scholarly journals Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Li Ping Zhou ◽  
Wei Wei Liu ◽  
Tian E. Zhang ◽  
Wei Hong Li ◽  
Ling Ling Tan ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Substitution Effect ◽  
Deficiency Syndrome ◽  
Trna Synthetase ◽  
Genomic Variation ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Kidney Yang Deficiency ◽  
Flanking Region ◽  
Nonsynonymous Variation

Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS).Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced.Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen.Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.

Identification of Linkage Disequilibrium SNPs from a Kidney-Yang Deficiency Syndrome Pedigree

2009 ◽  
Vol 37 (03) ◽  
pp. 427-438 ◽  
Author(s):  
Wei Jun Ding ◽  
Ying Zi Zeng ◽  
Wei Hong Li ◽  
Tian E. Zhang ◽  
Wei Wei Liu ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Homo Sapiens ◽  
Biological Activities ◽  
Protein Biosynthesis ◽  
Deficiency Syndrome ◽  
Trna Synthetase ◽  
National Standard ◽  
Genetic Traits ◽  
Definitive Evidence ◽  
Kidney Yang Deficiency

In order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required.

scholarly journals Anopheles gambiae Genome Conservation as a Resource for Rational Gene Drive Target Site Selection

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 97
Author(s):  
Nace Kranjc ◽  
Andrea Crisanti ◽  
Tony Nolan ◽  
Federica Bernardini
Keyword(s):  
Anopheles Gambiae ◽  
Data Storage ◽  
Genomic Variation ◽  
Malaria Vectors ◽  
Anopheles Coluzzii ◽  
Structural Constraints ◽  
Gene Drive ◽  
Genetic Traits ◽  
A Genome ◽  
Insight Into

The increase in molecular tools for the genetic engineering of insect pests and disease vectors, such as Anopheles mosquitoes that transmit malaria, has led to an unprecedented investigation of the genomic landscape of these organisms. The understanding of genome variability in wild mosquito populations is of primary importance for vector control strategies. This is particularly the case for gene drive systems, which look to introduce genetic traits into a population by targeting specific genomic regions. Gene drive targets with functional or structural constraints are highly desirable as they are less likely to tolerate mutations that prevent targeting by the gene drive and consequent failure of the technology. In this study we describe a bioinformatic pipeline that allows the analysis of whole genome data for the identification of highly conserved regions that can point at potential functional or structural constraints. The analysis was conducted across the genomes of 22 insect species separated by more than hundred million years of evolution and includes the observed genomic variation within field caught samples of Anopheles gambiae and Anopheles coluzzii, the two most dominant malaria vectors. This study offers insight into the level of conservation at a genome-wide scale as well as at per base-pair resolution. The results of this analysis are gathered in a data storage system that allows for flexible extraction and bioinformatic manipulation. Furthermore, it represents a valuable resource that could provide insight into population structure and dynamics of the species in the complex and benefit the development and implementation of genetic strategies to tackle malaria.

scholarly journals Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

2021 ◽  
Vol 9 (7) ◽  
pp. 1416
Author(s):  
Karen Leth Nielsen ◽  
Marc Stegger ◽  
Kristoffer Kiil ◽  
Berit Lilje ◽  
Karen Ejrnæs ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Genomic Variation ◽  
Whole Genome Sequencing Data ◽  
Phenotypic Traits ◽  
Recurrent Infections ◽  
Single Nucleotide ◽  
Recurrent Urinary Tract Infections ◽  
Tract Infections

Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.

scholarly journals Effects of Haima Duobian Pill in a Rat Model of Kidney Yang Deficiency Syndrome

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Yijia Zeng ◽  
Tingna Li ◽  
Xiaorui Zhang ◽  
Yuanyuan Ren ◽  
Qinwan Huang ◽  
...  
Keyword(s):  
Rat Model ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Cyclic Guanosine Monophosphate ◽  
Deficiency Syndrome ◽  
Guanosine Monophosphate ◽  
Network Pharmacology ◽  
Enzyme Linked Immunosorbent Assay ◽  
Therapeutic Effects ◽  
Kidney Yang Deficiency

