Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 413-419 ◽  
Author(s):  
Jin-Feng Chen ◽  
Fei Lu ◽  
Su-Shing Chen ◽  
Shi-Heng Tao
Keyword(s):  
Recombination Rate ◽  
Base Composition ◽  
Significant Positive Correlation ◽  
Gc Content ◽  
Pseudoautosomal Region ◽  
Positive Correlation ◽  
Coding Regions ◽  
Ideal System ◽  
Fixation Bias

This paper establishes that recombination drives the evolution of GC content in a significant way. Because the human P-arm pseudoautosomal region (PAR1) has been shown to have a high recombination rate, at least 20-fold more frequent than the genomic average of ~1 cM/Mb, this region provides an ideal system to study the role of recombination in the evolution of base composition. Nine non-coding regions of PAR1 are analyzed in this study. We have observed a highly significant positive correlation between the recombination rate and GC content (ρ = 0.837, p ≤ 0.005). Five regions that lie in the distal part of PAR1 are shown to be significantly higher than genomic average divergence. By comparing the intra- and inter-specific AT→GC – GC→AT ratios, we have detected no fixation bias toward GC alleles except for L254915, which has excessive AT→GC changes in the human lineage. Thus, we conclude that the high GC content of the PAR1 genes better fits the biased gene conversion (BGC) model.Key words: pseudoautosomal region, GC content, base composition, evolution, recombination.

scholarly journals Evolution of Nucleotide Composition in the SARS-CoV-2 Lineage: Implications for Vaccine Design

2020 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Base Composition ◽  
Scientific Community ◽  
Significant Positive Correlation ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Reverse Direction ◽  
Novel Coronavirus ◽  
Near Future ◽  
Systematic Reduction ◽  
Gc Contents

The worldwide outbreak of a novel coronavirus, SARS-CoV-2 has caused a pandemic of respiratory disease. Due to this emergency, researchers around the globe have been investigating the evolution of the genome of SARS-CoV-2 in order to design vaccines. Here I examined the evolution of GC content of SARS-CoV-2 by comparing the genomes of the members of the group Betacoronavirus. The results of this investigation revealed a highly significant positive correlation between the GC contents of betacoronaviruses and their divergence from SARS-CoV-2. The betacoronaviruses that are distantly related to SARS-CoV-2 have much higher GC contents than the latter. Conversely, the closely related ones have low GC contents, which are only slightly higher than that of SARS-CoV-2. This suggests a systematic reduction in the GC content in the SARS-CoV-2 lineage over time. The declining trend in this lineage predicts a much-reduced GC content in the coronaviruses that will descend/evolve from SARS-CoV-2 in the future. Due to the three consecutive outbreaks (MERS-CoV, SARS-CoV and SARS-CoV-2) caused by the members of the SARS-CoV-2, the scientific community is emphasizing the need for universal vaccines that are effective across many strains including those, that will inevitably emerge in the near future. The reduction in GC contents implies an increase in the rate of GC→AT mutations than that the mutational changes in the reverse direction. Therefore, understanding the evolution of base composition and mutational patterns of SARS-CoV-2 could be useful in designing broad-spectrum vaccines that could identify and neutralize the present and future strains of this virus.

Association of Vitamin D Status with Semen Parameters and Male Reproductive Hormones in Egyptian Infertile Men

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Doaa Abou-Taleb AE ◽  
◽  
Mahran AM ◽  
Mahmoud MA ◽  
Gaber MA ◽  
...  
Keyword(s):  
Vitamin D ◽  
Significant Positive Correlation ◽  
Reproductive Hormones ◽  
Male Reproduction ◽  
Semen Parameters ◽  
Unknown Etiology ◽  
Control Group ◽  
Positive Correlation ◽  
Infertile Men

Background: Although vitamin D receptor (VDR) is expressed in human sperm, little is known about the role of vitamin D (Vit. D) in male reproduction. Our objective was to assess Vit. D levels both in serum and seminal fluid and to establish the relation between serum and seminal Vit. D levels, semen parameters, male sex hormones and serum calcium level in Egyptian infertile men. Patients and Methods: We conducted a prospective case control study including 30 healthy fertile males as a control group and 60 male patients with infertility of unknown etiology. Semen samples were collected and semen parameters were evaluated. Also, seminal Vit. D level was measured. Blood samples were taken as serum levels of Vit. D, calcium, testosterone, Luteinizing Hormone (LH) and Follicle-Stimulating Hormone (FSH) were estimated. Results: There was significant decrease of both serum and seminal Vit. D level in groups of male infertility compared to control group. A significant positive correlation was found between serum and seminal Vit. D levels in different study groups. Also, significant positive correlation between serum Vit. D level and non-progressive sperm motility. Conclusion: Our results support the role of Vit. D in semen parameters and male fertility status.

