scholarly journals Cytosine methylation affects the mutability of neighbouring nucleotides in human, Arabidopsis, and rice

2019 ◽  
Author(s):  
Vassili Kusmartsev ◽  
Tobias Warnecke
Keyword(s):  
Cytosine Methylation ◽  
Gc Content ◽  
Patch Repair ◽  
Lesion Formation ◽  
Mutational Hotspots ◽  
The Difference ◽  
Rare Polymorphism ◽  
Species Specific ◽  
Mutagenic Effects ◽  
Mutation Dynamics

ABSTRACTMethylated cytosines deaminate at higher rates than unmethylated cytosines and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighbouring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3nt) of methylated cytosines mutate less frequently. In contrast, methylation is associated with increased neighbourhood mutation risk in A. thaliana and rice. The difference in mutation risk associated with methylation is less pronounced further away from the focal CpG, is modulated by regional GC content, and enhanced in heterochromatic regions. Our results are consistent with a model where elevated risk at neighbouring bases is linked to lesion formation at the focal cytosine and subsequent long-patch repair. Our results provide evidence that cytosine methylation has a broader mutational footprints than commonly assumed. They also illustrate that methylation is not intrinsically associated with higher mutation risk for surrounding bases, but that mutagenic effects reflect evolved species-specific and lesion-specific predispositions to elicit error-prone long-patch DNA repair.

scholarly journals Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma

Genetics ◽  
2020 ◽  
Vol 214 (4) ◽  
pp. 809-823 ◽  
Author(s):  
Vassili Kusmartsev ◽  
Magdalena Drożdż ◽  
Benjamin Schuster-Böckler ◽  
Tobias Warnecke
Keyword(s):  
Cytosine Methylation ◽  
Gc Content ◽  
Patch Repair ◽  
Methylation Data ◽  
Single Nucleotide Variants ◽  
Mutational Hotspots ◽  
The Difference ◽  
Rare Polymorphism ◽  
Mutation Dynamics ◽  
Neighborhood Mutation

Methylated cytosines deaminate at higher rates than unmethylated cytosines, and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighboring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3 bp) of methylated cytosines mutate less frequently. Reduced mutability around methylated CpGs is also observed in cancer genomes, considering single nucleotide variants alongside tissue-of-origin-matched methylation data. In contrast, methylation is associated with increased neighborhood mutation risk in A. thaliana and rice. The difference in neighborhood mutation risk is less pronounced further away from the focal CpG and modulated by regional GC content. Our results are consistent with a model where altered risk at neighboring bases is linked to lesion formation at the focal CpG and subsequent long-patch repair. Our findings indicate that cytosine methylation has a broader mutational footprint than is commonly assumed.

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

2021 ◽  
Author(s):  
Neetu Tyagi ◽  
Rahila Sardar ◽  
Dinesh Gupta
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Respiratory Illness ◽  
Respiratory Viruses ◽  
Nucleotide Composition ◽  
Health Crisis ◽  
Study Results ◽  
Usage Patterns ◽  
The Difference

AbstractThe Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.

scholarly journals Ba incorporation in benthic foraminifera

2017 ◽  
Author(s):  
Lennart J. de Nooijer ◽  
Anieke Brombacher ◽  
Antje Mewes ◽  
Gerald Langer ◽  
Gernot Nehrke ◽  
...  
Keyword(s):  
Trace Elements ◽  
Benthic Foraminifera ◽  
General Trend ◽  
Seawater Chemistry ◽  
Minor And Trace Elements ◽  
Foraminiferal Species ◽  
Element Partitioning ◽  
The Difference ◽  
Species Specific ◽  
New Applications

Abstract. Barium (Ba) incorporated in the calcite of many foraminiferal species is proportional to the concentration of Ba in seawater. Since the open ocean concentration of Ba closely follows seawater alkalinity, foraminiferal Ba/Ca can be used to reconstruct the latter. Alternatively, Ba/Ca from foraminiferal shells can also be used to reconstruct salinity in coastal settings where seawater Ba concentration corresponds to salinity as rivers contain much more Ba than seawater. Incorporation of a number of minor and trace elements is known to vary (greatly) between foraminiferal species and application of element/Ca ratios thus requires the use of species-specific calibrations. Here we show that calcite Ba/Ca correlates positively and linearly with seawater Ba/Ca in cultured specimens of two species of benthic foraminifera, Heterostegina depressa and Amphistegina lessonii. The slopes of the regression, however, vary 2–3 fold between these two species (0.33 and 0.78, respectively). This difference in Ba-partitioning resembles the difference in partitioning of other elements (Mg, Sr, B, Li and Na) in these foraminiferal taxa. A general trend across element partitioning for different species is described, which may help developing new applications of trace elements in foraminiferal calcite in reconstructing past seawater chemistry.

