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 A Quantitative Genomic View of the Coronaviruses: SARS-COV2

2020 ◽  
Author(s):  
Sk Sarif Hassan ◽  
Ranjeet Kumar Rout ◽  
Vipul Sharma
Keyword(s):  
Hurst Exponent ◽  
Hamming Distance ◽  
Gc Content ◽  
Large Family ◽  
Healthcare Facility ◽  
Viral Disease ◽  
Complete Sequences ◽  
Quantitative Understanding ◽  
The Common ◽  
Purine Pyrimidine

In 2020, the pandemic caused by the Coronaviruses (CoV) that are a large family of viruses that cause illness ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS-CoV2). The Coronavirus disease (COVID-19) is a new strain that was discovered in 2019 and has not been previously identified in humans. It is the high time to investigate the quantitative and/or qualitative genomic informations of the virus SARS-CoV2 in order to strengthen the healthcare facility to fight against this viral disease. In this article, a through quantitative understanding of the purine and pyrimidine spatial distribution/organization of all 89 complete sequences of SARS-CoV (available as on date in the NCBI virus database, is made using different parameters such as fractal dimension, Hurst exponent, Shannon entropy and GC content of the nucleotide sequences of the genome of SARS-CoV2. Also a cluster among all the the SARS-CoV sequences of nucleotide have been made based on their phylogeny made through their closeness (Hamming distance) based on respective purine-pyrimidine distribution.

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 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 Evaluating the Efficiency of gRNAs in CRISPR/Cas9 Mediated Genome Editing in Poplars

2019 ◽  
Vol 20 (15) ◽  
pp. 3623 ◽  
Author(s):  
Tobias Bruegmann ◽  
Khira Deecke ◽  
Matthias Fladung
Keyword(s):  
Genome Editing ◽  
Gene Editing ◽  
Constitutive Expression ◽  
Gc Content ◽  
Seed Region ◽  
Research Topics ◽  
Target Region ◽  
Cas9 Nuclease ◽  
Different Types ◽  
Poplar Hybrid

CRISPR/Cas9 has become one of the most promising techniques for genome editing in plants and works very well in poplars with an Agrobacterium-mediated transformation system. We selected twelve genes, including SOC1, FUL, and their paralogous genes, four NFP-like genes and TOZ19 for three different research topics. The gRNAs were designed for editing, and, together with a constitutively expressed Cas9 nuclease, transferred either into the poplar hybrid Populus × canescens or into P. tremula. The regenerated lines showed different types of editing and revealed several homozygous editing events which are of special interest in perennial species because of limited back-cross ability. Through a time series, we could show that despite the constitutive expression of the Cas9 nuclease, no secondary editing of the target region occurred. Thus, constitutive Cas9 expression does not seem to pose any risk to additional editing events. Based on various criteria, we obtained evidence for a relationship between the structure of gRNA and the efficiency of gene editing. In particular, the GC content, purine residues in the gRNA end, and the free accessibility of the seed region seemed to be highly important for genome editing in poplars. Based on our findings on nine different poplar genes, efficient gRNAs can be designed for future efficient editing applications in poplars.

scholarly journals A survey of qualitative spatial representations

2013 ◽  
Vol 30 (1) ◽  
pp. 106-136 ◽  
Author(s):  
Juan Chen ◽  
Anthony G. Cohn ◽  
Dayou Liu ◽  
Shengsheng Wang ◽  
Jihong Ouyang ◽  
...  
Keyword(s):  
Spatial Representation ◽  
Spatial Databases ◽  
Robot Navigation ◽  
Spatial Relations ◽  
Spatial Representations ◽  
Language Understanding ◽  
Different Types ◽  
Qualitative Spatial Representation ◽  
Autonomous Robot Navigation ◽  
Future Work

