Dynamic Structural Changes Research Articles

Meiotic DNA double-strand break-independent role of protein phosphatase 4 in Hop1 assembly to promote meiotic chromosome axis formation in budding yeast.

Dynamic changes in chromosomal structure that occur during meiotic prophase play an important role in the progression of meiosis. Among them, meiosis-specific chromosomal axis-loop structures are important as a scaffold for integrated control between the meiotic recombination reaction and the associated checkpoint system to ensure accurate chromosome segregation. However, the molecular mechanism of the initial step of chromosome axis-loop construction is not well understood. Here, we showed that, in budding yeast, protein phosphatase 4 (PP4) that primarily counteracts Mec1/Tel1 phosphorylation is required to promote the assembly of a chromosomal axis component Hop1 and Red1 onto meiotic chromatin via interaction with Hop1. PP4, on the other hand, less affects Rec8 assembly. Notably, unlike the previously known function of PP4, this PP4 function in Hop1/Red1 assembly was independent of meiotic DSB-dependent Tel1/Mec1 kinase activities. The defect in Hop1/Red1 assembly in the absence of PP4 function was not suppressed by dysfunction of Pch2, which removes Hop1 protein from the chromosome axis, suggesting that PP4 is required for the initial step of chromatin loading of Hop1 rather than stabilization of Hop1 on axes. These results indicate phosphorylation/dephosphorylation-mediated regulation of Hop1 recruitment onto chromatin during chromosome axis construction before meiotic double-strand break formation.

Long-term effects of planting density and site quality on timber assortment structure based on a 41-year plantation trial of Chinese fir

Stand density control coupled with site control is a key technique for cultivating large-diameter timber of Chinese fir trees, whose yield can be effectively increased by the optimal density and site management mode employed. This study aimed to evaluate the dynamic changes in timber assortment structure under differing initial planting densities and site quality based on growth data of a 41-year trial of Chinese fir plantations. Our results showed that the total timber yield and both large-diameter timber outturn and the outturn rate all increased with better site quality under the same initial planting density. Further, the outturn peak as well as outturn rate peak for both medium- and small-diameter timber was reached sooner with improved site quality. For the same site class, a lower initial planting density augmented the total timber outturn rate, and also resulted in less time required for the total timber outturn rate to reach a constant or maximum value. Finally, the total timber outturn rate of all density plots tended to be nearly identical. Using a high planting density increased the outturn of small-diameter timber, whose outturn peak was delayed in the denser plots. The bolstering effect of low density upon the growth of large-diameter timber was enhanced by higher site quality, with density-induced differences in large-diameter timber more pronounced; conversely, that promoting effect weakened under poor site quality conditions. The interaction between planting density and site index significantly influenced the growth of any timber assortment of Chinese fir in the early stage following its formation. Notably, the significant effect of site index on large-diameter timber lasted longer than that of other timber assortments. The optimal site conditions for cultivating large-diameter timber trees of Chinese fir consist of a site class ≥ 20 with a planting density limited to no more than 1667 trees/ha, whose stand rotation period must be over 26 years, so as to maximize the output of large-diameter timber yield. Our empirical findings will be helpful for the construction of an optimal cultivation mode for the density, site, and rotation age of large-diameter timber in Chinese fir plantations.

Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins.

Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress-relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamics in the deeply supercooled regime (T = 180 K), which is typically not accessible through equilibrium methods. The observed stimulated dynamic response is attributed to collective stress-relaxation as the system transitions from a jammed granular state to an elastically driven regime. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalized variance χT. The amplification of fluctuations is consistent with previous studies of hydrated proteins, which indicate the key role of density and enthalpy fluctuations in hydration water. Our study provides new insights into X-ray stimulated stress-relaxation and the underlying mechanisms behind spatiotemporal fluctuations in biological granular materials.

