content (e.g., raw data, source code), and scientific discipline [ 49 ]. A similar tool to help find a data archive specific to the field is FAIRsharing, based at Oxford University [ 102 ]. If there is no appropriate subject-specific data repository or one seems unsuitable for the data, there are general data repositories, such as Open Science Framework, figshare, Dryad, or Zenodo. To ensure that data stored in a repository can be found, a DOI is assigned to the data. Choosing the right license for the deposited code and data ensures that authors get credit for their work.

Publication and connection of all outcomes

If scientists have used all available open science tools during the research process, then publishing and linking all outcomes represents the well-deserved harvest ( Fig 2 ). At the end of a research process, researchers will not just have 1 publication in a journal. Instead, they might have a preregistration, a preprint, a publication in a journal, a dataset, and a protocol. Connecting these outcomes in a way that enables other scientists to better assess the results that link these publications will be key. There are many examples of good open science practices in laboratory animal science, but we want to highlight one of them to show how this could be achieved. Blenkuš and colleagues investigated how mild stress-induced hyperthermia can be assessed non-invasively by thermography in mice [ 103 ]. The study was preregistered with animalstudyregistry.org , which is referred to in their publication [ 104 ]. A deviation from the originally preregistered hypothesis was explained in the manuscript and the supplementary material was uploaded to figshare [ 105 ].

Application of open science practices can increase the reproducibility and visibility of a research project at the same time. By publishing different research outputs with more detailed information than can be included in a journal article, researchers enable peers to replicate their work. Reporting according to guidelines and using transparent visualization will further improve this reproducibility. The more research products that are generated, the more credit can be attributed. By communicating on social media or additionally publishing slides from delivered talks or posters, more attention can be raised. Additionally, publishing open access and making the work machine-findable makes it accessible to an even broader number of peers.

https://doi.org/10.1371/journal.pbio.3001810.g002

It might also be helpful to provide all resources from a project in a single repository such as Open Science Framework, which also implements other, different tools that might have been used, like GitHub or protocols.io.

Communicating your research

Once all outcomes of the project are shared, it is time to address the targeted peers. Social media is an important instrument to connect research communities [ 106 ]. In particular, Twitter is an effective way to communicate research findings or related events to peers [ 107 ]. In addition, specialized platforms like ResearchGate can support the exchange of practical experiences ( Table 1 ). When all resources related to a project are kept in one place, sharing this link is a straightforward way to reach out to fellow scientists.

With the increasing number of publications, science communication has become more important in recent years. Transparent science that communicates openly with the public contributes to strengthening society’s trust in research.

Conclusions

Plenty of open science tools are already available and the number of tools is constantly growing. Translational biomedical researchers should seize this opportunity, as it could contribute to a significant improvement in the transparency of research and fulfil their ethical responsibility to maximize the impact of knowledge gained from animal experiments. Over and above this, open science practices also bear important direct benefits for the scientists themselves. Indeed, the implementation of these tools can increase the visibility of research and becomes increasingly important when applying for grants or in recruitment decisions. Already, more and more journals and funders require activities such as data sharing. Several institutions have established open science practices as evaluation criteria alongside publication lists, impact factor, and h-index for panels deciding on hiring or tenure [ 108 ]. For new adopters, it is not necessary to apply all available practices at once. Implementing single tools can be a safe approach to slowly improve the outreach and reproducibility of one’s own research. The more open science products that are generated, the more reproducible the work becomes, but also the more the visibility of a study increases ( Fig 2 ).

As other research fields, such as social sciences, are already a step ahead in the implementation of open science practices, translational biomedicine can profit from their experiences [ 109 ]. We should thus keep in mind that open science comes with some risks that should be minimized early on. Indeed, the more open science practices become incentivized, the more researchers could be tempted to get a transparency quality label that might not be justified. When a study is based on a bad hypothesis or poor statistical planning, this cannot be fixed by preregistration, as prediction alone is not sufficient to validate an interpretation [ 110 ]. Furthermore, a boom of data sharing could disconnect data collectors and analysts, bearing the risk that researchers performing the analysis lack understanding of the data. The publication of datasets could also promote a “parasitic” use of a researcher’s data and lead to scooping of outcomes [ 111 ]. Stakeholders could counteract such a risk by promoting collaboration instead of competition.

During the COVID-19 pandemic, we have seen an explosion of preprint publications. This unseen acceleration of science might be the adequate response to a pandemic; however, the speeding up science in combination with the “publish or perish” culture could come at the expense of the quality of the publication. Nevertheless, a meta-analysis comparing the quality of reporting between preprints and peer-reviewed articles showed that the quality of reporting in preprints in the life sciences is at most slightly lower on average compared to peer-reviewed articles [ 112 ]. Additionally, preprints and social media have shown during this pandemic that a premature and overconfident communication of research results can be overinterpreted by journalists and raise unfounded hopes or fears in patients and relatives [ 113 ]. By being honest and open about the scope and limitations of the study and choosing communication channels carefully, researchers can avoid misinterpretation. It should be noted, however, that by releasing all methodological details and data in research fields such as viral engineering, where a dual use cannot be excluded, open science could increase biosecurity risk. Implementing access-controlled repositories, application programming interfaces, and a biosecurity risk assessment in the planning phase (i.e., by preregistration) could mitigate this threat [ 114 ].

Publishing in open access journals often involves higher publication costs, which makes it more difficult for institutes and universities from low-income countries to publish there [ 115 ]. Equity has been identified as a key aim of open science [ 116 ]. It is vital, therefore, that existing structural inequities in the scientific system are not unintentionally reinforced by open science practices. Early career researchers have been the main drivers of the open science movement in other fields even though they are often in vulnerable positions due to short contracts and hierarchical and strongly networked research environments. Supporting these early career researchers in adopting open science tools could significantly advance this change in research culture [ 117 ]. However, early career researchers can already benefit by publishing registered reports or preprints that can provide a publication much faster than conventional journal publications. Communication in social media can help them establish a network enabling new collaborations or follow-up positions.

Even though open science comes with some risks, the benefits easily overweigh these caveats. If a change towards more transparency is accompanied by the implementation of open science in the teaching curricula of the universities, most of the risks can be minimized [ 118 ]. Interestingly, we have observed that open science tools and infrastructure that are specific to animal research seem to mostly come from Europe. This may be because of strict regulations within Europe for animal experiments or because of a strong research focus in laboratory animal science along with targeted research funding in this region. Whatever the reason might be, it demonstrates the important role of research policy in accelerating the development towards 3Rs and open science.

Overall, it seems inevitable that open science will eventually prevail in translational biomedical research. Scientists should not wait for the slow-moving incentive framework to change their research habits, but should take pioneering roles in adopting open science tools and working towards more collaboration, transparency, and reproducibility.

Acknowledgments

The authors gratefully acknowledge the valuable input and comments from Sebastian Dunst, Daniel Butzke, and Nils Körber that have improved the content of this work.

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Low crude protein (CP) formulations with supplemental amino acids (AA) are used to enhance intestinal health, reduce costs, minimize environmental impact, and maintain growth performance of pigs. However, ext...

Effects of the kinetic pattern of dietary glucose release on nitrogen utilization, the portal amino acid profile, and nutrient transporter expression in intestinal enterocytes in piglets

Promoting the synchronization of glucose and amino acid release in the digestive tract of pigs could effectively improve dietary nitrogen utilization. The rational allocation of dietary starch sources and the ...

Global gene expression profiling of perirenal brown adipose tissue whitening in goat kids reveals novel genes linked to adipose remodeling

Brown adipose tissue (BAT) is known to be capable of non-shivering thermogenesis under cold stimulation, which is related to the mortality of animals. In the previous study, we observed that goat BAT is mainly...

Multi-omics integration identifies regulatory factors underlying bovine subclinical mastitis

Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry. Multi-omics approaches enable the comprehensive investigation of the complex interactions between mu...

Staphylococcus aureus and biofilms: transmission, threats, and promising strategies in animal husbandry

Staphylococcus aureus ( S. aureus ) is a common pathogenic bacterium in animal husbandry that can cause diseases such as mastitis, skin infections, arthritis, and other ailments. The formation of biofilms threatens...

In-depth proteome characterization of endometrium and extraembryonic membranes during implantation in pig

Proteome characterization of the porcine endometrium and extraembryonic membranes is important to understand mother-embryo cross-communication. In this study, the proteome of the endometrium and chorioallantoi...

High expression circRALGPS2 in atretic follicle induces chicken granulosa cell apoptosis and autophagy via encoding a new protein

The reproductive performance of chickens mainly depends on the development of follicles. Abnormal follicle development can lead to decreased reproductive performance and even ovarian disease among chickens. Ch...

Betaine addition to the diet alleviates intestinal injury in growing rabbits during the summer heat through the AAT/mTOR pathway

The aim of this experiment was to investigate the effect of different levels of betaine (Bet) inclusion in the diet on the intestinal health of growing rabbits under summer heat. A total of 100 weaned Qixing m...

Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens

Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality rate. Three-dimensional (3D) chromatin architecture takes part in disease processing by regulati...

Exploring the modulatory role of bovine lactoferrin on the microbiome and the immune response in healthy and Shiga toxin-producing E. coli challenged weaned piglets

Post-weaned piglets suffer from F18 + Escherichia coli ( E. coli ) infections resulting in post-weaning diarrhoea or oedema disease. Frequently used management strategies, including colistin and zinc oxide, have con...

Investigation of HCAR2 antagonists as a potential strategy to modulate bovine leukocytes

Dairy cows experiencing ketosis after calving suffer greater disease incidence and are at greater risk of leaving the herd. In vitro administration of beta-hydroxybutyric acid (BHBA; the primary blood ketone) ...

Novel uses of ensiled biomasses as feedstocks for green biorefineries

Perennial forage plants are efficient utilizers of solar radiation and nutrients so that there is a lot of scope to increase the production of green biomass in many areas. Currently, grasses are mainly used as...

Decreased eggshell strength caused by impairment of uterine calcium transport coincide with higher bone minerals and quality in aged laying hens

Deteriorations in eggshell and bone quality are major challenges in aged laying hens. This study compared the differences of eggshell quality, bone parameters and their correlations as well as uterine physiolo...

Dietary xylo-oligosaccharides and arabinoxylans improved growth efficiency by reducing gut epithelial cell turnover in broiler chickens

One of the main roles of the intestinal mucosa is to protect against environmental hazards. Supplementation of xylo-oligosaccharides (XOS) is known to selectively stimulate the growth of beneficial intestinal ...

Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post-weaning period

Nursery pigs undergo stressors in the post-weaning period that result in production and welfare challenges. These challenges disproportionately impact the offspring of primiparous sows compared to those of mul...

Two intestinal microbiota-derived metabolites, deoxycholic acid and butyrate, synergize to enhance host defense peptide synthesis and alleviate necrotic enteritis

Necrotic enteritis (NE) is a major enteric disease in poultry, yet effective mitigation strategies remain elusive. Deoxycholic acid (DCA) and butyrate, two major metabolites derived from the intestinal microbi...

tRNA Glu -derived fragments from embryonic extracellular vesicles modulate bovine embryo hatching

Transfer RNA-derived small RNAs (tsRNAs) have been shown to be involved in early embryo development and repression of endogenous retroelements in embryos and stem cells. However, it is unknown whether tsRNAs a...

