scholarly journals The Genetic and Environmental Adaptation of the Associated Liana Species Derris trifoliata Lour. (Leguminosae) in Mangroves

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1375
Author(s):  
Yun Zhang ◽  
Kun Xin ◽  
Baowen Liao ◽  
Xihang Ai ◽  
Nong Sheng
Keyword(s):  
Clonal Growth ◽  
Environmental Changes ◽  
Principal Component ◽  
Clonal Diversity ◽  
Control Measures ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Sexual Propagation ◽  
Specific Locus ◽  
And Control

Derris trifoliata Lour. is an indigenous and associated liana species of mangroves in China; however, its rapid dispersal is threatening mangrove survival. To explore and evaluate their persistence in past disturbances and their potential resistance to future climate and environmental changes, 120 D. trifoliata samples were collected from three sites in Guangdong Province, China, and they were used to develop single nucleotide polymorphic markers using specific-locus amplified fragment sequencing technology. A total of 351.59 Mb reads and 97,998 polymorphic specific-locus amplified fragment sequencing tags were identified, including 360,672 single nucleotide polymorphisms. The principal component analysis, phylogenetic tree, and genetic structure all clustered the samples according to their geographic positions. The three populations showed medium genetic diversity levels and high clonal diversity, indicating that sexual propagation played vital roles in the populations’ succession, although clonal growth was intense within the populations. An association analysis revealed that 9 out of 16 markers were correlated with nitrogen, which indicated the positive roles of nitrogen in population formation and maintenance. This study provides an ecological and molecular basis for understanding the outbreaks of D. trifoliata in mangroves. To control the further expansion of D. trifoliata in mangroves, preventive and control measures should be taken against clonal growth and sexual propagation, respectively; obstructing the clonal growth, especially that of the stolon, should be mainly considered at the junctions of D. trifoliata and mangroves.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

The G allele in IL-10-1082 G/A may have a role in lowering the susceptibility to panic disorder in female patients

2016 ◽  
Vol 28 (6) ◽  
pp. 357-361 ◽  
Author(s):  
Han-Joon Kim ◽  
Yong-Ku Kim
Keyword(s):  
Panic Disorder ◽  
Patient Group ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Female Patients ◽  
Immune System Activation ◽  
Tnf Α ◽  
System Activation ◽  
And Control

BackgroundImmune system activation is involved in the pathophysiology of panic disorder (PD). We investigated INF-γ+874 A/T, TNF-α-308 G/A, and IL-10-1082 G/A single nucleotide polymorphisms (SNPs) to determine their association with PD.MethodThis study enroled 135 PD patients and 135 healthy controls. INF-γ+874 A/T (rs2430561), TNF-α-308 G/A (rs1800629), and IL-10-1082 G/A (rs1800896) were genotyped.ResultsThere were no differences in genotypes or allele frequencies between the patient and control groups, regardless of accompanying agoraphobia. However, for female patients, the G allele frequency in IL-10 SNP was higher in the control group than in the patient group. Additionally, the female control group had a higher frequency of the A/G and G/G genotype in the IL-10 SNP than the female patient group.ConclusionWe suggest that the G allele in IL-10-1082 G/A might have a role in reducing the manifestations of PD in female patients. Further studies are needed to extend and confirm our findings.

scholarly journals Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
Author(s):  
Eunju Seo ◽  
Kipoong Kim ◽  
Tae-Hwan Jun ◽  
Jinsil Choi ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Useful Knowledge ◽  
Population Structure Analysis ◽  
Group 3 ◽  
Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

scholarly journals LB1. Regional Assessment and Containment of Candida auris Transmission in Post-Acute Care Settings—Orange County, California, 2019

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S993-S993 ◽  
Author(s):  
Ellora Karmarkar ◽  
Ellora Karmarkar ◽  
Kathleen O’Donnell ◽  
Christopher Prestel ◽  
Kaitlin Forsberg ◽  
...  
Keyword(s):  
Acute Care ◽  
Orange County ◽  
Invasive Disease ◽  
Nucleotide Polymorphisms ◽  
Nursing Facilities ◽  
Candida Auris ◽  
Single Nucleotide ◽  
Skilled Nursing ◽  
And Control

