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This opinion piece, written by ethnobiologists from different parts of the world, emphasizes the importance of ethnobiology research in advancing contemporary biology, natural resource management, biodiversity conservation, sustainable development, and, especially, contributing to the ecological transition and more just and inclusive world. To achieve these goals, it is essential to develop research and collaborate with social groups that live in close relationship with nature in research activities, such as Indigenous Peoples and Local Communities (IPLC), as well as Afro-descendants and other Marginalized, Minority or Minoritized Communities (AMMC). Ethnobiology can identify and provide locally appropriate solutions to local problems, enabling sustainable resource management at the landscape level. The text explores important aspects that need to be considered to guide the future of ethnobiology in the next 20 years, aiming to integrate and amplify previous discussions held in the discipline and identify points that demand ongoing attention. This paper highlights reflections from diverse researchers, emphasizing how ethnobiology can embrace different perspectives and employ rigorous analysis of complex phenomena toward effective policies and practices. This approach holds the potential to address the challenges the planet is currently facing in the coming decades. [ABSTRACT FROM AUTHOR]

Background: Circadian rhythms are important for all aspects of biology; virtually every aspect of biological function varies according to time of day. Although this is well known, variation across the day is also often ignored in the design and reporting of research. For this review, we analyzed the top 50 cited papers across 10 major domains of the biological sciences in the calendar year 2015. We repeated this analysis for the year 2019, hypothesizing that the awarding of a Nobel Prize in 2017 for achievements in the field of circadian biology would highlight the importance of circadian rhythms for scientists across many disciplines, and improve time-of-day reporting. Results: Our analyses of these 1000 empirical papers, however, revealed that most failed to include sufficient temporal details when describing experimental methods and that few systematic differences in time-of-day reporting existed between 2015 and 2019. Overall, only 6.1% of reports included time-of-day information about experimental measures and manipulations sufficient to permit replication. Conclusions: Circadian rhythms are a defining feature of biological systems, and knowing when in the circadian day these systems are evaluated is fundamentally important information. Failing to account for time of day hampers reproducibility across laboratories, complicates interpretation of results, and reduces the value of data based predominantly on nocturnal animals when extrapolating to diurnal humans. [ABSTRACT FROM AUTHOR]

On January 2020, the WHO Director General declared that the outbreak constitutes a Public Health Emergency of International Concern. The world has faced a worldwide spread crisis and is still dealing with it. The present paper represents a white paper concerning the tough lessons we have learned from the COVID-19 pandemic. Thus, an international and heterogenous multidisciplinary panel of very differentiated people would like to share global experiences and lessons with all interested and especially those responsible for future healthcare decision making. With the present paper, international and heterogenous multidisciplinary panel of very differentiated people would like to share global experiences and lessons with all interested and especially those responsible for future healthcare decision making. [ABSTRACT FROM AUTHOR]

Musk, the dried secretion from the musk sac gland which is located between the navel and genitals of mature male musk deer, is utilized as oriental medicine in east Asia. It has been utilized to treat conditions such as stroke, coma, neurasthenia, convulsions, and heart diseases in China since ancient times. This paper aims to provide a comprehensive overview of musk in zoology, chemical composition, pharmacology, clinical applications, and quality control according to the up-to-date literature. Studies found that musk mainly contains macrocyclic ketones, pyridine, steroids, fatty acids, amino acids, peptides, and proteins, whilst the main active ingredient is muscone. Modern pharmacological studies have proven that musk possesses potent anti-inflammatory effects, neuroprotective effects, anti-cancer effects, antioxidant effects, etc. Moreover, muscone, the main active ingredient, possesses anti-inflammatory, neuroprotective, antioxidant, and other pharmacological effects. In the quality control of musk, muscone is usually the main detection indicator, and the common analytical method is GC, and researchers have established novel and convenient methods such as HPLC-RI, RP-UPLC-ELSD, and Single-Sweep Polarography. In addition, quality evaluation methods based on steroids and the bioactivity of musk have been established. As for the identification of musk, due to various objective factors such as the availability of synthetic Muscone, it is not sufficient to rely on muscone alone as an identification index. To date, some novel technologies have also been introduced into the identification of musk, such as the electronic nose and DNA barcoding technology. In future research, more in vivo experiments and clinical studies are encouraged to fully explain the pharmacological effects and toxicity of musk, and more comprehensive methods are needed to evaluate and control the quality of musk. [ABSTRACT FROM AUTHOR]

