Course Of Evolution Research Articles

Докинз, мораль и религия Часть II. Проблема вагонетки

In an effort to substantiate the fundamental areligiosity of morality and the amo­rality of religion, Richard Dawkins develops the argument from a universal moral ability that has evolutionary genesis and is therefore inherent in people, re­gardless of their religious beliefs. In his book The God Delusion (2006), he uses the results of a thought experiment conducted by M. Hauser and P. Singer, who were the first to put forward this argument, claiming that their test did not reveal noticeable differences in the moral modus cogitandi of believers and atheists. The aim of the article is to give a critical analysis of that argument as based on a false presumption. It is reduced to opposition: either morality has arisen in the course of natural evolution, and then religion has nothing to do with it – or morality has been the supernatural gift of God, and then evolution has nothing to do with it. The author proves that the results of the experiment do not give grounds for the ideological conclusions that those advocates of atheism build on them.

The Major Facilitator Superfamily and Antimicrobial Resistance Efflux Pumps of the ESKAPEE Pathogen Staphylococcus aureus

The ESKAPEE bacterial pathogen Staphylococcus aureus has posed a serious public health concern for centuries. Throughout its evolutionary course, S. aureus has developed strains with resistance to antimicrobial agents. The bacterial pathogen has acquired multidrug resistance, causing, in many cases, untreatable infectious diseases and raising serious public safety and healthcare concerns. Amongst the various mechanisms for antimicrobial resistance, integral membrane proteins that serve as secondary active transporters from the major facilitator superfamily constitute a chief system of multidrug resistance. These MFS transporters actively export structurally different antimicrobial agents from the cells of S. aureus. This review article discusses the S. aureus-specific MFS multidrug efflux pump systems from a molecular mechanistic perspective, paying particular attention to structure-function relationships, modulation of antimicrobial resistance mediated by MFS drug efflux pumps, and direction for future investigation.

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders, and RNA-DNA interactions. These play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific families and subfamilies of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate sustained interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure. Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to shaping 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution.

Indirect partial volumetry in breast cancer-related lymphoedema: Distribution of oedema and clinical-diagnostic implications

Introduction and objectivesCurrently, the assessment of lymphoedema related to breast cancer (BCRL) is performed through the global perimeter volumetry. We implemented an additional system with partial measures (hand, forearm, and upper arm) that allows us to approximate the segmental distribution of oedema. We used this measurement tool to determine the oedema distribution and its evolution, as well as its possible impact on clinical assessment. MethodsWe carried out a retrospective observational study of the patients referred to our service with suspected BCRL. Inclusion criteriaUnilateral breast cancer, availability of global and partial digital medical record, and follow-up for a minimum of 24 months.Of the 210 selected patients, 190 were considered affected (≥10% excess volume). We analysed at three time points (initial, final, and peak involvement) the oedema distribution and segmental predominance and its relationship with the evolutionary course and the severity of the process. We subsequently examined, at the initial timepoint, the concordance of the global assessment with the partial assessment for the clinical classification of the 210 patients in the initial sample. ResultsThe BCRL oedema was characteristically irregular, with the forearm being the most affected segment and the hand the least affected (RM ANOVA: p<0.001). The irregularity was related to its severity (χ2: p<0.001) and the evolutionary course (Student t-test: p<0.005 for the hand). Overall, disagreement of 46.67% was observed between the clinical classification of the global and partial assessment. ConclusionsThis work supports the need to add partial volumetry to the commonly used global assessment.

An NlpC/P60 protein catalyzes a key step in peptidoglycan recycling at the intersection of energy recovery, cell division and immune evasion in the intracellular pathogen Chlamydia trachomatis.

The obligate intracellular Chlamydiaceae do not need to resist osmotic challenges and thus lost their cell wall in the course of evolution. Nevertheless, these pathogens maintain a rudimentary peptidoglycan machinery for cell division. They build a transient peptidoglycan ring, which is remodeled during the process of cell division and degraded afterwards. Uncontrolled degradation of peptidoglycan poses risks to the chlamydial cell, as essential building blocks might get lost or trigger host immune response upon release into the host cell. Here, we provide evidence that a primordial enzyme class prevents energy intensive de novo synthesis and uncontrolled release of immunogenic peptidoglycan subunits in Chlamydia trachomatis. Our data indicate that the homolog of a Bacillus NlpC/P60 protein is widely conserved among Chlamydiales. We show that the enzyme is tailored to hydrolyze peptidoglycan-derived peptides, does not interfere with peptidoglycan precursor biosynthesis, and is targeted by cysteine protease inhibitors in vitro and in cell culture. The peptidase plays a key role in the underexplored process of chlamydial peptidoglycan recycling. Our study suggests that chlamydiae orchestrate a closed-loop system of peptidoglycan ring biosynthesis, remodeling, and recycling to support cell division and maintain long-term residence inside the host. Operating at the intersection of energy recovery, cell division and immune evasion, the peptidoglycan recycling NlpC/P60 peptidase could be a promising target for the development of drugs that combine features of classical antibiotics and anti-virulence drugs.