scholarly journals Different Profile of Serum Leptin between Early Onset and Late Onset Preeclampsia

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Saeedeh Salimi ◽  
Farzaneh Farajian-Mashhadi ◽  
Anoosh Naghavi ◽  
Mojgan Mokhtari ◽  
Mahnaz Shahrakipour ◽  
...  
Keyword(s):  
Early Onset ◽  
Significant Positive Correlation ◽  
Late Onset ◽  
Maternal Serum ◽  
Serum Adiponectin ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serum Leptin ◽  
Positive Correlation ◽  
Early Onset Preeclampsia

Aim. This study was designed to clarify the role of leptin and adiponectin in preeclampsia (PE) pathogenesis and different subtypes of preeclampsia.Method. This case control study was performed in 45 PE patients and 45 healthy controls matched for age, BMI, and ethnicity. Serum leptin and adiponectin levels were determined by enzyme linked immunosorbent assay (ELISA).Results. Maternal serum leptin and adiponectin were significantly higher in PE women than controls. Serum leptin was elevated in early onset preeclampsia (EOPE) and late onset preeclampsia (LOPE) compared to controls. Among PE patients, serum leptin was higher in EOPE than LOPE women. However, serum adiponectin was not different between EOPE and LOPE women. The serum leptin was significantly higher in severe PE than mild PE. The serum adiponectin was significantly elevated in severe PE compared to controls. Significant positive correlation was observed between leptin and adiponectin and also between leptin and BMI in controls. Moreover significant positive correlation was observed between adiponectin and BMI in PE patients and controls.Conclusion. The present study showed that serum leptin level may play a significant role as a biomarker to differentiate early and late onset PE and also its relation to BMI and severity of disease.

Alpha 1 Antitrypsin, C Reactive Protein, and Hemolysis Markers: Association With Cytokines Profile In Sickle Cell Disease Patients In Steady-State and Crisis-State

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4701-4701
Author(s):  
Magda Carvalho ◽  
Wendell Vilas Boas ◽  
Bruno Antônio Veloso Cerqueira ◽  
Joao Oliveira Reis ◽  
Theo Araujo ◽  
...  
Keyword(s):  
Steady State ◽  
Sickle Cell Disease ◽  
Significant Positive Correlation ◽  
Clinical Manifestations ◽  
Cell Disease ◽  
C Reactive Protein ◽  
Positive Correlation ◽  
Reactive Protein ◽  
Alpha 1 Antitrypsin

Introduction Sickle cell disease (SCD) has a heterogeneous clinical picture, characterized by hemolysis, chronic inflammation and vaso-occlusive events and painful crisis. Aims Investigate the levels of Alpha 1 antitrypsin (A1AT), C reactive protein (CRP), hemolysis markers and its association with cytokines profile in SCD patients in steady-state and crisis-state. Methods It was developed a cross sectional study in a total of 72 SCD patients in steady-state (SP) and 23 SCD patients in crisis (CP) age-and-sex-matched. Hematological analysis was performed by automatic cell counter, hemoglobin profile by HPLC, and biochemistry analyses of inflammation and infection markers and lipid, hepatic, and kidney metabolism markers were investigated by immunochemistry assays. Plasma levels of TNFα, IFNγ, IL-10, IL-1β, IL-6 and IL-8 were measured using Cytometric Bead Array - CBA (BD Biosciences Pharmingen, USA) according to the manufacturer’s protocol. Results Statistical analysis showed that SCD steady-state patients group had the highest IL-12 concentration (p<0.0001) and there were a decrease in TNFα, IL-10, IL-1β, and IL-6 levels (p< 0.0001) when compared to CP group (figure 1). However, significant differences in IL-8 levels were not finding in the comparison between SCD in steady-state and crisis patients groups. Biomarkers analyses of SCD steady-state patients showed significant negative correlation between IL-8 with A1AT (r= -0.25; p= 0.03) and CRP (r= -0.24; p= 0.04) and significant positive correlation with lactate dehydrogenase (LDH) (r= 0.25; p= 0.03). The IL-6 showed significant positive correlation with white blood cell count (WBC) (r= 0.52; p< 0.0001), ferritin (r= 0.30; p= 0.001) and CRP (r= 0.42; p= 0.0002). TNFα showed a significant positive correlation with leukocyte count (r= 0.28; p= 0.02) and A1AT (r= 0.29; p= 0.01) and IL-10 showed a significant positive correlation with platelets count (r= 0.30; p= 0.01) and A1AT (r= 0.29; p= 0.01). Conclusions Immunological aspects of SCD patients have been increasingly studied. The high levels of Th2 cytokines (IL-6 and IL-10) and proinflammatory cytokines (TNFα and IL-1β) in SCD patients in crisis-state, possibly is related to severe clinical manifestations, despite the fundamental role of these cytokines in the pathophysiology is not yet completely clear. The correlation between these cytokines and biomarkers associated with important clinical manifestations in SCD, such as WBC, platelet count, A1AT and CRP, highlights the important role of inflammatory mediators in SCD and its possible association with an expression or activation of adhesion molecules in neutrophils and vascular endothelium. Disclosures: No relevant conflicts of interest to declare.