Dynamic changes of rumen microbiota and serum metabolome revealed increases in meat quality and growth performances of sheep fed bio-fermented rice straw

Providing high-quality roughage is crucial for improvement of ruminant production because it is an essential component of their feed. Our previous study showed that feeding bio-fermented rice straw (BF) improv...

Pig pangenome graph reveals functional features of non-reference sequences

The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-re...

Lactiplantibacillus plantarum FRT4 attenuates high-energy low-protein diet-induced fatty liver hemorrhage syndrome in laying hens through regulating gut-liver axis

Fatty liver hemorrhage syndrome (FLHS) becomes one of the most major factors resulting in the laying hen death for caged egg production. This study aimed to investigate the therapeutic effects of Lactiplantibacil...

Finding biomarkers of experience in animals

At a time when there is a growing public interest in animal welfare, it is critical to have objective means to assess the way that an animal experiences a situation. Objectivity is critical to ensure appropria...

Supplementation of vitamin E or a botanical extract as antioxidants to improve growth performance and health of growing pigs housed under thermoneutral or heat-stressed conditions

Heat stress has severe negative consequences on performance and health of pigs, leading to significant economic losses. The objective of this study was to investigate the effects of supplemental vitamin E and ...

Establishment of a chicken intestinal organoid culture system to assess deoxynivalenol-induced damage of the intestinal barrier function

Deoxynivalenol (DON) is a mycotoxin that has received recognition worldwide because of its ability to cause growth delay, nutrient malabsorption, weight loss, emesis, and a reduction of feed intake in livestoc...

Prevotella and succinate treatments altered gut microbiota, increased laying performance, and suppressed hepatic lipid accumulation in laying hens

This work aimed to investigate the potential benefits of administering Prevotella and its primary metabolite succinate on performance, hepatic lipid accumulation and gut microbiota in laying hens.

Probiotic cocktails accelerate baicalin metabolism in the ileum to modulate intestinal health in broiler chickens

Baicalin and probiotic cocktails are promising feed additives with broad application prospects. While probiotic cocktails are known to enhance intestinal health, the potential synergistic impact of combining b...

Excess dietary Lys reduces feed intake, stimulates jejunal CCK secretion and alters essential and non-essential blood AA profile in pigs

Commercial diets are frequently formulated to meet or exceed nutrient levels including those of limiting essential amino acids (AA) covering potential individual variations within the herd. However, the provis...

All- trans retinoic acid alleviates transmissible gastroenteritis virus-induced intestinal inflammation and barrier dysfunction in weaned piglets

Transmissible gastroenteritis virus (TGEV) is one of the main pathogens causing severe diarrhea of piglets. The pathogenesis of TGEV is closely related to intestinal inflammation. All- trans retinoic acid (ATRA) i...

Oils with different degree of saturation: effects on ileal digestibility of fat and corresponding additivity and bacterial community in growing pigs

Oils are important sources of energy in pig diets. The combination of oils with different degree of saturation contributes to improve the utilization efficiency of the mixed oils and may reduce the cost of oil...

Layer chicken microbiota: a comprehensive analysis of spatial and temporal dynamics across all major gut sections

The gut microbiota influences chicken health, welfare, and productivity. A diverse and balanced microbiota has been associated with improved growth, efficient feed utilisation, a well-developed immune system, ...

Effects of maternal methyl donor intake during pregnancy on ileum methylation and function in an intrauterine growth restriction pig model

Intrauterine growth retardation (IUGR) affects intestinal growth, morphology, and function, which leads to poor growth performance and high mortality. The present study explored whether maternal dietary methyl...

Vitamin A regulates mitochondrial biogenesis and function through p38 MAPK-PGC-1α signaling pathway and alters the muscle fiber composition of sheep

Vitamin A (VA) and its metabolite, retinoic acid (RA), are of great interest for their wide range of physiological functions. However, the regulatory contribution of VA to mitochondrial and muscle fiber compos...

Repeated inoculation with rumen fluid accelerates the rumen bacterial transition with no benefit on production performance in postpartum Holstein dairy cows

The dairy cow’s postpartum period is characterized by dramatic physiological changes, therefore imposing severe challenges on the animal for maintaining health and milk output. The dynamics of the ruminal micr...

Coated sodium butyrate ameliorates high-energy and low-protein diet induced hepatic dysfunction via modulating mitochondrial dynamics, autophagy and apoptosis in laying hens

Fatty liver hemorrhagic syndrome (FLHS), a fatty liver disease in laying hens, poses a grave threat to the layer industry, stemming from its ability to trigger an alarming plummet in egg production and usher i...

Sperm function, mitochondrial activity and in vivo fertility are associated to their mitochondrial DNA content in pigs

Despite their low abundance in sperm, mitochondria have diverse functions in this cell type, including energy production, signalling and calcium regulation. In humans, sperm mitochondrial DNA content (mtDNAc) ...

The chemical characteristics of different sodium iron ethylenediaminetetraacetate sources and their relative bioavailabilities for broilers fed with a conventional corn-soybean meal diet

Our previous studies demonstrated that divalent organic iron (Fe) proteinate sources with higher complexation or chelation strengths as expressed by the greater quotient of formation (Q f ) values displayed higher ...

Abomasal infusion of branched-chain amino acids or branched-chain keto-acids alter lactation performance and liver triglycerides in fresh cows

Dairy cows are at high risk of fatty liver disease in early lactation, but current preventative measures are not always effective. Cows with fatty liver have lower circulating branched-chain amino acid (BCAA) ...

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Journal of Animal Science and Biotechnology

ISSN: 2049-1891

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Why study Animal Science?

Since the emergence of modern humanity, the relationships between people and animals have been an integral part of our society, economy and culture. Animals provide us with food, clothing, recreation and companionship. Animal science—the study of the biological function of domestic and captive animals and their utilization by people—focuses on modern, efficient and humane ways to care for and make the best use of the animals who share our lives. Our undergraduate students work with animals regularly as they prepare for graduate school, veterinary school or a career in teaching, agricultural production or business.

Undergraduates can select one of three majors administered by the department:

• Agriculture & Environmental Education
• Animal Science
• Animal Science & Management

Our majors offer opportunities to students who enjoy animals and wish to study their biology and care and/or their management. A practical, as well as, a scientific understanding of domestic animals is obtained by completing a specialization: animal behavior, biochemistry, genetics, nutrition, physiology, aquatic animals, avian sciences, companion & captive animals, laboratory animals, equine science, livestock & dairy, or poultry. We pride ourselves in the experiential learning students obtain through our majors.

Knowledge is gained both in lecture classes and hands-on laboratories. The courses expose students to an integrated study of animal behavior, reproduction, growth, lactation, molecular biology, animal breeding, livestock judging, and many other aspects of animal biology. A wide array of formal and informal internship opportunities are available at the department's extensive animal facilities.

Animal science majors from UC Davis have entered careers as agricultural and natural resources consultants, agricultural and pharmaceutical sales staff, fisheries owners, lawyers, physicians, researchers, teachers, veterinarians and zookeepers.

Graduate students enroll in cross-cutting, disciplinary focused graduate groups. Graduate groups bring together scholars from across campus to address common research interests in a highly collaborative fashion. Department of Animal Science faculty host students in the following graduate groups: Agricultural & Environmental Chemistry, Animal Biology, Animal Behavior, Ecology, Forensic Science, Immunology, Integrative Genetics & Genomics, International Agricultural Development, Microbiology, Molecular, Cellular & Integrative Physiology, and Nutritional Biology.

The department is also home to the following Graduate Group:

• Animal Biology Graduate Group

More information about these and other affiliated Graduate Programs is available.

Animal Research Saves Lives

The benefits of studying animals.

Since the ancient Greeks first began studying animals to learn about anatomy and physiology around 500 BC, researchers and physicians have relied on animal studies as an irreplaceable source of scientific knowledge. Studying animals enables scientists to understand how living creatures, both human and animal, function. 

Studying animals helps us get an up-close look at living organisms, and how their physical, chemical and functional life systems work. Whether it’s dissecting a frog in high school biology class or conducting experiments on rats to find cures for cancer, studying living creatures remains an essential step in the continuous process of learning more about how to save lives, improve human and animal health, cure diseases, repair injuries and protect us from emerging diseases.

Animals in the laboratory

Animal rights groups have created an aura of controversy around the topic of biomedical research. However, in reality, there is little disagreement among qualified medical and scientific authorities that animal research is absolutely vital to human and animal health.

The National Institutes of Health (NIH) credits animal research with the recent first-time drop in annual cancer deaths, a 70 percent decline over the last 30 years in stroke deaths, and a 63 percent drop in deaths from coronary disease. 

Americans for Medical Progress (AMP) , a national advocacy and outreach organization for animal research, highlights some other impressive victories for animal research, including:

• The virtual eradication of polio through a vaccine developed using monkeys, and the creation of other vaccines to conquer measles, mumps, rubella, tetanus, diphtheria, and smallpox.
• The development and purification of insulin and new artificial pancreas technology to treat diabetes. Read more
• The development of Herceptin and Tamoxifen, two medicines that have saved the lives of thousands of women with breast cancer;
• The development of a respiratory therapy, pioneered in animal models, that has reduced by two-thirds the number of infant deaths due to respiratory distress syndrome;
• The development of treatments for childhood leukemia that have improved survival rates from 4 percent to 80 percent.

In addition to drugs and treatments, animal research has also been important in the development of surgical techniques and life-saving implants. Pacemakers, prosthetic limbs, artificial joints, spinal cord stimulators- these types of implants needed living animal models for early testing in order to monitor long-term safety. Not only is it important to make sure that these implants work effectively in a living animal, but when these devices were developed, they needed to be tested in ways that doctors would not be able to do in human patients. For example, when developing new types of implants using different materials for hip replacements, it was important to perform surgery and then do follow-up surgery at a later date to monitor the state of the implant. If the materials used to make the implant wore down sooner than expected, or the implant didn’t stay in place, it’s important for researchers to make adjustments before starting human trials in order to make sure that surgeries are successful as possible.

One Health Research  is an organization that communicates recent research to the public in an attempt to improve understanding of the way health care for humans, animals, and the environment are connected.

Understanding Animal Research offers Virtual Lab Animal Tours  of four locations, providing an invaluable mixture of transparency and education. Viewers can not only see multiple settings, they learn why animal research is necessary and valuable — and just as importantly, the animal welfare standards and considerations of lab animal science.

The National Association for Biomedical Research , an organization representing almost 300 public and private universities, medical and veterinary schools, teaching hospitals, voluntary health agencies, professional societies, pharmaceutical companies and other animal research-related firms, also speaks out on behalf of the responsible use of animals in research. The organization’s website clearly states its position:

The Association recognizes that now and in the foreseeable future it is not possible to completely replace the use of animals and that the study of the whole, living organisms is an indispensable element of biomedical research and testing that benefits all animals.

