Branches Of Life Research Articles

The definitive apparatus of law: some aspects of formation

The article is devoted to the review of the problems of formation of the definitive apparatus of law, that is, systems of definitions of categories and concepts of jurisprudence, through which the latter acquire specific meaning within the framework of legal theory or practice. In other words, the definitive apparatus of law is a necessary tool or means of knowing and understanding the relevant legal concepts and categories, and ensuring their certainty. The process of forming legal definitions implies the need to use a variety of methodological techniques, search for relevant information, hypotheses, theories and more. The definitive apparatus of law evolves in connection with a change in both law itself and a number of factors that to some extent influence the process of formation of concepts and their definitions in the legal system. In this regard, the determinants of the formation of the definitive apparatus of law should be sought primarily in those phenomena and processes that directly affect one or another of the content of legal concepts and categories and which are linked, on the one hand, to their more or less static within specific temporal and spatial dimensions, and, on the other, to their substantive diversity, which can manifest even at the level of the most important legal concepts (for example, state, law, legal responsibility etc.). In particular, it should be noted that technological progress has contributed to the emergence of new concepts and definitions that have already become widely used in the system of legislation of modern democratic states (for example, electronic document, electronic digital signature, electronic ticket, electronic settlement document, etc.). Similarly, the development of other spheres and branches of public life, in particular, medicine, business relations, education, etc., necessitates the development of legal definitions of relevant concepts and their consolidation in the legislation in order to ensure more effective legal regulation of social relations. In addition, one cannot ignore the subjective aspect in formulating certain legal definitions, the basis of which is the originality of the outlook of every person, including every scientist. After all, the content of certain concepts and categories, expressed in their definitions, is differently perceived and defined by the relevant subjects, which is determined primarily by their individual characteristics, which include, in particular, personal beliefs, ideals, values, etc. In this regard, we can say that the formation of a definitive apparatus of law is determined simultaneously by a number of objective and subjective factors that determine its specificity and ways and prospects for further development. Therefore, the formation of a definitive apparatus of law should be seen as an integral part of a more general law-formation process, the content of which is linked to those social factors and patterns that affect the development of legal regulation. In this case, the factors of formation of the definitive apparatus of law can be conditionally combined into two groups: internal and external. Internal factors are those facts and circumstances that are determined primarily by the specificity and dynamics of the development of law itself as a socio-normative phenomenon of social reality, and external include those phenomena that are related to the peculiarities of socio-cultural and natural development of society, in particular, with the level of progress of socio-humanities in general, with conditions of functioning of economic, political and other relations, with the content actually prevailing in society and the state ideology, with the specific relationship of law and other social regulators, etc. Keywords: law definitions, the definitive apparatus of law, law, law-formation, law concepts, methodology, law science.

Structural dynamics of pentapeptide repeat proteins.

Pentapeptide repeat proteins (PRPs) represent a large superfamily with more than 38 000 sequences in nearly 3500 species, the majority belonging to cyanobacteria but represented among all branches of life. PRPs contain at least eight consecutive pentapeptide repeats with the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K). PRPs fold into right-handed quadrilateral β helices, also known as repeat-five-residue (Rfr)-folds, with four consecutive pentapeptide repeats comprising a single coil, the ~90° change in polypeptide direction in square-shaped coils achieved by type I, II and IV β turns, and hydrogen bonds between coils establishing β ladders on each Rfr-fold face. PRPs are broadly categorized into group 1 and 2 involved in antibiotic resistance and group 3 currently having unknown functions. Motivated by their intriguing structures, we are investigating PRP biophysical characteristics, including Rfr-fold thermal stability, β turn and β ladder hydrogen bond amide exchange rates and backbone dynamics. Here, we present analysis of 20 ns molecular dynamics (MD) simulations and all atom normal mode analysis (aaNMA) calculations for four group 1 and group 2 and four group 3 PRPs whose structures have been determined by X-ray crystallography. The MD cross-correlation matrices and aaNMA indicated strong correlated motion between adjacent coils and weak coupled motion between coils separated by one or more intervening coils. Slow anticorrelated motions were detected between adjacent coils in aaNMA modes that we hypothesize are requisite to access exchange-competent states necessary to permit solvent exchange of amide hydrogens involved in β-ladder and β-turns hydrogen bonds, which can have lifetimes on the order of months.

