scholarly journals Emergence of multiple variants of SARS-CoV-2 with signature structural changes

2020 ◽  
Author(s):  
Debaleena Bhowmik ◽  
Sourav Pal ◽  
Abhishake Lahiri ◽  
Arindam Talukdar ◽  
Sandip Paul
Keyword(s):  
Structural Changes ◽  
Phylogenomic Analysis ◽  
Genetic Studies ◽  
Protein Coding ◽  
Coding Regions ◽  
Emergent Groups ◽  
Specific Proteins ◽  
Modelling Techniques ◽  
Divergence Pattern ◽  
The Impact

AbstractThis study explores the divergence pattern of SARS-CoV-2 using whole genome sequences of the isolates from various COVID-19 affected countries. The phylogenomic analysis indicates the presence of at least four distinct groups of the SARS-CoV-2 genomes. The emergent groups have been found to be associated with signature structural changes in specific proteins. Also, this study reveals the differential levels of divergence patterns for the protein coding regions. Moreover, we have predicted the impact of structural changes on a couple of important viral proteins via structural modelling techniques. This study further advocates for more viral genetic studies with associated clinical outcomes and hosts’ response for better understanding of SARS-CoV-2 pathogenesis enabling better mitigation of this pandemic situation.

scholarly journals Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2

2020 ◽  
Author(s):  
Matteo Chiara ◽  
David S. Horner ◽  
Carmela Gissi ◽  
Graziano Pesole
Keyword(s):  
Specific Protein ◽  
Phylogenomic Analysis ◽  
Founder Effects ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Geographic Locations ◽  
Coding Regions ◽  
Rapid Spread ◽  
Novel Virus ◽  
Genomic Regions

AbstractPhylogenomic analysis of SARS-CoV-2 as available from publicly available repositories suggests the presence of 3 prevalent groups of viral episomes (super-clades), which are mostly associated with outbreaks in distinct geographic locations (China, USA and Europe). While levels of genomic variability between SARS-CoV-2 isolates are limited, to our knowledge, it is not clear whether the observed patterns of variability in viral super-clades reflect ongoing adaptation of SARS-CoV-2, or merely genetic drift and founder effects. Here, we analyze more than 1100 complete, high quality SARS-CoV-2 genome sequences, and provide evidence for the absence of distinct evolutionary patterns/signatures in the genomes of the currently known major clades of SARS-CoV-2. Our analyses suggest that the presence of distinct viral episomes at different geographic locations are consistent with founder effects, coupled with the rapid spread of this novel virus. We observe that while cross species adaptation of the virus is associated with hypervariability of specific protein coding regions (including the RDB domain of the spike protein), the more variable genomic regions between extant SARS-CoV-2 episomes correspond with the 3’ and 5’ UTRs, suggesting that at present viral protein coding genes should not be subjected to different adaptive evolutionary pressures in different viral strains. Although this study can not be conclusive, we believe that the evidence presented here is strongly consistent with the notion that the biased geographic distribution of SARS-CoV-2 isolates should not be associated with adaptive evolution of this novel pathogen.

Y chromosomal fertility genes of Drosophila: a new type of eukaryotic genes

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 561-571 ◽  
Author(s):  
Wolfgang Hennig ◽  
Reindert C. Brand ◽  
Johannes Hackstein ◽  
Ron Hochstenbach ◽  
Hannie Kremer ◽  
...  
Keyword(s):  
Repeated Sequence ◽  
Protein Coding ◽  
Chromosomal Proteins ◽  
Coding Regions ◽  
Eukaryotic Genes ◽  
Chromosomal Genes ◽  
Specific Proteins ◽  
New Type ◽  
Fertility Genes ◽  
Lampbrush Loops

The Y chromosomal fertility genes of Drosophila are required for sperm differentiation. They are active only in primary spermatocytes where they form giant lampbrush loops. The molecular structure of these genes was investigated and revealed an unusual composition of DNA. Short, tandemly repeated sequence clusters are interrupted by longer and more heterogeneous sequences, which probably all represent transposable elements. No indication of the presence of protein-coding regions has been found within the fertility genes. However, the lampbrush loops bind site-specific proteins recognized by immunofluorescence techniques. This, together with other experimental data, led to the hypothesis that the Y chromosomal genes have a function in binding chromosomal proteins. The data and arguments in support of this gene model are summarized in this paper.Key words: Y chromosome, Drosophila, fertility genes, gene structure, lampbrush loops, spermatogenesis.