In this introduction article, we summarize the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference which was held on August 9–10, 2020 (virtual conference). We then briefly describe the nine research articles included in this supplement issue. ICIBM 2020 hosted four scientific sections covering current topics in bioinformatics, computational biology, genomics, biomedical informatics, among others. A total of 75 original manuscripts were submitted to ICIBM 2020. All the papers were under rigorous review (at least three reviewers), and highly ranked manuscripts were selected for oral presentation and supplement issues. This genomics supplement issue included nine manuscripts. These articles cover methods and applications for single cell RNA sequencing, multi-omics data integration for gene regulation, gene fusion detection from long-read RNA sequencing, gene co-expression analysis of metabolic pathways in cancer, integrative genome-wide association studies (GWAS) of subcortical imaging phenotype in Alzheimer's disease, as well as deep learning methods for protein structure prediction, metabolic pathway membership inference, and horizontal gene transfer (HGT) insertion sites prediction. [ABSTRACT FROM AUTHOR]

Background: Biomedical technologies have not just improved human health but also assisted in the creation of human life. Since the first birth of a healthy baby by in vitro fertilization (IVF) 40 years ago, IVF has been the mainstay treatment for couples struggling with infertility. This technology, in addition to increasingly accessible genetic testing, has made it possible for countless couples to have children. Since CRISPR-Cas9 gene editing was described in 2015, its potential for targeting genetic diseases has been much anticipated. However, the potential of using CRISPR-Cas9 for human germline modification has led to many fears of "designer babies" and widespread concerns for the impact of this technology on human evolution and its implications in Social Darwinism. In addition to these ethical/moral concerns, there remain many unknowns about CRISPR-Cas9 technology and endless unanticipated consequence to gene editing. Methods: In this paper, we analyze the current progresses of CRISPR-Cas9 technology and discuss the theoretical advantages of certain allelic variances in the C-C chemokine receptor 5 gene (CCR5) in the setting of recent ethical/moral concerns regarding gene editing using the CRISPR-Cas9 system. Results: These uncertainties have been highlighted recently by the birth of Chinese twins whose C-C chemokine receptor 5 (CCR5) gene had been inactivated via CRISPR-Cas9 to be theoretically protective against HIV infection. CCR5 signaling is critical for the successful infection of human immunodeficiency virus (HIV) and people with homozygous inactivating CCR5-Δ32 mutations have been shown to be protected against HIV infection. Those with the CCR5-Δ32/Δ32 mutation also have greater neuroplasticity, allowing for improved recovery from neurological trauma, and decreased Chagas cardiomyopathy. However, the CCR5-Δ32/Δ32 mutation has also been associated with earlier clinical manifestations for West Nile infection, ambiguous effects on osteoclast function, and a four-fold increased mortality from influenza infection. These detrimental health impacts, in addition to the confounding factor that these CRISPR babies do not carry this exact CCR5-Δ32/Δ32 mutation, lead to many questions regarding the children's future health and the moral conundrum of their birth. The creation and birth of these babies was not completed with any scientific, ethical, or governmental oversight, which has spurned the acceleration of talks regarding global regulations for human genetic editing. Conclusions: Although we can try to regulate for ethical, health-related only use of this technology, moral and governmental oversights need to be supplemented by technical regulations. For instance, whole genome sequencing needs to be used to eliminate off-target mutations that could affect the health and safety of infants born to this process. Like Pandora's Box, we cannot pretend to forget CRISPR-Cas9 technology, all we can do is ensure a safe, moral, and equitable used of this technology. [ABSTRACT FROM AUTHOR]