New Dielis species and structural dichotomy of the mitochondrial cox2 gene in Scoliidae wasps

Some mitochondrial protein-coding genes of protists and land plants have split over the course of evolution into complementary genes whose products can form heteromeric complexes that likely substitute for the undivided proteins. One of these genes, cox2, has also been found to have split in animals, specifically in Scoliidae wasps (Hymenoptera: Apocrita) of the genus Dielis (Campsomerini), while maintaining the conventional structure in related Scolia (Scoliini). Here, a hitherto unrecognized Nearctic species of Dielis, D. tejensis, is described based on its phenotype and mtDNA. The mitogenome of D. tejensis sp. nov. differs from that of the sympatric sibling species Dielis plumipes fossulana by the reduced size of the cox2-dividing insert, which, however, still constitutes the fifth part of the mtDNA; an enlarged nad2-trnW intergenic region; the presence of two trnKttt paralogues; and other features. Both species of Dielis have a unique insertion of a threonine in COXIIA, predicted to be involved in COXIIA-COXIIB docking, and substitutions of two hydrophobic residues with redox-active cysteines around the CuA centre in COXIIB. Importantly, the analysis of mtDNA from another Campsomerini genus, Megacampsomeris, shows that its cox2 gene is also split. The presented data highlight evolutionary processes taking place in hymenopteran mitogenomes that do not fall within the mainstream of animal mitochondrion evolution.

Проблемы становления Древнерусского государства в трудах С.А. Корфа

Considering the problem of the regularity of statehood S.A. Korf notes three levels of this problem: the first is the evolutionary forms of the social organization of society (from primitive to more complex forms); the next level is the emergence of new states among the existing ones; and the last level is the justification of the subjection of the individual to state power. The paper concludes that states arise in the course of a long evolution of social structures and represent the most perfect form of human social life. The state is understood as a form of social organization that functions according to the historically established system of social regulators, including law, and is the source of power of the subjects of management over other individuals. For the first time in the history of science, S.A. Korf tried to separate the concepts of state and statehood, by which he understood the qualitative characteristics of society at a certain stage of life.

Evolutionary Medicine

Evolutionary medicine is a growing area of research and practice; however, it is not widely discussed in introductory biology courses. Because of the interest in human biology, using evolutionary medicine is a great way to hold students’ interest, placing topics in context, making the subject of evolution relevant. Too often students lose interest in learning about evolution because they think it is not pertinent. The pedagogical technique of using case studies in the classroom engages students in a way that will grow their understanding of topics, in this case evolution, as well as helping students with critical thinking and process skills, growing their scientific literacy. The following case study is appropriate for an introductory biology course that focuses on evolution, an AP biology course, or an introductory evolution course for undergraduates. The case focuses on the evolutionary perspectives of what might be causing human ear infections, as well as the role of beneficial species of gut bacteria in maintaining a healthy immune system. It is advantageous for students to know about natural selection and coevolution before using the case study.

Development of ICT-Based Teaching Materials on Phylogeny Topic as Innovations in Evolution Courses: A need analysis

This study aims to collect and analyze the data needed for the development of ICT-based teaching materials in evolution courses on phylogeny topic. The methods used are systematic reviews and surveys. Based on the results of a systematic review, it can be concluded that the trend of research on evolution courses on phylogeny topic in scientific articles published in 2015-2021 is the mastery of tree thinking skills. The teaching materials developed to support the mastery of tree thinking skills are booklets, modules, and game cards. Based on the results of the survey, it can be concluded that the majority of students prefer to use smartphones instead of laptops to find and study evolution lecture materials and only a small percentage of students who have obstacles to accessing the internet both in the classroom and outside campus. The highest percentage of electronic teaching materials that students like the most are more diverse teaching materials. This need analysis provides information that can be used to develop ICT-based teaching materials on phylogeny topic

Why stars inflate to and deflate from red giant dimensions – II. Replies to critics

ABSTRACTIn a 1992 paper of ours, the role of opacity-driven thermal instabilities in shaping the course of stellar evolution was amply illustrated. This included the classical issue of ‘why stars become red giants’ as well as the subsequent formation of extended ‘Cepheids’ blue loops during the helium-burning phases. Our explanation of these evolutionary phenomena has occasionally been dismissed with just a few words in refereed or non-refereed publications. In a recent case, the fact that over the years I have not replied to these criticisms was interpreted as evidence that they were well founded. In this paper, it is made clear that this is not at all the case: the leading role of such instabilities is instead reaffirmed and the criticisms are shown to be insubstantial.