Increasing depth of neural networks for life-long learning

Purpose:We propose a novel method for continual learning based on the increasing depth of neural networks. This work explores whether extending neural network depth may be beneficial in a life-long learning setting. Methods:We propose a novel approach based on adding new layers on top of existing ones to enable the forward transfer of knowledge and adapting previously learned representations. We employ a method of determining the most similar tasks for selecting the best location in our network to add new nodes with trainable parameters. This approach allows for creating a tree-like model, where each node is a set of neural network parameters dedicated to a specific task. The Progressive Neural Network concept inspires the proposed method. Therefore, it benefits from dynamic changes in network structure. However, Progressive Neural Network allocates a lot of memory for the whole network structure during the learning process. The proposed method alleviates this by adding only part of a network for a new task and utilizing a subset of previously trained weights. At the same time, we may retain the benefit of PNN, such as no forgetting guaranteed by design, without needing a memory buffer. Results:Experiments on Split CIFAR and Split Tiny ImageNet show that the proposed algorithm is on par with other continual learning methods. In a more challenging setup with a single computer vision dataset as a separate task, our method outperforms Experience Replay. Conclusion:It is compatible with commonly used computer vision architectures and does not require a custom network structure. As an adaptation to changing data distribution is made by expanding the architecture, there is no need to utilize a rehearsal buffer. For this reason, our method could be used for sensitive applications where data privacy must be considered.

Nuclear envelope dynamics in connection to chromatin remodeling.

The nucleus is a central organelle of eukaryotic cells undergoing dynamic structural changes during cellular fundamental processes such as proliferation and differentiation. These changes rely on the integration of developmental and stress signals at the nuclear envelope (NE), orchestrating responses at the nucleo-cytoplasmic interface for efficient genomic functions such as DNA transcription, replication and repair. While in animals, correlation has already been established between NE dynamics and chromatin remodeling using last-generation tools and cutting-edge technologies, this topic is just emerging in plants, especially in response to mechanical cues. This review summarizes recent data obtained in this field with more emphasis on the mechanical stress response. It also highlights similarities/differences between animal and plant cells at multiples scales, from the structural organization of the nucleo-cytoplasmic continuum to the functional impacts of NE dynamics.

Study on the Trend in Microbial Changes during the Fermentation of Black Tea and Its Effect on the Quality.

The role of tea endophytes in black tea fermentation and their impact on black tea quality remain unclear. We collected fresh leaves of Bixiangzao and Mingfeng tea and processed them into black tea, while testing the biochemical composition of both the fresh leaves and the black tea. We also used high-throughput techniques, such as 16S rRNA, to analyze the dynamic changes in the microbial community structure and function during black tea processing in order to investigate the influence of dominant microorganisms on the quality of black tea formation. Our results showed that bacteria, such as Chryseobacterium and Sphingomonas, and Pleosporales fungi dominated the entire black tea fermentation process. Predicted functional analysis of the bacterial community indicated that glycolysis-related enzymes, pyruvate dehydrogenase, and tricarboxylic acid cycle-related enzymes were significantly elevated during the fermentation stage. Amino acids, soluble sugars, and tea pigment content also increased considerably during fermentation. Pearson's correlation analysis revealed that the relative bacterial abundance was closely related to the content of tea polyphenols and catechins. This study provides new insights into the changes in microbial communities during the fermentation of black tea and demonstrates understanding of the basic functional microorganisms involved in black tea processing.

Carbon Sequestration Characteristics Under Natural Vegetation Restoration in Ziwuling Area of the Loess Plateau