Regulators of Viral Frameshifting: More Than RNA Influences Translation Events.

Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.

Facing the University Environment with Covid Pandemic: A Comparative Analysis between Romania - South Korea

The Covid-19 determined pandemic has affected all branches of socio-economic life, and the educational environment has not been bypassed. The students' reaction to the measures of the total transfer of the teaching-learning process in the online environment, by universities closure, is proving to be one of the challenges determined by the current global pandemic manifestation. The impact is highlighted by major changes with obvious patterns in the short time period. The academic world is witnessing this changing from the position of forced adaptation, both teachers, administrative staff, and students being in the situation of reconsidering the entire system, in organization and functionality. The on-line platforms have replaced the classrooms, the communication is made exclusively virtual, and the reactions caused by this form of reconfiguration are felt in multiple ways. The present paper approaches the students' reaction to this necessity for adaptation, by comparison between the university environment from Romania and the one from South Korea. The results indicate multiple similarities and minor differences between these two countries. A main conclusion is that in technically, organizationally and emotionally-affective perspective, the situation is very similar, the differences being present only from a financial point of view and about the intention in student-teacher communication.

The Filament Forming Mechanism of SgrAI Endonuclease‐Structural and Kinetic Analysis

Filament formation by enzymes has recently emerged as a new paradigm of enzyme regulation 1.Wide‐spread reversible self‐assembly of enzymes in cells has also been shown to occur in all branches of life and diverse metabolic and biological pathways. We use the model system, SgrAI, to investigate the filament forming enzyme mechanism.Filaments formed by SgrAI have been structurally characterized using cryo‐electron microscopy 2 and the full reaction pathway including all rate constants has been determined using single turnover enzyme reactions, FRET, and global kinetic modeling 3– 4.The structural studies uncover the mechanism of activation of enzyme activity in SgrAI by filament formation, as well as the origin of the unusual expansion of substrate specificity in SgrAI within the filament. A conformational change in the SgrAI dimer, stabilized by protein‐protein and protein‐DNA contacts in the filament, leads directly to a shift in the active site, hypothesized to lead to stronger binding of a second catalytic Mg2+ ion. DNA structure and energetics is hypothesized to control substrate specificity and filament formation by SgrAI such that the secondary class of DNA sequences are cleaved by SgrAI only upon joining a filament formed by SgrAI bound to a primary class of DNA sequences. The full kinetic model showed a slow second order step in filament formation which is shown to control enzyme activity such that only invading phage DNA is cleaved, leaving the host genome untouched. This model also shows that the filament forming mechanism is superior in fast activation of enzyme activity upon initial recognition of primary DNA sequences.Using the SgrAI endonuclease as a model system to study filament forming enzymes, we have discovered that the enzyme is activated by stabilization of an activated conformation by contacts made within the filament. Control of the equilibrium between a low activity, non‐filamentous state and the high activity, filamentous state by DNA structural energetics gives rise to the unusual apparent expansion of DNA sequence specificity of SgrAI by filament formation. Simulations using the full kinetic pathway reveal an advantage in the filament mechanism over other non‐filamentous mechanisms in the speed of activation in response to invading phage DNA, giving strong evolutionary advantage to this filament forming mechanism.Support or Funding InformationThis work was supported by the National Science Foundation under Grant No. MCB‐1410355.

Glue till you drop – Experiments on Historical Adhesives

AbstractBereits seit mehreren Jahrtausenden verwenden Menschen Klebstoffe. Anfangs dienten diese vor allem der Fabrikation einfacher Werkzeuge und Jagdwaffen, während sie heute in beinahe allen Industrie‐ und Lebensbereichen zu finden sind. Dieser Beitrag stellt Experimente zur Herstellung einiger der ältesten Klebstoffe vor: das Birkenpech, Klebemixturen aus Baumharz und einen Glutinleim. Diese sind für den Chemie‐ bzw. Sachunterricht, insbesondere aber auch für AGs und Projekttage geeignet, um intermolekulare Wechselwirkungen auf abwechslungsreiche Weise zu thematisieren. Vor der Vorstellung der Experimente werden die chemischen und physikalischen Grundlagen des Klebens sowie die historischen Hintergründe der drei thematisierten Klebstoffe erläutert.