Influence of Freshwater Migration on the Reproductive Patterns of Anadromous Populations of Cisco (Coregonus artedii) and Lake Whitefish (C. clupeaformis)

1990 ◽  
Vol 47 (2) ◽  
pp. 335-345 ◽  
Author(s):  
Yvan Lambert ◽  
Julian J. Dodson
Keyword(s):  
Adult Mortality ◽  
Lake Whitefish ◽  
Age At Maturity ◽  
Predominant Role ◽  
Reproductive Patterns ◽  
Interspecific Differences ◽  
Survival And Reproduction ◽  
Coregonus Artedii ◽  
The Difference ◽  
Species Specific

We tested the hypothesis that differences in the cost of freshwater migration are responsible for the different reproductive patterns exhibited by the Eastmain River (James Bay) populations of anadromous cisco and lake whitefish, as predicted by species-specific migration costs that result in interspecific differences in energy allocation to growth, survival, and reproduction. In the Eastmain River, cisco spawn at a younger age and a smaller size, have a shorter life span and show a higher fecundity and a higher mortality than lake whitefish. Assuming that the two populations are stable (being only lightly exploited), the two species spawn at an age that maximizes their lifetime fecundity. Either juvenile (between three and age at maturity) and/or adult mortality is of major importance in moulding the observed age at maturity but adult mortality may play a predominant role. Adult mortality is associated with migration, an obligatory cost representing a major proportion of the energy loss experienced by reproductive individuals. The difference in the energy cost of migration between the two species suggests that migration may play a predominant role in producing the different reproductive patterns of cisco and lake whitefish in the Eastmain River and that within the physiological and size constraints of each species, these patterns represent optimal adaptations maximizing fitness.

Variations on a segmental theme: muscle receptor organs and extensor neuromusculature in the squat lobster Munida quadrispina (Anomura, Galatheidae)

1995 ◽  
Vol 198 (12) ◽  
pp. 2453-2463 ◽  
Author(s):  
E Wallis ◽  
D Paul ◽  
B Antonsen ◽  
R Hollenberg
Keyword(s):  
Relative Size ◽  
Extracellular Recording ◽  
Blue Staining ◽  
Squat Lobster ◽  
Muscle Receptor ◽  
Axial Muscles ◽  
Extensor Motoneurones ◽  
The Difference ◽  
Segmental Variation ◽  
Species Specific

Extensor neuromusculature and the muscle receptor organs (MROs) associated with them have been conserved during the evolution of malacostracan crustaceans, despite species-specific differences between homologous segments in divergent taxa. Investigations of these differences could provide insight into how sensory and neuromuscular elements are modified to accommodate changing behavioural patterns. The most obvious differences between squat lobsters (galatheid anomurans) and macruran decapods, such as crayfish, are the greater dorso-ventral flattening of the galatheid abdomen and its flexed resting posture. To investigate whether the evolution of this altered posture affected extensor neuromusculature and MRO morphology and physiology, we used Methylene Blue staining, cobalt backfilling and extracellular recording techniques to describe these elements in the caudal thoracic and six abdominal segments of the squat lobster Munida quadrispina and compared our results with published descriptions of homologous elements in macrurans. In M. quadrispina, there is segmental variation both in the orientation of the MROs along the abdomen and in their physiological responses to stretch: apparent sensitivity is higher in caudal than rostral MROs. Homologues of three of the four accessory neurones found in crayfish occur, but AN#1 has a major dendrite not present in crayfish. Intersegmental differences in size and morphology of extensor motoneurones occur in M. quadrispina, as have been reported in crayfish, but are dissimilar in the two: abdominal ganglion 5 extensor motoneurones are the largest in M. quadrispina and the smallest in crayfish; this difference correlates with the difference in relative size of axial muscles along the abdomen reported previously for these species. M. quadrispina also differs from macrurans in having a single tonic, and no phasic, MRO on each side of the last abdominal segment. Together, these observations suggest that galatheids have evolved modified or additional neurobehavioural control(s) for the abdomen and tailfan.