The aim of this study was to analyze the carbon sink effect under natural vegetation restoration and the influence of changes in vegetation community characteristics on ecosystem carbon density in ecologically fragile areas of the Loess Plateau. In this study, the changes in carbon sequestration of a vegetation-soil system under eight successional stages[slope cropland, abandoned cropland for 10 years, abandoned cropland for 20 years, Sophora davidii (Franch.) Skeels., Betula platyphylla Suk., Pinus tabulaeformis Carr., Quercus wutaishanic Mary+P. tabulaeformis Carr mixed forests, and Q. wutaishanic Mary] in Ziwuling area over 150 restoration periods were investigated using the common method of spatial and temporal substitution. This study also discussed the relationship between changes in vegetation community characteristics and vegetation-soil system carbon density. The results showed that the community coverage of the investigated vegetation fluctuated from 85% in the slope cropland stage to 100% in the arbor stage. The number of species, Margalef index, Shannon-Wiener index, Pielou index, and Simpson index initially increased rapidly, then declined slowly until becoming stable, and reached a peak in the middle of the succession (B. platyphylla Suk.). The biomass and carbon density of vegetation components (above-ground biomass, below-ground roots, and litter) increased exponentially during the succession, i.e., increased slowly before B. platyphylla Suk. but increased significantly in B. platyphylla Suk. and P. tabulaeformis Carr.(P<0.05). The biomass and carbon density reached the maximum values of 27858.08 g·m-2 and 13232.51 g·m-2, respectively, in Q. wutaishanic Mary+P. tabulaeformis Carr mixed forests and tended to be stable in the late succession stage. Soil organic carbon density showed a power function relationship with vegetation restoration, with the greatest increase in the stages of abandoned cropland for 10 years and B. platyphylla, but no significant changes in the subsequent stages (P>0.05). In the early succession stage, the carbon density of the farmland ecosystem was the lowest (4395.70 g·m-2), whereas the other seven stages increased by 55.54%, 40.37%, 69.96%, 202.48%, 326.35%, 357.43%, and 351.07%, respectively, compared with the farmland ecosystem. Community coverage, Margalef index, Shannon-Wiener index, above-ground biomass, root biomass, and litter biomass were significantly positively correlated with vegetation-soil system carbon density (P<0.05). The carbon sink effect of long-term natural restoration in Ziwuling Region was significant, and the carbon density of the vegetation-soil system under interspecific competition tended to be stable in the late succession stage. Dynamic changes in the vegetation community structure and plant diversity during the succession process increased vegetation carbon density and soil carbon density. This study helps to clarify the carbon sink effect of natural vegetation restoration in ecologically fragile areas of the Loess Plateau and provides a theoretical basis for promoting natural forest conservation and achieving carbon neutrality.

A Comprehensive Approach to Sample Preparation for Electron Microscopy and the Assessment of Mitochondrial Morphology in Tissue and Cultured Cells.

Mitochondria respond to metabolic demands of the cell and to incremental damage, in part, through dynamic structural changes that include fission (fragmentation), fusion (merging of distinct mitochondria), autophagic degradation (mitophagy), and biogenic interactions with the endoplasmic reticulum (ER). High resolution study of mitochondrial structural and functional relationships requires rapid preservation of specimens to reduce technical artifacts coupled with quantitative assessment of mitochondrial architecture. A practical approach for assessing mitochondrial fine structure using two dimensional and three dimensional high-resolution electron microscopy is presented, and a systematic approach to measure mitochondrial architecture, including volume, length, hyperbranching, cristae morphology, and the number and extent of interaction with the ER is described. These methods areused to assess mitochondrial architecture in cells and tissue with high energy demand, including skeletal muscle cells, mouse brain tissue, and Drosophila muscles. The accuracy of assessment isvalidated in cells and tissue with deletion of genes involved in mitochondrial dynamics.

3D genome perspective on cell fate determination, organ regeneration, and diseases

The nucleosome is the fundamental subunit of chromatin. Nucleosome structures are formed by the combination of histone octamers and genomic DNA. Through a systematic and precise process of folding and compression, these structures form a 30-nm chromatin fibre that is further organized within the nucleus in a hierarchical manner, known as the 3D genome. Understanding the intricacies of chromatin structure and the regulatory mode governing chromatin interactions is essential for unravelling the complexities of cellular architecture and function, particularly in relation to cell fate determination, regeneration, and the development of diseases. Here, we provide a general overview of the hierarchical structure of chromatin as well as of the evolution of chromatin conformation capture techniques. We also discuss the dynamic regulatory changes in higher-order chromatin structure that occur during stem cell lineage differentiation and somatic cell reprogramming, potential regulatory insights at the chromatin level in organ regeneration, and aberrant chromatin regulation in diseases.

Rational disposition effects: Theory and evidence

The disposition effect is a longstanding puzzle in financial economics. This paper demonstrates that it is not intrinsically at odds with rational behavior. In a rational expectations model with asymmetrically informed investors, trading strategies as predicted by the disposition effect can arise as an optimal response to dynamic changes in the information structure. The model predicts that the disposition behavior of uninformed investors weakens after events that reduce information asymmetries. The data, trading records of 50,000 clients at a German discount brokerage firm from 1995 to 2000, are consistent with this prediction.

Improving tyrosol production efficiency through shortening the allosteric signal transmission distance of pyruvate decarboxylase.