Arabidopsis tRNA-derived fragments as potential modulators of translation

ABSTRACT Transfer RNA-derived fragments (tRFs) exist in all branches of life. They are involved in RNA degradation, regulation of gene expression, ribosome biogenesis. In archaebacteria, kinetoplastid, yeast, and human cells, they were also shown to regulate translation. In Arabidopsis, the tRFs population fluctuates under developmental or environmental conditions but their functions are yet poorly understood. Here, we show that populations of long (30–35 nt) or short (19–25 nt) tRFs produced from Arabidopsis tRNAs can inhibit in vitro translation of a reporter gene. Analysing a series of oligoribonucleotides mimicking natural tRFs, we demonstrate that only a limited set of tRFs possess the ability to affect protein synthesis. Out of a dozen of tRFs, only two deriving from tRNAAla(AGC) and tRNAAsn(GUU) strongly attenuate translation in vitro. Contrary to human tRF(Ala), the 4 Gs present at the 5ʹ extremity of Arabidopsis tRF(Ala) are not implicated in this inhibition while the G18 and G19 residues are essential. Protein synthesis inhibition by tRFs does not require complementarity with the translated mRNA but, having the capability to be associated with polyribosomes, tRFs likely act as general modulation factors of the translation process in plants.

Highly Processive DNA Origami Nanoscale Motors

Biological motor proteins that convert chemical energy into controlled nanomechanical motion are essential and shared among all branches of life. Accordingly, there is considerable interest in developing synthetic analogues. Among the synthetic motors created thus far, unipedal and bipedal DNA walkers that undertake discrete steps on RNA tracks have shown the greatest promise with applications spanning from biosensing to cargo transport and cargo sorting. Nonetheless, DNA-based walkersfall short because of their limited speed, low endurance, and the lack of preferred directionality which is ultimately due to the lack of coordination between individual DNA legs. Herein, we uncover the design principles for creating autonomous, unidirectional and processive DNA motors. By taking advantage of the DNA origami three-dimensional self-assembly technique, we created a library of DNA motors that allow testing of structure-function relationships at the nanoscale. We tested the role of DNA-leg density, polyvalency, geometric distribution, and chassis rigidity. Importantly, the work reveals that the local density of DNA legs and not the absolute polyvalency, is the most important parameter contributing to effective motion. Furthermore, an anisotropic rigid chassis is necessary for unidirectional motion. This led to a rod-shaped DNA nanomotor that linearly and autonomously translocates micron distances without intervention through a forcefield or patterned track. These findings provide the rules for creating cooperative and more sophisticated synthetic molecular motors, thus reducing the gap in capabilities between biological and synthetic motors.

