Population Genetics Coupled Chemical Profiling for Conservation Implications of Decalepis salicifolia (Bedd. ex Hook.f.) Venter, an Endemic and Critically Endangered Species of Western Ghats, India.
Abstract Information on the genetic diversity and population structure is essential for developing conservational management programs, especially for threatened species. Decalepis salicifolia (Bedd. ex Hook.f.) Venter is a steno-endemic and critically endangered species of the south Western Ghats of India. The present study used ISSR markers as well as essential oil profiling to reveal the extent and distribution of genetic as well as the chemical diversity of all the twelve known populations of D. salicifolia. A total of 84 amplicons generated using 17 ISSR primers represented an overall 72.34% polymorphism. The ...
Source: Biochemical Genetics - March 27, 2020 Category: Genetics & Stem Cells Authors: Gokul S, Rodrigues V, Kumar A, Verma RS, Shukla AK, Sundaresan V Tags: Biochem Genet Source Type: research
Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics.
This study will provide information for further studies on taxonomy, phylogeny and patterns of adaptive evolution in the mitogenome of Trichiurus species. PMID: 32170439 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - March 13, 2020 Category: Genetics & Stem Cells Authors: Mukundan LP, Sukumaran S, Sebastian W, Gopalakrishnan A Tags: Biochem Genet Source Type: research
Genomic and Transcriptional Analysis of Banana Ovate Family Proteins Reveals Their Relationship with Fruit Development and Ripening.
Abstract Ovate Family Proteins (OFPs) belong to a plant-specific transcription factor family. They have been found to have significant roles in growth and development in Arabidopsis and tomato; however, little is known regarding their role in banana. Thus, a genome-wide study of OFP genes in banana was conducted for the first time in the present study. The results demonstrated that 49 OFP family members are unequally distributed across 11 chromosomes. Phylogenetic analysis grouped these genes into two subfamilies and eight subgroups, which was confirmed by the conserved motif and gene structure analysis. Furthermo...
Source: Biochemical Genetics - March 6, 2020 Category: Genetics & Stem Cells Authors: Zhang J, Miao H, Xie B, Wang J, Jia C, Zhang J, Xu B, Jin Z, Liu J Tags: Biochem Genet Source Type: research
Evaluating the Genetic Correlations Between Left-Handedness and Mental Disorder Using Linkage Disequilibrium Score Regression and Transcriptome-Wide Association Study.
In this study, linkage disequilibrium score regression (LDSC) analysis was conducted to evaluate the genetic correlations between left-handedness and multiple mental disorders. The significant genetic correlation was only observed between left-handedness and schizophrenia (SCZ). For the observed genetic correlation, transcriptome-wide association study (TWAS) was performed to identify the genes associated with left-handedness and SCZ, including brain RNA-seq (CBR) and brain RNA-seq splicing (CBRS). We detected several common genes associated with both left-handedness and SCZ, such as YWHAH, MAPT and ANO10. The common genes...
Source: Biochemical Genetics - February 25, 2020 Category: Genetics & Stem Cells Authors: Cheng B, Liang C, Li P, Liu L, Cheng S, Ma M, Zhang L, Qi X, Wen Y, Zhang F Tags: Biochem Genet Source Type: research
Molecular Characteristics, Phylogeny and Expression Profile of the PTEN Gene in Goats.
In this study, eight different tissues from E90, E135 and D90 female goats were collected to quantify the expression pattern of the PTEN gene using quantitative real-time PCR (qPCR), western blotting and FISH. In addition, the dynamic expression of PTEN was also determined during the differentiation of goat precursor adipose cells. A 1212-bp fragment (accession number MG923848), encoding a 403-amino acid protein with a putative molecular weight of 47.14 kDa, was identified in Jianzhou Daer goats by reverse-transcription polymerase chain reaction (RT-PCR). The phylogenetic tree showed that caprine PTEN had a relatively...
Source: Biochemical Genetics - February 4, 2020 Category: Genetics & Stem Cells Authors: Zhong T, Zhou J, Zhan S, Wang L, Niu L, Guo J, Li L, Zhang H Tags: Biochem Genet Source Type: research
WBSCR22 Competes with Long Non-coding RNA Linc00346 for miR-509-5p Binding Site to Regulate Cancer Stem Cell Phenotypes of Colorectal Cancer.
