scholarly journals Introduction pages

2021 ◽  
Vol 49 (4) ◽  
pp. 12605
Author(s):  
Radu E. SESTRAS
Keyword(s):  
Life Science ◽  
Genome Wide Association Study ◽  
Chemical Compounds ◽  
Carthamus Tinctorius ◽  
Molecular Techniques ◽  
Cotton Production ◽  
Yield And Quality ◽  
Genome Wide ◽  
Trait Locus

The papers published in Notulae Botanicae Horti Agrobotanici Cluj-Napoca, Issue 4, Volume 49, 2021 represent new exciting researches in different topics of life science, respectively in plant science, horticulture, agronomy and crop science. Among the interesting articles we invite you to find news about: Cotton versus climate change: the case of Greek cotton production; Agronomic and genetic approaches for enhancing tolerance to heat stress in rice; Insights on solanaceous resistance against tomato leafminer (Tuta absoluta), with emphasis on chemical compounds useful in integrated pest management; Role of conventional and molecular techniques in soybean yield and quality improvement - A critical review; Assessment of cold stress tolerance in maize through quantitative trait locus, genome-wide association study and transcriptome analysis; Beneficial microorganisms enhance the growth of basil (Ocimum basilicum L.) under greenhouse conditions; Genome-wide identification and expression profiling of duplicated flavonoid 3'-hydroxylase gene family in Carthamus tinctorius L.; Comparative analysis of genetic diversity in Norway spruce (Picea abies) clonal seed orchards and seed stands, etc.

scholarly journals Inflammation and JNK's Role in Niacin-GPR109A Diminished Flushed Effect in Microglial and Neuronal Cells With Relevance to Schizophrenia

2021 ◽  
Vol 12 ◽  
Author(s):  
Sabrina H. Ansarey
Keyword(s):  
Inflammatory Mediators ◽  
Neuronal Death ◽  
Microglial Activation ◽  
Negative Symptoms ◽  
Genome Wide Association Study ◽  
Genetic Mutation ◽  
Genome Wide ◽  
Ultra High Risk ◽  
Altered Proteins

Schizophrenia is a neuropsychiatric illness with no single definitive aetiology, making its treatment difficult. Antipsychotics are not fully effective because they treat psychosis rather than the cognitive or negative symptoms. Antipsychotics fail to alleviate symptoms when patients enter the chronic stage of illness. Topical application of niacin showed diminished skin flush in the majority of patients with schizophrenia compared to the general population who showed flushing. The niacin skin flush test is useful for identifying patients with schizophrenia at their ultra-high-risk stage, and understanding this pathology may introduce an effective treatment. This review aims to understand the pathology behind the diminished skin flush response, while linking it back to neurons and microglia. First, it suggests that there are altered proteins in the GPR109A-COX-prostaglandin pathway, inflammatory imbalance, and kinase signalling pathway, c-Jun N-terminal kinase (JNK), which are associated with diminished flush. Second, genes from the GPR109A-COX-prostaglandin pathway were matched against the 128-loci genome wide association study (GWAS) for schizophrenia using GeneCards, suggesting that G-coupled receptor-109A (GPR109A) may have a genetic mutation, resulting in diminished flush. This review also suggests that there may be increased pro-inflammatory mediators in the GPR109A-COX-prostaglandin pathway, which contributes to the diminished flush pathology. Increased levels of pro-inflammatory markers may induce microglial-activated neuronal death. Lastly, this review explores the role of JNK on pro-inflammatory mediators, proteins in the GPR109A-COX-prostaglandin pathway, microglial activation, and neuronal death. Inhibiting JNK may reverse the changes observed in the diminished flush response, which might make it a good therapeutic target.

scholarly journals The FAM171A2 gene is a key regulator of progranulin expression and modifies the risk of multiple neurodegenerative diseases