The Association’s sister organization, the Foundation for Biomedical Research , notes the benefits of biomedical research for animal health as well as human medical progress. According to the Foundation, many lifesaving and life-extending treatments for cats, dogs, farm animals, wildlife, and endangered species were developed through research on animals. Pacemakers, artificial joints, organ transplants, and freedom from arthritic pain are just a few of the breakthroughs made in veterinary medicine thanks to animal research.

The most commonly used animals in research—more than 98 percent—are rodents, reptiles, and fish. Contrary to the claims of animal rights proponents, the number of dogs, cats and non-human primates used in research comprise less than one percent of all animals studied. 

Over the past 50 years, the total number of animals in research has declined by about 30 percent. In recent years, scientists have worked hard on what they call “the three R’s”—Reducing the number of animals needed; Replacing animals with other models whenever possible, and Refining techniques to improve animal welfare. Before researchers can even begin to work with animals, they need to prove that there are no acceptable alternatives. They also need to justify the number of animals necessary for their research. The institution’s Animal Care and Use Committee reviews a research proposal before approving any animal work, making sure that the research protocol complies with the Animal Welfare Act, the Public Health Service Policy on Humane Care and Use of Laboratory Animals, the Guide for the Care and Use of Laboratory Animals, as well as any applicable FDA, USDA, OLAW, and institutional regulations.

The Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC) is a private, nonprofit organization that promotes the humane treatment of animals in science through voluntary accreditation and assessment programs. Over 950 companies, agencies and research institutions with animal research programs have received AAALAC accreditation. This accreditation speaks volumes about these research institutions, as participation is voluntary. AAALAC accreditation demonstrates accountability, stimulates continuous improvement through in-depth peer review, and communicates a commitment to excellence and quality within the scientific community.

While AAALAC accreditation is a way for organizations to show their commitment to excellence, the American Association for Laboratory Animal Science (AALAS) provides ways for animal care technicians to show this commitment on an individual level. Most animal care technicians have a strong background working with animals, and this type of job tends to attract animal lovers who really enjoy their day-to-day interactions with their animals. AALAS offers several certification levels for animal care technicians who are interested in furthering their careers and continuing education.

Through AALAS, individuals can achieve certification at the following levels, with content increasing in difficulty: Assistant Laboratory Animal Technician (ALAT), Laboratory Animal Technician (LAT), Laboratory Animal Technologist (LATG), and Certified Manager of Animal Resources (CMAR). After achieving these certifications, technicians and managers earn continuing education credits by attending seminars, workshops, and training programs in order to stay on top of new information in the field.

It is well known that physiological responses to stress can affect experimental data, so excellent animal care is extremely important to animal care technicians and scientists. All animals, including research animals, have very specific physical, social, and emotional needs, and animal care technicians work hard to provide their animals with the best care possible. Programs that focus on ways to create enriching and stimulating habitats are important to animal welfare, and a critical component of any animal research program. Compassion and an understanding of the animal and its needs are also extremely important to the success of animal-based research.

Understanding an entire living system is essential to research that will lead to treatments for human and animal diseases. You can study cancer cells in a dish (in vitro) and try to figure out whether or not a new drug will kill those cells, but that alone doesn’t give you enough information to determine whether or not the drug will kill those cancer cells safely in the body. Bleach will kill cancer cells in a dish, but I hope you wouldn’t use that information to inject bleach into a human patient. There have to be steps in between these two points, and those steps need to give researchers information that computer systems and cell cultures can’t. Drug A might kill breast cancer cells in culture, but what if estrogen affects the way Drug A works? What if it causes kidney failure or brain damage? These are all questions that need answers before Drug A is put into human clinical trials.

Often, arguments are made that computer technology is so advanced that we shouldn’t need to rely on animals for testing. Fortunately, past animal testing has provided extensive information that has allowed scientists to develop computer models that can improve the quality of research. Researchers can pre-screen compounds to determine which ones will be the most effective, and this screening has been able to reduce the number of animals needed for early testing. But while computers have been able to give us valuable information, they have limits. As AMP notes, “Even the most sophisticated computers cannot simulate physiological functions that must be studied to understand how compounds may affect an entire living system.” To program a computer to behave like a living system, the programmers need to completely understand the living system they’re trying to model. The brain and body are so complex that we still don’t completely understand how and why they work the way they do. It’s like trying to write a screenplay for a movie that is supposed to accurately depict the 2020 Presidential election. We might be able to guess who some of the candidates will be, or accurately predict some of the hot topic issues that will be argued, but until it’s actually 2020 and the election has been won, we can’t say that our movie will be accurate. It’s more likely that the movie will turn into a comedy of errors that we’d laugh at. But the consequences of attempting to use a predictive computer model to determine drug safety, medication interactions, or treatment outcomes could be devastating.

At this point in time, even IF researchers had a complete understanding of the living system they were trying to model, processing speed is another limiting factor.  Researchers working to model HALF a mouse brain said that it put “tremendous constraints on computation, communication and memory capacity of any computing platform.” And this was only modeling HALF a mouse brain! Their simulation wasn’t able to run at full speed, either; it ran about ten times slower than real life. It also lacked structures seen in real mouse brains. It seems more reasonable to say that computer modeling can help reduce the number animals used in research by replacing some early stages of testing, but ultimately, it’s not at the point where it can replace animals completely.

Researchers don’t make the decision to work with animals out of convenience. Computer models or cell cultures require less care and maintenance than live animals. If there’s a power outage, chances are, your computer will restart when the power is restored and you’ll be right where you left off. In vitro experiments (cells in a dish) can be timed around when it’s convenient for the lab members. In vivo (in living animals) experiments usually don’t have that flexibility. If the power goes out, someone needs to ensure that animals have an adequate supply of food and water and that the ventilation and habitat temperatures stay at acceptable levels for the animals to remain healthy and happy. Animal research requires round the clock attention and specialized care. Researchers that work with animals do so because animals are the best models for their research.

However, one doesn’t need to be a researcher or scientist to recognize the need for animal research. Would any of us want to undergo surgery at the hands of a surgeon who had never operated on a live being before? Would we want a veterinarian who had never used a scalpel on a live animal operating on our dog or cat? Of course not. And after understanding the limitations of computer models and in vitro cell research, we probably wouldn’t want to receive a new medication or treatment without knowing that it had already been successfully tested in a living animal (in vivo).

Researchers are able to create animal models of human disease in an attempt to model disease mechanisms. A mouse model of bronchopulmonary dysplasia is helping researchers develop ways of preventing lung and heart problems in premature human infants .

Nematode worms and humans have the same protein on the surface of their sperm cells; this protein helps the egg recognize the sperm, and research with these worms may lead to a better understanding of human infertility .

Animal models for late-onset diseases, such as Alzheimer’s, are particularly important. For example, laboratory mice have much shorter lifespans than humans, so researchers can determine whether or not a particular drug or treatment will work in a matter of weeks or months instead of years or decades. In a research setting, variables can be carefully controlled, so scientists can determine exactly which variable made a difference. Mice have given scientists clues about the role of estrogen , the immune system , and certain enzymes  that may play a role in Alzheimer’s disease in humans.

Information gained through animal research does more than help humans - it also helps animals. The Foundation for Biomedical Research reports that dogs, cats, sheep, and cattle now live healthier lives because of vaccines for rabies, distemper, parvovirus, hepatitis, anthrax, tetanus, and feline leukemia, all developed through animal research. New treatments for glaucoma, heart disease, cancer, hip dysplasia, and traumatic injuries are saving, extending, and enhancing the lives of beloved pets.

In addition, animal research has led to advanced techniques that have helped preserve and protect threatened and endangered species. The National Zoo, a program of the Smithsonian Institution, operates two important research centers. The Center for Species Survival conducts basic and applied research, especially in the fields of reproductive science and animal management, to understand biological mysteries and to implement practical solutions to help rare species survive in zoos so that they will not become extinct in the wild.  Scientists at the Center for Conservation and Evolutionary Genetics  specialize in genetic research to help manage wild and captive populations to maintain their genetic diversity. Improving knowledge of the genetics of threatened and endangered species enables scientists to understand how genetic variations affect their ability to survive and to identify effective approaches for sustaining these species in the wild.

Animal research has played an important role in our understanding of diseases that affect humans and animals today, and it will continue to be important in the development of new drugs, treatments, and therapies in the future. At this point in time, there is no substitute for live animal models at necessary stages of research. The message here, though, is that animal-based research is carefully regulated and performed by individuals who believe that animal welfare is a top priority. To perform animal research responsibly, one must have a respect for the animals in their care and for what those animals are able to teach us.

There are a lot of misunderstandings surrounding animal-based research, in part because it’s difficult for members of the scientific community to communicate their work. Unfortunately, there have been a lot of negative perceptions surrounding animal research, mostly due to this lack of understanding. Please do some research for yourself, and learn more about the ways that animals continue to advance science and medicine.

Animals in the classroom

The leading national organization representing science teachers has examined carefully the pros and cons and effectiveness of live study, textbook learning, computer models and other approaches and has taken a position supporting the inclusion of live animals as well as dissection in the classroom. The National Science Teachers Association (NSTA)  contends that having students interact with animals is “one of the most effective methods of achieving many of the goals outlined in the National Science Education Standards.” 

Educators recommend that dissection activities be conducted in a way that helps students develop hands-on skills of observation and comparison; understand the shared as well as unique structures and processes of specific organisms, and develop an enhanced appreciation for the complexity of life.

Teaching students respect for animals and an ethical awareness of their obligation for humane treatment is an important byproduct of dissection activities. The NSTA sets forth a number of recommendations for teachers who include dissection activities in their classes. They include:

• Conducting laboratory and dissection activities with consideration and appreciation for the organism;
• Planning laboratory and discussion activities that are appropriate to the maturity level of the students;
• Using specimens from reputable and reliable scientific supply companies or FDA-inspected facilities;
• Ensuring that dissection occurs in a clean and organized workspace with proper ventilation, lighting, equipment, and access to hot water and soap for clean-up;
• Using personal safety protective equipment such as gloves, goggles, and aprons, and ensuring the safe and appropriate use of scissors, scalpels and other tools.
• Ensuring that specimens are handled and disposed of properly;
• Addressing issues such as allergies or squeamishness about dealing with animal specimens;
• Basing laboratory and dissection activities on carefully planned and educationally sound curriculum objectives;

Most science educators agree that it is important to offer alternatives to dissection for students who might be uncomfortable handling real animals in this way. Modern computer simulations make “virtual dissection” a lesser option for those students. However, the NSTA continue to support the decision of science teachers and schools to integrate live animals and dissection in the classroom and opposes any rules or laws that would deny students the best opportunity to learn biology: through actual animal dissection.

One Miraculous Moment

Diabetes is a very manageable illness; in fact, it is so common for people with diabetes to lead long, healthy lives today, it might be shocking to learn that the disease was a death sentence less than 100 years ago. At that time, an adult diagnosed with diabetes would be lucky to live another decade, and the recommended treatment was a strict starvation diet , which at best merely prolonged your life.