ADMINISTRATIVE AND LEGAL PRINCIPLES OF THE FINANCIAL SYSTEM OF UKRAINE

In the course of its economic and legal development, the formation and improvement of the financial system from a legal perspective continues to occur in Ukraine. Today, political transformations in one aspect or another affect the state of the financial system, that is, in some cases, they stabilize it, and in others, unfortunately, lead to its imbalance. At the same time, it should be noted that the financial system of Ukraine, as well as its functions in modern conditions, usually develop in close interaction with other links. Their interaction with the budget system is especially important for the functioning of the financial system itself since it contributes to the financial support of various branches of public life in Ukraine. At the same time, the axiology of the financial system of Ukraine requires analysis of its functional component, since in the legal and economic literature the specified category is still debatable. In addition, the concept of “financial system” is absent both in scientific sources and in the current legislation. The problems of the financial system have already been the subject of research by individual scholars. However, an analysis of their work shows that the administrative and legal aspects of the financial system are only partially revealed. That is why the purpose of this article is to analyze the very concept of the financial system and its components, as well as to study the impact on it of the relevant administrative and legal principles. As a result, it is concluded that finance, as well as the financial system as a whole, is crucial for the development of the state. They serve as the economic basis for the existence of even the state itself. The notion of “finance” is applied not only to the sphere of state property but also to the sphere of the effect of private relations, because in Ukraine the market relations develop. In this regard, finance is regarded as a public-law and private-law category, which is the very foundation of Ukraine’s financial system. Nowadays in Ukraine, there is a tendency of scientific research of peculiarities of legal regulation of a certain type of activity, including financial, because the latter has state-defined elements. Given that the main elements of the financial system include finance: state, local, economic entities of all forms of ownership, the non-productive sphere of activity, the population of the financial market, as well as financial infrastructure, it is possible to improve the definition of the content of the financial system as a set regulated by financial and legal norms individual units of financial relations and financial institutions through which the state creates, distributes and uses centralized and decentralized funds. This definition directly indicates that there is a specific model of legal influence created by a special combination of legal regulation of financial relations in Ukraine. The aforementioned allows convincingly to assert that in Ukraine there is an administrative-legal regime of the financial system, which is functionally oriented to the performance of functions and actions of the authorized state bodies in the implementation and provision of all elements of the financial system. Keywords: administrative and legal principles of the financial system, financial system, finances, money.

ТЕОРЕТИКО-МЕТОДОЛОГІЧНІ КОНЦЕПЦІЇ ФОРМУВАННЯ ЛЮДСЬКОГО КАПІТАЛУ ЗАКЛАДУ ОХОРОНИ ЗДОРОВ’Я

Introduction. Health care is one of the strategic branches of socio-economic life in Ukraine. It is a basis for formation of national human capital, since the health status is one of the factors for its formation. From the development level of health institutions and their activity, from the medical workers’ activity and from the development of the healthcare network depends the quality of medical care in any country. But nevertheless, the medical personnel are a key element of such system. They are the providers of health services and thus, the analysis of theoretical and methodological concepts of forming human capital of medical staff is urgent nowadays. Purpose of this paper is to form theoretical and methodological concepts for forming the human capital in the medical establishment. The methodological basis of the paper is the complex of methods, including methods of scientific cognition, analysis and synthesis, systematization and scientific abstraction. The informational basis of the conducted research is the scientific works of the domestic and foreign scientists in the sphere of management and organization of health care, personnel management, statistical data of the State Statistics Service of Ukraine, legal and regulatory documents of Ministry of Health of Ukraine. Results. In the paper definitions of the human capital are analyzed. Channeling investment to the human capital is defined. The formula for evaluation of the human capital’s cost is proposed; it is universal for the all organizations of different property forms and activities. The problem of development of human capital in the medical establishment is analyzed separately, namely its staff’s professionalization. The concept of continuing medical education is considered. The conditions of forming human capital at the medical establishment are researched. Originality. Directions of human capital’s development in the medical establishment are proposed, taking into account the modern reformation of health sphere. Conclusion. Practical importance of the scientific research results lies in defining the modern paradigm of personnel management for healthcare facilities, which is important for the further development of the healthcare sphere, labour market of medical staff and improvement of the healthcare facilities’ activity in Ukraine.

Polymeric materials in sustainable development – from the need to use to the need for wear. Part I. There is no turning back from plastics

The Packet for Circular Economy accepted by EU in 2015 is actually the most mature form for the realization of the Strategy for Sustainable Development. For the implementation of its assumption plastics play the role of the aim of the activity as well as of the aid for it. The importance of polymeric materials for the contemporary world as a constructional material omnipresent in all branches of economy, everyday life and culture was demonstrated within this study. Moreover, their unrecognized and often underestimated significance for the environment protection was depicted. It was also revealed that science and technology still did not find any substitutes allowing, even partially, for the replacement for material of millennium as plastics are in their commercial applications with simultaneous reduction of the environmental impact of end-life wastes. The real reasons of the accumulation of these wastes in the nature were also discussed in detail.