2020 ◽  
Vol 6 (43) ◽  
pp. eabb3063
Author(s):  
Wei Xu ◽  
Si-Da Han ◽  
Can Zhang ◽  
Jie-Qiong Li ◽  
Yan-Jiang Wang ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Genome Wide Association Study ◽  
In Vitro Study ◽  
Genome Wide ◽  
A Genome ◽  
Increased Risk ◽  
Pathophysiological Role ◽  
Independent Cohort

Progranulin (PGRN) is a secreted pleiotropic glycoprotein associated with the development of common neurodegenerative diseases. Understanding the pathophysiological role of PGRN may help uncover biological underpinnings. We performed a genome-wide association study to determine the genetic regulators of cerebrospinal fluid (CSF) PGRN levels. Common variants in region of FAM171A2 were associated with lower CSF PGRN levels (rs708384, P = 3.95 × 10−12). This was replicated in another independent cohort. The rs708384 was associated with increased risk of Alzheimer’s disease, Parkinson’s disease, and frontotemporal dementia and could modify the expression of the FAM171A2 gene. FAM171A2 was considerably expressed in the vascular endothelium and microglia, which are rich in PGRN. The in vitro study further confirmed that the rs708384 mutation up-regulated the expression of FAM171A2, which caused a decrease in the PGRN level. Collectively, genetic, molecular, and bioinformatic findings suggested that FAM171A2 is a key player in regulating PGRN production.

scholarly journals A compendium of uniformly processed human gene expression and splicing quantitative trait loci

2021 ◽  
Vol 53 (9) ◽  
pp. 1290-1299
Author(s):  
Nurlan Kerimov ◽  
James D. Hayhurst ◽  
Kateryna Peikova ◽  
Jonathan R. Manning ◽  
Peter Walter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Cell Types ◽  
Summary Statistics ◽  
Genome Wide ◽  
Cell Type Specific ◽  
Trait Locus ◽  
Complex Human Traits

AbstractMany gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues.

scholarly journals Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture

2016 ◽  
Vol 68 (4) ◽  
pp. 932-943 ◽  
Author(s):  
Marta E. Alarcón-Riquelme ◽  
Julie T. Ziegler ◽  
Julio Molineros ◽  
Timothy D. Howard ◽  
Andrés Moreno-Estrada ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Association Study ◽  
Lupus Erythematosus ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Systemic Lupus ◽  
Genome Wide

scholarly journals Trans-Ethnic Mapping of BANK1 Identifies Two Independent SLE-Risk Linkage Groups Enriched for Co-Transcriptional Splicing Marks

2018 ◽  
Vol 19 (8) ◽  
pp. 2331 ◽  
Author(s):  
Manuel Martínez-Bueno ◽  
Nina Oparina ◽  
Mikhail Dozmorov ◽  
Miranda Marion ◽  
Mary Comeau ◽  
...  
Keyword(s):  
B Cell ◽  
Genome Wide Association Study ◽  
Susceptibility Gene ◽  
Eqtl Analysis ◽  
Minimal Set ◽  
Genome Wide ◽  
Trait Locus ◽  
Independent Effects ◽  
Ethnic Mapping ◽  
Splice Junctions

BANK1 is a susceptibility gene for several systemic autoimmune diseases in several populations. Using the genome-wide association study (GWAS) data from Europeans (EUR) and African Americans (AA), we performed an extensive fine mapping of ankyrin repeats 1 (BANK1). To increase the SNP density, we used imputation followed by univariate and conditional analysis, combined with a haplotypic and expression quantitative trait locus (eQTL) analysis. The data from Europeans showed that the associated region was restricted to a minimal and dependent set of SNPs covering introns two and three, and exon two. In AA, the signal found in the Europeans was split into two independent effects. All of the major risk associated SNPs were eQTLs, and the risks were associated with an increased BANK1 gene expression. Functional annotation analysis revealed the enrichment of repressive B cell epigenomic marks (EZH2 and H3K27me3) and a strong enrichment of splice junctions. Furthermore, one eQTL located in intron two, rs13106926, was found within the binding site for RUNX3, a transcriptional activator. These results connect the local genome topography, chromatin structure, and the regulatory landscape of BANK1 with co-transcriptional splicing of exon two. Our data defines a minimal set of risk associated eQTLs predicted to be involved in the expression of BANK1 modulated through epigenetic regulation and splicing. These findings allow us to suggest that the increased expression of BANK1 will have an impact on B-cell mediated disease pathways.

