The evolution of Genetic Molecular Map and phylogenetic tree of Coronavirus (COVID-19)

The aim of this article is to set a macro-historical narrative concerning the emergence of warfare and social ethics as symplesiomorphic features in the lineage of Homo sapiens. This means that these two behavioral aspects, representative of a very selected branch in the phylogenetic tree of the Primate order, are shared by the two lineages of great African apes that diverged from a common ancestor around six million years in the past, leading to extant humans and chimpanzees. Therefore, this article proposes an ethological understanding of warfare and social ethics, as both are innate to the social high-specialized modular mind present in the species of genera Pan and Homo. However behavioral restraints to intersocietal coalitionary violence seems to be an exclusive aspect of the transdominial modular cognition that characterizes modern humans. Thus, if in the evolutionary long durée, warfare and restrictions to intrasocial violence both appear to be ethologically common to humans and chimpanzees to a certain extent, an ethics of warfare - and, of course, the cognitive capability for intersocietal peace - seems to be distinctly human.

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Identification of novel mitochondrial and mitochondrial related genetic loci associated with exercise response in the Gene SMART study

10.1101/2020.02.20.957340 ◽

2020 ◽

Author(s):

NR Harvey ◽

S Voisin ◽

RA Lea ◽

X Yan ◽

MC Benton ◽

...

Keyword(s):

Mitochondrial Genome ◽

Exercise Training ◽

Genetic Variants ◽

Principal Component ◽

Genetic Sequencing ◽

Association Testing ◽

Smart Study ◽

Exercise Response ◽

Intracellular Energy ◽

Mtdna Variants

ABSTRACTMitochondria supply intracellular energy requirements during exercise. Specific mitochondrial haplogroups and mitochondrial genetic variants have been associated with athletic performance, and exercise responses. However, these associations were discovered using underpowered, candidate gene approaches, and consequently have not been replicated. Here, we used whole-mitochondrial genome sequencing, in conjunction with high-throughput genotyping arrays, to discover novel genetic variants associated with exercise responses in the Gene SMART (Skeletal Muscle Adaptive Response to Training) cohort (n=62 completed). We performed a Principal Component Analysis of cohort aerobic fitness measures to build composite traits and test for variants associated with exercise outcomes. None of the mitochondrial genetic variants but nine nuclear encoded variants in eight separate genes were found to be associated with exercise responses (FDR<0.05) (rs11061368: DIABLO, rs113400963: FAM185A, rs6062129 and rs6121949: MTG2, rs7231304: AFG3L2, rs2041840: NDUFAF7, rs7085433: TIMM23, rs1063271: SPTLC2, rs2275273: ALDH18A1). Additionally, we outline potential mechanisms by which these variants may be contributing to exercise phenotypes. Our data suggest novel nuclear-encoded SNPs and mitochondrial pathways associated with exercise response phenotypes. Future studies should focus on validating these variants across different cohorts and ethnicities.AUTHOR SUMMARYPrevious exercise genetic studies contain many flaws that impede the growth in knowledge surrounding change in exercise outcomes. In particular, exercise studies looking at mtDNA variants have looked at very small portions of the mitochondrial genome. Mitochondria are the ‘power house’ of the cell and therefore understanding the mitochondrial genetics behind adaptations to training can help us fill knowledge gaps in current research. Here, we utilised a new mitochondrial genetic sequencing technique to examine all mitochondrial and mitochondrial related genetic variations. We have shown that there were no mitochondrial specific variants that influenced exercise training however there were 9 related variants that were significantly associated with exercise phenotypes. Additionally, we have shown that building composite traits increased the significance of our association testing and lead to novel findings. We will be able to understand why response to training is so varied and increase the effectiveness of exercise training on a host of metabolic disorders.

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Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

10.1101/2021.02.24.21252386 ◽

2021 ◽

Author(s):

◽

Philip W Fowler

Keyword(s):

Genetic Variants ◽

Susceptibility Testing ◽

Drug Susceptibility ◽

Drug Susceptibility Testing ◽

Broth Microdilution ◽

Wild Type ◽

Genetic Sequencing ◽

Indicator Tube ◽

Cutoff Values ◽

Type Population

AbstractDrug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. There are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, including quantifying the magnitude of effect conferred by genetic variants and being able to identify isolates with elevated MICs that can still be treated with standard therapy. It is necessary, however, to measure the epidemiological cutoff values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-TB compounds, including bedaquiline and delamanid, derived from 20,637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to the majority of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression. The proposed ECOFF/ECV values were then validated by comparing to the MIC distributions of high-confidence genetic variants that confer resistance and to qualitative drug susceptibility tests obtained via Mycobacterial Growth Indicator Tube and the Microscopic-Observation Drug-Susceptibility assay.

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S4-01-05: The 28-amino acid form of an APLP1-derived abeta-like peptide is a surrogate marker for Abeta42 production

Alzheimer s & Dementia ◽

10.1016/j.jalz.2011.05.1946 ◽

2011 ◽

Vol 7 ◽

pp. S675-S675

Author(s):

Masayasu Okochi

Keyword(s):

Amino Acid ◽

Surrogate Marker ◽

Acid Form ◽

Amino Acid Form

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(S)-2,2,5,5-Tetramethylthiazolidine-4-carboxylic acid: a compound which exists in the amino acid rather than the zwitterion form

Canadian Journal of Chemistry ◽

10.1139/v85-399 ◽

1985 ◽

Vol 63 (9) ◽

pp. 2411-2419 ◽

Cited By ~ 4

Author(s):

Helen Elaine Howard-Lock ◽

Colin James Lyne Lock ◽

Philip Stuart Smalley

Keyword(s):