Methodological issues related to the formation of preschool children’s ecological culture within the coordinates of the modern educational ideas

The planet’s ecological situation demands an immediate change of mankind’s, each country communities’ and each person’s attitude to the natural environment, to the saving of the natural resources, to the necessity to form an active position which would deal with the renovation and withstand the loss of the nature’s elements, which might lead to the destruction of the ecological balance. The radical change of the situation towards people’s destroying activities can be stopped on condition that all social institutions consolidate, specialists in all fields and branches of life undertake common actions, efforts in the fields of science, economics, politics and culture are integrated. In our opinion, the most responsible mission facilitating the solution of the ecological problem belongs to education, since it is to educate a personality who is able to radically change the ecological trends, to build a personality possessing a new type of thinking, new moral orientations, ecological consciousness and culture (being typical of this personality). Preschool education has a great responsible for raising person’s ecological consciousness and culture. During the preschool period, when fundamentals of the future adult life are formed, the child masters those values, ethical norms, knowledge which will allow him / her to develop his / her own new style of interacting with the surrounding world, to develop the ecologically expedient models of behaviour. We consider the widening of the connections between preschoolers’ ecological education and natural sciences, philosophy and psychology to be the way to increase its efficiency. The content-based and technological aspects of the ecological education methodology should be grounded, in great extent, on the fundamentals of the philosophy of eco-centrism. They must recreate the natural knowledge of the out-ecology (individual attitude to ecology) and synecology about living organisms, their interconnection with the environmental habitat, about organisms’ adaptation to environment, about ecosystem, biocenosis, etc. The process of ecological education is to be developed as the real practice of child’s contacting with the elements of nature during which psychological feeling, as if being involved into the natural environment and being part of nature, is formed; a subject attitude to all nature elements as to important and equal ones in their rights is built; the demand for non-pragmatic interaction with nature is cultivated. Keywords: ecological consciousness, ecological culture, eco-centrism, ecological involvement, subjective attitude, non-pragmatic interaction.

Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II.

Type II topoisomerases are ubiquitous enzymes in all branches of life that can alter DNA superhelicity and unlink double-stranded DNA segments during processes such as replication and transcription. In cells, type II topoisomerases are particularly useful for their ability to disentangle newly-replicated sister chromosomes. Growing lines of evidence indicate that eukaryotic topoisomerase II (topo II) activity is monitored and regulated throughout the cell cycle. Here, we discuss the various roles of topo II throughout the cell cycle, as well as mechanisms that have been found to govern and/or respond to topo II function and dysfunction. Knowledge of how topo II activity is controlled during cell cycle progression is important for understanding how its misregulation can contribute to genetic instability and how modulatory pathways may be exploited to advance chemotherapeutic development.

Metagenomic and chemical characterization of soil cobalamin production

Cobalamin (vitamin B12) is an essential enzyme cofactor for most branches of life. Despite the potential importance of this cofactor for soil microbial communities, the producers and consumers of cobalamin in terrestrial environments are still unknown. Here we provide the first metagenome-based assessment of soil cobalamin-producing bacteria and archaea, quantifying and classifying genes encoding proteins for cobalamin biosynthesis, transport, remodeling, and dependency in 155 soil metagenomes with profile hidden Markov models. We also measured several forms of cobalamin (CN-, Me-, OH-, Ado-B12) and the cobalamin lower ligand (5,6-dimethylbenzimidazole; DMB) in 40 diverse soil samples. Metagenomic analysis revealed that less than 10% of soil bacteria and archaea encode the genetic potential for de novo synthesis of this important enzyme cofactor. Predominant soil cobalamin producers were associated with the Proteobacteria, Actinobacteria, Firmicutes, Nitrospirae, and Thaumarchaeota. In contrast, a much larger proportion of abundant soil genera lacked cobalamin synthesis genes and instead were associated with gene sequences encoding cobalamin transport and cobalamin-dependent enzymes. The enrichment of DMB and corresponding DMB synthesis genes, relative to corrin ring synthesis genes, suggests an important role for cobalamin remodelers in terrestrial habitats. Together, our results indicate that microbial cobalamin production and repair serve as keystone functions that are significantly correlated with microbial community size, diversity, and biogeochemistry of terrestrial ecosystems.

Genetic Logic Gates Enable Patterning of Amyloid Nanofibers.