Children suffering from diabetes passed more quickly than adults. They were often kept in large hospital wards with 50 or more other children, visited by family as they wasted away toward a tragic, inevitable death. This was the reality of diabetes in early 1922.

But in 1922, in one of the most dramatic moments in the history of medicine, that reality was changed forever. Three men visited one of these hospital wards, traveling from bed to bed giving each child an injection… a shot that proved so effective, by the time the men reached the last child in the ward, some of the first children to receive the injection had already awakened from their comas. For these children and their families, diabetes – just like that – was no longer a death sentence.

How did this happen?

The three men, Frederick Banting, Charles Best, and James Collip, had recently discovered how to treat diabetes with insulin following research trials with dogs and the purification of animal insulin. Having restored normal glucose levels in a near-death 14-year-old boy , and armed with enough insulin for multiple patients, it was time to treat larger groups. To the grateful joy of parents and their awakening children, insulin was, quite literally, a new lease on life.

Thanks to the work of these scientists, diabetes – a confounding disease that had been described in medical literature for thousands of years – transformed from a death sentence into manageable disease virtually overnight. Today, it is estimated that 29 million people in the United States have diabetes and their generation may be the first to experience cures as well as treatments.

For more information:

• The Foundation for Biomedical Research (FBR)
• Americans for Medical Progress
• The American Diabetes Association
• Diabetes UK
• National Animal Interest Alliance

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Scientists push new paradigm of animal consciousness, saying even insects may be sentient

Bees play by rolling wooden balls — apparently for fun . The cleaner wrasse fish appears to recognize its own visage in an underwater mirror . Octopuses seem to react to anesthetic drugs and will avoid settings where they likely experienced past pain. 

All three of these discoveries came in the last five years — indications that the more scientists test animals, the more they find that many species may have inner lives and be sentient. A surprising range of creatures have shown evidence of conscious thought or experience, including insects, fish and some crustaceans. 

That has prompted a group of top researchers on animal cognition to publish a new pronouncement that they hope will transform how scientists and society view — and care — for animals. 

Nearly 40 researchers signed “ The New York Declaration on Animal Consciousness ,” which was first presented at a conference at New York University on Friday morning. It marks a pivotal moment, as a flood of research on animal cognition collides with debates over how various species ought to be treated. 

The declaration says there is “strong scientific support” that birds and mammals have conscious experience, and a “realistic possibility” of consciousness for all vertebrates — including reptiles, amphibians and fish. That possibility extends to many creatures without backbones, it adds, such as insects, decapod crustaceans (including crabs and lobsters) and cephalopod mollusks, like squid, octopus and cuttlefish.

“When there is a realistic possibility of conscious experience in an animal, it is irresponsible to ignore that possibility in decisions affecting that animal,” the declaration says. “We should consider welfare risks and use the evidence to inform our responses to these risks.” 

Jonathan Birch, a professor of philosophy at the London School of Economics and a principal investigator on the Foundations of Animal Sentience project, is among the declaration’s signatories. Whereas many scientists in the past assumed that questions about animal consciousness were unanswerable, he said, the declaration shows his field is moving in a new direction. 

“This has been a very exciting 10 years for the study of animal minds,” Birch said. “People are daring to go there in a way they didn’t before and to entertain the possibility that animals like bees and octopuses and cuttlefish might have some form of conscious experience.”

From 'automata' to sentient

There is not a standard definition for animal sentience or consciousness, but generally the terms denote an ability to have subjective experiences: to sense and map the outside world, to have capacity for feelings like joy or pain. In some cases, it can mean that animals possess a level of self-awareness. 

In that sense, the new declaration bucks years of historical science orthodoxy. In the 17th century, the French philosopher René Descartes argued that animals were merely “material automata” — lacking souls or consciousness.

Descartes believed that animals “can’t feel or can’t suffer,” said Rajesh Reddy, an assistant professor and director of the animal law program at Lewis & Clark College. “To feel compassion for them, or empathy for them, was somewhat silly or anthropomorphizing.” 

In the early 20th century, prominent behavioral psychologists promoted the idea that science should only study observable behavior in animals, rather than emotions or subjective experiences . But beginning in the 1960s, scientists started to reconsider. Research began to focus on animal cognition, primarily among other primates. 

Birch said the new declaration attempts to “crystallize a new emerging consensus that rejects the view of 100 years ago that we have no way of studying these questions scientifically.” 

Indeed, a surge of recent findings underpin the new declaration. Scientists are developing new cognition tests and trying pre-existing tests on a wider range of species, with some surprises. 

Take, for example, the mirror-mark test, which scientists sometimes use to see if an animal recognizes itself. 

In a series of studies, the cleaner wrasse fish seemed to pass the test . 

The fish were placed in a tank with a covered mirror, to which they exhibited no unusual reaction. But after the cover was lifted, seven of 10 fish launched attacks toward the mirror, signaling they likely interpreted the image as a rival fish. 

After several days, the fish settled down and tried odd behaviors in front of the mirror, like swimming upside down, which had not been observed in the species before. Later, some appeared to spend an unusual amount of time in front of the mirror, examining their bodies. Researchers then marked the fish with a brown splotch under the skin, intended to resemble a parasite. Some fish tried to rub the mark off. 

“The sequence of steps that you would only ever have imagined seeing with an incredibly intelligent animal like a chimpanzee or a dolphin, they see in the cleaner wrasse,” Birch said. “No one in a million years would have expected tiny fish to pass this test.”

In other studies, researchers found that zebrafish showed signs of curiosity when new objects were introduced into their tanks and that cuttlefish could remember things they saw or smelled . One experiment created stress for crayfish by electrically shocking them , then gave them anti-anxiety drugs used in humans. The drugs appeared to restore their usual behavior.

Birch said these experiments are part of an expansion of animal consciousness research over the past 10 to 15 years. “We can have this much broader canvas where we’re studying it in a very wide range of animals and not just mammals and birds, but also invertebrates like octopuses, cuttlefish,” he said. “And even increasingly, people are talking about this idea in relation to insects.”

As more and more species show these types of signs, Reddy said, researchers might soon need to reframe their line of inquiry altogether: “Scientists are being forced to reckon with this larger question — not which animals are sentient, but which animals aren’t?” 

New legal horizons

Scientists’ changing understanding of animal sentience could have implications for U.S. law, which does not classify animals as sentient on a federal level, according to Reddy. Instead, laws pertaining to animals focus primarily on conservation, agriculture or their treatment by zoos, research laboratories and pet retailers.

“The law is a very slow moving vehicle and it really follows societal views on a lot of these issues,” Reddy said. “This declaration, and other means of getting the public to appreciate that animals are not just biological automatons, can create a groundswell of support for raising protections.” 

State laws vary widely. A decade ago, Oregon passed a law recognizing animals as sentient and capable of feeling pain, stress and fear, which Reddy said has formed the bedrock of progressive judicial opinions in the state.  

Meanwhile, Washington and California are among several states where lawmakers this year have considered bans on octopus farming, a species for which scientists have found strong evidence of sentience. 

British law was recently amended to consider octopuses sentient beings — along with crabs and lobsters .

“Once you recognize animals as sentient, the concept of humane slaughter starts to matter, and you need to make sure that the sort of methods you’re using on them are humane,” Birch said. “In the case of crabs and lobsters, there are pretty inhumane methods, like dropping them into pans of boiling water, that are very commonly used.”

Evan Bush is a science reporter for NBC News. He can be reached at [email protected].

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Computer model: a computer program designed to predict what might happen based off of collected data.

Ethical: relating to a person's moral principles.

Morals: a person's beliefs concerning what is right and wrong.

Zoologist: a person who studies animals.

Scientists learn a lot about snakes and other animals through basic research. Image by the Virginia State Park staff.

“Don’t worry, they aren’t dangerous” you hear the zoologist say as she leads you and a group of others toward an area with a number of different snakes. She removes a long snake from a larger glass enclosure and asks who would like to hold it. You take a step back, certain that holding a snake is the last thing you’d like to do.

"But how do you know they aren’t dangerous?” you ask. The zoologist looks up and smiles. She explains that scientists have studied this type of snake, and so we actually know quite a bit about it. This type of snake rarely bites and does not produce venom, so it isn’t dangerous to people. You nod along as she talks about the snakes, their natural habitats, and other details like what they eat.

Animals in the Research Process

How do we know so much about snakes or other animals? Animals are all unique, and scientists study them to learn more about them. For example, by studying snakes we have learned that they stick their tongues out because they are trying to pick up odors around them. This helps them sense food, predators, and other things that may be nearby. When research is performed to expand our understanding of something, like an animal, we call it basic research .

Scientists study animals for other reasons too. What we learn about animals can actually help us find solutions to other problems or to help people. For example, studying snakes helps us understand which ones are venomous so that humans know what kinds of snakes they shouldn't touch. Scientists also study animals to find new treatments to diseases and other ailments that affect both people and animals. If we learn what is in snake venom, we can create a medicine to give to people that have been bitten as a treatment to help them feel better. Using what we know about an animal or thing to help us solve problems or treat disease is called  applied research .

Scientists use many other tools, such as computer models, in addition to animals to study different topics. Image by Andreas Horn.

No matter what type of research is being performed, scientists must consider many things when they study animals.  

Do Scientists Need to Study Animals?

Of course we can learn a lot from using animals for research, but are there alternative options? Sometimes there are. For example, scientists could use some other method, like cells or computer models, to study a particular topic instead of using animals. However, for a number of reasons , scientists have found that using animals is sometimes the best way to study certain topics.

What If Scientists Harm Animals for Research?

Some research using animals only requires scientists to watch behavior or to take a few samples (like blood or saliva) from the animal. These activities may cause the animals some stress, but they are unlikely to harm the animals in any long-term way. Studies of the behavior or physiology of an animal in its natural environment is an example of such research.

In other cases, scientists may need to harm or kill an animal in order to answer a research question. For example, a study could involve removing a brain to study it more closely or giving an animal a treatment without knowing what effects it may have. While the intention is never to purposely harm animals, harm can be necessary to answer a research question.

How Do Scientists Decide When It’s OK to Study Animals?

Many animals are used in research. But there is still debate on whether they should be used for this purpose. Image by the United States Department of Agriculture.

There are  many guidelines  for when it’s ok to use animals in research. Scientists must write a detailed plan of why and how they plan to use animals for a research project. This information is then reviewed by other scientists and members of the public to make sure that the research animals will be used for has an important purpose. Whatever the animals are used for, the scientists also make sure to take care of animal research subjects as best as they can.

Even with rules in place about using animals for research, many people (both scientists and non-scientists) continue to debate whether animals should be used in research. This is an ethical question, or one that depends on a person's morals. Because the way each person feels about both research and animals may be different, there is a range of views on this matter.

• Some people argue that it doesn’t matter that there are rules in place to protect animals. Animals should never be used for research at all, for any reason. 
• Others say we should be able to use animals for any kind of research because moving science forward is more important than the rights or well-being of animals. 
• Lastly, there are people whose opinions sit somewhere in the middle. They might argue that it’s ok to use animals for research, but only in some cases. For example, if the results of the research are very likely to help treat something that affects people, then it may be okay to use animals.