AbstractRepresentation and reasoning with qualitative spatial relations is an important problem in artificial intelligence and has wide applications in the fields of geographic information system, computer vision, autonomous robot navigation, natural language understanding, spatial databases and so on. The reasons for this interest in using qualitative spatial relations include cognitive comprehensibility, efficiency and computational facility. This paper summarizes progress in qualitative spatial representation by describing key calculi representing different types of spatial relationships. The paper concludes with a discussion of current research and glimpse of future work.

scholarly journals INFORMATION AND MEMORY-BASED ANALYSIS FOR DECODING OF THE HUMAN LEARNING BETWEEN NORMAL AND VIRTUAL REALITY (VR) CONDITIONS

Fractals ◽  
2021 ◽  
Vol 29 (03) ◽  
pp. 2150163
Author(s):  
HAMIDREZA NAMAZI ◽  
MOHAMMAD HOSSEIN BABINI ◽  
KAMIL KUCA ◽  
ONDREJ KREJCAR
Keyword(s):  
Virtual Reality ◽  
Shannon Entropy ◽  
Mathematical Analysis ◽  
Strong Correlation ◽  
Hurst Exponent ◽  
Human Learning ◽  
Learning Ability ◽  
Eeg Signals ◽  
2D And 3D ◽  
Electroencephalogram Eeg

In this paper, we investigated the learning ability of students in normal versus virtual reality (VR) watching of videos by mathematical analysis of electroencephalogram (EEG) signals. We played six videos in the 2D and 3D modes for nine subjects and calculated the Shannon entropy of recorded EEG signals to investigate how much their embedded information changes between these modes. We also calculated the Hurst exponent of EEG signals to compare the changes in the memory of signals. The analysis results showed that watching the videos in a VR condition causes greater information and memory in EEG signals. A strong correlation was obtained between the increment of information and memory of EEG signals. These increments also have been verified based on the answers that subjects gave to the questions about the content of videos. Therefore, we can say that when subjects watch a video in a VR condition, more information is transferred to their brains that cause increments in their memory.

scholarly journals Identifying genome level variation in generalist and specialist bacteria and their relationship to abiotic conditions in European freshwater ecosystems

2021 ◽  
Vol 4 ◽  
Author(s):  
Manan Shah ◽  
Till Bornemann ◽  
Julia Nuy ◽  
Alexander Probst ◽  
Daniela Beisser ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Genetic Basis ◽  
Abiotic Factors ◽  
Gc Content ◽  
Nutrient Content ◽  
Freshwater Ecosystems ◽  
Different Types ◽  
Genome Level ◽  
Physical Changes ◽  
Insight Into

Microbial biodiversity is one of the increasingly studied fields, yet we are unable to accurately pinpoint the intricacies of how the biotic landscape changes with its abiotic counterpart. Every organism reacts differently to physical changes in its surrounding(Zeglin (2015)). While there are some generalist microbes that can grow in limited capacity in many different types of environment, there are also some specialists that can flourish in very specific environments(Monard et al. (2016)). We hypothesize that both generalists and specialists have developed advanced strategies that allow them thrive under diverse conditions or in very specific niches, and that these changes should be traceable on the genomic level. We expect to see variations in factors like genome sizes, number of genes, GC content, metabolic pathways that yield growth and replication advantages in nutrient deficient niches and defense mechanisms. We also expect to identify genomic streamlining in organisms that survive in nutrient deficient environments. We are currently studying the genetic basis of why these generalists are so universally present though in smaller numbers, and what allows the specialists to efficiently exploit the abiotic factors of their specific environment in order to flourish. To pursue this, we have sampled and sequenced metagenomes from 47 lakes spread across Europe with strongly diverging environmental conditions such as pH, temperature, organic and nutrient content, elevation, and conductivity. We’ve identified reads from more than 9000 taxonomically unique organisms, of which 700 were identified as generalists and 1200 as specialists, based on niche width permutations. In total we have assembled 313 high quality Metagenome Assembled Genomes (MAGs). Which now allow us to get a more detailed insight into the genetic basis and specific adaptations of these organisms.