Abstract Background Patients in long-term acute care hospitals (LTACHs) and skilled nursing facilities with ventilator units (VSNFs) are at high risk for Candida auris colonization; among patients colonized with this emerging pathogen, 5%–10% develop invasive disease with >45% mortality. In September 2018, a California LTACH-affiliated laboratory began enhanced C. auris surveillance by classifying species of Candida isolated from routine urine specimens. In February 2019, the first known Southern California case was detected in an Orange County (OC) LTACH; the patient had not traveled outside the region, indicating local acquisition. We performed point prevalence surveys (PPS) and infection prevention (IP) assessments at all OC LTACHs and VSNF subacute units to identify patients colonized with C. auris and control transmission. Methods During March–August 2019, we conducted PPS at facilities by collecting composite axilla and groin swabs for C. auris polymerase chain reaction testing and reflex culture from all patients who assented. Facilities with ≥1 C. auris-colonized patient repeated a PPS every 2 weeks to assess for new transmission. Isolate relatedness was assessed by whole-genome sequencing (WGS). We evaluated hand hygiene (HH) adherence, access to alcohol-based hand rubs (ABHR), and cleaning of high-touch surfaces to guide IP recommendations. Results The first PPS at all OC LTACHs (n = 3) and adult VSNFs (n = 14) identified 45 C. auris-colonized patients in 3 (100%) LTACHs and 6 (43%) VSNFs; after repeated PPS, the total count reached 124. Most patients (70%) were at 2 facilities (Table 1). Three of 124 patients developed candidemia. To date, isolates from 48 patients have completed WGS; all were highly related (<11 single-nucleotide polymorphisms) in the African clade. Of 9 facilities with C. auris, 5 had HH adherence < 50%, 3 had limited ABHR, and at 2, <60% of assessed high-touch surfaces were clean. We recommended regular HH and cleaning audits, and increased ABHR. Conclusion Our investigation, prompted by enhanced surveillance, identified C. auris at 9 OC facilities. WGS indicated a single introduction and local transmission. Early detection, followed by rapid county-wide investigation and IP support, enabled containment efforts for C. auris in OC. Disclosures All authors: No reported disclosures.

scholarly journals Evaluation of the Association between Programmed Cell Death-1 Gene Polymorphisms and Hepatocellular Carcinoma Susceptibility in Turkish Subjects. A Pilot Study

2020 ◽  
Author(s):  
Abdullah Fatih Demirci ◽  
Coskun Ozer Demirtas ◽  
Fatih Eren ◽  
Demet Yilmaz ◽  
Caglayan Keklikkiran ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Death ◽  
Programmed Cell Death ◽  
Turkish Population ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Programmed Cell Death 1 ◽  
Significant Difference ◽  
And Control

Background and Aims: Programmed cell death-1 (PD-1) has a vital role in regulating T-cell function, and immune escape mechanism of cancer cells. It was shown that there could be a relationship between single nucleotide polymorphisms (SNPs) in the PD-1 gene and susceptibility to hepatocellular carcinoma (HCC) based on various studies. We aimed to investigate the role of three SNPs within the PD-1 gene in susceptibility to HCC in the Turkish population. Methods: Single nucleotide polymorphisms of PD-1.1, 1.5, and 1.6 were genotyped by using TaqMan Allelic Discrimination Assays in blood samples of 137 HCC and 136 control subjects, matched for age and gender. The genotype, allele and haplotype frequencies were compared in HCC and control groups using logistic regression analysis. Results: Genotype distributions of PD-1.1, PD-1.5 and PD-1.6 SNPs were in Hardy-Weinberg equilibrium. No significant difference was observed in the genotype distribution of PD-1.1, PD-1.5 and PD-1.6 polymorphisms among gender and age-matched HCC (M/F: 96/41; mean age: 61.4 ±11.7 years) and control group (M/F: 94/42; mean age: 61.4±10.1). In the haplotype analysis of PD-1.1/PD-1.5/PD-1.6, no significant difference was found among HCC and control group adjusted for sex and age (all p values>0.1). Conclusion: Our findings, firstly reporting the association of PD-1.5 polymorphism with HCC, and PD-1.1 and PD-1.6 with HCC in the Turkish population, suggest that PD-1 polymorphisms are not predisposing factors for HCC development. Future studies with larger sample sizes and different ethnic populations are required to validate our findings.

scholarly journals POLYMORPHISMS IN THE GENES OF REPARATIONS AMONG EMPLOYEES OF THE ATOMIC INDUSTRY OF KAZAKHSTAN

2020 ◽  
Vol 1 (337) ◽  
pp. 5-10
Author(s):  
D. M. Botbаeyev ◽  
А. M. Belkozhаev ◽  
A. K. Khanseitova ◽  
A. Zh. Borbayeva ◽  
N. А. Аitkhozhinа
Keyword(s):  
Nuclear Industry ◽  
Repair System ◽  
Nucleotide Polymorphisms ◽  
Low Dose Radiation ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Variable Regions ◽  
And Control ◽  
Dose Radiation