Along with this debate, there are many advantages and disadvantages of doing animal research . Scientists must weigh these options when performing their research.

Additional Images via Wikimedia Commons. White rat image by Alexandroff Pogrebnoj.

Read more about: Using Animals in Research

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• Article: Using Animals in Research
• Author(s): Patrick McGurrin and Christian Ross
• Publisher: Arizona State University School of Life Sciences Ask A Biologist
• Site name: ASU - Ask A Biologist
• Date published: December 4, 2016
• Date accessed: May 2, 2024
• Link: https://askabiologist.asu.edu/explore/Animal-use-in-Research

Patrick McGurrin and Christian Ross. (2016, December 04). Using Animals in Research. ASU - Ask A Biologist. Retrieved May 2, 2024 from https://askabiologist.asu.edu/explore/Animal-use-in-Research

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Patrick McGurrin and Christian Ross. "Using Animals in Research". ASU - Ask A Biologist. 04 December, 2016. https://askabiologist.asu.edu/explore/Animal-use-in-Research

MLA 2017 Style

Patrick McGurrin and Christian Ross. "Using Animals in Research". ASU - Ask A Biologist. 04 Dec 2016. ASU - Ask A Biologist, Web. 2 May 2024. https://askabiologist.asu.edu/explore/Animal-use-in-Research

Animals are an important part of research. But many argue about whether it's ethical to use animals to help advance scientific progress.

Using Animals in Research

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Animal behavior research is getting better at keeping observer bias from sneaking in – but there’s still room to improve

Professor and Associate Head of Psychology, University of Tennessee

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Todd M. Freeberg does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

University of Tennessee provides funding as a member of The Conversation US.

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Animal behavior research relies on careful observation of animals. Researchers might spend months in a jungle habitat watching tropical birds mate and raise their young. They might track the rates of physical contact in cattle herds of different densities. Or they could record the sounds whales make as they migrate through the ocean.

Animal behavior research can provide fundamental insights into the natural processes that affect ecosystems around the globe, as well as into our own human minds and behavior.

I study animal behavior – and also the research reported by scientists in my field. One of the challenges of this kind of science is making sure our own assumptions don’t influence what we think we see in animal subjects. Like all people, how scientists see the world is shaped by biases and expectations, which can affect how data is recorded and reported. For instance, scientists who live in a society with strict gender roles for women and men might interpret things they see animals doing as reflecting those same divisions .

The scientific process corrects for such mistakes over time, but scientists have quicker methods at their disposal to minimize potential observer bias. Animal behavior scientists haven’t always used these methods – but that’s changing. A new study confirms that, over the past decade, studies increasingly adhere to the rigorous best practices that can minimize potential biases in animal behavior research.

Biases and self-fulfilling prophecies

A German horse named Clever Hans is widely known in the history of animal behavior as a classic example of unconscious bias leading to a false result.

Around the turn of the 20th century , Clever Hans was purported to be able to do math. For example, in response to his owner’s prompt “3 + 5,” Clever Hans would tap his hoof eight times. His owner would then reward him with his favorite vegetables. Initial observers reported that the horse’s abilities were legitimate and that his owner was not being deceptive.

However, careful analysis by a young scientist named Oskar Pfungst revealed that if the horse could not see his owner, he couldn’t answer correctly. So while Clever Hans was not good at math, he was incredibly good at observing his owner’s subtle and unconscious cues that gave the math answers away.

In the 1960s, researchers asked human study participants to code the learning ability of rats. Participants were told their rats had been artificially selected over many generations to be either “bright” or “dull” learners. Over several weeks, the participants ran their rats through eight different learning experiments.

In seven out of the eight experiments , the human participants ranked the “bright” rats as being better learners than the “dull” rats when, in reality, the researchers had randomly picked rats from their breeding colony. Bias led the human participants to see what they thought they should see.

Eliminating bias

Given the clear potential for human biases to skew scientific results, textbooks on animal behavior research methods from the 1980s onward have implored researchers to verify their work using at least one of two commonsense methods.

One is making sure the researcher observing the behavior does not know if the subject comes from one study group or the other. For example, a researcher would measure a cricket’s behavior without knowing if it came from the experimental or control group.

The other best practice is utilizing a second researcher, who has fresh eyes and no knowledge of the data, to observe the behavior and code the data. For example, while analyzing a video file, I count chickadees taking seeds from a feeder 15 times. Later, a second independent observer counts the same number.

Yet these methods to minimize possible biases are often not employed by researchers in animal behavior, perhaps because these best practices take more time and effort.

In 2012, my colleagues and I reviewed nearly 1,000 articles published in five leading animal behavior journals between 1970 and 2010 to see how many reported these methods to minimize potential bias. Less than 10% did so. By contrast, the journal Infancy, which focuses on human infant behavior, was far more rigorous: Over 80% of its articles reported using methods to avoid bias.

It’s a problem not just confined to my field. A 2015 review of published articles in the life sciences found that blind protocols are uncommon . It also found that studies using blind methods detected smaller differences between the key groups being observed compared to studies that didn’t use blind methods, suggesting potential biases led to more notable results.

In the years after we published our article, it was cited regularly and we wondered if there had been any improvement in the field. So, we recently reviewed 40 articles from each of the same five journals for the year 2020.

We found the rate of papers that reported controlling for bias improved in all five journals , from under 10% in our 2012 article to just over 50% in our new review. These rates of reporting still lag behind the journal Infancy, however, which was 95% in 2020.

All in all, things are looking up, but the animal behavior field can still do better. Practically, with increasingly more portable and affordable audio and video recording technology, it’s getting easier to carry out methods that minimize potential biases. The more the field of animal behavior sticks with these best practices, the stronger the foundation of knowledge and public trust in this science will become.

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Researchers create a bodywide map of molecular changes linked to exercise and health

A Stanford Medicine-led effort to learn more about exercise’s molecular effects paints the broadest picture yet of why, in the health arena, sweat is king.

May 1, 2024 - By Krista Conger

Researchers at Stanford Medicine and their colleagues conducted nearly 10,000 measurements in nearly 20 types of tissues, learning about the   effects of exercise on the immune system, stress response, energy production and metabolism. Alan Poulson Photography/Shutterstock.com

Exercise. It’s associated with increased muscle strength, improved heart health, lower blood sugar and just about every other physical improvement you can name. But how does regularly puffing away on a treadmill, biking up a steep hill or going for a brisk lunchtime walk confer such a dizzying array of health benefits?

We’re now closer to finding out, thanks to a vast new study led by Stanford Medicine. Researchers conducted nearly 10,000 measurements in nearly 20 types of tissues to uncover the effect of eight weeks of endurance exercise in laboratory rats trained to run on rodent-sized treadmills.

Their results highlight striking effects of exercise on the immune system, stress response, energy production and metabolism. They uncovered significant links between exercise, molecules and genes already known to be involved in myriad human diseases and tissue recovery.

The study is one of a series of papers published May 1 by members of a multicenter research group meant to lay the groundwork for understanding — on a bodywide, molecular level — exactly how our tissues and cells react when we push them to perform.

“We all know exercise is beneficial for us,” said professor of pathology Stephen Montgomery , PhD. “But we don’t know much about the molecular signals that manifest across the body when people exercise, or how they may change when people train. Our study is the first to take a holistic, bodywide look at molecular changes, from proteins to genes to metabolites to fats and energy production. It’s the broadest profiling yet of the effects of exercise, and it creates an essential map to how it changes the body.”

Montgomery, who is also a professor of genetics and of biomedical data science, is a senior author of the  paper , which published on May 1 in  Nature . Other senior authors are  Michael Snyder , PhD, the Stanford W. Ascherman, MD, FACS Professor in Genetics, and associate professor of medicine  Matthew Wheeler , MD. First authors are former genetics PhD student Nicole Gay, PhD; former postdoctoral scholar David Amar, PhD; and Pierre Jean Beltran, PhD, a former postdoctoral scholar at the Broad Institute.

Additional papers by Stanford Medicine researchers include a related published report in  Nature Communications  investigating the effect of exercise-induced changes in genes and tissues known to be involved in disease risk as well as a  paper  published on May 2 in  Cell Metabolism , which focuses on the effects of exercise on the cellular energy factors called mitochondria in various tissues. Montgomery is the senior author of the  Nature Communications  paper and postdoctoral scholar  Nikolai Vetr , PhD, is its lead author. Instructor of cardiovascular medicine  Malene Lindholm , PhD, is the senior author of the  Cell Metabolism  paper, and Amar is the lead author.

Stephen Montgomery

“These papers further highlight the multiple impacts exercise training has on metabolism and health,” Montgomery said.

A coordinated look at exercise

The researchers involved in the study and the other simultaneous publications are part of a national group called the Molecular Transducers of Physical Activity Consortium, or MoTrPAC, organized by the National Institutes of Health. The effort was launched in 2015 to investigate in detail exactly how physical exercise improves health and prevents disease.

The Stanford Medicine team took on a lot of the heavy lifting, studying the effects of eight weeks of endurance training on gene expression (the transcriptome), proteins (the proteome), fats (the lipidome), metabolites (the metabolome), the pattern of chemical tags placed on DNA (the epigenome), the immune system (the…you get the idea).

Let’s just call it the sweat-ome.

They performed 9,466 analyses on multiple tissues in rats as the animals were trained to run increasing distances and compared the results with those of rats that loafed about in their cages. They paid special attention to the muscles of the leg, the heart, the liver, the kidney and a type of fat called white adipose tissue (the kind of fat that accumulates as pounds pile on); other tissues included the lungs, brain and brown adipose tissue (a more metabolically active type of fat that helps burn calories). The combination of multiple assays — think of all those -omes! — and tissue types pumped out results numbering in the hundreds of thousands for non-epigenetic changes to more than 2 million distinct changes in the epigenome. The results will keep scientists hopping for years.

Although this study served primarily to create a database for future analysis, some interesting nuggets vaulted to the top. First, they noted that the expression of 22 genes changed with exercise in all six of the tissues they focused on. Many of these genes were involved in what are known as heat shock pathways, which stabilize the structure of proteins when cells undergo stress including changes in temperature (feel that burn?), infection or tissue remodeling (hello new muscle fibers!). Others have been implicated in pathways that reduce blood pressure and increase the body’s sensitivity to insulin, which lowers blood sugar levels.

The researchers also noted that the expression of several genes involved in Type 2 diabetes, heart disease, obesity and kidney disease was reduced in exercising rats as compared with their sedentary counterparts — a clear link between their studies and human health.

Sex differences

Finally, they identified sex differences in how multiple tissues in male and female rats responded to exercise. Male rats lost about 5% of their body fat after eight weeks of exercise while female rats didn’t lose a significant amount. (They did, however, maintain their starting fat percentage while the sedentary females packed on an additional 4% of body fat during the study period.) But the largest difference was observed in gene expression in the rats’ adrenal glands. After one week, genes associated with the generation of steroid hormones like adrenaline and with energy production increased in male rats but decreased in female rats.