Background: Plants, like all living organisms, metamorphose their bodies during their lifetime. All the developmental and growth events in a plant's life are connected to specific points in time, be it seed germination, seedling emergence, the appearance of the first leaf, heading, flowering, fruit ripening, wilting, or death. The onset of automated phenotyping methods has brought an explosion of such time-to-event data. Unfortunately, it has not been matched by an explosion of adequate data analysis methods. Results and discussion: In this paper, we introduce the Bayesian approach towards time-to-event data in plant biology. As a model example, we use seedling emergence data of maize under control and stress conditions but the Bayesian approach is suitable for any time-to-event data (see the examples above). In the proposed framework, we are able to answer key questions regarding plant emergence such as these: (1) Do seedlings treated with compound A emerge earlier than the control seedlings? (2) What is the probability of compound A increasing seedling emergence by at least 5 percent? Conclusion: Proper data analysis is a fundamental task of general interest in life sciences. Here, we present a novel method for the analysis of time-to-event data which is applicable to many plant developmental parameters measured in field or in laboratory conditions. In contrast to recent and classical approaches, our Bayesian computational method properly handles uncertainty in time-to-event data and it is capable to reliably answer questions that are difficult to address by classical methods. [ABSTRACT FROM AUTHOR]

Background: Because of diverse topographical habitats, the Chenab River wetland harbors a wealth of medicinal and food plant species. This paper presents first quantitative assessment on the ethnobotanical use of plants by the local peoples residing in the Chenab riverine area. Methods: The ethnobotanical data were collected from six parts of the Chenab River wetland: Mandi Bahuddin, Gujranwala, Gujrat, Sargodha, and Sialkot during 2014 to 2015, using semi-structured interviews. Quantitative indices including informant consensus factor (FCI), relative frequency of citation (RFC), relative importance level (RIL), use value (UV), fidelity level (FL), and corrected fidelity level (CFL) were used to analyze the data. Results: On the whole, 129 medicinal plant species belonging to 112 genera of 59 families were reported, with herbs as dominant life forms (51%). Poaceae was the leading family with 13 species, and leaves were the most frequently utilized plant parts (28%). Herbal medicines were mostly used in the form of powder or decoction, and were mainly taken orally. Withania somnifera, Solanum surattense, Solanum nigrum, Azadirachta indica, Ficus benghalensis, Morus nigra, Morus alba, Polygonum plebeium, and Tribulus terrestris were among the highly utilized plant species, with highest UV, RFC, RIL, FL, and CFL values. The reported ailments were grouped into 11 categories based on FCI values, whereas highest FIC was recorded for gastrointestinal diseases and glandular diseases (0.41 and 0.34, respectively). The use report (UR) and frequency of citation (FC) depicted strong positive correlation (r = 0.973; p = 0.01). The value of determination (r2 = 0.95) indicating 95% variation in UR can be explained in terms of the FC. Conclusion: The significant traditional knowledge possessed by local communities depicts their strong relation with phytodiversity. Reported data could be helpful in sustainable use and protection of plant species in the Chenab wetland, with special emphasis on medicinal plants. Furthermore, screening of plant-borne active ingredients and in vivo/in vitro pharmacological activities could be of interest for novel drug synthesis. [ABSTRACT FROM AUTHOR]

