Biological Disciplines Research Articles

DiMo: discovery of microRNA motifs using deep learning and motif embedding.

MicroRNAs are small regulatory RNAs that decrease gene expression after transcription in various biological disciplines. In bioinformatics, identifying microRNAs and predicting their functionalities is critical. Finding motifs is one of the most well-known and important methods for identifying the functionalities of microRNAs. Several motif discovery techniques have been proposed, some of which rely on artificial intelligence-based techniques. However, in the case of few or no training data, their accuracy is low. In this research, we propose a new computational approach, called DiMo, for identifying motifs in microRNAs and generally macromolecules of small length. We employ word embedding techniques and deep learning models to improve the accuracy of motif discovery results. Also, we rely on transfer learning models to pre-train a model and use it in cases of a lack of (enough) training data. We compare our approach with five state-of-the-art works using three real-world datasets. DiMo outperforms the selected related works in terms of precision, recall, accuracy and f1-score.

Sexual harassment disproportionately affects ecology and evolution graduate students with multiple marginalized identities in the United States

Abstract Sexual harassment within academic institutions has profound impacts that may lead to the attrition of groups historically excluded from the biological sciences and related disciplines. To understand sexual harassment's effects on vulnerable communities within academia, we examined graduate student experiences with sexual harassment. In a survey of ecology and evolutionary biology programs across the United States, we found that 38% of the graduate student respondents were sexually harassed during their time in these programs. Sexual harassment disproportionately affected graduate students with multiple intersecting marginalized identities, and these experiences led to delays in completing graduate programs and shifts away from their desired careers. Our research highlights the need for academic institutions, and science more broadly, to make widespread changes to sexual harassment policies, including treating sexual harassment as scientific misconduct and creating resources for individuals within students’ informal support networks, in tandem with efforts to dismantle barriers to advancing diversity, equity, and inclusion.

Cross-species microbial genome transfer: a Review.

Synthetic biology combines the disciplines of biology, chemistry, information science, and engineering, and has multiple applications in biomedicine, bioenergy, environmental studies, and other fields. Synthetic genomics is an important area of synthetic biology, and mainly includes genome design, synthesis, assembly, and transfer. Genome transfer technology has played an enormous role in the development of synthetic genomics, allowing the transfer of natural or synthetic genomes into cellular environments where the genome can be easily modified. A more comprehensive understanding of genome transfer technology can help to extend its applications to other microorganisms. Here, we summarize the three host platforms for microbial genome transfer, review the recent advances that have been made in genome transfer technology, and discuss the obstacles and prospects for the development of genome transfer.

The First University School of Russian Genetics

Professor Yu.A. Filipchenko founded the first department of genetics (then genetics and experimental zoology) in Russia in 1919. The first department of genetics in Russia made its first steps in the context of world science was facilitatedthrough contacts between leading scientists in genetics, who today are recognized as classics of genetics – T.H. Morgan, Yu.A. Filipchenko, N.I. Vavilov, W. Bateson, G.A. Levitsky, G.D. Karpechenko, F.G. Dobzhansky, H.J. Muller, M.E. Lobashev and others. The modern scientific and educational activities of the department are predetermined by its previous history and the staff of the department continues to develop the traditions of the educational and scientific complex. Teaching work is link inextricably with research work within the framework of a common problem – “Mechanisms of the genetic processes integration”. The formulation of a broad problem makes it possible to resist centrifugal tendencies, the cause of which may be the differentiation of interests and specific tasks of researchers, what, in turn, is fraught with the danger of training narrow specialists. The formularization of some unifying problem is traditional for the department and preserves the basis of mutual understanding between different geneticists, and emphasizes that geneticsis one of the most important general biological disciplines.

Advances in Integration, Wearable Applications, and Artificial Intelligence of Biomedical Microfluidics Systems.

Microfluidics attracts much attention due to its multiple advantages such as high throughput, rapid analysis, low sample volume, and high sensitivity. Microfluidics has profoundly influenced many fields including chemistry, biology, medicine, information technology, and other disciplines. However, some stumbling stones (miniaturization, integration, and intelligence) strain the development of industrialization and commercialization of microchips. The miniaturization of microfluidics means fewer samples and reagents, shorter times to results, and less footprint space consumption, enabling a high throughput and parallelism of sample analysis. Additionally, micro-size channels tend to produce laminar flow, which probably permits some creative applications that are not accessible to traditional fluid-processing platforms. The reasonable integration of biomedical/physical biosensors, semiconductor microelectronics, communications, and other cutting-edge technologies should greatly expand the applications of current microfluidic devices and help develop the next generation of lab-on-a-chip (LOC). At the same time, the evolution of artificial intelligence also gives another strong impetus to the rapid development of microfluidics. Biomedical applications based on microfluidics normally bring a large amount of complex data, so it is a big challenge for researchers and technicians to analyze those huge and complicated data accurately and quickly. To address this problem, machine learning is viewed as an indispensable and powerful tool in processing the data collected from micro-devices. In this review, we mainly focus on discussing the integration, miniaturization, portability, and intelligence of microfluidics technology.