Despite these early, tantalizing associations, the researchers caution that exercise science is nowhere near the finish line. It’s more like the starting gun has just fired. But the future is exciting.

“In the long term, it’s unlikely we will find any one magic intervention that reproduces what exercise can do for a person,” Montgomery said. “But we might get closer to the idea of precision exercise — tailoring recommendations based on a person’s genetics, sex, age or other health conditions to generate beneficial whole-body responses.”

A full list of researchers and institutions involved in the study can be found online.

The MoTrPAC study is supported by the National Institutes of Health (grants U24OD026629, U24DK112349, U24DK112342, U24DK112340, U24DK112341, U24DK112326, 612 U24DK112331, U24DK112348, U01AR071133, U01AR071130, 613 U01AR071124, U01AR071128, U01AR071150, U01AR071160, U01AR071158, U24AR071113, U01AG055133, U01AG055137, 615 U01AG055135, 5T32HG000044, P30AG044271 and P30AG003319), the National Science Foundation, and the Knut and Alice Wallenberg Foundation.

About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit med.stanford.edu .

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How Do We Know What Animals Are Really Feeling?

Animal-welfare science tries to get inside the minds of a huge range of species — in order to help improve their lives.

Credit... Photo Illustration by Zachary Scott

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By Bill Wasik and Monica Murphy

Bill Wasik is the magazine’s editorial director and Monica Murphy is a veterinarian and writer.

• April 23, 2024

What makes a desert tortoise happy? Before you answer, we should be more specific: We’re talking about a Sonoran desert tortoise, one of a few species of drab, stocky tortoises native to North America’s most arid landscapes. Adapted to the rocky crevices that striate the hills from western Arizona to northern Mexico, this long-lived reptile impassively plods its range, browsing wildflowers, scrub grasses and cactus paddles during the hours when it’s not sheltering from the brutal heat or bitter cold. Sonoran desert tortoises evolved to thrive in an environment so different from what humans find comfortable that we can rarely hope to encounter one during our necessarily short forays — under brimmed hats and layers of sunblock, carrying liters of water and guided by GPS — into their native habitat.

Listen to this article, read by Gabra Zackman

This past November, in a large, carpeted banquet room on the University of Wisconsin’s River Falls campus, hundreds of undergraduate, graduate and veterinary students silently considered the lived experience of a Sonoran desert tortoise. Perhaps nine in 10 of the participants were women, reflecting the current demographics of students drawn to veterinary medicine and other animal-related fields. From 23 universities in the United States and Canada, and one in the Netherlands, they had traveled here to compete in an unusual test of empathy with a wide range of creatures: the Animal Welfare Assessment Contest.

That morning in the banquet room, the academics and experts who organize the contest (under the sponsorship of the American Veterinary Medical Association, the nation’s primary professional society for vets) laid out three different fictional scenarios, each one involving a binary choice: Which animals are better off? One scenario involved groups of laying hens in two different facilities, a family farm versus a more corporate affair. Another involved bison being raised for meat, some in a smaller, more managed operation and others ranging more widely with less hands-on human contact.

Then there were the tortoises. On screens along the room’s outer edge, a series of projected slides laid out two different settings: one, a desert museum exhibiting seven Sonoran specimens together in a large, naturalistically barren outdoor enclosure; the other, a suburban zoo housing a group of four tortoises, segregated by sex, in small indoor and outdoor pens furnished with a variety of tortoise toys and enticements. Into the slides had been packed an exhausting array of detail about the care provided for the tortoises in each facility. Only contestants who had prepared thoroughly for the competition — by researching the nutritional, environmental, social and medical needs of the species in question — would be able to determine which was doing a better job.

“Animal welfare” is sometimes misused as a synonym for “animal rights,” but in practice the two worldviews can sometimes be at cross purposes. From an animal rights perspective, nearly every human use of animals is morally suspect, but animal-welfare thinkers take it as a given that animals of all kinds do exist in human care, for better or worse, and focus on how to treat them as well as possible. In the past half century, an interdisciplinary group of academics, working across veterinary medicine and other animal-focused fields, have been trying to codify what we know about animal care in a body of research referred to as “animal-welfare science.”

The research has unlocked riddles about animal behavior, spurred changes in how livestock are treated and even brought about some advances in how we care for our pets: Studies of domestic cats, for example, have found that “puzzle feeders,” which slow consumption and increase mental and physical effort while eating, can improve their health and even make them friendlier. The discipline has begun to inform policy too, including requirements for scientists receiving federal grants for their animal-based research, regulations governing transport and slaughter of livestock, accreditation standards for zoos and aquariums and guidelines for veterinarians performing euthanasia.

Contest organizers hope to help their students, who might someday go into a range of animal-related jobs — not just as vets but in agribusiness, conservation, government and more — employ data and research to improve every aspect of animal well-being. Americans own an estimated 150 million dogs and cats, and our policies and consumption patterns determine how hundreds of millions of creatures from countless other species will live and die. The Animal Welfare Assessment Contest tries to introduce students to that enormous collective responsibility, and to the complexity of figuring out what each of these animals needs, especially when — as in the case of reptiles living in a shell — their outlook differs radically from our own.

The effort to improve the lives of America’s animals began more than 150 years ago. As it happens, a hundred or so turtles figured in one of the most important events in the early history of animal activism in America. It was May 1866 — the heyday of turtle soup, a dish so beloved at the time that restaurants in New York would take out newspaper ads, or even maintain special outdoor signage, declaring the hour at which the day’s batch would be ready. And so this group of unlucky sea turtles, after being captured by hunters in Florida, was brought to New York upside down on a schooner. To further immobilize them, holes were pierced through their fins with cords run through them.

The turtles would have assumed a tranquil, passive demeanor under such conditions, perhaps making it possible for the ship’s crew to believe that the creatures weren’t suffering. But there is every reason to believe they were. Evolution has equipped the marine turtle for a life afloat, with a large lung capacity filling the space beneath the shell, to enable long dives. When the turtles were on their backs, the weight of their organs would have put pressure on these lungs, forcing their breathing to become deliberate and deep.

The American Society for the Prevention of Cruelty to Animals started up the month before. Its president and founder, a Manhattan shipbuilding heir named Henry Bergh, spent its early weeks focusing on domestic species — above all, horses, the rough treatment of which in 19th-century streets was the main inspiration for his activism. But when he became aware of these suffering sea turtles for sale at Fulton Market, he decided to extend his campaign to a wildlife species that then barely rated more consideration than a cockroach, if not a cabbage.

Bergh made a case that the infliction of prolonged pain and distress upon sea turtles bound for the soup pot was illegal as well as immoral. As with other “mute servants of mankind” providing labor, locomotion, meat or milk to human beings, the turtle was entitled to be treated with compassion. But when Bergh hauled the ship’s captain in front of a judge, the defense argued (successfully!) that turtles were not even “animals,” but rather a form of fish, and thereby did not qualify under the new animal-cruelty law that Bergh succeeded in passing earlier that year.

Still, the case became a media sensation — and signaled to New Yorkers that Bergh’s campaign on behalf of animals was going to force them to account for the suffering of all animals, not just the ones they already chose to care about.

It’s perhaps no accident that Bergh turned to activism after a failed career as a dramatist. There’s something irreducibly imaginative in considering questions of animal welfare, regardless of how much science we marshal to back up our conclusions. George Angell of Boston, his fellow titan of that founding generation of animal advocates, pirated a 13-year-old British novel called “Black Beauty” and turned it into one of the century’s best-selling books, touting it as “the ‘Uncle Tom’s Cabin’ of the Horse” — though its real innovation was its use of an animal as a first-person narrator, thrusting readers into a working horse’s perspective and forcing them to contemplate how the equines all around them might see the world differently.

But how far does imagination really get us? The philosopher Thomas Nagel famously explored this problem in an essay called “What Is It Like to Be a Bat?” which took up that question only to dramatize the impossibility of answering it to anyone’s satisfaction. “It will not help,” he wrote, “to try to imagine that one has webbing on one’s arms, which enables one to fly around at dusk and dawn catching insects in one’s mouth; that one has very poor vision, and perceives the surrounding world by a system of reflected high-frequency sound signals; and that one spends the day hanging upside down by one’s feet in an attic. Insofar as I can imagine this (which is not very far), it tells me only what it would be like for me to behave as a bat behaves.”

In the case of chelonians like turtles — and their encarapaced brethren, the tortoises — we may know even less about how they experience the world than we do about bats. Take their vision, for example: Among those species that have been studied, scientists have found evidence of broad-spectrum color vision, sometimes including ultraviolet wavelengths invisible to the human eye. And while chelonians can see well beyond their pointed beaks, where edible vegetation or predators may await notice, their brains process these visual signals slowly — a quality of certain animal brains that might, some experts have theorized, result in a sped-up perception of time. (In chelonian eyes, do grasses wave frenetically in the breeze and clouds race across the sky?)

Next to vision, smell is probably the sense turtles and tortoises rely upon most. Their sensitive nasal epithelium, distributed between two chambers, can detect odors diffused in a warm desert breeze or dissolved in a cold ocean current. Chelonian ears are where you’d expect them to be, but buried beneath their scaled reptilian skin. They hear well at low frequencies, even if they don’t register the high notes of twittering birds, humming mosquitoes or the whistling wind. Some chelonians seem to have the power of magnetoreception, which means that somewhere in their anatomy — perhaps their eyes, or their nervous systems, or elsewhere — there are chemicals or structures that allow them to sense the earth’s geomagnetic field and navigate by it.

The chelonian sense of touch presents fewer mysteries. Specialized receptors in the skin and on the shell detect mechanical, temperature and pain stimuli and send messages to the nervous system — just as they do in humans and a wide variety of other species. Recognition of pain, in particular, is considered a primordial sense, essential to the survival of animals on every limb of the evolutionary tree. But even here, there are differences separating species: What does the nervous system do with signals from its nociceptors? Does the desert tortoise withdraw its foot from the scorpion’s tail only reflexively, or does it consciously register the pain of the sting? What suffering does a turtle endure when its shell is struck by the sharp edges of a boat propeller?

As Nagel argued, there is no way to meaningfully narrow the gulch in understanding that exists around “what it is like to be” such a creature. The strategy of animal-welfare science is to patiently use what we can observe about these other kinds of minds — what they choose to eat and to do, how they interact with their environments, how they respond to certain forms of treatment — looking for objective cues to show experts what imagination cannot.

Upstairs from the banquet hall, student competitors nervously milled around carpeted corridors. One by one they were called into conference rooms to face a judge, who sat at a table beside a digital chronograph. In one room, a neatly dressed young woman in owlish glasses took a breath as the display began counting up hundredths of seconds in bright red digits. Catherine LeBlond, a second-year student at Atlantic Veterinary College at Canada’s University of Prince Edward Island, began her presentation about the bison scenario.

She was allowed to refer only to a single 3-by-5 index card, which she had packed with information based on a “summary sheet” of takeaways that she and her teammates worked up together, with key phrases emphasized and sources cited, all of it broken down by category: social behavior (“Bison are a very social species with strong matriarchal divisions”), handling guidelines (“Prods should not be used to move bison unless safety is an issue”), facility design (“Ensure that there is a sufficient number of gates within facilities to slow the animals”), euthanasia (“The recommended euthanasia method of a bison is gunshot”) and more.