scholarly journals Gene duplication confers enhanced expression of 27-kDa γ-zein for endosperm modification in quality protein maize

2016 ◽  
Vol 113 (18) ◽  
pp. 4964-4969 ◽  
Author(s):  
Hongjun Liu ◽  
Junpeng Shi ◽  
Chuanlong Sun ◽  
Hao Gong ◽  
Xingming Fan ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Genetic Selection ◽  
Quality Protein Maize ◽  
Genome Wide ◽  
Mapping Analysis ◽  
Enhanced Expression ◽  
Selection For ◽  
Trait Locus ◽  
Maize Domestication

The maize opaque2 (o2) mutant has a high nutritional value but it develops a chalky endosperm that limits its practical use. Genetic selection for o2 modifiers can convert the normally chalky endosperm of the mutant into a hard, vitreous phenotype, yielding what is known as quality protein maize (QPM). Previous studies have shown that enhanced expression of 27-kDa γ-zein in QPM is essential for endosperm modification. Taking advantage of genome-wide association study analysis of a natural population, linkage mapping analysis of a recombinant inbred line population, and map-based cloning, we identified a quantitative trait locus (qγ27) affecting expression of 27-kDa γ-zein. qγ27 was mapped to the same region as the major o2 modifier (o2 modifier1) on chromosome 7 near the 27-kDa γ-zein locus. qγ27 resulted from a 15.26-kb duplication at the 27-kDa γ-zein locus, which increases the level of gene expression. This duplication occurred before maize domestication; however, the gene structure of qγ27 appears to be unstable and the DNA rearrangement frequently occurs at this locus. Because enhanced expression of 27-kDa γ-zein is critical for endosperm modification in QPM, qγ27 is expected to be under artificial selection. This discovery provides a useful molecular marker that can be used to accelerate QPM breeding.

scholarly journals Identification of candidate genes that underlie the QTL on chromosome 1 that mediates genetic differences in stress-ethanol interactions

2015 ◽  
Vol 47 (8) ◽  
pp. 308-317 ◽  
Author(s):  
Melloni N. Cook ◽  
Jessica A. Baker ◽  
Scott A. Heldt ◽  
Robert W. Williams ◽  
Kristin M. Hamre ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Zinc Finger Protein ◽  
Genetic Differences ◽  
Chromosome 1 ◽  
Protein Tyrosine ◽  
Finger Protein ◽  
Genome Wide ◽  
Trait Locus ◽  
Tyrosine Phosphate

Alcoholism, stress, and anxiety are strongly interacting heritable, polygenetic traits. In a previous study, we identified a quantitative trait locus (QTL) on murine chromosome (Chr) 1 between 23.0 and 31.5 Mb that modulates genetic differences in the effects of ethanol on anxiety-related phenotypes. The goal of the present study was to extend the analysis of this locus with a focus on identifying candidate genes using newly available data and tools. Anxiety-like behavior was evaluated with an elevated zero maze following saline or ethanol injections (1.8 g/kg) in C57BL/6J, DBA2J, and 72 BXD strains. We detected significant effects of strain and treatment and their interaction on anxiety-related behaviors, although surprisingly, sex was not a significant factor. The Chr1 QTL is specific to the ethanol-treated cohort. Candidate genes in this locus were evaluated using now standard bioinformatic criteria. Collagen 19a1 ( Col19a1) and family sequence 135a ( Fam135a) met most criteria but have lower expression levels and lacked biological verification and, therefore, were considered less likely candidates. In contrast, two other genes, the prenylated protein tyrosine phosphate family member Ptp4a1 (protein tyrosine phosphate 4a1) and the zinc finger protein Phf3 (plant homeoDomain finger protein 3) met each of our bioinformatic criteria and are thus strong candidates. These findings are also of translational relevance because both Ptp4a1 and Phf3 have been nominated as candidates genes for alcohol dependence in a human genome-wide association study. Our findings support the hypothesis that variants in one or both of these genes modulate heritable differences in the effects of ethanol on anxiety-related behaviors.