Bioeconomic modelling in tilapia aquaculture: A review

AbstractThe global production of aquatic resources is increasing at the rate of 3.3 million tons per year, main thanks to aquaculture. However, this industry is considered by financial institutions as high risk due to failures caused by epizootics, natural disasters and poor planning and monitoring. Bioeconomic modelling is a progressive branch of social science that seeks to integrate the disciplines of economics and biology to create theories that better explain economic events using a biological basis and vice versa. This should be used in aquaculture to plan, monitor, and determine cost‐effectiveness and risk, to reduce uncertainty and increase profits of ongoing or new projects. A meta‐analysis of the literature on bioeconomic modelling in aquaculture during 26 years (1994─2020) was performed, using four search engines. Sixty‐eight articles were published in 23 journals, on 25 groups of species or species. The most studied were shrimp, tilapia, seabream, salmon and carp. From these, 12 articles dealt with tilapia models that shared similar biological, management and economic sub‐models. In the 26‐year analysis, the global scientific productivity in this field is low (2.6 articles/year) in relation to the growth of world aquaculture. Bioeconomic modelling peaked during the decade from 2004 to 2014 with 5.6 papers/year, but then declined to only 0.83 articles/year from 2015 to 2020. This is possibly due to the low diffusion among producers, planners and financial institutions of the advantages of the models and the difficulty to use them if friendly and readily available software is lacking.

ДЕЯКІ ОСОБЛИВОСТІ ДИСТАНЦІЙНОГО НАВЧАННЯ СТУДЕНТІВ ПРИ ВИВЧЕННІ БІОЛОГІЧНИХ ДИСЦИПЛІН

The article examines the theoretical aspects of distance learning of the educational process participants, in particular, the peculiarities of conducting classes for students of biological specialties. The authors outline the main issues of this scientific field; attention is focused on the most convenient, flexible and accessible learning technologies, which allow to realize a full-fledged educational process in tough conditions of military setting. It is noted that the development of information technologies allows to implement fundamentally new approaches to high school students education. It is emphasized that a remote organization of the educational process implies a slightly different approach to learning on the part of students, which is independent research, analysis, systematization and generalization of information, self-management and self-monitoring. Studying natural sciences in general and biology in particular with the help of information and communication technologies enables to perform a number of didactic tasks with sufficient quality. Thus, a wide range of educational and scientific platforms, such as LearningApps, Scilab, e- Anatomy, "Interesting Science", TeamLabBody, makes it possible to study biological phenomena and processes using computer graphics, modeling and simulation of biological processes (PhET interactive simulation platform ) as well as to carry out experiments in virtual laboratories on the platforms Labster, LabsLand, Go-Lab, VirtualBiologyLab, LabBench Activities by Pearson, Classzone. Based on the analysis of numerous research findings, it was noted that when teaching biological disciplines, it is advisable to divide the independent study material into sections, modules or blocks, create clear instructions, develop methodological recommendations for work performing and results presenting, and motivate students to constant self-monitoring. The article stresses the importance of competency-based tasks, which are student-centered and, therefore, focused on the hands-on application of theoretical knowledge. They provide students with the necessary means and tools for their implementation, contribute to increasing cognitive activity, forming skills in the analysis of biological phenomena and processes developing critical thinking, revealing the personality of a future specialist.

A real data-driven simulation strategy to select an imputation method for mixed-type trait data.