LeBlond began by declaring her choice: The wilder facility provided a more humane environment for its animals. She felt it was helping bison “live a more natural life”: The more spacious grounds would support wallowing behavior, she reasoned, and allow the animals to choose their social grouping, an important policy given bisons’ strong sense of social structure. She also praised the operation for enabling bison to avoid “aversive life events,” by using drones, rather than ranchers on horseback, to monitor the animals in the field, and also by slaughtering the animals on-site to avoid the distress they experience in transport. As she ran through her presentation, she took care to hit two important rhetorical notes that judges look for: “granting” some areas in which the other institution excelled and offering positive advice about how it might improve.

One way to think about her reasoning is through the lens of “the five freedoms,” a rubric that animal-welfare thinkers have long embraced to consider all the different obligations that humans have to the animals in their care. They are: 1. the freedom from hunger and thirst; 2. the freedom from discomfort; 3. the freedom from pain, injury or disease; 4. the freedom to express normal behavior; and 5. the freedom from fear and distress. In fact, it was arguably the articulation of these five freedoms — in the Brambell Report, a document put out by a British government committee in 1965 to assess the welfare conditions of the nation’s livestock — that inaugurated the whole field of animal-welfare science.

What made this list of “freedoms” so influential, in retrospect, was that it created a context for other, more targeted thinking about how a species might experience each freedom or its violation. What sort of environment will offer “freedom from discomfort” to a beef steer, on the one hand, and a freedom “to express normal behavior” on the other? Trying to answer such questions in a rigorous way involves considerations of veterinary medicine but also of evolutionary history, behavioral observation, physiology (scientists have begun using proxies like cortisol levels as an indication of animal stress), neuroscience and more.

In her bison presentation, by citing “a more natural life” and avoiding “aversive life events,” LeBlond was emphasizing Freedoms 4 and 5, the freedom to express normal behavior and the freedom from distress. In the scenario about tortoises, though, Freedoms 4 and 5 seemed to be at odds. When LeBlond addressed the judge for that category, she awarded the edge to the zoo — weighing its better health outcomes and stimulating enrichments over the more naturalistic setting at the museum. She zeroed in on the zoo’s visitor program, which gave the tortoises a novel method of choosing whether or not they wanted to interact with humans: Staff put out a transport crate, and over the course of 20 minutes, tortoises could decide to climb into the crate to be taken to the human guests, and later receive a special biscuit for their service.

And she linked this to a behavioral difference, illustrated by a set of charts comparing how readily each set of tortoises moved toward a “novel object” (like an enrichment toy) or a “novel person” in their midst. The numbers showed that the zoo’s tortoises were far more drawn to interactions with people. “This indicates that they have less fear of humans,” LeBlond pointed out, “which could be because they are given a choice about whether or not they get to participate in educational programs, and those that do are positively reinforced with high-value rewards.”

Most of the students followed a similar logic and chose the zoo. The judges, however, disagreed. As one of them explained later at the awards ceremony — at which LeBlond took second place among vet students — the facility may have seemed to be offering their tortoises a consensual choice, but it was more accurate to see it as heavy-handed operant conditioning, which lured them into submitting to human contact with the promise of a biscuit. In scenarios involving domestic animals, a documented comfort around humans is a sign of positive treatment, but when it comes to wild animals, the goal is the opposite: to acclimate them as little to human contact as possible. Another way of putting it is this: Biscuits might make a desert tortoise “happy,” insofar as we can even imagine what that means, but happiness isn’t ultimately what humane treatment is about.

Each year at the contest, competitors are asked to perform one “live” assessment: a situation with real animals in it. This time, the species of choice was the laboratory rat. We joined Kurt Vogel, head of the Animal Welfare Lab at University of Wisconsin-River Falls, on a tour of the scenario that he and a colleague, Brian Greco, had constructed in a warren of rooms a few buildings over from the competition site.

They had brought a great deal of brio to the task. In the first room, where several rats snoozed in containers, Vogel and Greco had left a panoply of welfare infractions for eagle-eyed students to find. One cage was missing a water bottle, while others housed only a single rat, a violation of best practices (rats prefer to be housed in groups). Feed bags sat on the floor with detritus all around, and a note in a lab journal indicated that pest rodents had been observed snacking on it.

In subsequent rooms, the horrors became more baroque. A euthanasia chamber had the wrong size lid on it, and a nearby journal described a rat escaping in the middle of its extermination. Paperwork in an office laid out the nature of the study being performed, which involved prolonged deprivation of food and water, forced swimming and exposure to wet bedding. Diagrams showed that the rats’ brains were being studied through physical implants, and students could see that the operating room was a nightmare, littered with unsterile implements and the researchers’ food trash (the remnants of Vogel’s bagel sandwich, deliberately left behind). None of the abuse was real — Vogel and Greco were even taking care to cycle the rats in and out of the fake scenario, in order to avoid undue stress from the parade of students who came through taking notes.

Happiness isn’t ultimately what humane treatment is about.

Rodents did not always play the role in labs that they do today. In the late 19th century, experiments were carried out on a whole host of species, including a high proportion of dogs — a fact that animal-welfare activists publicized to turn the “vivisection” debate into a political issue, to the point that even some prominent doctors became galvanized to restrict or ban the practice. In the 20th century, as research shifted to carefully bred rats and mice, optimized for predictability and uniformity, animal experimentation receded as an issue in the public discourse. Today animal-welfare advocates struggle to motivate their base on the matter of rodents: the Humane Society’s website illustrates its section on “Taking Suffering Out of Science” (which sits at the very end in its list of the group’s current “fights”) with a picture of a beagle in a cage, despite the fact that roughly 95 percent of all lab mammals are now rats or mice.

Lab rodents are maybe the most vivid example of a species whose suffering is hard to know how to weigh against the benefits it provides us. Studies using rat and mouse models have sought to answer basic scientific questions across diverse fields of inquiry: psychology, physiology, pathology, genetics. Look into any new advance in human health care, and you’re likely to find that it’s built on years of experimentation that consumed the lives of literally thousands of rodents. We may now be on the cusp of innovations that could allow that toll to be radically reduced — by essentially replacing animal models with some combination of virtual simulations and lab-grown tissue and organs — but it’s hard to imagine a world anytime soon where human patients would be subject to therapies that have never been tested on hundreds of animals. No one even reliably counts how many rodents are killed in U.S. labs every year, but the estimates range from 10 million up to more than 100 million.

This question of scale especially haunts the problem of livestock, which is an area where many of the contest’s student competitors will eventually find jobs. America is currently home to roughly 87 million cattle and 75 million pigs: populations that exceed those of dogs and cats in scale, but the welfare of which commands so much less of our moral attention.

When the practice of centralized, industrialized livestock management began in earnest after the Civil War, the treatment of the animals, especially during slaughter, could be barbaric. Pigs were simply hoisted up and their throats cut, and after some point were assumed to be dead enough to dump into boiling water so that the sharp bristles on their skin could be scraped away. There was little doubt that some of them were still conscious at the point that they were plunged into the water, as was reported in a broad exposé in 1880 by The Chicago Tribune: “Not infrequently,” the reporter noted, “a hog reaches the scalding-tub before life is extinct; in fact, they sometimes are very full of life when they reach the point whence they are dumped into the seething tub.”

After 1906, when Upton Sinclair’s “The Jungle” exposed the industry’s unsanitary practices, a series of reforms did lead to significant improvements in the lives and deaths of American livestock. Thanks to the Humane Slaughter Act of 1958, federal law now requires that animals be “rendered insensible to pain” before the act of killing; with pigs, this is generally done either with electrocution or by suffocation in a carbon-dioxide chamber, while with cattle, the method of choice is the captive-bolt gun. And since the 1970s, animal-welfare science has led to some considerable reforms. Perhaps the most transformational work has been done by Temple Grandin, the animal behaviorist whose research into how food animals experience and respond to their environment — particularly during transport and slaughter — has changed the way that meat and dairy producers operate.

Still, despite years of promises to end the practice, many sows are still kept almost permanently in 7-feet-by-2-feet “gestation crates,” too small to turn around in. And the rise of concentrated animal feeding operations (CAFOs) has doomed millions of pigs, cattle and chickens to lives spent cheek to jowl in the stench of their own waste — waste that also threatens the health of nearby communities and ecosystems.

At the contest, many attendees were excited about the gains that artificial intelligence could bring to the animal-welfare field. Pilot studies have indeed shown great promise: For example, with A.I. assistance, 24-hour video surveillance can help pinpoint sick or injured animals much more quickly so they can be pulled out for veterinary care. Last year, a group of European researchers announced that based on 7,000 recordings of more than 400 pigs, they had made significant progress in understanding the meaning of their grunts. “By training an algorithm to recognize these sounds, we can classify 92 percent of the calls to the correct emotion,” one of the scientists remarked.

That well may be, but given what we know about pigs — specifically, their remarkable intelligence, which rivals (if not exceeds) that of a dog, to the point that a group of scientists recently trained some to play video games — there is no amount of A.I.-driven progress that can reconcile their short, crowded life as an American industrial food animal with any definition of what a “good” life looks like for such brainy creatures, all 75 million of them.

The laying hen, among the four species considered at the contest, is the one that lives among us in the largest numbers: There are an estimated 308 million of them in the United States alone, or nine for every 10 Americans. In a backyard flock, these hens could be expected to live six to eight years, but a vast majority of them toil in industrial operations that will slaughter them after only two to three years, once their productivity (six eggs a week) declines — and chickens, notably, are not covered by the Humane Slaughter Act. Poor air quality, soiled litter, nutritional stress and conflict with other chickens can contribute to dietary deficiencies, infectious diseases, egg-laying complications, self-mutilation, even cannibalism. And even in the best laying-hen operations, including the “cage-free” ones imagined in the contest scenario, these are short lives spent under 16 hours a day of artificial lighting in extremely close quarters with other birds.

More than in the other scenarios, the organizers had made the laying-hen choice a straightforward one. The corporate farm offered fewer amenities for the birds, which were also observed rarely to use the dirt-floored, plastic-covered “veranda” that was supposed to serve as a respite from their long hours laying in the aviary. The more commodious verandas of the family farm, covered with synthetic grass, proved more popular with their chickens, and in warm weather, its birds made use of a screened “garden” as well.

In her presentation, Catherine LeBlond correctly picked the family farm, for many of the same reasons that the judges did. Again, she “granted” some positive qualities of the corporate farm and offered it some advice — reflecting, after all, the values of the veterinary profession that she was training to enter, a field that takes on the advising of everyone who has animals in their care, not only the most conscientious.

Even so, at the very end, LeBlond briefly stepped back to ask a true ethical question, one that troubled the entire premise of a multibillion-dollar global industry: “whether or not it is ethical to keep these hens for the sole purpose of egg-laying, only to have them slaughtered at the end.” Among the scores of students we watched over the course of a weekend, LeBlond and her teammates from the Atlantic Veterinary College were the only ones who, in the final seconds of their talks, raised deep questions about the scenario’s entire premise — about whether, in the end, these fictional animals should have been put in these fictional situations in the first place.