A linear reciprocal relationship between robustness and plasticity in homeostatic biological networks.

In physics of living systems, a search for relationships of a few macroscopic variables that emerge from many microscopic elements is a central issue. We evolved gene regulatory networks so that the expression of core genes (partial system) is insensitive to environmental changes. Then, we found the expression levels of the remaining genes autonomously increase to provide a plastic (sensitive) response. A feedforward structure from the non-core to core genes evolved autonomously. Negative proportionality was observed between the average changes in core and non-core genes, reflecting reciprocity between the macroscopic robustness of homeostatic genes and plasticity of regulator genes. The proportion coefficient between those genes is represented by their number ratio, as in the "lever principle", whereas the decrease in the ratio results in a transition from perfect to partial adaptation, in which only a portion of the core genes exhibits robustness against environmental changes. This reciprocity between robustness and plasticity was satisfied throughout the evolutionary course, imposing an evolutionary constraint. This result suggests a simple macroscopic law for the adaptation characteristic in evolved complex biological networks.

Phycobilisomes and Phycobiliproteins in the Pigment Apparatus of Oxygenic Photosynthetics: From Cyanobacteria to Tertiary Endosymbiosis.

Eukaryotic photosynthesis originated in the course of evolution as a result of the uptake of some unstored cyanobacterium and its transformation to chloroplasts by an ancestral heterotrophic eukaryotic cell. The pigment apparatus of Archaeplastida and other algal phyla that emerged later turned out to be arranged in the same way. Pigment-protein complexes of photosystem I (PS I) and photosystem II (PS II) are characterized by uniform structures, while the light-harvesting antennae have undergone a series of changes. The phycobilisome (PBS) antenna present in cyanobacteria was replaced by Chl a/b- or Chl a/c-containing pigment-protein complexes in most groups of photosynthetics. In the form of PBS or phycobiliprotein aggregates, it was inherited by members of Cyanophyta, Cryptophyta, red algae, and photosynthetic amoebae. Supramolecular organization and architectural modifications of phycobiliprotein antennae in various algal phyla in line with the endosymbiotic theory of chloroplast origin are the subject of this review.

Endogenous Retroviruses as Modulators of Innate Immunity.

Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that are highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% of the genome and over the course of evolution, HERV elements underwent positive selection and accrued mutations that rendered them non-infectious; thereby, the genome could co-opt them into constructive roles with important biological functions. In the past two decades, with the help of advances in sequencing technology, ERVs are increasingly considered to be important components of the innate immune response. While typically silenced, expression of HERVs can be induced in response to traumatic, toxic, or infection-related stress, leading to a buildup of viral transcripts and under certain circumstances, proteins, including functionally active reverse transcriptase and viral envelopes. The biological activity of HERVs in the context of the innate immune response can be based on the functional effect of four major viral components: (1) HERV LTRs, (2) HERV-derived RNAs, (3) HERV-derived RNA:DNA duplexes and cDNA, and (4) HERV-derived proteins and ribonucleoprotein complexes. In this review, we will discuss the implications of HERVs in all four contexts in relation to innate immunity and their association with various pathological disease states.

Iterative Drawing Reveals Diversity and Change in Student Thinking About Evolution

One theoretical framework for learning is that knowledge exists in pieces. Understanding emerges by developing a coherent and stable integration of multiple ideas. When learning gains are evaluated iteratively, over time, it is clear that the mental constructs representing key ideas are dynamic. Here we describe an assessment framework that enables estimation of the dynamic nature of mental constructs as students make gains towards coherency of knowledge and understanding. The framework emphasizes the value of iterative assessment combined with multivariate methods borrowed from ecology for revealing and following gains in student thinking. We applied our framework for monitoring and describing student gains in their abilities to visualize and describe the process of evolution. Our approach was observational. We evaluated 276 drawings and accompanying text-based descriptions of evolution generated by 102 students by implementing the same open-ended assessment question four times in two sections of an upper division evolutionary biology course during spring 2021. Based on a binary rubric of 10 key ideas, students showed evidence of gains and losses of key ideas over time, and their learning trajectories were diverse and dynamic. Our findings revealed students take a multitude of pathways to concept mastery and that they struggled to succinctly construct and communicate comprehensive evolutionary models. Based on our study, we recommend using iterative free-response assessment with an explicit rubric and multivariate non-metric dimensional scale data visualization for revealing student thinking and guiding data-driven revision of curriculum, teaching strategies, and assessment for achieving greater coherency and stability of knowledge.