scholarly journals The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Geng Zou ◽  
Bernardo Bello-Orti ◽  
Virginia Aragon ◽  
Alexander W. Tucker ◽  
Rui Luo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Simple Sequence Repeats ◽  
Potential Role ◽  
Gc Content ◽  
Nucleotide Metabolism ◽  
Coding Regions ◽  
Purine Nucleotide Metabolism ◽  
Go Terms ◽  
Simple Sequence

Abstract Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3 and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

scholarly journals Enterprises’ R&D Investment, Venture Capital Syndication and IPO Underpricing

2021 ◽  
Vol 13 (13) ◽  
pp. 7290
Author(s):  
Xuemeng Guo ◽  
Kai Li ◽  
Siyi Yu ◽  
Bolu Wei
Keyword(s):  
Venture Capital ◽  
Information Asymmetry ◽  
Adverse Selection ◽  
Significant Positive Correlation ◽  
Ipo Underpricing ◽  
Positive Correlation ◽  
The Relationship ◽  
D Investment

Based on the data of companies that got ChiNext listed from 2009 to 2018, this paper empirically studies the relationship among R&D investment, venture capital (VC) syndication and IPO underpricing. It is found that there is a significant positive correlation between R&D investment and IPO underpricing, indicating that the higher the R&D investment is, the higher the IPO underpricing degree is; the intervention of VC syndication plays a role of “adverse selection” instead of giving play to its advantages of sharing information, which intensifies the positive correlation between R&D investment and IPO underpricing. Further analysis shows that the reputation of the leading VC in syndication can play a negative regulating role; the higher the reputation of the leading VC is, the more it can play the “certification effect”, reduce the information asymmetry caused by R&D investment, therefore alleviating the IPO underpricing caused by R&D investment.

scholarly journals Comparisons of Coding and Noncoding Sequences to infer the Origin of Codon usage Bias

2017 ◽  
Author(s):  
Prashant Mainali ◽  
Sobita Pathak
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Mutation Bias ◽  
Translation Process ◽  
Noncoding Regions ◽  
Coding Regions ◽  
Synonymous Codons ◽  
Shed Light

ABSTRACTCodon usage bias is the preferential use of the subset of synonymous codons during translation. In this paper, the comparisons of normalized entropy and GC content between the sequence of coding regions of Escherichia coli k12 and noncoding regions (ncRNA, rRNA) of various organisms were done to shed light on the origin of the codon usage bias.The normalized entropy of the coding regions was found significantly higher than the noncoding regions, suggesting the role of the translation process in shaping codon usage bias. Further, when the position specific GC content of both coding and noncoding regions was analyzed, the GC2 content in coding regions was lower than GC1 and GC2 while in noncoding regions, the GC1, GC2, GC3 contents were approximately equal. This discrepancy is explained by the biased mutation coupled with the presence and absence of selection pressure. The accumulation of CG content occurs in the sequences due to mutation bias in DNA repair and recombination process. In noncoding regions, the mutation is harmful and thus, selected against while due to the degeneracy of codons in coding regions, a mutation in GC3 is neutral and hence, not selected. Thus, the accumulation of GC content occurs in coding regions, and thus codon usage bias occurs.

scholarly journals FAKTOR-FAKTOR YANG BERHUBUNGAN DENGAN KEIKUTSERTAAN SUAMI DALAM KELUARGA BERENCANA DI WILAYAH PUSKESMAS KECAMATAN PULOGADUNG JAKARTA TIMUR

2017 ◽  
Vol 5 (1) ◽  
pp. 107-118
Author(s):  
Willa Follona Follona
Keyword(s):  
Family Planning ◽  
Role Models ◽  
Significant Positive Correlation ◽  
Health Workers ◽  
P Value ◽  
Positive Correlation ◽  
Number Of Children ◽  
Family Planning Programs ◽  
The Relationship