scholarly journals Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans

2020 ◽  
Vol 8 (6) ◽  
pp. 900
Author(s):  
Gema Carrasco ◽  
Sara Monzón ◽  
María San Segundo ◽  
Enrique García ◽  
Noelia Garrido ◽  
...  
Keyword(s):  
16S Rrna ◽  
Topoisomerase Ii ◽  
Gc Content ◽  
Amino Acid Identity ◽  
Beta Lactams ◽  
Nocardia Species ◽  
Antimicrobial Susceptibilities ◽  
The Difference ◽  
Subunit B ◽  
Genomic Gc Content

Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).

BIOSYSTEMATICS OF THE GENUS EUXOA (LEPIDOPTERA: NOCTUIDAE). XVIH. COMPARATIVE BIOLOGY AND EXPERIMENTAL TAXONOMY OF THE SIBLING SPECIES EUXOA RIDMGSIANA (GRT.) AND EUXOA MAIMES (SM.)

1985 ◽  
Vol 117 (4) ◽  
pp. 481-493 ◽  
Author(s):  
J.R. Byers ◽  
D.L. Struble ◽  
J.D. Lafontaine
Keyword(s):  
Life Cycle ◽  
Reproductive Isolation ◽  
Sibling Species ◽  
Mate Recognition ◽  
Recognition System ◽  
Flight Period ◽  
Interspecific Differences ◽  
Mate Recognition System ◽  
The Difference ◽  
Species Specific

AbstractThe species previously recognized as Euxoa ridingsiana (Grt.) is shown to be composed of a sympatric pair of sibling species, Euxoa ridingsiana (Grt.) and Euxoa maimes (Sm.), which in the laboratory will produce viable F1 hybrids but no F2. Results of F1 sib and backcrosses show that the F1 males are fertile and the F1 females are infertile. In mating-bias tests conducted in laboratory cages, 74% of matings were conspecific and 26% interspecific. Differences in the diel periodicities of mating, which are about 2 h out of phase, may account for the mating bias. The duration of development of E. ridingsiana in the laboratory and its seasonal flight period in the field are about 2 weeks in advance of that of E. maimes. However, there is considerable overlap of the flight periods and, with the tendency of females of both species to mate several times, it is unlikely that the difference in seasonal emergence is enough to effect reproductive isolation. It is evident that, under natural conditions, reproductive isolation can be maintained entirely by species-specific sex pheromones. This mechanism of reproductive isolation is, however, apparently ineffective when moths are confined in cages in the laboratory.Biogeographic considerations suggest that the differences in life-cycle timing and mating periodicities might have been adaptations to adjust development and reproduction to prevailing ancestral environments. If the initial differentiation of the 2 species occurred in isolation and included at least an incipient shift in the pheromonal mate-recognition system, it is possible that upon reestablishment of contact between ancestral populations the differences in life-cycle timing and mating periodicities acting in concert could have effected substantial, albeit incomplete, reproductive isolation. Subsequent selection to reinforce assortative mating to preserve coadapted gene complexes could then have resulted in differentiation of discrete pheromonal systems and attainment of species status.

METHYL ACTIVATION AND sRNA METHYLATION BY SOLUBLE FRACTIONS OF SEVERAL VERTEBRATE LIVERS

1967 ◽  
Vol 45 (10) ◽  
pp. 1513-1522 ◽  
Author(s):  
R. L. Hancock
Keyword(s):  
Mouse Liver ◽  
Specific Interaction ◽  
Adult Rabbit ◽  
X Chromosomes ◽  
E Coli ◽  
Lower Vertebrates ◽  
The Difference ◽  
Species Specific ◽  
Methylase Activity