Metamorphosis differences of caudiciform plants as an adaptation to arid conditions

In the course of evolution, the formation of succulent variations in the underground and surface parts of plants in different taxa could occur simultaneously under the influence of similar abiotic factors, in particular as an adaptation to arid conditions, and similar structural features even in distant families are a manifestation of convergent evolution. Along with this, the development of such adaptive structures in ontogeny can occur in different ways in different taxa. Studying the anatomical and morphological features of the vegetative organs of Fockea edulis (Asclepiadoideae, Apocynaceae) at the early stages of ontogenesis and comparing them with those of other plants will improve the understanding of the features of growth and development of caudex-like plants. The research was conducted on seedlings, juvenile and immature plants of F. edulis. When comparing the features of the development of vegetative parts of three representatives of the Apocynaceae family, we found that the strategy of succulent traits development in F. edulis at the organ level is characterized by the active development of the hypocotyl already at the seedling stage, similar to Adenium obesum, and the subsequent formation of an expanded basal part of the stem due to the combined cortex-pith thickening and radish-like root due to the growth of xylem parenchyma. However, Petopentia natalensis is characterized by a mesophytic seedling. It was established that secondary thickening in the basal part of the stem occurs in two individual ways: in Adenium obesum, the cambium generates solid rings of phloem and parenchymatized xylem; in P. natalensis and F. edulis, the bundle type of conducting elements is preserved. The thickening of the tap root in F. edulis is similar to that in A. obesum.

Computational protein design repurposed to explore enzyme vitality and help predict antibiotic resistance.

In response to antibiotics that inhibit a bacterial enzyme, resistance mutations inevitably arise. Predicting them ahead of time would aid target selection and drug design. The simplest resistance mechanism would be to reduce antibiotic binding without sacrificing too much substrate binding. The property that reflects this is the enzyme "vitality", defined here as the difference between the inhibitor and substrate binding free energies. To predict such mutations, we borrow methodology from computational protein design. We use a Monte Carlo exploration of mutation space and vitality changes, allowing us to rank thousands of mutations and identify ones that might provide resistance through the simple mechanism considered. As an illustration, we chose dihydrofolate reductase, an essential enzyme targeted by several antibiotics. We simulated its complexes with the inhibitor trimethoprim and the substrate dihydrofolate. 20 active site positions were mutated, or "redesigned" individually, then in pairs or quartets. We computed the resulting binding free energy and vitality changes. Out of seven known resistance mutations involving active site positions, five were correctly recovered. Ten positions exhibited mutations with significant predicted vitality gains. Direct couplings between designed positions were predicted to be small, which reduces the combinatorial complexity of the mutation space to be explored. It also suggests that over the course of evolution, resistance mutations involving several positions do not need the underlying point mutations to arise all at once: they can appear and become fixed one after the other.

Foredune growth and storm surge protection potential at the Eiderstedt Peninsula, Germany

In the context of climate change and associated sea level rise, coastal dunes can provide an essential contribution to coastal protection against wave attack and flooding. Since dunes are highly dynamic systems, their potential safety levels are related to their long-term development, varying in time and space, however pertinent research that ties those aspects together are generally scarce. The objective of this study is to analyze the long-term development of a young coastal foredune at the Eiderstedt peninsula, Germany and assess its coastal protection potential. This research presents (i) a novel semi-automated Dune Toe Tracking (DTT) method to systematically extract dune toes from cross-shore elevation profiles; (ii) established tools to derive the extraction of characteristic dune parameters and (iii) a newly defined Critical Storm Surge Level (CSSL) to relate spatio-temporal dune growth with coastal storm surge protection. Based on geospatial survey data, initial dune formation was identified in the 1980s. By 2015, the foredune had developed over a 6.5 km coastal stretch with a mean annual growth of 7.4m³/m. During the course of dune evolution, the seaward dune toe shifted seaward by an average of 2.3m/yr, while simultaneously increasing in height by an average of 1.1 cm/yr. Overall, the foredune formation established a new line of defense in front of an existing dike/dune line that provides spatially varying protection against a mean CSSL of 3.4m + NHN and can serve as an additional buffer against wave attack during severe storm events.