Tyrosol is an important chemical in medicine and chemical industries, which can be synthesized by a four-enzyme cascade pathway constructed in our previous study. However, the low catalytic efficiency of pyruvate decarboxylase from Candida tropicalis (CtPDC) in this cascade is a rate-limiting step. In this study, we resolved the crystal structure of CtPDC and investigated the mechanism of allosteric substrate activation and decarboxylation of this enzyme toward 4-hydroxyphenylpyruvate (4-HPP). In addition, based on the molecular mechanism and structural dynamic changes, we conducted protein engineering of CtPDC to improve decarboxylation efficiency. The conversion of the best mutant, CtPDCQ112G/Q162H/G415S/I417V (CtPDCMu5), had over two-fold improvement compared to the wild-type. Molecular dynamic (MD) simulation revealed that the key catalytic distances and allosteric transmission pathways were shorter in CtPDCMu5 than in the wild type. Furthermore, when CtPDC in the tyrosol production cascade was replaced with CtPDCMu5, the tyrosol yield reached 38 g·L-1 with 99.6% conversion and 1.58 g·L-1·h-1 space-time yield in 24 h through further optimization of the conditions. Our study demonstrates that protein engineering of the rate-limiting enzyme in the tyrosol synthesis cascade provides an industrial-scale platform for the biocatalytic production of tyrosol. KEY POINTS: • Protein engineering of CtPDC based on allosteric regulation improved the catalytic efficiency of decarboxylation. • The application of the optimum mutant of CtPDC removed the rate-limiting bottleneck in the cascade. • The final titer of tyrosol reached 38 g·L-1 in 24 h in 3 L bioreactor.

The mitochondrial genome of the diploid oat Avena longiglumis

BackgroundAvena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species.ResultsThe complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100–31,235 bp) and medium (144–792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts.ConclusionsComparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.

Mouse Cardiac Arrest Model for Brain Imaging and Brain Physiology Monitoring During Ischemia and Resuscitation.

Most cardiac arrest (CA) survivors experience varying degrees of neurologic deficits. To understand the mechanisms that underpin CA-induced brain injury and, subsequently, develop effective treatments, experimental CA research is essential. To this end, a few mouse CA models have been established. In most of these models, the mice are placed in the supine position in order to perform chest compression for cardiopulmonary resuscitation (CPR). However, this resuscitation procedure makes the real-time imaging/monitoring of brain physiology during CA and resuscitation challenging. To obtain such critical knowledge, the present protocol presents a mouse asphyxia CA model that does not require the chest compression CPR step. This model allows for the study of dynamic changes in blood flow, vascular structure, electrical potentials, and brain tissue oxygen from the pre-CA baseline to early post-CA reperfusion. Importantly, this model applies to aged mice. Thus, this mouse CA model is expected to be a critical tool for deciphering the impact of CA on brain physiology.

Analysis for 3-D morphology structural changes for underwater topographical in Culebrita Island

ABSTRACT In order to discover how a storm impacts underwater topographic changes, the underwater terrain morphological and structural changes in Culebrita Island were analysed. Airborne bathymetry LiDAR (Light Detection and Ranging) data from the National Oceanic and Atmospheric Administration (NOAA) with a 1.0 m spatial resolution at different time intervals (2016, 2018, 2019) were used to create three-dimensional (3D) terrain models. Four types of terrain feature attributes, water depth, slope, aspect and rugosity, were analysed to investigate terrestrial structure changes caused by the storms. The variation of underwater topography at each time interval was discussed by five profiles, the volume of deposition and erosion between different water depth intervals was investigated to derive the rate of net volume change per unit area (), spatial patterns of underwater topography dynamics are discussed and dynamic changes in topography structure and changes in topographic erosion deposition are observed and detected. The analysis of the topographic feature attributes for each year discovered an increase in topographic complexity. Analysis of the profiles has discovered that the topographic deposition with an average rate of 0.53 from 2016 to 2018 and an average topographic erosion rate of 0.34 from 2018 to 2019. In addition, it is also found that the deposition was greater than erosion from 2016 to 2018, and the erosion was greater than deposition from 2018 to 2019, with a net volume change of+48794 and a net volume change rate of+0.042. Investigation also found that such large changes in the deposition were mainly due to the sediment carried by the storms.