International trade: Research of the reasons for the fall

2019 ◽  
pp. 79-91 ◽  
Author(s):  
V. S. Nazarov ◽  
S. S. Lazaryan ◽  
I. V. Nikonov ◽  
A. I. Votinov
Keyword(s):  
Growth Rate ◽  
International Trade ◽  
Exchange Rate ◽  
Global Economy ◽  
Structural Changes ◽  
Global Value Chains ◽  
Value Chains ◽  
Negative Contribution ◽  
Basic Commodity ◽  
The Impact

The article assesses the impact of various factors on the growth rate of international trade. Many experts interpreted the cross-border flows of goods decline against the backdrop of a growing global economy as an alarming sign that indicates a slowdown in the processes of globalization. To determine the reasons for the dynamics of international trade, the decompositions of its growth rate were carried out and allowed to single out the effect of the dollar exchange rate, the commodities prices and global value chains on the change in the volume of trade. As a result, it was discovered that the most part of the dynamics of international trade is due to fluctuations in the exchange rate of the dollar and prices for basic commodity groups. The negative contribution of trade within global value chains in 2014 was also revealed. During the investigated period (2000—2014), such a picture was observed only in the crisis periods, which may indicate the beginning of structural changes in the world trade.

THE IMPACT OF UKRAINE'S EXCISE DUTY POLICY ON THE TRANSFORMATION PROCESSES OF THE TOBACCO MARKET

2020 ◽  
Vol 2020 (10) ◽  
pp. 19-33
Author(s):  
Nadiia NOVYTSKA ◽  
◽  
Inna KHLIEBNIKOVA ◽  
Keyword(s):  
Structural Changes ◽  
Tax Avoidance ◽  
Transformation Process ◽  
State Regulation ◽  
Tobacco Products ◽  
Excise Duty ◽  
Increasing Demand ◽  
High Level ◽  
The Impact ◽  
Transformation Processes

The market of tobacco products in Ukraine is one of the most dynamic and competitive. It develops under the influence of certain factors that cause structural changes, therefore, the aim of the article is to conduct a comprehensive analysis of transformation processes in the market of tobacco and their alternatives in Ukraine and identify the factors that cause them. The high level of tax burden and the proliferation of alternative products with a potentially lower risk to human health, including heating tobacco products and e-cigarettes, are key factors in the market’s transformation process. Their presence leads to an increase in illicit turnover of tobacco products, which accounts for 6.37% of the market, and the gradual replacement of cigarettes with alternative products, which account for 12.95%. The presence on the market of products that are not taxed or taxed at lower rates is one of the reasons for the reduction of excise duty revenues. According to the results of 2019, the planned indicators of revenues were not met by 23.5%. Other reasons for non-fulfillment of excise duty revenues include: declining dynamics of the tobacco products market; reduction in the number of smokers; reorientation of «cheap whites» cigarette flows from Ukraine to neighboring countries; tax avoidance. Prospects for further research are identified, namely the need to develop measures for state regulation and optimization of excise duty taxation of tobacco products and their alternatives, taking into account the risks to public health and increasing demand of illegal products.

Effekt of blood flow shutdown on the vein damage when exposed to HIFU

2017 ◽  
pp. 46-50
Author(s):  
Н.Н. Петрищев ◽  
Д.Ю. Семенов ◽  
А.Ю. Цибин ◽  
Г.Ю. Юкина ◽  
А.Е. Беркович ◽  
...  
Keyword(s):  
Blood Flow ◽  
Structural Changes ◽  
Focused Ultrasound ◽  
Vena Cava ◽  
Posterior Wall ◽  
High Intensity Focused Ultrasound ◽  
Vein Wall ◽  
Ultrasound Exposure ◽  
Isolated Segment ◽  
The Impact

