scholarly journals Spatial Distribution of Amino Acids of the SARS-CoV2 Proteins

2020 ◽  
Author(s):  
Ranjeet Kumar Rout ◽  
Sk Sarif Hassan
Keyword(s):  
Amino Acids ◽  
Spatial Distribution ◽  
Frequency Distribution ◽  
Shannon Entropy ◽  
Hurst Exponent ◽  
Spatial Representation ◽  
Protein Sequences ◽  
Healthcare Facility ◽  
Spatial Representations ◽  
The World

The world is now undergoing through a global emergency due to COVID-19 which needs immediate remedies in order to strengthen the healthcare facility to save the nations. Looking towards to the remedies, research on different aspects including the genomic and proteomic level characterizations of the SARS-CoV2 are necessarily important. In this present study, the spatial representation/composition of twenty amino acids across the primary protein sequences of SARS-CoV2 have been looked into through different parameters viz. Shannon entropy, Hurst exponent in order to fetch the autocorrelation and amount of information over the spatial representations. Also frequency distribution of each of the amino acids over the protein sequences have been chalked out.

scholarly journals Spatial Distribution of Amino Acids of the SARS-CoV2 Proteins

2020 ◽  
Author(s):  
Sk Sarif Hassan ◽  
Ranjeet Kumar Rout
Keyword(s):  
Amino Acids ◽  
Spatial Distribution ◽  
Frequency Distribution ◽  
Shannon Entropy ◽  
Hurst Exponent ◽  
Spatial Representation ◽  
Protein Sequences ◽  
Healthcare Facility ◽  
Spatial Representations ◽  
The World

The world is now undergoing through a global emergency due to COVID-19 which needs immediate remedies in order to strengthen the healthcare facility to save the nations. Looking towards to the remedies, research on different aspects including the genomic and proteomic level characterizations of the SARS-CoV2 are necessarily important. In this present study, the spatial representation/composition of twenty amino acids across the primary protein sequences of SARS-CoV2 have been looked into through different parameters viz. Shannon entropy, Hurst exponent in order to fetch the autocorrelation and amount of information over the spatial representations. Also frequency distribution of each of the amino acids over the protein sequences have been chalked out.

scholarly journals A Quantitative Comparisons of $\beta$-Coronavirus Genomes and Their Associated Genes

2020 ◽  
Author(s):  
Sk Sarif Hassan ◽  
Ranjeet Kumar Rout
Keyword(s):  
Density Estimation ◽  
Shannon Entropy ◽  
Hurst Exponent ◽  
Gc Content ◽  
Spatial Representations ◽  
Human Coronavirus ◽  
Precise Understanding ◽  
Different Types ◽  
Purine Pyrimidine ◽  
Nucleotide Bases

A precise understanding of the genes and associated genomes of SARS-CoV2 is important for various reasons such as discovering origin of the virus and virulence and so on. A thorough descriptive understanding of the SARS-CoV2 genomes and other coronavirus of the beta-coronavirus genus is primarily important. In this article, a set of ten genomes of four CoVs and their associated genes are considered for this present study. A spatial representations of nucleotide bases including purine-pyrimidine representations of the different genes of the corresponding genomes are quantified using Hurst exponent, Shannon entropy and density estimation of different nucleotides including GC content, in order to draw a comparison and contrast among the ten genomes of different types of CoVs which include MERS, SARS-CoV, HKU1 (Human Coronavirus) and associated their genes.

scholarly journals Feature-extraction and analysis based on spatial distribution of amino acids for SARS-CoV-2 Protein sequences

2021 ◽  
pp. 105024
Author(s):  
Ranjeet Kumar Rout ◽  
Sk Sarif Hassan ◽  
Sabha Sheikh ◽  
Saiyed Umer ◽  
Kshira Sagar Sahoo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Feature Extraction ◽  
Spatial Distribution ◽  
Protein Sequences

scholarly journals Features of lysine inheritance in grain sorghum hybrids of the second generation

2020 ◽  
Vol 21 (3) ◽  
pp. 273-282
Author(s):  
A. V. Alabushev ◽  
V. V. Kovtunov ◽  
P. I. Kostylev ◽  
N. A. Kovtunova ◽  
N. S. Kravchenko
Keyword(s):  
Amino Acids ◽  
Frequency Distribution ◽  
Second Generation ◽  
Essential Amino Acids ◽  
Grain Sorghum ◽  
Spontaneous Mutant ◽  
The World ◽  
Feed Value ◽  
Sorghum Grain ◽  
Sorghum Protein