The responsibility of men in terms of family planning is very important in the role of family planning programs. However, there is an imbalance in the number of contraceptive participation in female and male FP acceptors. The participation of men is still very low, compared to female. The purpose of this study is to analyze the relationship between husband characteristics seen from the factors of age, education, occupation, ethnicity, religion, income, number of children, also about husband knowledge, attitudes husband and wife / family support, and access to media / participation of husband as KB acceptor. This is across sectional study of 90 husbands chosen purposively in Pulogadung Sub District in September 2016. The results showed that there was a significant positive correlation between knowledge with the participation of respondents as Family Planning acceptors, the higher the knowledge level, the higher the participation of husband as the acceptors of family planning with p value 0.022 (OR = 4,818; 95% CI 1.476 to 15.728). There was a significant positive correlation between attitudes with the participation of respondents as familyplanning acceptors, the higher the attitudes they have, the higher the participation of husbands as the acceptors of family planning p value 0,007 (OR = 13,813; 95% CI 2,286 to 66,111). Health workers are expected to further promote the promotion of male KB acceptor services, through the provision of family planning education in the form of counseling and family approaches concerning the importance of family planning for men. For those have become acceptors are expected to be role models by spreading to their peer.

scholarly journals Role of weather parameters on seasonal abundance of insects in a mangobased agroforestry in Bangladesh, with particular reference to mango hopper

2017 ◽  
Vol 42 (2) ◽  
pp. 197-205
Author(s):  
S Namni ◽  
MR Amin ◽  
MRU Miah ◽  
MF Rahman ◽  
SJ Suh
Keyword(s):  
Relative Humidity ◽  
Significant Positive Correlation ◽  
Fruit Set ◽  
Species Abundance ◽  
Significant Negative Correlation ◽  
Seasonal Abundance ◽  
Insect Species ◽  
Positive Correlation ◽  
Weather Parameters

Weekly sweeping was done by sweep net in order to collect insects to study the effect of weather parameters on the seasonal abundance of total insect species as well as mango hopper population in a mango-based agroforestry in Bangladesh during January to June 2013. The total insect species abundance was the highest during April to May, following the flushing of inflorescence and fruit set. At that time temperature and relative humidity were comparatively higher and there was rainfall. Mango hopper population was the highest in May and synchronized to fruit set. The abundance of total insect species and mango hopper population showed significant positive correlation with temperature, and relative humidity, while significant negative correlation with light intensity and non-significant positive correlation with rainfall. Multiple linear regression equation based on weather parameters revealed 59.2% and 61.7% role on population build up of total insect species and mango hopper, respectively. Temperature was found to be the most important effect which individually contributed 31.3% on population abundance of total insect species and 29.9% on mango hopper.Bangladesh J. Agril. Res. 42(2): 197-205, June 2017

The role of non-dipterous insects in the pollination of cocoa in Brazil

1978 ◽  
Vol 68 (4) ◽  
pp. 559-574 ◽  
Author(s):  
J. A. Winder
Keyword(s):  
Distribution Pattern ◽  
Significant Positive Correlation ◽  
Favourable Effect ◽  
Positive Correlation ◽  
Treated Area ◽  
Untreated Area ◽  
Toxoptera Aurantii ◽  
Mosaic Distribution

AbstractField collections in Bahia State, Brazil, of open cocoa flowers from an untreated plantation and one treated with insecticide and fungicide showed that Homoptera, including the cicadellid Xesrocephalus ancorifer Linnavuori, the aphidid Toxoptera aurantii (Boy.), and species of Pseudococcidae and Margarodidae (Coccoidea), constituted 96% of the total number of insects collected. In the untreated area, Wasmannia rochai Ford formed 22% of the ants collected and Brachymyrmex pictus Mayr, Crernatogaster ? parabiotica Forel,Iridomyrmex sp., Pheidole sp. and Solenopsis sp., a further 48%, whereas in the treated area, 47% were C. parabiotica, 14% W. rochai and 9% B. heeri Forel. There was evidence of a mosaic distribution pattern for the ant species. No cocoa pollen was found on any of the insects collected. Total pollination ranged between 7·4 and 8·1 % and effective pollination between 3·7 and 2·8 % in the treated and untreated areas, respectively. Approximately 76% of the pollen masses were stylar, with 38% of the ball type and 54% of the smear type, whereas the 16% stigmatic pollen masses consisted of 63% ball and 29% smear types; 44% of the stigmatic pollinations were effective, compared with only 33 % of the stylar ones. Some quadrats were more attractive to pollinators than others, and there was a significant positive correlation between percentage effective pollination and insolation, probably due to the favourable effect of sunshine on Forcipomyia activity.

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