scholarly journals The HLA complex non-coding RNA HCG4 is differentially expressed in the blood of patients with coronavirus co-infections.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Influenza A ◽  
Differentially Expressed ◽  
Human Coronavirus ◽  
Gene Encoding ◽  
Non Coding Rna ◽  
Different Types ◽  
Family Gene ◽  
Human Coronaviruses ◽  
One Year

The human coronavirus SARS-CoV-2 (1) has resulted in the death of over 200,000 Americans in less than one year (2). Infection of a person already suffering from a viral infection, a phenomena known as co-infection can potentially pose a problem during the upcoming influenza season. We mined published microarray data (3) to identify genes most differentially expressed in the whole blood of patients suffering from human coronavirus co-infections. We found that the gene encoding the HLA complex non-coding RNA HCG4 was among those whose expression changed most significantly transcriptome-wide when comparing the blood of patients suffering from three different types of co-infections: human coronavirus NL63 and rhinovirus, human coronavirus HKU1 and rhinovirus, as well as in human coronavirus OC43 and influenza A co-infection. We previously reported significant transcriptome-wide changes in HLA family gene expression (4), as well as in changes in gene expression of the cathepsins in viral co-infection (5). Together, these data suggest the process of antigen presentation could be altered during viral co-infections involving the human coronaviruses.

scholarly journals Wavelet-Based Entropy Measures to Characterize Two-Dimensional Fractional Brownian Fields

Entropy ◽  
2020 ◽  
Vol 22 (2) ◽  
pp. 196 ◽  
Author(s):  
Orietta Nicolis ◽  
Jorge Mateu ◽  
Javier E. Contreras-Reyes
Keyword(s):  
Shannon Entropy ◽  
Simulation Study ◽  
Hurst Exponent ◽  
Wavelet Spectrum ◽  
Two Dimensional ◽  
Entropy Measures ◽  
Rényi Entropies ◽  
Self Similar ◽  
Fractional Brownian Field ◽  
Renyi Entropies

The aim of this work was to extend the results of Perez et al. (Physica A (2006), 365 (2), 282–288) to the two-dimensional (2D) fractional Brownian field. In particular, we defined Shannon entropy using the wavelet spectrum from which the Hurst exponent is estimated by the regression of the logarithm of the square coefficients over the levels of resolutions. Using the same methodology. we also defined two other entropies in 2D: Tsallis and the Rényi entropies. A simulation study was performed for showing the ability of the method to characterize 2D (in this case, α = 2 ) self-similar processes.

scholarly journals Diagnosis of Lung Cancer by Fractal Analysis of Damaged DNA

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Hamidreza Namazi ◽  
Mona Kiminezhadmalaie
Keyword(s):  
Lung Cancer ◽  
Dna Sequences ◽  
Hurst Exponent ◽  
The Body ◽  
Cancer Genes ◽  
A Genome ◽  
Different Types ◽  
Diagnosis Of Lung Cancer ◽  
Dna Walk ◽  
Damaged Dna

Cancer starts when cells in a part of the body start to grow out of control. In fact cells become cancer cells because of DNA damage. A DNA walk of a genome represents how the frequency of each nucleotide of a pairing nucleotide couple changes locally. In this research in order to study the cancer genes, DNA walk plots of genomes of patients with lung cancer were generated using a program written in MATLAB language. The data so obtained was checked for fractal property by computing the fractal dimension using a program written in MATLAB. Also, the correlation of damaged DNA was studied using the Hurst exponent measure. We have found that the damaged DNA sequences are exhibiting higher degree of fractality and less correlation compared with normal DNA sequences. So we confirmed this method can be used for early detection of lung cancer. The method introduced in this research not only is useful for diagnosis of lung cancer but also can be applied for detection and growth analysis of different types of cancers.

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