Distinct spatial patterning of naturally produced materials is observed in many cellular structures and even among communities of microorganisms. Reoccurrence of spatially organized materials in all branches of life is clear proof that organization is beneficial for survival. Indeed, organisms can trick the evolutionary process by using organized materials in ways that can help the organism to avoid unexpected conditions. To expand the toolbox for synthesizing patterned living materials, Boolean type "AND" and "OR" control of curli fibers expression is demonstrated using recombinases. Logic gates are designed to activate the production of curli fibers. The gates can be used to record the presence of input molecules and give output as CsgA expression. Two different curli fibers (CsgA and CsgA-His-tag) production are then selectively activated to explore distribution of monomers upon coexpression. To keep track of the composition of fibers, CsgA-His-tag proteins are labeled with nickel-nitrilotriacetic acid (Ni-NTA-) conjugated gold nanoparticles. It is observed that an organized living material can be obtained upon inducing the coexpression of different CsgA fibers. It is foreseen that living materials with user-defined curli composition hold great potential for the development of living materials for many biomedical applications.

Next-generation transcriptome assembly and analysis: Impact of ploidy.

Whole genome duplications (WGD) occur widely in plants, but the effects of these events impact all branches of life. WGD events have major evolutionary impacts, often leading to major structural changes within the chromosomes and massive changes in gene expression that facilitate rapid speciation and gene diversification. Even for species that currently have diploid genomes, the impact of ancestral duplication events is still present in the genomes, especially in the context of highly similar gene families that are retained from WGD. However, the impact of these ploidies on various bioinformatics workflows has not been studied well. In this review, we overview biological significance of polyploidy in different organisms. We describe the impact of having polyploid transcriptomes on bioinformatics analyses, especially focusing on transcriptome assembly and transcript quantification. We discuss the benefits of using simulated benchmarking data when we examine the performance of various methods. We also present an example strategy to generate simulated allopolyploid transcriptomes and RNAseq datasets and how these benchmark datasets can be used to assess the performance of transcript assembly and quantification methods. Our benchmarking study shows that all transcriptome assembly methods are affected by having polyploid genomes. Quantification accuracy is also impacted by polyploidy depending on the method. These simulated datasets can be adapted for testing, such as, read mapping, variant calling, and differential expression using biologically realistic conditions.

THE IDEALIZED MODELS OF SOFTWARE SYSTEMS REENGINEERING

Content. Software systems are used in a variety of branches of life and human activities, but they are most widely used in industries where it is necessary to work with many routine operations – this applies to industry, production, transportation, training and info communications. Of course, in the process of exploiting these systems there is an evolutionary aging of the different types of security. This trend leads to a deterioration of high-speed, information-communication, graphic, time and other characteristics, up to the complete failure of the software system. The subject of the article is aimed to the design of ergative systems, project management and programs for re-designing or improving these systems. Reengineering allows the system to evolve, by making positive changes to its structure in order to improve operational characteristics and technical support. Objective. To form a representation of the estimation of resource cost parameters for the reengineering of software systems with the help of a mathematical tools for describing design models. Method. The idea of the article is based on the Boehm method and the principles of building an Archimedes spiral. Author’s research led to the idea of combining Boehm and Archimedes structures, adapting them to the software engineering methodology and transferring them to a cylindrical coordinate system. The basis of the obtained models is laid spiral principle of the organization of the reference. Results. The article deals with the process of creating and visualizing mathematical models in relation to the process of reengineering software systems. Transactions with these models can occur in projections of time and cost, in the isometric projection of software components, and in the logarithmic projection of lines of software code. Conclusions. For the first time, idealized models of reengineering have been formed, which will allow to increase the accuracy of cost estimation from the redesign of software systems. The model of cost visualization for reprogramming of software systems has been improved, which will increase the efficiency of forecasting the order of expenses. For the first time dependencies were obtained on the construction of the graphical cost model trajectory from the introduced reengineering automation coefficient and the similarity coefficient of the components that would make changes to the configuration of the model. The proposed idealized models for reengineering of software system security are evolutionary spirals, which are constructed in a cylindrical coordinate system. Reengineering, which will be accomplished with the help of developed idealized reengineering models, will not only reduce the cost of reprogramming software systems, but also increase the efficiency of technical support, increase the life cycle of software systems which are already in service and overcome the contradictions between the rapid pace of development of science, technology and processes of designing new software systems.