Missing observations in trait datasets pose an obstacle for analyses in myriad biological disciplines. Considering the mixed results of imputation, the wide variety of available methods, and the varied structure of real trait datasets, a framework for selecting a suitable imputation method is advantageous. We invoked a real data-driven simulation strategy to select an imputation method for a given mixed-type (categorical, count, continuous) target dataset. Candidate methods included mean/mode imputation, k-nearest neighbour, random forests, and multivariate imputation by chained equations (MICE). Using a trait dataset of squamates (lizards and amphisbaenians; order: Squamata) as a target dataset, a complete-case dataset consisting of species with nearly complete information was formed for the imputation method selection. Missing data were induced by removing values from this dataset under different missingness mechanisms: missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR). For each method, combinations with and without phylogenetic information from single gene (nuclear and mitochondrial) or multigene trees were used to impute the missing values for five numerical and two categorical traits. The performances of the methods were evaluated under each missing mechanism by determining the mean squared error and proportion falsely classified rates for numerical and categorical traits, respectively. A random forest method supplemented with a nuclear-derived phylogeny resulted in the lowest error rates for the majority of traits, and this method was used to impute missing values in the original dataset. Data with imputed values better reflected the characteristics and distributions of the original data compared to complete-case data. However, caution should be taken when imputing trait data as phylogeny did not always improve performance for every trait and in every scenario. Ultimately, these results support the use of a real data-driven simulation strategy for selecting a suitable imputation method for a given mixed-type trait dataset.

Half a century of evolutionary games: a synthesis of theory, application and future directions.

Half a century of evolutionary games: a synthesis of theory, application and future directions.

A primer on pollen assignment by nanopore-based DNA sequencing

The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device.

A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea).

Environmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits the potential simultaneous retrieval of vast amounts of molecular data from many different organisms and species, thus contributing to a wide range of biological disciplines. Environmental DNA protocols designed for protists often focused on the highly conserved small subunit of the ribosome gene, that does not permit species-level assignments. On the other hand, eDNA protocols aiming at species-level assignments allow a fine level ecological resolution and reproducible results. These protocols are currently applied to organisms living in marine and shallow lotic freshwater ecosystems, often in a bioindication purpose. Therefore, in this study, we present a species-level eDNA protocol designed to explore diversity of Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa that is based on mitochondrial cytochrome oxidase subunit I (COI). These organisms are widespread in lentic water bodies and soil ecosystems. We applied this protocol to 42 samples from peatlands, estuaries and soil environments, recovering all the infraorders in Glutinoconcha (with COI data), except for Hyalospheniformes. Our results revealed an unsuspected diversity in morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With this protocol we expect to revolutionize the design of modern distributional Arcellinida surveys. Our approach involves a rapid and cost-effective analysis of testate amoeba diversity living in contrasted ecosystems. Therefore, the order Arcellinida has the potential to be established as a model group for a wide range of theoretical and applied studies.

Achievements in virus research

This paper brings a brief survey of the achievements in virology as published from the second half of 20th century til now. In beginning, the virus research has been performed at framework of microbiology and/or closely by related biological disciplines, such as parasitology, pathology, mycology and/or cytology. The reason why virologists have been involved in many related scientific disciplines, has been, in addition, because viruses infect not only great many mammalian species, but also lower vertabrates (such as birds and reptiles) and/or certain plants. Even though there could be difficult to assess such great variety of scientific information, a great proportion a great proportion of authors at least has attempted doing with success. Needless to mention that though precise origin of viruses has not been cleared till now, they have probably sequestrated from cellular organelles and then sequently underwent to own (rather independent) evolution

Facilitating biodiversity conservation through partnerships to achieve transformative outcomes.

Conservation biology is a mission-driven discipline that must navigate a new relationship between conservation and science. Because conservation is a social and political as well as an ecological project, conservation biologists must practice interdisciplinarity and collaboration. In a comparative study of 7 cases (Jaguars in the Chaco, Grevy's zebra in Kenya, Beekeeping in Tanzania, Andean cats in Argentina, Jaguars in Mexico, Lobster fishing, and Black bears in Mexico), we examined motivations for collaboration in conservation, who can collaborate in conservation, and how conservation professionals can work well together. In 5 case studies, successful conservation outcomes were prioritized over livelihood benefits. In the other 2 cases, livelihoods were prioritized. All case studies employed participatory approaches. There were multiple external actors, including local and Indigenous communities, nongovernmental organizations, agencies, regional and national governments, and international organizations, which enhanced conservation and wider sustainability outcomes. Key collaboration aspects considered across the case studies were time (mismatch between relationship building and project schedules), trust required for meaningful partnerships, tools employed, and transformative potential for people, nature, and the discipline of conservation biology. We developed guidelines for successful collaboration, including long-term commitment, knowledge integration, multiscalar and plural approaches, cultivation of trust, appropriate engagement, evaluation, supporting students, and efforts for transformation.