The amount of liver ATP: L-methionine S-adenosyltransferase activity varies widely in vertebrates from trace amounts in certain lower vertebrates, e.g. shark or turtle, to relatively large quantities in mammals, e.g. mouse or rabbit. The liver from male mice of a particular stock had only two-thirds the activity of female mouse liver. This difference is not explained by the difference between the sexes in number of X-chromosomes, since female mice with only one X-chromosome (X/0) had the same levels of liver S-adenosyltransferase activity as normal females with two X-chromosomes.sRNA methylase activity from mouse, shark, and rabbit liver supernatant fractions were studied with mouse, shark, and Escherichia coli sRNA. Highspeed supernatant fractions from both rabbit embryonic liver and mouse hepatoma hypermethylated E. coli sRNA which had been previously methylated by adult rabbit or mouse liver supernatant fractions. Hepatoma methylase(s) acts in an analogous manner to that of a species-specific interaction with heterologous and homologous sRNA.A calculation is made comparing the amount of sRNA methylase activity detected in vitro with mouse liver sRNA, with one which is theoretically derived; similar values are obtained. The variation found in vertebrate liver with respect to methyl activation and sRNA methylation is discussed.

scholarly journals Perbedaan pH, Viskositas dan Volume Saliva setelah Berkumur dengan Obat Kumur Sintetik yang Mengandung Chlorhexidine dan Larutan Propolis pada Anak Usia 11-12 Tahun

2020 ◽  
Vol 7 (3) ◽  
pp. 158
Author(s):  
Shinta Dinyanti ◽  
Roedy Budirahardjo ◽  
Raditya Nugroho
Keyword(s):  
Side Effects ◽  
Dental Caries ◽  
Oral Cavity ◽  
Synthetic Compounds ◽  
The Difference ◽  
Mutagenic Effects

Dental caries is a process that begins with dissolution of enamel causing damage to the dental component by several factors, such as saliva. The occurrence of diseases in the oral cavity is prevented by the use of synthetic mouthwash containing chlorhexidie, but the using of synthetic compounds causes mutagenic effects on the oral cavity, so it needs alternative by using natural ingredients that have antibacterial power and smaller side effects. The purpose of the study was to investigate the difference of pH, viscosity and volume saliva after gargling with synthetic mouthwash containing of chlorhexidine and propolis solution for children age 11-12 years in Pondok Pesantren Nurul Islam Antirogo Jember. This study used pra-experimental One Shoot Case Study with total sampling in Pondok pesantren Nurul Islam Antirogo Jember. As many 25 students were recruited for the study. The result showed that after gargling with propolis solution can be increase of pH saliva, decrease of viscosity saliva and increase of volume saliva for children age 11-12 years in Pondok Pesantren Nurul Islam Antirogo Jember.

scholarly journals Bamboo Water Transport Assessed with Deuterium Tracing

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 623 ◽  
Author(s):  
Tingting Mei ◽  
Dongming Fang ◽  
Alexander Röll ◽  
Dirk Hölscher
Keyword(s):  
Water Transport ◽  
Water Use ◽  
Extended Period ◽  
Sap Flux ◽  
Short Term ◽  
The Difference ◽  
Highly Correlated ◽  
Species Specific ◽  
Water Use Rates ◽  
Deuterium Tracing

Bamboo water transport comprises the pathway rhizomes-culms-leaves as well as transfer among culms via connected rhizomes. We assessed bamboo water transport in three big clumpy bamboo species by deuterium tracing. The tracer was injected into the base of established culms, and water samples were collected from leaves of the labeled culms and from neighboring culms. From the base of labeled culms to their leaves, the average tracer arrival time across species was 1.2 days, maximum tracer concentration was reached after 1.8 days, and the tracer residence time was 5.6 days. Sap velocities were high (13.9 m d−1). Daily culm water use rates estimated by the tracer method versus rates measured by a calibrated sap flux method were highly correlated (R2 = 0.94), but the tracer estimates were about 70% higher. Elevated deuterium concentrations in studied neighbor culms point to deuterium transfer among culms, which may explain the difference in culm water use estimates. We found no differences in deuterium concentrations between neighbor-established and neighbor freshly sprouted culms of a given species. In two species, elevated concentrations in both neighbor-established and neighbor freshly sprouted culms were observed over an extended period. An applied mixing model suggests that five neighbor culms received labeled water. In contrast, for the third species, elevated concentrations in neighbor culms were only observed at the earliest sampling date after labeling. This could indicate that there was only short-term transfer and that the tracer was distributed more widely across the rhizome network. In conclusion, our deuterium tracing experiments point to water transfer among culms, but with species-specific differences.

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