Background: Southeast Asia is known for its rich linguistic, cultural and biological diversity. While ethnobiology in the west has benefitted greatly from intellectual and methodological advances over the last decades, the status of Southeast Asian ethnobiology is largely unknown. This study aims to provide an analysis of the current status of ethnobiology in Southeast Asia and outlines possibilities for future advancements. Methods: We accessed papers cited in the Scopus and Web of Science databases for the period of 1960 to 2014 using the current as well as previous names of the 11 Southeast Asian countries and various disciplines of ethnobiology as key words. We juxtaposed the number of publications from each country against its number of indigenous groups and languages, to see if ethnobiology research has addressed this full spectrum of ethnical diversity. The available data for the last ten years was analysed according to the five phases concept to understand the nature of studies dominating Southeast Asian ethnobiology. Results and conclusions: A total number of 312 publications were recorded in the databases for the period 1960-2014. Indonesia ranks highest (93 studies), followed by Thailand (68), Malaysia (58) Philippines (42), Vietnam (31), Laos (29), and other Southeast Asian countries (44). A strong correlation was found between the number of publications for each country, the number of indigenous groups, and the number of endangered languages. Comparing the data available for the period 2005-2009 with 2010-2014, we found a strong increase in the number of phase 5 publications. However, papers with bioprospecting focus were also on the rise, especially in Malaysia. Our study indicates that ethnobiologists still need to realise the full potential of the Biocultural Diversity of Southeast Asia, and that there is a strong need to focus more on socially relevant research. [ABSTRACT FROM AUTHOR]

Background: A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic materials between different species. Horizontal gene transfer has been found prevalent in prokaryotes but very rare in eukaryote. In this paper, we investigate horizontal gene transfer in the human genome. Results: From the pair-wise alignments between human genome and 53 vertebrate genomes, 1,467 human genome regions (2.6 M bases) from all chromosomes were found to be more conserved with non-mammals than with most mammals. These human genome regions involve 642 known genes, which are enriched with ion binding. Compared to known horizontal gene transfer regions in the human genome, there were few overlapping regions, which indicated horizontal gene transfer is more common than we expected in the human genome. Conclusions: Horizontal gene transfer impacts hundreds of human genes and this study provided insight into potential mechanisms of HGT in the human genome. [ABSTRACT FROM AUTHOR]

Background: An absent word with respect to a sequence is a word that does not occur in the sequence as a factor; an absent word is minimal if all its factors on the other hand occur in that sequence. In this paper we explore the idea of using minimal absent words (MAW) to compute the distance between two biological sequences. The motivation and rationale of our work comes from the potential advantage of being able to extract as little information as possible from large genomic sequences to reach the goal of comparing sequences in an alignment-free manner. Findings: We report an experimental study on the use of absent words as a distance measure among biological sequences. We provide recommendations to use the best index based on our analysis. In particular, our analysis reveals that the best performers are: the length weighted index of relative absent word sets, the length weighted index of the symmetric difference of the MAW sets, and the Jaccard distance between the MAW sets. We also found that during the computation of the absent words, the reverse complements of the sequences should also be considered. Conclusion: The use of MAW to compute the distance between two biological sequences has potential advantage over alignment based methods. It is expected that this potential advantage would encourage researchers and practitioners to use this as a (dis)similarity measure in the context of sequence comparison and phylogeny reconstruction. Therefore, we present here a comparison among different possible models and indexes and pave the path for the biologists and researchers to choose an appropriate model for such comparisons. [ABSTRACT FROM AUTHOR]

Background: Fluorescence molecular tomography (FMT) is an optical imaging technique that reveals biological processes within small animals through non-invasively reconstructing the distributions of fluorescent agents. The primary problem in FMT with non-stationary fluorescent yield is the increase of the unknown parameters to be reconstructed. In this paper, a method is proposed to reconstruct dynamic fluorescent yield.Methods: A shape-based reconstruction method that recovers dynamic fluorescent yield with a level set method is proposed for FMT. To reduce the number of unknown parameters, a level set function is introduced to describe the shape of target and a small number of parameters are used to describe the fluorescent yields at different time points.Results: Results of simulations and phantom experiments demonstrate that the proposed method can recover well the dynamic fluorescent yields, shapes and locations of the target.Conclusions: The proposed method can handle the cases with non-stationary fluorescent yields and recover the fluorescent yields at each projection angle. [ABSTRACT FROM AUTHOR]