Comparison of the Literacy Level on Major Environmental Issues of the G.C.E. (A/L) Students of Different Disciplines in Kandy District, Sri Lanka

The study aims to examine the environmental literacy level of G.C.E A/L students (comparable to British Advanced Level) in the Kandy District, Sri Lanka, and to evaluate environment modules embedded into the curriculum. Furthermore, we find the relationships between environmental literacy level and socioeconomic and discipline levels. A survey with a sample of 300 students was selected randomly from four different disciplines, with 25 students in each subject (biological science, mathematics, arts, and commerce) from three different types of schools (Public, Private, and International). A piloted, self-administered, and structured questionnaire with 44 items under six sections (personal background, environmental issues, attitudes, behavior, suggestion, and mitigation) was randomly distributed among the study sample. Results showed that most respondents reside in an urban area, the education level of parents was positioned in the G.C.E. (A/L) category, and the monthly total family income was more than SLR 90,000.00. Overall, the environmental literacy (EL) was similar among students of three different types of schools. The type of permanent residence, discipline, and educational background of parents were recognized as determining factors of EL levels (p < 0.05). The environmental literacy knowledge of biological science students was the highest (44%), followed by mathematics (36%), art (32%), and commerce (28%). Furthermore, the EL of the biology discipline was significantly different from commerce (18%) and art (14%) students. Students acquired environmental knowledge from television and radio (44%), internet (22%), school (27%), and parents (7%). The A/L Curriculum evaluation results proved that much less environment-related components were included in the commerce, art, and mathematics subjects. Of the disciplines, geography (35%) and biological science (11%) included a higher amount of EL knowledge, comparatively. Students suggested that recycling/ reuse of waste conserves natural resources, the green building concept, and the use of public transportation to conserve the environment. This study recommends that environmental concepts should be integrated with formal G.C.E A/L syllabus with activity learning, especially for non-science disciplines, and that environment-related television and radio programs should be enhanced.

Towards an integrative approach to understanding collective behaviour in caterpillars.

To evolve, and remain adaptive, collective behaviours must have a positive impact on overall individual fitness. However, these adaptive benefits may not be immediately apparent owing to an array of interactions with other ecological traits, which can depend on a lineage's evolutionary past and the mechanisms controlling group behaviour. A coherent understanding of how these behaviours evolve, are exhibited, and are coordinated across individuals, therefore requires an integrative approach spanning traditional disciplines in behavioural biology. Here, we argue that lepidopteran larvae are well placed to serve as study systems for investigating the integrative biology of collective behaviour. Lepidopteran larvae display a striking diversity in social behaviour, which illustrates critical interactions between ecological, morphological and behavioural traits. While previous, often classic, work has provided an understanding of how and why collective behaviours evolve in Lepidoptera, much less is known about the developmental and mechanistic basis of these traits. Recent advances in the quantification of behaviour, and the availability of genomic resources and manipulative tools, allied with the exploitation of the behavioural diversity of tractable lepidopteran clades, will change this. In doing so, we will be able to address previously intractable questions that can reveal the interplay between levels of biological variation. This article is part of a discussion meeting issue 'Collective behaviour through time'.

Outer Membrane Integrity-Dependent Fluorescence of the Japanese Eel UnaG Protein in Live Escherichia coli Cells.

Reporter genes are important tools in many biological disciplines. The discovery of novel reporter genes is relatively rare. However, known reporter genes are constantly applied to novel applications. This study reports the performance of the bilirubin-dependent fluorescent protein UnaG from the Japanese eel Anguilla japonicas in live Escherichia coli cells in response to the disruption of outer membrane (OM) integrity at low bilirubin (BR) concentrations. Using the E. coli wild-type strain MC4100, its isogenic OM-deficient mutant strain NR698, and different OM-active compounds, we show that BR uptake and UnaG fluorescence depend on a leaky OM at concentrations of 10 µM BR and below, while fluorescence is mostly OM integrity-independent at concentrations above 50 µM BR. We suggest that these properties of the UnaG-BR couple might be applied as a biosensor as an alternative to the OM integrity assays currently in use.