Single nucleotide polymorphisms (SNPs) are the most convenient marker and the widespread subject of polymorphism testing. To identify the presence or absence of the effects of chronic low-dose radiation on nuclear industry personnel, the occurrence of single-nucleotide substitutions at the polymorphic sites of the genes of the repair system 3 and 6 of the introns of the APC gene P53.11 gene, in positions -2549 of the VEGF gene, XPD gene rs313181 ( Lys751Gln) and rs25487 of the XRCC gene (Аrg399Gln) were compared. Analysis of allele frequencies and distribution of genotypes in the variable regions of the tested genes was performed by the method of polymerase chain reaction (PCR), followed by determination of restriction fragment length polymorphism (RFLP). When com-paring the frequencies of alleles and the distribution of genotypes between the second group of miners (11–20 years’ experience) and control, differences in the distribution of genotypes in the rs25487 XRCC plot (χ2 = 7.11, p = 0.028) were revealed. These differences satisfy the criterion p <0.05 and, accordingly, are statistically significant. Key words: polymorphism, genes, a nuclear industry.

scholarly journals Association of p53Pro72Arg (rs1042522) and MDM2309 (rs2279744) polymorphisms with risk for cervical intraepthelial lesions and cervical cancer development in Macedonian women

2016 ◽  
Vol 62 (2) ◽  
pp. 49-58
Author(s):  
Sotirija Duvlis ◽  
Marija Hiljadnikova Bajro ◽  
Dijana Plaseska Karanfilska
Keyword(s):  
Cervical Cancer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Significant Difference ◽  
Promoter Gene ◽  
The Republic ◽  
Cervical Cancer Development ◽  
Negative Controls ◽  
And Control ◽  
Intraepithelial Lesions

High risk Human Papillomavirus (HPV) is an important etiological factor in initiation of squamous intraepithelial lesions (SIL), but not enough for malignant progression to cervical cancer (CCa). Single nucleotide polymorphisms (SNPs): rs1042522 within the codon 72 of p53 and rs2279744 within MDM2 promoter gene are plausible factors for development of SIL or CCa conferring increased attenuation of p53 pathway. We investigated the association of these SNPs with the HPV positive SIL and CCa among women from the Republic of Macedonia. Using a multiplex PCR SNaPShot analysis we genotyped rs1042522 and rs2279744 in 131 HPV positive women with SIL or CCa and 110 HPV and cytologicaly negative controls subject. No significant difference in either genotype or allelic frequencies for rs1042522 and rs2279744 between cases and control was found. The stratification of patients on the basis of the lesion grade revealed lower frequency of CC genotype and C allele of rs1042522 in HSIL and CCa compared to LSIL [GG vs CC; p=0.001, OR=0.4; CG vs CC; p=0.04, OR=0.03 and CG+ GG vs CC; p=0.004, OR=0.2]. Additionally TT genotype and T allele of MDM2 309 showed significantly lower frequency in HSIL and CCa group then in LSIL [G vs T p=0.02, OR=0.52; GG vs TT; p=0.04, OR=0.29; ТТ vs ТG+GG; p=0.007, OR=0.34].The Arg variant of rs1042522 and T allele/TT genotype of rs2279744 are associated with progression to LSIL to HSIL or CCa and may be used as prediction markers in CCa management, but the clinical relevant warrants further validation in large and well-designed studies

scholarly journals Variations in MHC-DRB1 exon2 and associations with Brucellosis susceptibility in Chinese Merino sheep

2016 ◽  
Author(s):  
Yue’e Chen ◽  
Wanyun Xu ◽  
Chuangfu Chen ◽  
Hugh T Blair ◽  
Jianfeng Gao
Keyword(s):  
Haplotype Analysis ◽  
Nucleotide Polymorphisms ◽  
Control Groups ◽  
Single Nucleotide ◽  
Merino Sheep ◽  
Pcr Products ◽  
Polymerase Chain ◽  
And Control ◽  
Control Samples ◽  
Online Software

MHC-DRB1 exon2 was amplified by polymerase chain reaction (PCR) from 126 healthy and 67 Brucellosis-infected Chinese Merino sheep. PCR products were analyzed using the SSCP technique, and then cloned to allow sequencing of the different alleles. For each SNP, allelic and genotypic frequencies were compared between case and control samples, in addition the association with Brucellosis susceptibility was determined. Haplotypes and their frequencies were established and analyzed by SHEsis online software. There were forty-one single nucleotide polymorphisms (SNPs) in the 270 bp DNA sequence. The distribution of C>T alleles at locus 109 was significantly different between case and control samples. The linkage disequilibrium (LD) analysis showed that there were nine LD blocks in MHC-DRB1 exon2 and strong LD between SNPs existed in every Block. Haplotype analysis identified nine haplotypes with strong LD, but only Hap8 and Hap9 in case-control groups were significantly different (P<0.05); neither haplotype contained the C>T allele at locus 109. In conclusion, genetic variants of MHC-DRB1 gene exon2 demonstrated associations with Brucellosis susceptibility, indicating that further research is warranted.