Sorghum is one of the most important grain crops in the world. Sorghum grain is characterized by a low percentage of essential amino acids in protein, primarily lysine, which significantly reduces its feed value. There are two known mutant genes with a large lysine percentage, namely the spontaneous mutant hl gene, which was originally identified in Ethiopian lines, and the P721 gene, which is induced by ethylmethanesulfonate. The purpose of the current study was to identify the patterns of inheritance of the lysine percentage in grain sorghum hybrids of the second generation which were obtained by hybridization according to two 4x4 diallelic schemes (I - SPZS-11, Sb-126/4, 144 f/8, Zernogradskoe 204; II - ZSK-4, Belozernoe 100, Otbor 100, 34045). The hybridological analysis has established that in lysine percentage in sorghum protein there are genetic differences of 1-3 genes between the parental samples included in the hybridization. The greatest differences (3 genes) were identified between sorghum grain samples 34045 and 144 f/8. In most hybrid combinations there have been identified monogenic and digenic differences between the samples involved in hybridization. The estimation of dominance degree has identified the value of the gene manifestation, that controls lysine percentage in sorghum protein. There has been determined the dominance of both large and small values of the trait. The frequency distribution curves of the studied hybrids were within the variability of the parental forms, however, there were positive transgressions in some combinations. In the combinations Sb-126/4 × SPZS-11, Zernogradskoe 204 × SPZS-11 there have been identified the forms with a large lysine percentage in grain (more than 3.5%) for further breeding process.

North Atlantic Oscillation; a Climatic Indicator to Predict Hydropower Availability in Scandinavia

2002 ◽  
Vol 33 (5) ◽  
pp. 415-424 ◽  
Author(s):  
Cintia B. Uvo ◽  
Ronny Berndtsson
Keyword(s):  
Climate Change ◽  
Spatial Distribution ◽  
Climate Variability ◽  
North Atlantic Oscillation ◽  
North Atlantic ◽  
Winter Precipitation ◽  
Model Driven ◽  
The World ◽  
Hydropower Production ◽  
Precipitation And Temperature

Climate variability and climate change are of great concern to economists and energy producers as well as environmentalists as both affect the precipitation and temperature in many regions of the world. Among those affected by climate variability is the Scandinavian Peninsula. Particularly, its winter precipitation and temperature are affected by the variations of the so-called North Atlantic Oscillation (NAO). The objective of this paper is to analyze the spatial distribution of the influence of NAO over Scandinavia. This analysis is a first step to establishing a predictive model, driven by a climatic indicator such as NAO, for the available water resources of different regions in Scandinavia. Such a tool would be valuable for predicting potential of hydropower production one or more seasons in advance.

A Study on Host Tropism Determinants of Influenza Virus Using Machine Learning

2020 ◽  
Vol 15 (2) ◽  
pp. 121-134 ◽  
Author(s):  
Eunmi Kwon ◽  
Myeongji Cho ◽  
Hayeon Kim ◽  
Hyeon S. Son
Keyword(s):  
Machine Learning ◽  
Amino Acids ◽  
Influenza Virus ◽  
Random Forest ◽  
Physicochemical Properties ◽  
Protein Sequences ◽  
Influenza Viruses ◽  
Host Tropism ◽  
Post Hoc ◽  
Ha Protein

Background: The host tropism determinants of influenza virus, which cause changes in the host range and increase the likelihood of interaction with specific hosts, are critical for understanding the infection and propagation of the virus in diverse host species. Methods: Six types of protein sequences of influenza viral strains isolated from three classes of hosts (avian, human, and swine) were obtained. Random forest, naïve Bayes classification, and knearest neighbor algorithms were used for host classification. The Java language was used for sequence analysis programming and identifying host-specific position markers. Results: A machine learning technique was explored to derive the physicochemical properties of amino acids used in host classification and prediction. HA protein was found to play the most important role in determining host tropism of the influenza virus, and the random forest method yielded the highest accuracy in host prediction. Conserved amino acids that exhibited host-specific differences were also selected and verified, and they were found to be useful position markers for host classification. Finally, ANOVA analysis and post-hoc testing revealed that the physicochemical properties of amino acids, comprising protein sequences combined with position markers, differed significantly among hosts. Conclusion: The host tropism determinants and position markers described in this study can be used in related research to classify, identify, and predict the hosts of influenza viruses that are currently susceptible or likely to be infected in the future.