Impact of fractional strain on medium containing spherical cavity in the framework of generalized thermoviscoelastic diffusion

Viscoelastic materials (elastomers, resins, and polycrystalline metals) are of significant importance due to their numerous applications in biology, civil, and mechanical engineering alongwith other scientific disciplines. Viscoelastic materials possess strong relation with temperature and diffusion phenomenon and their mechanical properties exhibit memory dependence. With this view, fractional order strain is considered to study thermoviscoelastic diffusion interactions in the context of hyperbolic two-temperature-three-phase lag model. The investigation is carried out for an infinite, homogeneous, isotropic medium containing a spherical cavity. Initially, the medium is held quiescent. The boundary of the cavity is subjected to continuous concentration and ramp type thermal load in stress-free state. The problem is solved in Laplace transformed domain. The aim of this article is to analyze the behavior of field variables under thermoelastic models with different fractional order strain, ramping, and viscosity parameters. Physical data of Copper material is considered for numerical inversion technique and obtained results are plotted graphically. Here it is revealed that fractional order strain parameters lead to lower perturbations of stress and viscous effects result in higher temperature. One temperature and hyperbolic two temperature theories produce similar solutions. Ramp type thermal loading at the boundary significantly influences the temporal profile.

Features of Fractal Conformity and Bioconsolidation in the Early Myogenesis Gene Expression and Their Relationship to the Genetic Diversity of Chicken Breeds.

Elements of fractal analysis are widely used in scientific research, including several biological disciplines. In this study, we hypothesized that chicken breed biodiversity manifests not only at the phenotypic level, but also at the genetic-system level in terms of different profiles of fractal conformity and bioconsolidation in the early myogenesis gene expression. To demonstrate this effect, we developed two mathematical models that describe the fractal nature of the expression of seven key genes in the embryonic breast and thigh muscles in eight breeds of meat, dual purpose, egg and game types. In the first model, we produced breed-specific coefficients of gene expression conformity in each muscle type using the slopes of regression dependencies, as well as an integral myogenesis gene expression index (MGEI). Additionally, breed fractal dimensions and integral myogenesis gene expression fractal dimension index (MGEFDI) were determined. The second gene expression model was based on plotting fractal portraits and calculating indices of fractal bioconsolidation. The bioconsolidation index of myogenesis gene expression correlated with the chick growth rate and nitric oxide (NO) oxidation rate. The proposed fractal models were instrumental in interpreting the genetic diversity of chickens at the level of gene expression for early myogenesis, NO metabolism and the postnatal growth of chicks.

Integrating imaging physics into undergraduate STEM education

Physics is a notoriously challenging subject that plays a critical and ubiquitous role in our lives. Undergraduate educators thus need new approaches that will encourage college students to study physics. At Lewis & Clark College, we have addressed this need through the development of a novel undergraduate physics course and supporting textbook that cover the principles, practice, and application of prominent “biophysical” and “biomedical” imaging techniques (i.e., light microscopy and medical imaging) and explore their extensive connections to physics. We chose to focus on imaging because it is a powerful, ubiquitous approach used in biology, medicine, and many other scientific disciplines, and because it has strong foundational ties to physics. Imaging also arises frequently in everyday life in connection with vision, cameras, and the diagnosis and treatment of disease and injury, so students are interested in the topic and appreciate its importance. The physical foundations of imaging often are established using sophisticated theoretical approaches suited for graduate physics and engineering students. However, they also can be established using introductory (largely conceptual) or intermediate (combined conceptual and theoretical) approaches suited for undergraduate students. Our course uses an intermediate approach accessible to most STEM majors and is very enthusiastically received by students at our institution majoring in biology, biochemistry, chemistry, and/or physics, making it our most popular upper-division physics course. This success suggests that other institutions also would profit from offering a course in the spirit of Biomedical Imaging. Here we describe the course content, including highly popular hands-on activities, to help pave the way for other educators who are interested in teaching a similar course.

The common morphospecies Cypridopsis vidua (O.F. MÜLLER, 1776) (Crustacea, Ostracoda) is not an obligate parthenogen

The common non-marine ostracod Cypridopsis vidua (O.F. Müller, 1776) is used as a proxy in various biological disciplines, such as (palaeo-)ecology, evolutionary biology, ecotoxicology and parasitology. This morphospecies was considered to be an obligate parthenogen. We report on the discovery of the first population of C. vidua with males from Woods Hole (MA, USA) and determine that it is a population with mixed reproduction. We describe the morphology of the males and of the sexual and asexual females. We illustrate a copula of a male and a sexual female as well insemination in a sexual female, showing that males are functional. Therefore, Cypridopsis vidua is a morphospecies with mixed reproduction, not a full apomictic parthenogen. We use, for the first time, polychromatic polarization microscope technology to illustrate soft parts of ostracods. In addition, we compare the sexual species C. bisexualis, C. okeechobei, C. howei and C. schwartzi and conclude that these species, especially the latter three, are morphologically very close to C. vidua.