Background: Morphogenesis is a developmental process in which cells organize into shapes and patterns. Complex, non-linear and multi-factorial models with images as output are commonly used to study morphogenesis. It is difficult to understand the relation between the uncertainty in the input and the output of such 'black-box' models, giving rise to the need for sensitivity analysis tools. In this paper, we introduce a workflow for a global sensitivity analysis approach to study the impact of single parameters and the interactions between them on the output of morphogenesis models. Results: To demonstrate the workflow, we used a published, well-studied model of vascular morphogenesis. The parameters of this cellular Potts model (CPM) represent cell properties and behaviors that drive the mechanisms of angiogenic sprouting. The global sensitivity analysis correctly identified the dominant parameters in the model, consistent with previous studies. Additionally, the analysis provided information on the relative impact of single parameters and of interactions between them. This is very relevant because interactions of parameters impede the experimental verification of the predicted effect of single parameters. The parameter interactions, although of low impact, provided also new insights in the mechanisms of in silico sprouting. Finally, the analysis indicated that the model could be reduced by one parameter. Conclusions: We propose global sensitivity analysis as an alternative approach to study the mechanisms of morphogenesis. Comparison of the ranking of the impact of the model parameters to knowledge derived from experimental data and from manipulation experiments can help to falsify models and to find the operand mechanisms in morphogenesis. The workflow is applicable to all 'black-box' models, including high-throughput in vitro models in which output measures are affected by a set of experimental perturbations. [ABSTRACT FROM AUTHOR]

Background: Multiscale approaches for integrating submodels of various levels of biological organization into a single model became the major tool of systems biology. In this paper, we have constructed and simulated a set of multiscale models of spatially distributed microbial communities and study an influence of unevenly distributed environmental factors on the genetic diversity and evolution of the community members. Results: Haploid Evolutionary Constructor software http://evol-constructor.bionet.nsc.ru/ was expanded by adding the tool for the spatial modeling of a microbial community (1D, 2D and 3D versions). A set of the models of spatially distributed communities was built to demonstrate that the spatial distribution of cells affects both intensity of selection and evolution rate. Conclusion: In spatially heterogeneous communities, the change in the direction of the environmental flow might be reflected in local irregular population dynamics, while the genetic structure of populations (frequencies of the alleles) remains stable. Furthermore, in spatially heterogeneous communities, the chemotaxis might dramatically affect the evolution of community members. [ABSTRACT FROM AUTHOR]

Background: A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in Saccharomyces cerevisiae using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in S. cerevisiae demonstrated the generality of our method. Conclusion: We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify genetic parts to fine-tune gene expression rates is crucial to the design of biological systems, such a tool may play an important role in the success of synthetic biology going forward. [ABSTRACT FROM AUTHOR]

Background: The founders of Hereditas envisioned that race biology would be a major subject that had social applications with utmost importance in the near future. Anthropometrics was in this context understood to be the pure and eugenics the applied science. Sweden had a long tradition in physical anthropometry. Herman Lundborg, member of the advisory board of Hereditas, united the anthropometric and eugenic approaches in a synthesis. He was the first head of the Institute for Race Biology in Sweden. The contents of Hereditas reflect the development of race biology in the Nordic countries. Conclusions: The initial enthusiasm for applied race biology did not last long. In the 1920's Hereditas carried papers on both physical anthropology and eugenics. Most paper dealt, however, with human genetics without eugenic content. Two papers, published in 1921 and 1939 show how the intellectual climate had changed from positive to negative. Finally only human genetics prevailed as the legitimate study of the human race or humankind. A belated defense of eugenics published in 1951 did not help; geneticists had abandoned anthropometrics for good around the year 1940 and eugenics about a decade later. In spite of that, eugenic legislation was amended astonishingly late, in the 1970's. The development was essentially similar in all Nordic countries. [ABSTRACT FROM AUTHOR]