A Long-Running Arms Race between APOBEC1 Genes and Retroviruses in Tetrapods.

Activation-induced cytidine deaminase/apolipoprotein B mRNA editing catalytic polypeptide-like (AID/APOBEC) proteins are cytosine deaminases implicated in diverse biological functions. APOBEC1 (A1) proteins have long been thought to regulate lipid metabolism, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. Endogenous retroviruses (ERVs) document past retroviral infections and are ubiquitous within the vertebrate genomes. Here, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in ERVs, and interrogate the evolutionary arms race between A1 genes and ERVs across vertebrate species. We find that A1 genes are widely present in tetrapods, recurrently amplified and lost in certain lineages, suggesting that A1 genes might have originated during the early evolution of tetrapods. A1-mediated mutation footprints can be detected in ERVs across tetrapods. Moreover, A1 genes appear to have experienced episodic positive selection in many tetrapod lineages. Taken together, we propose that a long-running arms race between A1 genes and retroviruses might have persisted throughout the evolutionary course of tetrapods. IMPORTANCE APOBEC3 (A3) genes have been thought to function in defense against retroviruses, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. In this study, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in endogenous retroviruses (ERVs), and explore the evolutionary arms race between A1 genes and ERVs across vertebrate species. We found A1 proteins originated during the early evolution of tetrapods, and detected the footprints of A1-induced hypermutations in retroviral fossils. A1 genes appear to have experienced pervasive positive selection in tetrapods. Our study indicates a long-running arms race between A1 genes and retroviruses taking place throughout the evolutionary course of tetrapods.

Petrology of Palaeoarchaean mafic–ultramafic rock suites of the western Iron Ore Group, Singhbhum Craton, eastern India, using the chemistry of minerals

AbstractThe petrogenesis of Palaeoarchaean mafic–ultramafic rock suites from the western Iron Ore Group, Singhbhum Craton, eastern India, has been evaluated based on the chemistry of constituent mineral phases. The rock suites include basaltic rocks and mafic (gabbro) to ultramafic (serpentinized peridotite) intrusive rocks, which occur in host rocks covering phyllite, ferruginous shale, banded haematite quartzite and jasper. The constituent clinopyroxene shows dominant uralitization, whereas plagioclase grains are generally saussuritized, being marked by relatively tiny granular aggregates of albite, chlorite, epidote and K-feldspar. The ultramafic intrusive rocks are overwhelmingly serpentinized. Clinopyroxene compositions are augitic, whereas relict plagioclase is typically bytownite. Amphiboles of the investigated rock suites are divisible into the ‘uralite’ type (occurring peripherally to clinopyroxene) and the ‘completely changed-over amphibole’ type (with no traces of initial clinopyroxene). Both the amphibole types belong to the ‘calcic group’, showing a compositional spectrum from actinolite–magnesiohornblende–ferrohornblende–ferroactinolite. Opaque minerals include magnetite (both Cr-magnetite and Al-magnetite), chromite (Al-chromite) and ilmenite, whereas serpentine (belonging to the ultramafic intrusive rocks) corresponds to lizardite. Looking at the mineral compositions of the pyroxene, glass and amphibole, the studied rock suites show a wide equilibration temperature–pressure domain range (∼750 °C to ∼1400 °C at ∼0.26 kbar to ∼21 kbar), which corresponds to an ascending magma that underwent a ‘hydration event’ at a shallow level. The assessment of the clinopyroxene and spinel chemistry characteristically suggests an arc setting for the parent magma that has undergone both equilibrium and fractional crystallization in the course of magmatic evolution. During differentiation, the magmatic density remains almost constant, with variable oxygen fugacity.

Escape from Parsimony of a Double-Cut-and-Join Genome Evolution Process.

We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. Not only do our models allow different types of operations generated by DCJs (including reversals, translocations, transpositions, fissions, and fusions) to take different weights during the course of evolution, but they also let these weights fluctuate over time. We compare the number of operations along the evolutionary trajectory with the DCJ distance of the genome from its ancestor at each step, and determine at what point they diverge: the process escapes from parsimony. Adapting the method developed by Berestycki and Durrett, we approximate the number of cycles in the breakpoint graph of a random genome at time t and its ancestral genome by the number of tree components in a random graph (not necessarily an Erdös-Rényi one) constructed from the model of evolution. In both models, the process on a genome of size n is bound to its parsimonious estimate up to steps.