The purpose. In the study we investigated the impact of the partial blood flow shutdown on structural changes in the rabbit vena cava posterior wall after exposure to high-intensity focused ultrasound (HIFU). Methods. Ultrasound Exposure: frequency of 1.65 MHz, the ultrasound intensity in the focus of 13.6 kW/cm, the area of the focal spot 1 mm, continuous ultrasound, exposure for 3 seconds. Results. Immediately after HIFU exposure all layers of the vein wall showed characteristic signs of thermal damage. A week after exposure structural changes in the intima, media and adventitia was minimal in the part of vessel with preserved blood flow, and after 4 weeks the changes were not revealed. A week after HIFU exposure partial endothelium destruction, destruction of myocytes, disorganization and consolidation of collagen fibers of the adventitia were observed in an isolated segment of the vessel, and in 4 weeks endothelium restored and signs of damage in media and adventitia persisted, but were less obvious than in a week after exposure. Conclusion. The shutdown of blood flow after exposure to HIFU promotes persistent changes in the vein wall. Vein compression appears to be necessary for the obliteration of the vessel, when using HIFU-technology.

scholarly journals The open targets post-GWAS analysis pipeline

2020 ◽  
Vol 36 (9) ◽  
pp. 2936-2937 ◽  
Author(s):  
Gareth Peat ◽  
William Jones ◽  
Michael Nuhn ◽  
José Carlos Marugán ◽  
William Newell ◽  
...  
Keyword(s):  
Drug Targets ◽  
Gene Expression Regulation ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Protein Coding ◽  
Data Resource ◽  
Coding Regions ◽  
Genome Wide ◽  
Causal Genes ◽  
Interactive Data

Abstract Motivation Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. Results We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. Availability and implementation The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.

scholarly journals KUALITAS AIR SUNGAI DI KAWASAN WISATA PANTAI PETITENGET, KEROBOKAN KABUPATEN BADUNG BALI

2018 ◽  
Vol 12 (2) ◽  
pp. 226
Author(s):  
Wayan Budiarsa Suyasa ◽  
Sri Kunti Pancadewi G. A ◽  
Iryanti E. Suprihatin ◽  
Dwi Adi Suastuti G. A.
Keyword(s):  
Water Quality ◽  
Structural Changes ◽  
Pollution Index ◽  
Basic Structure ◽  
Physical Damage ◽  
E Coli ◽  
Pollutant Source ◽  
Quality Category ◽  
Index Value ◽  
The Impact

In order to maintain the environmental carrying capacity of coastal tourism, this research was conducted to determine the condition of river water environmental pollution in the Petitenget beach area and pollutant source activities. Determination of water quality is carried out by analyzing the water quality taken at several sampling points in the four rivers that lead to the Petitenget beach. Determined the pollution index value (IP) of the physical chemical and biological pollution parameters. The results showed that the four rivers that flow into the Petitenget Beach area had been contaminated with indications of pH, BOD, COD, ammonia, Coliform and E. coli which exceeded water quality category III class quality (PerGub Bali No 16 Year 2016). The four rivers are included in the criteria of severe contamination. The four rivers have experienced physical damage or structural changes that have very high discharge fluctuations both in quantity and quality. Slimy basic structure, smelly and slum aesthetic waters. While the indication of the impact of pollution is waste water which is directly discharged into the river from hotels, restaurants, homestays, commercial centers and settlements.

Statistical Approaches to Structural Change in Regional Interindustry Models

1986 ◽  
Vol 18 (9) ◽  
pp. 1189-1207
Author(s):  
B Ó Huallacháin
Keyword(s):  
Structural Change ◽  
Structural Changes ◽  
Washington State ◽  
Multivariate Statistical Analyses ◽  
Input Output ◽  
Multivariate Statistical ◽  
State Data ◽  
System A ◽  
Statistical Approaches ◽  
The Impact

The conventional approach to assessing structural change in regional input – output tables is to measure the impact of coefficient change on the estimation of outputs and multipliers. The methods developed and tested in this paper focus exclusively on the coefficients. Univariate and multivariate statistical analyses can be used to identify and measure various types of changes ranging from coefficient instability to changes in interindustry relationships as a system. A distinction is made between structural changes in input relationships and those in output relationships. The methods are tested by using Washington State data for the years 1963 and 1967. The results are compared with previous analyses of change in these data.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

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