scholarly journals ESR1, WT1, WNT4, ATM and TERT loci are major contributors to uterine leiomyoma predisposition

2018 ◽  
Author(s):  
Niko Välimäki ◽  
Heli Kuisma ◽  
Annukka Pasanen ◽  
Oskari Heikinheimo ◽  
Jari Sjöberg ◽  
...  
Keyword(s):  
Estrogen Receptor Alpha ◽  
Genome Wide Association Study ◽  
Benign Tumors ◽  
Risk Alleles ◽  
Estrogen Exposure ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Level ◽  
Genomic Risk

ABSTRACTUterine leiomyomas (ULs) are benign tumors that are a major burden to women’s health. A genome-wide association study on 5,417 UL cases and 331,791 controls was performed, followed by replication of the genomic risk in two cohorts. Effects of the identified risk alleles were evaluated in view of molecular and clinical features.Five loci displayed a genome-wide significant association; the previously reported TNRC6B, and four novel loci ESR1 (ERα), WT1, WNT4, and ATM. The sixth hit TERT is also a conceivable target. The combined polygenic risk contributed by these loci was associated with MED12 mutation-positive tumors. The findings link genes for uterine development and genetic stability to leiomyomagenesis. While the fundamental role of sex hormones in UL aetiology has been clear, this work reveals a connection to estrogen receptor alpha on genetic level and suggests that determinants of UL growth associated with estrogen exposure have an inherited component.

scholarly journals TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling

2021 ◽  
Author(s):  
Duan Liu ◽  
Thanh Thanh Le Nguyen ◽  
Huanyao Gao ◽  
Huaizhi Huang ◽  
Daniel C. Kim ◽  
...  
Keyword(s):  
Body Mass Index ◽  
Bipolar Disorder ◽  
Body Mass ◽  
Genome Wide Association Study ◽  
Induced Pluripotent Stem Cell ◽  
Sequencing Data ◽  
Peripheral Tissues ◽  
Genome Wide ◽  
A Genome ◽  
Trait Locus

AbstractBipolar disorder (BD) and obesity are highly comorbid. We previously performed a genome-wide association study (GWAS) for BD risk accounting for the effect of body mass index (BMI), which identified a genome-wide significant single-nucleotide polymorphism (SNP) in the gene encoding the transcription factor 7 like 2 (TCF7L2). However, the molecular function of TCF7L2 in the central nervous system (CNS) and its possible role in the BD and BMI interaction remained unclear. In the present study, we demonstrated by studying human induced pluripotent stem cell (hiPSC)-derived astrocytes, cells that highly express TCF7L2 in the CNS, that the BD-BMI GWAS risk SNP is associated with glucocorticoid-dependent repression of the expression of a previously uncharacterized TCF7L2 transcript variant. That transcript is a long non-coding RNA (lncRNA-TCF7L2) that is highly expressed in the CNS but not in peripheral tissues such as the liver and pancreas that are involved in metabolism. In astrocytes, knockdown of the lncRNA-TCF7L2 resulted in decreased expression of the parent gene, TCF7L2, as well as alterations in the expression of a series of genes involved in insulin signaling and diabetes. We also studied the function of TCF7L2 in hiPSC-derived astrocytes by integrating RNA sequencing data after TCF7L2 knockdown with TCF7L2 chromatin-immunoprecipitation sequencing (ChIP-seq) data. Those studies showed that TCF7L2 directly regulated a series of BD risk genes. In summary, these results support the existence of a CNS-based mechanism underlying BD-BMI genetic risk, a mechanism based on a glucocorticoid-dependent expression quantitative trait locus that regulates the expression of a novel TCF7L2 non-coding transcript.

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