C-A test of DNA force fields

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.Comment: 14 pages, 4 figures plus one TOC picture, 5 table

Dynamics of Soliton-Like Excitations in a Chain of a Polymer Crystal: Influence of Neighbouring Chains Mobility

We investigate influence of mobility of neighbouring chains on dynamics of soliton-like excitations in a chain of the simplest polymer crystal (polyethylene in the “united atoms ” approximation) using molecular dynamics simulation. We present results for point-like structural defects: static and moving at low, medium and high velocities; and examine howthe structure of a crystal will affect them. 1Introduction The present work is concerned with the behaviour of a system presumed to be close to an integrable one, namely Sine-Gordon system. Sine-Gordon equation is well known to be the simplest continual one-dimensional model of a dislocation in a crystal (the well known Frenkel–Kontorova model). It can be equally used to describe nonlinear dynamics of a directed macromolecular chain subjected to a periodic potential [1, 2]. Because it is a periodic potential which is generated by immobile neighbouring chains in a polymer crystal, it was supposed that one can identify topological solitons of Sine-Gordon type with point defects in a polymer chain (vacancies and inclusions) which are caused by loca

Diversity and distribution of European whitefish (<i>Coregonus lavaretus</i>) in the watercourses of Murmansk region

European whitefish (Coregonus lavaretus) is a highly polymorphic species, but the wider scale diversity and distribution of sympatric morphs in subarctic lakes of northwestern Russia has not been recently studied and analyzed. The aim of the present study was to investigate diversity and distribution of whitefish morphs in different sized lakes and watercourses of Murmansk region. Our study of the water bodies in four major river basins of Murmansk region revealed the presence of two whitefish morphs: sparsely rakered (sr) and medium rakered (mr). The mr morph is less common and observed only alongside the sr whitefish. In general, in sr whitefish the number of gill rakers ranges between 15 and 31, and in mr whitefish between 27 and 44. Among whitefishes with 27 to 31 gill rakers, both sr and mr morphs were observed and distinguishable by the shape of the rakers. In the studied sr whitefish populations, relatively long and short rakered whitefish morphs were found. In Lake Kuetsyarvi (Pasvik River basin), the sr and mr whitefish formed additional slow- and fast-growing ecological morphs. The four whitefish morphs in Lake Kuetsyarvi specialize to different ecological niches correlating with morphological and behavioral differences. The observed diversity and distribution of whitefish in the Murmansk region requires genetic studies of the population to assess the origins of divergence

Bronchopulmonary Pathology Prevalence Among Premature infants and Estimation of Prophylactic Efficacy and Reactogenicity of 13-Valent Pneumococcal Conjugate Vaccine in Premature infants with Bronchopulmonary Dysplasia

Background. The most frequent chronic lung pathology among infants and especially in premature children with extremely low and very low body weight is bronchopulmonary dysplasia (BPD). The aim of the study is to study the prevalence of bronchopulmonary pathology among premature children and justify the need to vaccinate against pneumococcal disease premature children suffering from BPD. Methods. The official statistics (Form №32) and data from annual reports of the catamnesis department of “the Honourary order” Perm Regional Clinical Hospital were used in order to measure the number of premature children born alive in Perm region in 2015-2017 yy. The estimation of prophylactic efficacy and reactogenicity of 13-valent pneumococcal conjugate vaccine (PCV13) at immunization of premature children with BPD. Results. The study group included vaccinated premature children with BPD (n=29), the experimental group included non-vaccinated premature children with BPD (n=29) and 30 vaccinated term children. Administration of PCV13 in premature children suffering from BPD has revealed its high prophylactic efficacy (no cases of community-acquired pneumonia among vaccinated children during the prospective study for 3 years), high tolerability (no cases of broncho-obstructive syndrome or negative effects on respiratory system such as apnoea or desaturation among vaccinated children). Low reactogenicity (17.2 ± 0.57%) and similar vaccine tolerance with term children (16.5 ± 0.55%) has been revealed as well. The combination of PCV13 with other vaccines from immunisation schedule did not increase the number of vaccine-induced diseases in comparison with administration of PCV13 alone. Conclusion. The scientific necessity of vaccination of premature children with BPD against pneumococcal disease has been proved. The high prophylactic efficacy and low reactogenicity of PCV13 in this children group at tertiary neonatological care (catamnesis department of perinatal center) has been established within the national immunisation schedule

Increased importance of cool-water fish at high latitudes emerges from individual-level responses to warming

High latitude ecosystems are experiencing the most rapid warming on earth, expected to trigger a diverse array of ecological responses. Climate warming affects the ecophysiology of fish, and fish close to the cold end of their thermal distribution are expected to increase somatic growth from increased temperatures and a prolonged growth season, which in turn affects maturation schedules, reproduction, and survival, boosting population growth. Accordingly, fish species living in ecosystems close to their northern range edge should increase in relative abundance and importance, and possibly displace cold-water adapted species. We aim to document whether and how population-level effects of warming are mediated by individual-level responses to increased temperatures, shift community structure, and composition in high latitude ecosystems. We studied 11 cool-water adapted perch populations in communities dominated by cold-water adapted species (whitefish, burbot, and charr) to investigate changes in the relative importance of the cool-water perch during the last 30 years of rapid warming in high latitude lakes. In addition, we studied the individual-level responses to warming to clarify the potential mechanisms underlying the population effects. Our long-term series (1991-2020) reveal a marked increase in numerical importance of the cool-water fish species, perch, in ten out of eleven populations, and in most fish communities perch is now dominant. Moreover, we show that climate warming affects population-level processes via direct and indirect temperature effects on individuals. Specifically, the increase in abundance arises from increased recruitment, faster juvenile growth, and ensuing earlier maturation, all boosted by climate warming. The speed and magnitude of the response to warming in these high latitude fish communities strongly suggest that cold-water fish will be displaced by fish adapted to warmer water. Consequently, management should focus on climate adaptation limiting future introductions and invasions of cool-water fish and mitigating harvesting pressure on cold-water fish.Peer reviewe

Long-Term Environmental Monitoring in an Arctic Lake Polluted by Metals under Climate Change

Lake Kuetsjarvi (in the lower reaches of the Pasvik River, Murmansk Region, Russia) in the border area between Russia and Norway, is one of the most polluted water reservoirs in the European Arctic. The operation of the Pechenganikel Smelter located on its shores has led to the extremely high concentrations of heavy metals observed in the waters and sediments of the lake. Long-term comprehensive studies of the ecosystem of Lake Kuetsjarvi have made it possible to identify the response of its components to the global and regional change in the environment and climate as a whole, resulting in increased water toxicity and eutrophication, reduction in the number of stenobiont species of aquatic organisms against the background of an increase in the number of eurybiontic and invasive species. Modern communities of Lake Kuetsjarvi are the result of a combination of long-term changes in the abiotic environment and biotic interactions. Heavy-metal pollution of Lake Kuetsjarvi, observed since the 1930s, has led to the formation of a community that is resistant to this type of impact and supports large populations of adapted species. Adaptations of communities to the dynamics of the environmental conditions that their members are exposed to include changes in the species composition, quantitative indicators, ratios between individual taxonomic groups, and the population structure. The development of sympatric forms that differ in the ecological niches they occupy, morphology, and life cycle strategies, including the transition to a short-cycle survival strategy, allows whitefish to remain the dominant species and maintain high population numbers. Unlike the organismal level, responses to medium-term environmental changes on the population and community level are less specific and characterized by stronger inertia