Genetic Basis of Differential Heat Resistance between Two Species of Congeneric Freshwater Snails: Insights from Quantitative Proteomics and Base Substitution Rate Analysis

Abstract Using BEAST v1.X, we constructed a credible timetree of 115 specimens of Odonata and five species of Ephemeroptera (Paleoptera; Pterygota) and two species of Archaeognatha and three species of Zygentoma (Apterygota). 88 specimens we ourselves analyzed were collected from the Ryukyu islands, Taiwan, Japan, and China, and the resting sequence data were mostly from whole mitochondrial data found in GenBank / DDJB. The combined gene (not concatenated gene) analysis of the mitochondrial COI (795 bp), COII (548 bp), and 16S rRNA (517 bp), and the nuclear 28S rRNA (825 bp) were performed. Using the calibration function of BEAST v1.X, the timetree was constructed by applying a 1.55 Ma geological event (isolation of the Ryukyu islands from China), in addition to chronologically robust fossil dates ranging from 400 Ma for Archaeognatha, 300 Ma for Ephemeroptera, and 200 Ma for Odonata and to 1.76 Ma for Calopterygidae, for a total of 13 calibration points (event: 6, fossil: 12; Quaternary 7, pre Quaternary 11). The resultant timetree showed that molecular clock was not uniformly progressed, and the base substitution rate has exponentially increased from ca. 20 Ma to the Recent by over an order of magnitude. Our new and attractive finding indicates that the Quaternary severe climatic change including a start of glacial and interglacial cycle might have resulted in the extensive radiation and speciation of Odonata, and consequently increased the biodiversity. C4 pores generated in the Miocene effectively decreased atmospheric CO2, and triggered the Quaternary glaciation. Another peak of base substitution rate was found in the Carboniferous time around 320 Ma, and this may be analogous to the late Paleozoic icehouse. This glaciation has been triggered by the development of terrestrial plants to form thick coal layers, because this process also reduced the atmospheric CO2.

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Cicada timetree by BEAST v1.X verified the recently and exponentially increasing base substitution rates

10.1101/2020.12.03.409599 ◽

2020 ◽

Author(s):

Soichi Osozawa ◽

John Wakabayashi

Keyword(s):

Substitution Rate ◽

Phylogenetic Trees ◽

Base Substitution ◽

C4 Grasses ◽

Calibration Function ◽

Clock Model ◽

Exponential Increase ◽

Geological Event ◽

Relaxed Clock ◽

Base Substitution Rate

AbstractFollowing the recent publication of global cicada phylogenetic trees by Marshall et al. (2018), Łukasik et al. (2018), and Simon et al. (2019), we developed a new dated tree incorporating mostly endemic east Asian cicada data for totally 113 specimens, using the mostly advanced BEAST v1.X software applied the relaxed clock model. Fossil calibrations as old as Triassic were adopted after Moulds (2018), and a Quaternary geological event calibration was adopted following Osozawa et al. (2012), applying the calibration function of BEAST. Our timetree suggests that Tettigarctidae had cicada basal lineage as old as 200 Ma, and Derotettiginae was next as old as 100 Ma. Tibicininae was a sister of the resting Cicadidae, and Tettigomyiinae, Cicadettinae, and Cicadina started simultaneous branching and radiation around 40 Ma. We made a base substitution rate vs age diagram based on the timetree using the BEAST function, and it strongly suggested an exponential increase of base substitution rate approaching the present. The consequent increased cicada biodiversity including generation of cryptic species might have been driven by the generation and spreading of C4 grasses and the following Quaternary glaciations and severe environmental change.