Unveiling the Impact of the Core Circadian Clock Protein FREQUENCY on Output in Neurospora crassa

Circadian rhythms are cellular oscillations that tune an organism's biology to the 24‐hour light/dark cycle on Earth. This cellular time‐keeping mechanism aids in the anticipation of environmental changes and increases organismal survival. These rhythms are maintained by a transcriptional/translational negative feedback loop, called the core circadian clock, that is evolutionarily conserved throughout most branches of life. In this core clock, positive arm proteins act to transcriptionally activate negative arm proteins. The negative arms proteins act back on the positive arm, in a time specific manner, to halt the negative arm's activation before degradation and re‐initiation, thus setting the period of the clock. Beyond this core clock, positive arm proteins also act to transcriptionally activate a variety of other genes that do not participate in the core clock mechanism in a time dependent manor, referred to as clock‐controlled genes (ccgs.) Most research into the mechanisms of circadian regulation on output has focused on transcriptional activation by the positive arm proteins. However, recently published work has demonstrated that there are many oscillating proteins for which the corresponding mRNA is not rhythmic. This has led to the theory that the regulation of circadian output is also accomplished via post‐translational mechanisms, which we hypothesize are imparted by the negative arm proteins.In the model organism Neurospora crassa, the negative arm comprises FREQUENCY (FRQ), Frequency‐Interacting RNA Helicase (FRH), and Casein Kinase 1 (CK‐1). Importantly, FRQ has been computationally and experimentally proven to be an intrinsically disordered protein (IDP). Aside from lacking a single, predetermined three‐dimensional structure, IDPs play key roles in cellular signaling and regulation due, in part, to the transient but highly specific and varied interacting partners they have. These attributes make FRQ a prime candidate to impart post‐translational circadian regulation. The aim of this study is to characterize protein complexes, centered around FRQ, that change in a time specific manner, to determine the impact these interactions could impart post‐translationally on circadian regulatory pathways. To this end, Neurospora samples where crosslinked and purified through co‐immunoprecipitation before protein identification through liquid chromatography mass spectrometry. Initial results suggest that FRQ plays a role in post‐translational regulation on metabolism, the cell cycle, and a variety of other functions.Support or Funding InformationThis work was funded through the support of the NIGMS/NIH R35GM128687 grant and the Rensselaer Polytechnic Institue Start Up Fund.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Single Amino Acid Substitutions Dramatically Shift Equilibria of Physiologically Relevant Alternate Protein Assemblies

Increasing numbers of proteins are being revealed to “shape shift” in physiologically relevant ways that do not dramatically alter secondary structure. As each has been discovered they have been called morpheeins, transformers, metamorphic polymorphs, and others. In each case the alternate assemblies have different functions ranging from “on vs. off” to “moonlighting”. These examples continue to surprise their discoverers because they defy the “one sequence, one structure, one function” paradigm in an unexpected way. These alternate assemblies are likely physiologically relevant as their interconversion is thermodynamically feasible and the equilibrium of alternate assemblies is responsive to biological signals (e.g. pH, ligands). Experience now teaches that single amino acid substitutions can also dramatically shift an equilibrium of alternate assemblies. In some cases this shift is reasonably hypothesized, or established, to contribute to diseases such as inborn errors of metabolism and cancer.We present examples culled both from our work and the literature of such shape‐shifting proteins whose equilibria respond to single amino acid substitutions. Prime examples come from diverse branches of life, including viral proteins, bacterial proteins, and human metabolic enzymes. The growing number of such examples suggests that alternate assemblies, which have been called the fifth level of protein structure, may be a common factor in protein structure‐function relationships. Experience teaches that this fifth level of structure, for a given protein, may be revealed by the unexpected biophysical behavior of single amino acid variants.Support or Funding InformationNIH R01 NS100081 (EKJ)NIH R01 AI118016 (EOS)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Fungi in the Marine Environment: Open Questions and Unsolved Problems.

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.