Objective. Modern research shows that Haima Duobian pill (HDP) can relieve the kidney yang deficiency syndrome (KYDS), but the mechanism is still unclear. The aim of this work was to study the effects of HDP in a rat model of KYDS. Materials and Methods. The network pharmacology methods were used to predict the therapeutic effects of Haima Duobian pill. Adenine was used to establish the rat model of kidney yang deficiency syndrome. The general physical signs of rats were observed after different doses of Haima Duobian pill (HDP) were given. Serum cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), luteinizing hormone (LH), follicle-stimulating hormone (FSH), testosterone (T), estradiol (E2), and gonadotropin-releasing hormone (GnRH) levels were determined using enzyme-linked immunosorbent assay (ELISA) kits. Then, the histopathologic changes and sperm activity were detected. Results. HDP could improve the general signs of kidney yang deficiency syndrome rats. After the rats were treated with HDP, the expression of cGMP and E2 was significantly inhibited and the expression of cAMP and T was significantly increased. The pathological damage of testis, epididymis, and seminal vesicle was alleviated, and the sperm activity was improved. Conclusion. For adenine-induced kidney yang deficiency syndrome in rats, HDP had a significant therapeutic effect.

Two Novel Polymorphisms in 5' Flanking Region of the Mesothelin Gene are Associated with Soluble Mesothelin-Related Peptide (SMRP) Levels

2011 ◽  
Vol 26 (2) ◽  
pp. 117-123 ◽  
Author(s):  
Alfonso Cristaudo ◽  
Rudy Foddis ◽  
Alessandra Bonotti ◽  
Silvia Simonini ◽  
Agnese Vivaldi ◽  
...  
Keyword(s):  
Healthy Subjects ◽  
Fold Increase ◽  
High Rate ◽  
Pleural Mesothelioma ◽  
Clinical Use ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Elisa Kit ◽  
Surveillance Programs ◽  
Flanking Region

Background and aims Increased concentrations of soluble mesothelin-related peptides (SMRP) have been found in sera of patients with malignant pleural mesothelioma (MPM) even if a relatively high rate of false positives has hampered their clinical use as a tumor marker. Individual SMRP levels could be affected by polymorphic elements. The aim of this study was to investigate the association between single nucleotide polymorphisms within the promoter-5'UTR regions and SMRP levels in healthy asbestos-exposed individuals and patients suffering from MPM. Methods The promoter-5'UTR regions of the mesothelin gene were genotyped in 59 healthy asbestos-exposed subjects and 27 MPM patients. SMRP levels were measured using a commercially available ELISA kit. Results Two novel polymorphisms, an A>C variant (called New1) and a C>T variant (called New2), were identified. In healthy subjects, high SMRP levels were associated with the C-variant of New1, with an average 1.62-fold increase compared with AA homozygotes (p<0.0001). Most of the C-allele carriers had SMRP levels above the threshold of 1.00 nM. We set two different SMRP cutoffs on the basis of the combined New1+New2 genotypes. Conclusions New1-New2 genotypes could be employed as markers for setting individualized and appropriate thresholds of “normality” when SMRP is used in surveillance programs of asbestos-exposed people.

RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG

2020 ◽  
Vol 61 (7) ◽  
pp. 1262-1272
Author(s):  
Hiromi Kajiya-Kanegae ◽  
Hideki Takanashi ◽  
Masaru Fujimoto ◽  
Motoyuki Ishimori ◽  
Norikazu Ohnishi ◽  
...  
Keyword(s):  
Linkage Map ◽  
High Density ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Map Construction ◽  
Days To Heading ◽  
High Density Linkage Map ◽  
Sorghum Bicolor L

Abstract Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

scholarly journals BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

2013 ◽  
Vol 10 (2) ◽  
pp. 103-116 ◽  
Author(s):  
Goksel Misirli ◽  
Anil Wipat ◽  
Joseph Mullen ◽  
Katherine James ◽  
Matthew Pocock ◽  
...  
Keyword(s):  
Laboratory Strain ◽  
Nucleotide Polymorphisms ◽  
Genetic Circuits ◽  
Positive Bacterium ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Data Resource ◽  
Data Integration System ◽  
Bacterium Bacillus Subtilis ◽  
Bacterium Bacillus

Summary BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.

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