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Post-Triassic Spermatophyta Timetree Adding the Quaternary Radiated Asarum Wild Gingers

10.21203/rs.3.rs-99466/v1 ◽

2020 ◽

Author(s):

Soichi Osozawa ◽

Cunio Nackejima ◽

John Wakabayashi

Keyword(s):

Adaptive Radiation ◽

Substitution Rate ◽

Evolutionary History ◽

Base Substitution ◽

C4 Grasses ◽

Glacial Period ◽

Fossil Calibration ◽

Geologic Time ◽

Exponential Increase ◽

Base Substitution Rate

Abstract BackgroundAngiospermae radiation was known as the mid-Cretaceous event, but adaptive radiation of Asarum is also expected in the Quaternary. In order to know such the Angiospermae evolutionary history through the time, we constructed a whole Spermatophyta timetree employing BEAST v1. X associated with robust fossil calibration function.ResultsWe successfully and precisely dated the Spermatophyta phylogeny, and the Angiospermae topology was concordant to the APG system. Using another function of BEAST, we discovered the exponential increase in base substitution rate in recent geologic time, and another rise of rate at the mid-Cretaceous time. These increasing events correspond to the Quaternary and mid-Cretaceous Angiospermae radiations.ConclusionsA probable cause of the recently increasing rate and the consequent radiation was ultimately generation of C4 grasses, reduction of atomospheric CO2, and the start of the Quaternary glacial period. Mid-Cretaceous event was explained by co-radiation with insect beetles as the food plant.

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Novel Insights Into Heat Tolerance Using Microbiome and Metabolomics Analyses in Dairy Cows Rumen Fluid

10.21203/rs.3.rs-847239/v1 ◽

2021 ◽

Author(s):

Zichen Wang ◽

Leizhen Liu ◽

Fanglin Pang ◽

Zhuo Zheng ◽

Zhanwei Teng ◽

...

Keyword(s):

Heat Stress ◽

Heat Resistance ◽

Dairy Cows ◽

Propionic Acid ◽

Heat Tolerance ◽

Function Analysis ◽

Rumen Fluid ◽

Diagnostic Tools ◽

Differential Heat ◽

Rumen Microbiome

Abstract Background: Heat stress is a key issue of growing concern for livestock industry worldwide due to its negative effects not only on milk production, fertility, health, welfare, and economic returns of dairy cows, but also on the microbial communities in the rumen. However, the underlying relationship between rumen microbiome and its associated metabolism with heat tolerance in cow have not been extensively described yet. Therefore, the main objective of this study was to investigate differential heat resistance in Holstein cows using rumen microbiome and metabolome analyses.Methods: We performed both principal component analysis and membership function analysis to select 7 heat-tolerant (HT) and 7 heat-sensitive (HS) cows. The ruminal fluid samples of two groups were collected at two hours post feeding on 7th day of heat stress period, for analyses including rumen fermentation parameters, rumen microbiome and nontargeted metabolomics.Results: Under heat stress conditions, the HT cows had a significantly higher propionic acid content than the HS cows; whereas measures of the respiratory rate (RR), rectal temperature (RT), acetic,butyric acid and acetic acid to propionic acid ratio (A:P) in the HT cows were lower compared with the HS cows. Omics sequencing revealed that the relative abundance of Rikenellaceae_RC9_gut_group, Succiniclasticum, Ruminococcaceae_NK4A214_group and Christensenellaceae_R-7_group were significantly higher in the HT than HS cows; whereas Prevotella_1, Ruminococcaceae_UCG-014, and Shuttleworthia were significantly higher in the HS cows compared to HT cows. Substances mainly involved in carbohydrate metabolism, including glycerol, mannitol, and maltose, showed significantly higher content in the HT cows compared to that in the HS cows. Simultaneously, RR was significantly correlated with both differential microorganisms and distinct metabolites, suggesting three metabolites could be potential biomarkers for determining heat resistance that require further research.Conclusion: Overall, distinct changes in the rumen microbiome and metabolomics in the HT cows may be associated with better adaptability to heat stress. These findings suggest their use as diagnostic tools of heat tolerance in dairy cattle breeding schemes.