Mergers and acquisitions in supply bases

Mergers and acquisitions (M&amp;As) by first‐tier suppliers, referred to as the supply base, are dynamic and drastic changes in supply chain structure and relationships that affect focal firm performance. In particular, the impact of M&amp;As in a supply base depends on the concentration and differentiation of the supply base, which affects power–dependence relationships in the supply chain. This study examines the effect of supply base M&amp;As on focal firms’ cost of goods sold (COGS). In addition, this study explores the role of power relationships by investigating the moderating effects of supply base concentration and differentiation. Using secondary panel data assembled from four different data sources, this study constructs econometric models and empirically examines the relationship between supply base M&amp;As and focal firm cost efficiency. Our findings indicate that supply base M&amp;As are positively associated with focal firm COGS. This result suggests that potential efficiency gains from M&amp;As in supply bases may not translate to benefits for the focal firm because suppliers may also gain bargaining power from M&amp;As. However, the effect of supply base M&amp;As on focal firm COGS is attenuated when the supply base is less concentrated in terms of their transaction percentage with suppliers and more differentiated in terms of industry and business scopes. These are situations where suppliers less effectively obtain or employ bargaining power from M&amp;As. These findings make important contributions to the operations management literature.

Reversible and irreversible transformations of Ni-based electrocatalysts during the oxygen evolution reaction

Nickel-based catalysts for the alkaline oxygen evolution reaction (OER) demonstrate excellent catalytic performance and stability. However, a lack of fundamental understanding of the dynamic electronic and structural changes that occur under OER conditions inhibits the rational design of new materials. Recent advances in operando spectroscopy and computational modelling techniques have helped to elucidate the electrochemically-driven transformations of Ni-based materials. For reversible transformations, this encompasses an increased understanding of the redox transformations of Ni/Fe centers, the adsorption and desorption of reaction intermediates, oxygen vacancy dynamics, phase transformations, and the mechanism of dissolution and redeposition of surface atoms. Likewise, there have been great advances in scientific understanding of irreversible transformations including phase transformations related to ageing, as well as operando surface reconstruction which involves the growth of new OER active phases.

Engineering D-allulose 3-epimerase from Clostridium cellulolyticum for improved thermostability using directed evolution facilitated by a nonenzymatic colorimetric screening assay

D-Allulose 3-epimerase (DAEase) is a biocatalyst of concern for D-allulose enzymatic synthesis; however, it exhibits comparatively low thermal stability. To facilitate the directed evolution of DAEase, a nonenzymatic colorimetric assay was developed for high-throughput screening of enhanced DAEase mutants. One desirable mutant, MT4 (S38F/F42N/A70P/T119P), was screened based on purifying selection of the randomly mutagenesis library and positive screening of the randomly shuffled library. Compared to the wild-type, the combinational mutant MT4 had higher catalytic activity (1.23-fold) and showed 5, 6.2, and 6.92 °C increases in Topt, T50, and Tm values, respectively. Furthermore, at 60 °C, the t1/2 value of mutant MT4 was 7.30nullh, exhibiting an 11.4-fold increase in comparison to the wild-type. When the mutant MT4 was used in D-allulose production, the yield reached 28.3%, higher than the 25.1% achieved by the wild-type. Dynamic property and structural change analysis demonstrated that the enhanced properties of mutant MT4 were largely attributed to the β4-α4 loop rigidification and active-site tunnel entrance constriction. This work expands the industrial application value of DAEase and provides a robust method as the basis for further protein engineering to achieve better performance of this enzyme.