A recent paper in BMC Biology entitled "A tissue level atlas of the healthy human virome" by Kumata et al. describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project. Using a workflow that maps the GTEx sequences to the human genome, then screens unmapped sequences to detect viral transcripts, the authors present a quantitative analysis of the presence of different viruses in the non-diseased tissues of over 500 individuals and assess the impact of these viruses on host gene expression. Here we draw attention to an issue not acknowledged in this study. Namely, by relying solely on GTEx datasets, which are enriched for transcripts with poly(A) tails, the analysis will have missed non-poly(A) viral transcripts, rendering this tissue level atlas of the virome incomplete. A commentary on Kumata et al. (BMC Biol 18:55, 2020). [ABSTRACT FROM AUTHOR]

Frameworks that govern the development and application of novel products, such as the products of synthetic biology, should involve all those who are interested or potentially affected by the products. The governance arrangements for novel products should also provide a democratic mechanism that allows affected parties to express their opinions on the direction that innovation does or does not take. In this paper we examine rationales, obstacles and opportunities for public participation in governance of novel synthetic biology products. Our analysis addresses issues such as uncertainties, the considering of alternative innovations, and broader social and environmental implications. The crucial issues in play go beyond safety alone, to include contending social values around diverse notions of benefit and harm. The paper highlights the need for more inclusive social appraisal mechanisms to inform governance of Synthetic Biology and alternative products, and discusses a few practical methods to help achieve this goal. [ABSTRACT FROM AUTHOR]

Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function. It is the study of the composition of all components of a biological system and their interactions under specific conditions. The core of systems biology is holistic and systematic research, which is different from the manner of thinking and research of all other branches of biology to date. Chinese herbal formulae (CHF) are the main form of Chinese medicine and are composed of single Chinese herbal medicines (CHMs) with pharmacological and pharmacodynamic compatibility. When single CHMs are combined into CHF, the result is different from the original effect of a single drug and can be better adapted to more diseases with complex symptoms. CHF represent a complex system with multiple components, targets and effects. Therefore, the use of systems biology is conducive to revealing the complex characteristics of CHF. With the rapid development of omics technologies, systems biology has been widely and increasingly applied to the study of the basis of the pharmacological substances, action targets and mechanisms of CHF. To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and metagenomics and their applications in research on CHF. [ABSTRACT FROM AUTHOR]

The development and use of genetic technologies is regulated by countries according to their national laws and governance structures. Legal frameworks require comprehensive technical evidence to be submitted by an applicant on the biology of the organism, its safety to human, animal health and the environment in which it will be released. Some countries also require information on socio-economic and trade impacts. One of the key elements that assists decision-making under those legal frameworks is the use of risk assessments. The risk assessment paradigm of problem formulation based on risk hypothesis, and the assessment of plausible scientific pathways leading to potential environmental and human harms being realised, has been used widely to assess potential risks of genetic technologies to human health and the environment, from crops to mosquitoes. This paper uses the case study of a genetically modified self-limiting olive fly ( Bactrocera oleae ) for a first deliberate release in Spain to examine the regulatory processes and stakeholders involved in the assessment of risk. It is anticipated that existing risk assessment frameworks are equally applicable to gene drive technologies that may spread and persist in the environment and cross-national borders, but it is the governance structures surrounding the involvement of civil society in regulatory processes that must be administered in a more transparent and defined manner. [ABSTRACT FROM AUTHOR]

How organs grow to be the right size for the animal is one of the central mysteries of biology. In a paper in BMC Biology, Khammash et al. propose a mechanism for escaping from the deficiencies of feedback control of growth as a mechanism. [ABSTRACT FROM AUTHOR]

Selected papers from the 13th International Conference on Bioinformatics (InCoB2014), July 31-2 August, 2014 in Sydney, Australia have been compiled in this supplement. These range from network analysis and gene regulatory networks to systems level biological analysis, providing the 2014 update to InCoB's computational systems biology research. [ABSTRACT FROM AUTHOR]