Conclusion

2018 ◽  
Author(s):  
Chris Barrett
Keyword(s):  
Early Modern ◽  
Spatial Representation ◽  
Regional Area ◽  
The World ◽  
Richard Hakluyt

While Chapters 1–3 examine early modern texts that take the work of spatial representation as an opportunity to consider the labor, dangers, and possibilities of representation, the Conclusion (which takes its title from remarks by Richard Hakluyt in describing how as a child he became fascinated by maps) considers three contemporary objects: a mug, a Mapparium, and recent revisions to the famous boot-shaped silhouette of Louisiana. Each of these objects represents a global or regional area in some novel way: foregrounding their artifice in order to exploit the same cartographic anxieties of representation articulated in works by Spenser, Drayton, and Milton, these objects suggest that the contemporary moment’s efforts to reimagine the space of the world in rhetorically affecting if overtly non-mimetic ways reflects the triumph of an early modern poetics of anxiety, a poetics that might be generative still, in the Anthropocene.

A Pandemic of Violence? The Impact of COVID-19 on Conflict

2020 ◽  
Vol 26 (3) ◽  
Author(s):  
Sara M.T. Polo
Keyword(s):  
Spatial Distribution ◽  
Real Time ◽  
Case Studies ◽  
Armed Conflict ◽  
Event Data ◽  
Social Unrest ◽  
Johns Hopkins University ◽  
The World ◽  
Political Advantage ◽  
The Impact

AbstractThis article examines the impact and repercussions of the COVID-19 pandemic on patterns of armed conflict around the world. It argues that there are two main ways in which the pandemic is likely to fuel, rather than mitigate, conflict and engender further violence in conflict-prone countries: (1) the exacerbating effect of COVID-19 on the underlying root causes of conflict and (2) the exploitation of the crisis by governments and non-state actors who have used the coronavirus to gain political advantage and territorial control. The article uses data collected in real-time by the Armed Conflict Location & Event Data Project (ACLED) and the Johns Hopkins University to illustrate the unfolding and spatial distribution of conflict events before and during the pandemic and combine this with three brief case studies of Afghanistan, Nigeria, and Libya. Descriptive evidence shows how levels of violence have remained unabated or even escalated during the first five months of the pandemic and how COVID-19-related social unrest has spread beyond conflict-affected countries.

scholarly journals Determinants of adenine-mutagenesis in diversity-generating retroelements

2020 ◽  
Author(s):  
Sumit Handa ◽  
Andres Reyna ◽  
Timothy Wiryaman ◽  
Partho Ghosh
Keyword(s):  
Amino Acids ◽  
Dark Matter ◽  
Reverse Transcription ◽  
Genetic Information ◽  
Human Microbiome ◽  
Protein Sequences ◽  
Catalytic Efficiency ◽  
Natural World ◽  
In Vitro System

Abstract Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.

Climate, ticks and disease

2021 ◽  
Keyword(s):  
Climate Change ◽  
Spatial Distribution ◽  
Disease Ecology ◽  
Future Climate Change ◽  
Climate Change Scenarios ◽  
Expert Opinions ◽  
The World ◽  
Host Pathogen ◽  
The Future ◽  
Impacts Of Climate Change

Abstract This book is a collection of 77 expert opinions arranged in three sections. Section 1 on "Climate" sets the scene, including predictions of future climate change, how climate change affects ecosystems, and how to model projections of the spatial distribution of ticks and tick-borne infections under different climate change scenarios. Section 2 on "Ticks" focuses on ticks (although tick-borne pathogens creep in) and whether or not changes in climate affect the tick biosphere, from physiology to ecology. Section 3 on "Disease" focuses on the tick-host-pathogen biosphere, ranging from the triangle of tick-host-pathogen molecular interactions to disease ecology in various regions and ecosystems of the world. Each of these three sections ends with a synopsis that aims to give a brief overview of all the expert opinions within the section. The book concludes with Section 4 (Final Synopsis and Future Predictions). This synopsis attempts to summarize evidence provided by the experts of tangible impacts of climate change on ticks and tick-borne infections. In constructing their expert opinions, contributors give their views on what the future might hold. The final synopsis provides a snapshot of their expert thoughts on the future.

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