Biomechanisms of cervical remodeling and current approaches to maturity assessment

The cervical remodeling process is unique and consists of softening, ripening, dilation at fetal birth, and repair to the original state, which is a dense long tubular structure. In this review, the problem of impaired cervical remodeling is discussed in both preterm birth and delayed transformation, which leads to the unpreparedness of the cervix for childbirth and prolongation of pregnancy. Histological, immunological and structural dynamic changes in the cervix begin long before delivery and are noted as early as the first trimester of gestation. There are a few ways to assess the maturity of the cervix. In the second and third trimester, in order to predict preterm birth, these are ultrasound cervicometry and a cervical phosphorylated insulin-like growth factor binding protein-1 test. At full term, in order to determine its readiness for delivery, this is a palpation assessment. Inadequate assessment of the cervical characteristics is one of the factors of untimely prevention of preterm birth, and at full term leads to inappropriate choice of method of preparation for labor. It is necessary to develop new approaches to the comprehensive assessment of the cervix, using existing methods, and to discover new ways to assess its maturity.&#x0D; In this review, the problem of cervical maturation diagnosis is considered based on literature data from such databases as PubMed, ResearchGate, and Google Scholar, as well as from electronic resources of the M. Gorky Scientific Library (St. Petersburg State University, Russia). This review analyzes data on molecular, biochemical and histophysiological processes occurring during cervical maturation at all stages of gestation.&#x0D; It is generally accepted that the main role in cervical changes at all stages of gestation is played by: collagen fiber restructuring / desorganization, decreased concentrations of collagen and elastin, high molecular weight hylauronic acid cleavage, increased aquaparin level and tissue hydrophilicity, increased cervical vascularization, as well as changes in glycosaminoglycan and matrix metalloproteinase content. Palpatory technique and ultrasound cervicometry are the most common methods of determining the cervical length, which have insufficient sensitivity, probably because they do not cover all pathogenetic pathways of remodeling and cannot assess all cervical characteristics. Improvement of efficiency is possible through the introduction of combined techniques and the use of promising methods such as elastography, ultrasound diagnosis of the cervix with Doppler assessment of its vessels, determination of a disintegrin and metalloprotease with thrombospondin-like repeats-1 and placental 1-microglobulin in cervical secretion, and relaxin in maternal blood.&#x0D; Understanding the molecular, biochemical and histophysiological processes that occur during cervical remodeling is crucial for predicting preterm birth, diagnosing isthmic-cervical insufficiency, understanding the lack of timely cervical readiness, and choosing tactics the method of preinduction and induction of labor if necessary. The lack of clinical methods and their lack of objectivity require a combined approach and the search for new prognostic markers of cervical maturation.

In Silico Analysis of SARS-CoV-2 Spike Proteins of Different Field Variants.

Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein software to understand the changes produced in the protein structure. The SOPMA web server was used to predict the secondary structure of the proteins. Tertiary structure details of the selected proteins were analyzed using the web server SWISS-MODEL. Sequencing results showed numerous single nucleotide polymorphisms in the surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein while the envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes had no or few SNPs. Contigs were used to identify variations in the Alpha and Delta variants of SARS-CoV-2 with the reference strain (Wuhan). Some of the secondary structures of the SARS-CoV-2 proteins were predicted by using Sopma software and were further compared with reference strains of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plots. Through the Swiss-model, a comparison of the tertiary structure model of the SARS-CoV-2 spike protein of the Alpha and Delta variants was made with the reference strain (Wuhan). Alpha and Delta variants of the SARS-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with the reference strain, and 3D structure mapping of the spike glycoprotein and mutations in the amino acids were seen. The surprisingly increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employed in silico computational tools to analyze the SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in the functionality, immunological, physicochemical, and structural variations in the SARS-CoV-2 isolates. However, the real impact of these SNPs can only be determined further by experiments. Our results can aid in vivo and in vitro experiments in the future.

Histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 proteins affect plant growth under nitrogen deficient conditions in Arabidopsis thaliana.

Nitrogen (N) availability is one of the most important factors regulating plant metabolism and growth as it affects global gene expression profiles. Dynamic changes in chromatin structure, including histone modifications and nucleosome assembly/disassembly, have been extensively shown to regulate gene expression under various environmental stresses in plants. However, the involvement of chromatin related changes in plant nutrient responses has been demonstrated only in a few studies to date. In this study, we investigated the function of histone chaperone NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) proteins under N deficient conditions in Arabidopsis. In the nap1;1 nap1;2 nap1;3 triple mutant (m123-1), the expression of N-responsive marker genes and growth of lateral roots were decreased under N deficient conditions. In addition, the m123-1 plants showed a delay in N deficiency-induced leaf senescence. Taken together, these results suggest that NAP1s affect plant growth under N deficient conditions in Arabidopsis.