Amino Acid ◽

Carboxylic Acid ◽

Raman Spectra ◽

Cooh Group ◽

Infrared And Raman Spectra ◽

Acid Form ◽

Hydrogen Atoms ◽

Cell Dimensions ◽

Amino Acid Form ◽

C Nmr

The X-ray crystal structure of (S)-2,2,5,5-tetramethylthiazolidine-4-carboxylic acid, 1, has been determined. Crystals are monoclinic, P21, with cell dimensions a = 11.351(4) b = 8.303(2), c = 11.969(3) Å, β = 116.69(2)°, and Z = 4. The structure was solved by standard methods and refined to R1 = 0.0774, R2 = 0.0670 for 2388 independent reflections. Compound 1 exists in the amino-acid form as shown by two distinctly different C—O bond lengths, 1.209 and 1.309 Å, typical of the COOH group, and by the positions of the hydrogen atoms. The amino-acid form of 1 found in the solid also exists in solution as shown by infrared and Raman spectra. The mass spectra, and 1H and 13C nmr spectra are reported, as well as detailed infrared and Raman spectra for the title compound and several deuterated species.

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Warfare, Ethics, Ethology Evolutionary fundamentals for conflict and cooperation

10.31234/osf.io/mez2f ◽

2020 ◽

Author(s):

Daniel Barreiros

Keyword(s):

Phylogenetic Tree ◽

Common Ancestor ◽

Homo Sapiens ◽

Social Ethics ◽

Historical Narrative ◽

Conflict And Cooperation ◽

African Apes ◽

The Past ◽

Cognitive Capability ◽

The Social

The aim of this article is to set a macro-historical narrative concerning the emergence of warfare and social ethics as symplesiomorphic features in the lineage of Homo sapiens. This means that these two behavioral aspects, representative of a very selected branch in the phylogenetic tree of the Primate order, are shared by the two lineages of great African apes that diverged from a common ancestor around six million years in the past, leading to extant humans and chimpanzees. Therefore, this article proposes an ethological understanding of warfare and social ethics, as both are innate to the social high-specialized modular mind present in the species of genera Pan and Homo. However behavioral restraints to intersocietal coalitionary violence seems to be an exclusive aspect of the transdominial modular cognition that characterizes modern humans. Thus, if in the evolutionary long durée, warfare and restrictions to intrasocial violence both appear to be ethologically common to humans and chimpanzees to a certain extent, an ethics of warfare - and, of course, the cognitive capability for intersocietal peace - seems to be distinctly human.

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Phylogenetic Analysis of Spike and Envelope Proteins for a Number of Bat Coronaviruses for Understanding the Hypothesis of Possible Origin for the Novel 2019-nCoV

Kurdistan Journal of Applied Research ◽

10.24017/science.2020.ichms2020.15 ◽

2020 ◽

pp. 137-144

Author(s):

Salar Ibrahim Ali

Keyword(s):

Hong Kong ◽

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Tree ◽

Envelope Protein ◽

Spike Protein ◽

Phylogenetic Tree Analysis ◽

Tree Analysis ◽

Close Relationship ◽

Bat Coronavirus

Coronavirus Disease 19 (COVID-19) emergence reveals globally a great health issue and due to the limited information and knowledge on the origin of this novel coronavirus 2019 (2019-nCoV). Therefore, this study aims to investigate the evolution and analysis of molecular epidemiology for both Spike and Envelope proteins of 20 available complete genome sequences of different bat coronaviruses including 2019-nCoV in order to find out which type of bat coronaviruses is more likely to be the origin of this new 2019-nCoV and also multiple amino acid sequences of Envelope protein for all bat coronaviruses were aligned for the purpose of finding the greater probability of novel 2019-nCoV original host among bat coronaviruses. Phylogenetic tree analysis for Spike protein revealed that all 2019-nCoV related coronaviruses isolated from these species of species are discovered in China and Hong Kong and the Middle East bat are less likely to contribute in spreading or to become the origin of 2019-nCoV and all coronaviruses that from Hong Kong and China are located into one clade next to the clade that contains 2019-nCoV coronaviruses which indicates that this group of coronaviruses are genetically different for 2019-nCoV; moreover, Hong Kong and USA bat coronaviruses does not contain the bat coronavirus from China and are located into one clade far from the clade that contains 2019-nCoV indicates that all coronaviruses are genetically very different from 2019-nCoV, and USA bat coronavirus may has no role in generating of 2019-nCoV. The phylogenetic trees analysis of Envelope protein showed that Envelope protein of different coronaviruses are more similar in comparison to Spike protein, USA bat coronavirus has a relatively closeness relationship to 2019-nCoV. Furthermore, Envelope protein alignment showed the closely related amino acid sequence which confirms that the outcomes of phylogenetic tree analysis in which that these bat coronaviruses have genetically close relationship together and more interestingly amino acid sequence (MG772934.1) shows 100% identity with the amino acid sequence of 2019-nCoV (NC 045512.2) and the same virus has a close relationship in both Spike and Envelope due to that in both phylogenetic tree analysis are neighbored with 2019-nCoV in the same clade.

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Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

10.21203/rs.3.rs-33194/v1 ◽

2020 ◽

Author(s):

Tingting Li ◽

Dongxia Liu ◽

Yadi Yang ◽

Jiali Guo ◽

Yujie Feng ◽

...

Keyword(s):

Phylogenetic Tree ◽

Common Ancestor ◽

Virus Disease ◽

Evolutionary Relationship ◽

Critical Issue ◽

Last Common Ancestor ◽

Genome Sequences ◽

Phylogenetic Tree Analysis ◽

Origin And Evolution ◽

Bat Coronavirus

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

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