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Optimal substitution rate analysis of submarine natural gas hydrates considering geological and hydrological conditions

Arabian Journal of Geosciences ◽

10.1007/s12517-021-06588-4 ◽

2021 ◽

Vol 14 (5) ◽

Author(s):

Yuan Li ◽

Yuhu Sun

Keyword(s):

Natural Gas ◽

Gas Hydrates ◽

Substitution Rate ◽

Hydrological Conditions ◽

Rate Analysis ◽

Natural Gas Hydrates

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Clostridium sporogenes PA 3679 and Its Uses in the Derivation of Thermal Processing Schedules for Low-Acid Shelf-Stable Foods and as a Research Model for Proteolytic Clostridium botulinum

Journal of Food Protection ◽

10.4315/0362-028x.jfp-11-391 ◽

2012 ◽

Vol 75 (4) ◽

pp. 779-792 ◽

Cited By ~ 21

Author(s):

JANELLE L. BROWN ◽

NAI TRAN-DINH ◽

BELINDA CHAPMAN

Keyword(s):

Heat Resistance ◽

Thermal Processing ◽

Clostridium Botulinum ◽

Genetic Basis ◽

Thermal Processes ◽

Research Model ◽

Clostridium Sporogenes ◽

Fail Safe ◽

Shelf Stable ◽

Resistance Data

The putrefactive anaerobe Clostridium sporogenes PA 3679 has been widely used as a nontoxigenic surrogate for proteolytic Clostridium botulinum in the validation of thermal processes for low-acid shelf-stable foods, as a target organism in the derivation of thermal processes that reduce the risk of spoilage of such foods to an acceptable level, and as a research model for proteolytic strains of C. botulinum. Despite the importance of this organism, our knowledge of it has remained fragmented. In this article we draw together the literature associated with PA 3679 and discuss the identity of this organism, the phylogenetic relationships that exist between PA 3679 and various strains of C. sporogenes and proteolytic C. botulinum, the heat resistance characteristics of PA 3679, the advantages and limitations associated with its use in the derivation of thermal processing schedules, and the knowledge gaps and opportunities that exist with regard to its use as a research model for proteolytic C. botulinum. Phylogenetic analysis reviewed here suggests that PA 3679 is more closely related to various strains of proteolytic C. botulinum than to selected strains, including the type strain, of C. sporogenes. Even though PA 3679 is demonstrably nontoxigenic, the genetic basis of this nontoxigenic status remains to be elucidated, and the genetic sequence of this microorganism appears to be the key knowledge gap remaining to be filled. Our comprehensive review of comparative heat resistance data gathered for PA 3679 and proteolytic strains of C. botulinum over the past 100 years supports the practice of using PA 3679 as a (typically fail-safe) thermal processing surrogate for proteolytic C. botulinum.

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A Thr359Met mutation in factor VII of a patient with a hereditary deficiency causes defective secretion of the molecule

Blood ◽

10.1182/blood.v87.12.5085.bloodjournal87125085 ◽

1996 ◽

Vol 87 (12) ◽

pp. 5085-5094 ◽

Cited By ~ 30

Author(s):

AA Arbini ◽

M Mannucci ◽

KA Bauer

Keyword(s):

Genetic Basis ◽

Chinese Hamster Ovary Cells ◽

Chinese Hamster ◽

Factor Vii ◽

Base Substitution ◽

Severe Bleeding ◽

Ovary Cells ◽

The Media ◽

Type Factor ◽

Intron 4

We elucidated the genetic basis responsible for factor VII deficiency in an Italian woman with a severe bleeding diathesis. In the allele inherited from the patient's father, we identified a G to A mutation at nucleotide 6070 at the 5′ splice site of intron 4 and a G to A substitution at nucleotide 10976 resulting in the Arg353Gln polymorphism. The maternal allele demonstrated a C to T substitution at nucleotide 10994 resulting in Thr359Met. The mutation at nucleotide 6070 alters an invariant GT dinucleotide and disrupts normal mRNA processing. To investigate the mechanism by which Thr359Met reduces factor VIl levels, we expressed wild type factor VII cDNA (FVIIwt) and a mutant factor VII cDNA containing the base substitution resulting in Met359 (FVII359M) in Chinese hamster ovary cells (CHO). In cells transfected with the mutant factor VII cDNA, FVII359M accumulated intracellularly, and no factor VII was detected in the media after 3 hours of chase. The carbohydrate side chains associated with FVII359M were sensitive to Endo H digestion, which indicates that the protein is retained in the endoplasmic reticulum. Analysis of cell lysates also showed that FVII359M was associated with the 78 kD protein corresponding to GRP78/BiP. We conclude that a Thr359Met mutation in factor VII results in a severe secretion defect that probably results from abnormal folding of the molecule.

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