Abstract Various Long non-coding RNAs (lncRNAs) and MicroRNAs (miRNAs) have been demonstrated to be involved in colorectal cancer stem cells (CSCs). WBSCR22 is a key gene we previously found that functions in colorectal cancer (CRC). This paper aims to investigate the effects of WBSCR22 and its corresponding miRNA and lncRNA in CRC. The expression of WBSCR22 was detected by Western blot and qRT-PCR analysis. Tumor sphere formation assays, CCK-8 analysis, and Transwell assays were applied to examine the colorectal cancer stem cell properties. Luciferase assay and biotin RNA pulldown assay were used to detect the in...
Source: Biochemical Genetics - February 1, 2020 Category: Genetics & Stem Cells Authors: Zhao H, Su W, Sun Y, Wu Z Tags: Biochem Genet Source Type: research
Association Between the Polymorphism of Aldehyde Dehydrogenase 2 Gene and Cerebral Infarction in a Hakka Population in Southern China.
In conclusion, these findings support an association of ALDH2 gene polymorphisms with ischemic stroke in a Chinese Hakka population. In particular, homozygote ALDH2*2/*2 may be a risk factor for cerebral infarction in males, but contribute to reduced risk for cerebral infarction in females. PMID: 32006143 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - January 31, 2020 Category: Genetics & Stem Cells Authors: Hou JY, Zhong ZX, Deng QT, Liu SD, Lin LF Tags: Biochem Genet Source Type: research
Small Molecules with Big Impacts on Cardiovascular Diseases.
Abstract Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Although in recent years there has been a significant progress in the diagnosis, treatment, and prognosis of CVD, but due to their complex pathobiology, developing novel biomarkers and therapeutic interventions are still in need. MicroRNAs (miRNAs) are a fraction of non-coding RNAs that act as micro-regulators of gene expression. Mounting evidences over the last decade confirmed that microRNAs were deregulated in several CVDs and manipulating their expression could affect homeostasis, differentiation, and function o...
Source: Biochemical Genetics - January 29, 2020 Category: Genetics & Stem Cells Authors: Mirzadeh Azad F, Arabian M, Maleki M, Malakootian M Tags: Biochem Genet Source Type: research
Functional Analysis of Sheep POU2F3 Isoforms.
The objective of this study was to determine the tissue expression pattern of the four POU2F3 transcript variants in sheep and to investigate the functional differences in cell proliferation among the three POU2F3 isoforms. Quantitative RT-PCR analysis showed that the four POU2F3 transcripts were ubiquitously expressed in all tested adult sheep tissues, and POU2F3-1 exhibited higher expression level than the other three POU2F3 transcript variants in skin (P
Source: Biochemical Genetics - December 31, 2019 Category: Genetics & Stem Cells Authors: Ma GW, Chu YK, Yang H, Yan XH, Rong EG, Li H, Wang N Tags: Biochem Genet Source Type: research
Genetic Diversity and Structure Analysis Assessed by SSR Markers in a Large Collection of Vitis Cultivars from the Island of Crete, Greece.
In this study, Vitis cultivars collected from the island of Crete were characterized using microsatellite markers. A broad germplasm collection representing 44 inferred Vitis cultivars, a total of 163 accessions, from the area of Crete including 37 wine and 7 table cultivars were fingerprinted employing thirteen (13) standardized simple sequence repeat (SSR, microsatellite) loci. SSR allelic analysis and a similarity dendrogram construction (cluster analysis) was followed by a hierarchical STRUCTURE analysis. The mean observed (Ho) and expected heterozygosity (He) were 0.7372 and 0.7686, respectively. The cumulative probab...
Source: Biochemical Genetics - November 28, 2019 Category: Genetics & Stem Cells Authors: Bibi AC, Gonias ED, Doulis AG Tags: Biochem Genet Source Type: research
Epigenetic Modifications in Head and Neck Cancer.
Abstract Head and neck squamous cell carcinoma (HNSCC) is the sixth most common human malignancy in the world, with high mortality and poor prognosis for patients. Among the risk factors are tobacco and alcohol intake, human papilloma virus, and also genetic and epigenetic modifications. Many studies show that epigenetic events play an important role in HNSCC development and progression, including DNA methylation, chromatin remodeling, histone posttranslational covalent modifications, and effects of non-coding RNA. Epigenetic modifications may influence silencing of tumor suppressor genes by promoter hypermethylat...
Source: Biochemical Genetics - November 11, 2019 Category: Genetics & Stem Cells Authors: Gaździcka J, Gołąbek K, Strzelczyk JK, Ostrowska Z Tags: Biochem Genet Source Type: research
Haplogroup Structure and Genetic Variation Analyses of 60 Mitochondrial DNA Markers in Southern Shaanxi Han Population.