scholarly journals Description of breed ancestry and genetic health traits in arctic sled dog breeds

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Joseph A. Thorsrud ◽  
Heather J. Huson
Keyword(s):  
Principal Component ◽  
Factor Vii ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Characteristics ◽  
Dna Test ◽  
Sled Dogs ◽  
Sled Dog ◽  
Arctic Exploration ◽  
And Performance

Abstract Background This study describes the presence and frequency of health traits among three populations of dogs traditionally used for sledding and explores their ancestry and breed composition as provided by the commercially available Embark dog DNA test. The three populations include the purebred Siberian Husky and the admixed populations of Alaskan sled dogs and Polar Huskies. While the Siberian Husky represents a well-established breed with extensive historical and health data, the Alaskan sled dog is less studied but has been the subject of nutritional, physiological, and genetic studies related to ancestry and performance. In contrast, the Polar Husky is a relatively obscure and rare group of dogs used for arctic exploration with very little-known information. The three populations were compared using Embark results, providing new insight into the health traits circulating within the populations and the potential ancestral linkage of the health traits between the sledding populations. Embark results are based upon 228,588 single-nucleotide polymorphisms (SNPs) spanning the canine genome, characterized using a custom-designed Illumina beadchip array. Results Specifically, breed composition was summarized for the two admixed populations with most of the dogs being predominantly categorized as Alaskan husky- type dog or “Supermutt”. Mitochondrial and Y chromosome haplogroups and haplotypes were found with Alaskan sled dogs carrying most of the haplogroups and types found in Siberian and Polar Huskies. Genomic principal component analysis reflected population structure corresponding to breed and substructure within the Alaskan sled dogs related to sprint or distance competition. Genetic markers associated with Alanine Aminotransferase activity, Alaskan Husky Encephalopathy, dilated cardiomyopathy, Collie eye anomaly, degenerative myelopathy, ichthyosis, and factor VII deficiency were identified in the populations of sledding breeds. Conclusion These results provide a preliminary description of genetic characteristics found in sledding breeds, improving the understanding and care of working sled dogs.

Association between Polymorphic Variation at the IL5RA Locus and the Severity of FIP1L1-PDGFRA Positive Chronic Eosinophilic Leukaemia

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1544-1544
Author(s):  
Sonja Burgstaller ◽  
Sebastian Kreil ◽  
Katherine Waghorn ◽  
Georgia Metzgeroth ◽  
Claude Preudhomme ◽  
...  
Keyword(s):  
Multiple Testing ◽  
Fusion Gene ◽  
Blood Eosinophil ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Peripheral Blood Eosinophil ◽  
Blood Eosinophil Count ◽  
Level Of Significance ◽  
And Control ◽  
Lower Expression

Abstract FIP1L1-PDGFRA is a cytogenetically cryptic fusion gene seen in a minority of patients with chronic eosinophilic leukaemia (CEL). Observations in mice have suggested that FIP1L1-PDGFRA alone is insufficient to induce all features of the human disease, and that a secondary event associated with IL-5 overexpression may be required for the full phenotype. In this study we have investigated the hypothesis that constitutional genetic variation in IL-5 signalling may be associated with the development or severity of FIP1L1-PDGFRA positive CEL in humans. We genotyped six single nucleotide polymorphisms (SNP) within or close to the IL5RA or IL5 genes in 82 European patients with FIP1L1-PDGFRA positive CEL plus, as controls, healthy individuals (n=100), patients with FIP1L1-PDGFRA negative eosinophilia (n=100) or patients with chronic myeloid leukaemia (n=100). We found no association between SNP allele frequency between FIP1L1-PDGFRA positive and control cases. However for FIP1L1-PDGFRA cases, we found an association between the genotype at rs4054760, a SNP in the 5′UTR of IL5RA, and peripheral blood eosinophil count (P=0.026) as well as the presence or absence of tissue infiltration (P=0.032). Although these associations fell below the level of significance once corrected for multiple testing, no such association was seen in FIP1L1-PDGFRA negative cases and no difference in allele frequencies for rs4054760 was seen in control populations across Europe. Furthermore, in an analysis of 128 patients with CML, there was a trend towards lower expression of IL5RA expression in cases with a c/t or t/t genotype compared to those who were c/c (P=0.08). These data suggest that the constitutional IL5RA genotype may be associated with the severity of FIP1L1-PDGFRA disease.

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