It was a question that the judges of the Animal Welfare Assessment Contest had no doubt considered, but it also was one that seemed to lie outside the contest’s purview: In its either-or structure, the contest is helping train future professionals how to improve, rather than remove, the ties that bind animals into human society. Unless the day arrives when there is no need for laboratory rats, or poultry barns, or facilities to house desert tortoises and other captive wildlife, the animals of North America will be in the hands of veterinarians and animal scientists like LeBlond and her classmates, to help shape their situations the very best way they can.

Parts of this article are adapted from “Our Kindred Creatures: How Americans Came to Feel the Way They Do About Animals,” by Bill Wasik and Monica Murphy, published this month by Knopf.

Read by Gabra Zackman

Narration produced by Krish Seenivasan and Emma Kehlbeck

Engineered by Lance Neal

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Artificial intelligence, machine learning boost animal science research

Supercomputers and artificial intelligence aren't typically thought to go with animal science, but they are among the tools for a relatively new field of science called bioinformatics that can be used to improve animal health and productivity.

Jumping from human-focused medical research at Yale University and Stanford University, Aranyak Goswami is a bioinformatics specialist who recently became an assistant professor for the Arkansas Agricultural Experiment Station. He will work with three different departments to boost the research arm of the U of A System Division of Agriculture.

"Artificial intelligence and machine learning are at the forefront of many aspects of animal and poultry production," said Michael Looper, head of the Animal Science Department. "Dr. Goswami's expertise in these key areas complements our current research programs in animal health, genetics and well-being."

Like putting together a jigsaw puzzle from millions of small pieces, Goswami implements data analysis tactics to make sense of data generated from complex research like genetic sequencing. The field known as bioinformatics, or computational biology, links biological data with information storage, distribution and analysis to support many scientific research areas.

Use of the term bioinformatics began in the 1970s , based on foundations laid in the 1960s .

Looper said collaborations between the fields of computational biology and animal science will "greatly benefit producers in Arkansas and beyond." Goswami is already working with Jiangchao Zhao, a professor of animal science, on a collaboration that will study animal microbiomes that regulate digestion, reproduction and infection resistance, to name a few.

"One of my main interests will be to explore microbiomes to improve cattle and poultry health," Goswami said. "There are a lot of genomes which are coming out that need to be sequenced, and there are several gaps in this field."

Genome sequencing is a method used to determine the entire genetic makeup of a specific organism to find comparative changes of the genome. For example, Goswami's research would examine different gene expression patterns.

"You can study the biological pathways that are activated and those that are not," Goswami explained. "And what are the specific metabolic pathways they are using? And what are their protein interactions? What can we find to make them healthier or improve meat productivity?"

With gut health in mind, Goswami's analysis will help animal scientists pinpoint a specific class of bacteria or virus affecting an animal to help design probiotics and other therapeutic approaches.

As a computational biologist, Goswami said he wants to apply his experiences in human health research and machine learning to animal health.

"Whatever is exciting in the human field in general is more exciting for the animal field because the genomes are not standardized," Goswami said. "There is a lot of sequencing that needs to be done and a lot of methods that need to be developed. So that's a lot of exciting work for a computational biologist."

Machine learning in agriculture

Goswami will teach courses through the Dale Bumpers College of Agricultural, Food and Life Sciences. Through the experiment station, he will conduct research in the Animal Science and Poultry Science departments and the Center for Agricultural Data Analytics.

"We are thrilled to have Dr. Goswami join our programs here in Bumpers College and the Arkansas Agricultural Experiment Station," said David Caldwell, head of the Poultry Science Department and director of the Center of Excellence for Poultry Science. "We believe ongoing research in the areas of poultry food safety and disease prevention that involve high-throughput sequencing or omics data will gain significant benefits from Dr. Goswami's expertise in bioinformatics."

Goswami said he looks forward to helping develop the Center for Agricultural Data Analytics as a "world-class center in machine learning, statistical learning and mathematical modeling with respect to agriculture."

"Most of our students have never had the opportunity to take a course in artificial intelligence," Looper said. "Through his teaching responsibility, Dr. Goswami also will expose our students to the exciting field of machine learning in the agricultural sciences."

New field with potential growth

Bioinformatics is a relatively new field of science, but there is a lot of potential expansion, Goswami said. In 2017, Goswami completed his doctorate in bioinformatics, focusing on microbial ecology, evolution and genomics at the Indian Institute of Chemical Biology under Chitra Dutta in Kolkata. Goswami said Dutta is a pioneer in bioinformatics and computational biology in India, with a theoretical physics and mathematical sciences background.

Goswami has served in postdoctoral positions at Yale University, working with psychiatrists, epidemiologists and physicians focused on cardiovascular, genetics and internal medicine research. His most recent position was as a Stanford University postdoctoral fellow and research scientist.

At Stanford University, Goswami was involved in an initiative known as the "Long-Range Planning Report" to highlight the rights of postdoctoral faculty in aspects such as salary, health care, security and career development.

"Our efforts have the potential to catalyze transformative changes in the broader landscape of postdoctoral experiences throughout the United States," Goswami said.

Provided by University of Arkansas

'Animal-centred internet' may be possible, scientists suggest

New research found that parrots preferred live video calls over recorded video messages - which may lay the foundations for an online world for animals, researchers said.

News reporter @niamhielynch

Thursday 2 May 2024 02:55, UK

An "animal-centred internet" - which could allow pets to interact with each other as well as humans - may be possible, scientists have suggested.

The findings come following a new study by researchers at the University of Glasgow found that parrots may prefer live chats with their friends over recorded messages - part of wider research that they said could pave the way for an online world for animals.

Scientists believe parrots prefer the video calls because they may be able to tell the difference between live chats and pre-recorded messages.

Lead author Dr Ilyena Hirskyj-Douglas, from the University of Glasgow's School of Computing Science, said the internet holds "a great deal of potential for giving animals agency to interact with each other in new ways".

But she warned "the systems we build to help them do that need to be designed around their specific needs and physical and mental abilities".

"Studies like this could help to lay the foundations of a truly animal-centred internet."

Dr Hirskyj-Douglas added: "Our previous research had shown that parrots seem to benefit from the opportunity to video call each other, which could help reduce the mental and physical toll that living in domestic situations can take on them.

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"In the wild, they live in flocks and socialise with each other constantly.

"As pets, they're often kept on their own, which can cause them to develop negative behaviours like excessive pacing or feather-plucking."

The study, which also involved a team from Northeastern University in the US , aimed to explore the online social lives of nine pet parrots.

Each bird had a profile created with their photo and tablets were provided to their owners so the birds could make video calls on Facebook Messenger.

The parrots were trained to ring a bell when they wanted to interact with the screen and also took part in a "meet and greet" session where they were introduced to other birds.

Over six months, the birds were then given access to 12 video sessions, six of which were live calls with their Facebook friends while the remaining involved watching pre-recorded videos of their bird contacts.

Findings showed the parrots preferred live chats to pre-recorded sessions, as they spent a total of 561 minutes on live calls compared with 142 minutes on playback video.

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The birds initiated 65 calls out of a possible 108 in the live phase, but just 40 in the pre-recorded sessions, the team said.

Dr Hirskyj-Douglas said the study "has given us new insight into how these intelligent birds react to the complex stimulus digital tablets can provide".

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"Their behaviour while interacting with another live bird often reflected behaviours they would engage in with other parrots in real life, which wasn't the case in the pre-recorded sessions."

ORIGINAL RESEARCH article

This article is part of the research topic.

Climate and Environmental Changes in Circum-Mediterranean Regions

Bibliometric Analysis of Publications on the Effect of Animal Production on Climate Change from Past to Present Provisionally Accepted

• 1 Bingöl University, Türkiye

The final, formatted version of the article will be published soon.

Bibliometrics and scientific mapping methods using R software, the biblioshiny web program, Scopus and VOSviewer were used to analyze the works of literature referenced and analyzed by the Web of Science during 1990-2023 in order to provide a thorough overview of the effect of animal production on climate change research from 1990 to 2023. A bibliometric analysis of 6558 publications that were published on the Web of Science database was done in order to determine which articles, authors, and journals were the most important. It also provided information on future study themes and gaps, as well as present topic trends. The most productive nations are China, the USA, and Australia; the most productive journals are Global Change Biology, The Science of the Total Environment, and Environmental Science and Pollution Research International. The analysis's findings show that, over the course of the study period, there was a noticeable rise in the number of research publications discussing how animal production is impacted by climate change, along with a steady expansion of the study area. The level of cooperation and research projects in this field among nations has increased, which has improved the caliber of publications over time. Important publications, writers, and journals in the area of how animal production affects climate change were also tallied. The problem of animal production and climate change will become significantly more dependent on new data, techniques, and technology.

Keywords: Bibliometrics, Climate Change, Animal production, Web of Science, trend

Received: 17 Mar 2024; Accepted: 02 May 2024.

Copyright: © 2024 Çelik. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Mx. Şenol Çelik, Bingöl University, Bingöl, Türkiye

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Sumatran orangutan becomes first wild animal seen using medicinal plant to treat wound

A Sumatran orangutan has become the first wild animal seen self-medicating with a plant to heal a wound.

The male orangutan, named Rakus, had sustained a wound on his cheek pad, most likely from fighting other males, researchers said in a study published in the journal Scientific Reports.

Rakus was seen chewing liana leaves without swallowing them, then using his fingers to apply the resulting juice onto the wound, the researchers said.

Finally, he covered the wound up completely with a paste he had made by chewing the leaves and continued feeding on the plant.

Five days after he was seen applying the leaf paste onto the wound it was closed, and a month later barely visible.

Rakus is seen with a facial wound below his eye.

Two months later the wound was almost invisible.

It is the first documented case of active wound treatment by a wild animal with a plant known to have medicinal qualities.

The leaves were from a liana known as akar kuning ( Fibraurea tinctoria in Latin), which is used in traditional medicine to relieve pain, reduce fever and treat various diseases, such as diabetes and malaria.

It also has antibacterial, anti-inflammatory, antifungal and antioxidant properties.

"To the best of our knowledge, there is only one report of active wound treatment in non-human animals, namely in chimpanzees," the researchers wrote.

"This possibly innovative behaviour presents the first systematically documented case of active wound treatment with a plant species known to contain biologically active substances by a wild animal and provides new insights into the origins of human wound care."

The orangutan's behaviour was recorded in 2022 by Ulil Azhari, a co-author and field researcher at the Suaq Project in Medan, Indonesia.

Scientists have been observing orangutans in Indonesia's Gunung Leuser National Park since 1994, but they hadn't previously seen this behaviour.

It's possible Rakus learned the technique from other orangutans living outside the park and away from scientists' daily scrutiny, said co-author Caroline Schuppli at Max Planck.

Rakus was born and lived as a juvenile outside the study area. Researchers believe the orangutan got hurt in a fight with another animal. It's not known whether Rakus earlier treated other injuries.

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