scholarly journals Contrasting gene‐level signatures of selection with reproductive fitness

2021 ◽  
Author(s):  
Stephen J. Bush ◽  
Courtney J. Murren ◽  
Araxi O. Urrutia ◽  
Paula X. Kover
Keyword(s):  
Reproductive Fitness ◽  
Gene Level ◽  
Signatures Of Selection

Fragmentation and matching of human microRNA sequences in 3’utr

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
M.S. Parker ◽  
A. Balasubramaniam ◽  
F.R. Sallee ◽  
S.L. Parker
Keyword(s):  
Time Scale ◽  
Point Mutations ◽  
Physical Separation ◽  
Gene Level ◽  
Mature Micrornas

: Matches of mature microRNAs (m-miRs) in human 3’utr can be traced to mutations producing fragments of original m-miR sequences without physical separation. (The by far fewer m-miR matches in 5’utr and cds follow similar patterns.) The sense and antisense m-miR fragments in 3’utr occur at quite similar levels. The fragmentation occurs at gene level by mutation within one of the paired m-miRs, which upon transcription results in increased interactive capability for both former pre-micro (pre-mir) RNA stem partners. The non-mutated stem partner can persist in 3’utr sequences, as is apparent from significant presence of miR-619-5p and miR-5096 and some conservation of 20 other simian-specific m-miR sequences. However, most of m-mir sequences in 3’utr are extensively fragmented, with low preservation of long matches. In flanks of individual m-miR embeds the mutated pre-mir positions are to a degree defined specifically. The m-mir matches of various sizes in 3’utr apparently reflect accumulation, on a phylogenetic time scale, of in-sequence point mutations. Across human 3’utr this fragmentation is significantly less for evolutionarily recent human m-miRs that originate in simians compared to human m-miRs first appearing in lower primates, and especially to human m-miRs introduced in non-primates.

Inbreeding reduces reproductive fitness

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Natural Selection ◽  
Inbreeding Depression ◽  
Reproductive Fitness ◽  
Heterozygote Advantage ◽  
Small Populations ◽  
Population Bottlenecks ◽  
Risk Of Extinction ◽  
Survival And Reproduction

The harmful impacts of inbreeding are generally greater in species that naturally outbreed compared to those in inbreeding species, greater in stressful than benign environments, greater for fitness than peripheral traits, and greater for total fitness compared to its individual components. Inbreeding reduces survival and reproduction (i.e., it causes inbreeding depression), and thereby increases the risk of extinction. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Natural selection may remove (purge) the alleles that cause inbreeding depression, especially following inbreeding or population bottlenecks, but it has limited effects in small populations and usually does not completely eliminate inbreeding depression. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies.

scholarly journals Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ege Ülgen ◽  
Özge Can ◽  
Kaya Bilguvar ◽  
Cemaliye Akyerli Boylu ◽  
Şirin Kılıçturgay Yüksel ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Clinical Interpretation ◽  
Germline Variants ◽  
Whole Exome ◽  
Gene Level ◽  
Analysis Workflow ◽  
Tumor Mutational Burden ◽  
Diffuse Gliomas

Abstract Background In the clinical setting, workflows for analyzing individual genomics data should be both comprehensive and convenient for clinical interpretation. In an effort for comprehensiveness and practicality, we attempted to create a clinical individual whole exome sequencing (WES) analysis workflow, allowing identification of genomic alterations and presentation of neurooncologically-relevant findings. Methods The analysis workflow detects germline and somatic variants and presents: (1) germline variants, (2) somatic short variants, (3) tumor mutational burden (TMB), (4) microsatellite instability (MSI), (5) somatic copy number alterations (SCNA), (6) SCNA burden, (7) loss of heterozygosity, (8) genes with double-hit, (9) mutational signatures, and (10) pathway enrichment analyses. Using the workflow, 58 WES analyses from matched blood and tumor samples of 52 patients were analyzed: 47 primary and 11 recurrent diffuse gliomas. Results The median mean read depths were 199.88 for tumor and 110.955 for normal samples. For germline variants, a median of 22 (14–33) variants per patient was reported. There was a median of 6 (0–590) reported somatic short variants per tumor. A median of 19 (0–94) broad SCNAs and a median of 6 (0–12) gene-level SCNAs were reported per tumor. The gene with the most frequent somatic short variants was TP53 (41.38%). The most frequent chromosome-/arm-level SCNA events were chr7 amplification, chr22q loss, and chr10 loss. TMB in primary gliomas were significantly lower than in recurrent tumors (p = 0.002). MSI incidence was low (6.9%). Conclusions We demonstrate that WES can be practically and efficiently utilized for clinical analysis of individual brain tumors. The results display that NOTATES produces clinically relevant results in a concise but exhaustive manner.

scholarly journals An Overview of Equine Influenza in South America

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 888
Author(s):  
Cecilia Olguin-Perglione ◽  
María Edith Barrandeguy
Keyword(s):  
South America ◽  
Disease Surveillance ◽  
Economic Losses ◽  
South American ◽  
Respiratory Pathogens ◽  
Equine Influenza Virus ◽  
Equine Influenza ◽  
Vaccine Manufacturer ◽  
Gene Level ◽  
Control Procedures

Equine influenza virus (EIV) is one of the most important respiratory pathogens of horses as outbreaks of the disease lead to significant economic losses worldwide. In this review, we summarize the information available on equine influenza (EI) in South America. In the region, the major events of EI occurred almost in the same period in the different countries, and the EIV isolated showed high genetic identity at the hemagglutinin gene level. It is highly likely that the continuous movement of horses, some of them subclinically infected, among South American countries, facilitated the spread of the virus. Although EI vaccination is mandatory for mobile or congregates equine populations in the region, EI outbreaks continuously threaten the equine industry. Vaccine breakdown could be related to the fact that many of the commercial vaccines available in the region contain out-of-date EIV strains, and some of them even lack reliable information about immunogenicity and efficacy. This review highlights the importance of disease surveillance and reinforces the need to harmonize quarantine and biosecurity protocols, and encourage vaccine manufacturer companies to carry out quality control procedures and update the EIV strains in their products.

Cytogenetic Observations in Infertile Men Working with Insecticidal Compounds

1978 ◽  
Vol 27 ◽  
pp. 51-56 ◽  
Author(s):  
Fiorella Shabtai ◽  
Shlomo Bichacho ◽  
Isaac Halbrecht
Keyword(s):  
Y Chromosome ◽  
Male Fertility ◽  
Reproductive Fitness ◽  
Negative Influence ◽  
Chromosomal Breakage ◽  
Infertile Men ◽  
Chemically Induced ◽  
The Individual ◽  
Chromosomal Variants ◽  
Insecticidal Compounds

The negative influence of some insecticides on male fertility has been noted. We report our cytogenetic observations on a group of infertile insecticide workers. Increased chromosomal breakage was a constant finding and the Y chromosome was especially damaged. This may account for impaired spermatogenesis. Furthermore, the involvement of heterochromatic chromosomal variants both in the individual susceptibility to the chemically induced damage and in the reproductive fitness is emphasized.

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