In conclusion, the panel comprising 60 mtDNA markers could be utilized for forensic applications in Southern Shaanxi Han population. PMID: 31696339 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - November 6, 2019 Category: Genetics & Stem Cells Authors: Wei YY, Ren ZP, Jin XY, Cui W, Chen C, Guo YX, Meng HT, Zhu BF Tags: Biochem Genet Source Type: research
Retraction Note to: Inferring Phylogenetic Relationships of Indian Citron (Citrus medica L.) Based on rbcL and matK Sequences of Chloroplast DNA.
Abstract The Editor-in-Chief and the publisher have retracted this article  because of significant overlap with previously published articles [2-5]. Ajit Uchoi, Surendra Kumar Malik, Ravish Chaudhary, Susheel Kumar, M.R. Rohini, Digvender Pal, and Sezai Ercisli disagree with the retraction. The publisher was not able to get in contact with Rekha Chaudhury, she did not respond to any correspondence about this retraction. PMID: 31650275 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - October 24, 2019 Category: Genetics & Stem Cells Authors: Uchoi A, Malik SK, Choudhary R, Kumar S, Rohini MR, Pal D, Ercisli S, Chaudhury R Tags: Biochem Genet Source Type: research
Association of the Variant rs7561317 Downstream of the TMEM18 Gene with Overweight/Obesity and Related Anthropometric Traits in a Sample of Pakistani Population.
Abstract Obesity is a multifactorial disorder and requires favorable environment for its expression. However, some individuals are more prone to weight gain than others in an obesogenic environment. Thus, at individual level, who becomes overweight or obese is mostly determined by genetic factors. The current study was undertaken to explore for the first time the association of the TMEM18 rs7561317 variant with overweight/obesity and related anthropometric, metabolic, physical, and behavioral traits in a sample of Pakistani population with association between the rs7561317 and many traits was not investigated befo...
Source: Biochemical Genetics - October 18, 2019 Category: Genetics & Stem Cells Authors: Rana S, Sultana A Tags: Biochem Genet Source Type: research
Association Between MTHFR Gene Common Variants, Serum Homocysteine, and Risk of Early-Onset Coronary Artery Disease: A Case-Control Study.
This study was designed to investigate the associations of MTHFR in Chinese populations with early-onset coronary artery disease (EOCAD). The two common variants of the MTHFR gene were genotyped in 875 EOCAD patients and 956 controls using PCR, followed by direct sequencing of the PCR product. Serum levels of Hcy were measured using an automatic biochemistry analyzer. A significant association between the MTHFR-677C/T variant and the risk of EOCAD was detected in CC versus TT (odds ratio (OR) 1.456, 95% confidence interval (CI) 1.120-1.892), dominant genetic model (OR 1.266, 95% CI 1.027-1.546), and recessive genetic model...
Source: Biochemical Genetics - September 24, 2019 Category: Genetics & Stem Cells Authors: Zhang SY, Xuan C, Zhang XC, Zhu J, Yue K, Zhao P, He GW, Lun LM, Tian QW Tags: Biochem Genet Source Type: research
Disruption of the Molecular Circadian Clock and Cancer: An Epigenetic Link.
a-Vélez MV Abstract The circadian clock is regulated at the molecular level by feedback circuits of a group of genes known as "clock genes", which establish a mechanism that controls circadian cellular physiology to maintain the balance between cell proliferation, response to DNA damage and apoptosis. Alterations in the expression of clock genes due to genetic or epigenetic mechanisms have been associated with multiple diseases including cancer. Even some clock genes such as the Per1, Per2, Bmal1 genes have been proposed as tumor suppressor genes, with a relevant role during carcinogenesis. At the...
Source: Biochemical Genetics - September 24, 2019 Category: Genetics & Stem Cells Authors: Hernández-Rosas F, López-Rosas CA, Saavedra-Vélez MV Tags: Biochem Genet Source Type: research
Characterization and Analysis of Mammalian AKR7A Gene Promoters: Implications for Transcriptional Regulation.
Abstract Aldo-keto reductase (AKR) superfamily is responsible for preventing mammalian cells from the toxic and carcinogenic effect of different genotoxic and non-genotoxic chemicals by reducing them, though the inducibility of these genes are different in different species. The aim of this paper is to compare the gene regulation mechanisms of AKR superfamily genes in different species and to identify the conserved areas, which are responsible for gene regulations in the presence of antioxidant, toxicants, and non-genotoxic carcinogens. At the beginning of the analysis AKR genes found in different species were div...
Source: Biochemical Genetics - September 16, 2019 Category: Genetics & Stem Cells Authors: Rajib SA, Sharif Siam MK Tags: Biochem Genet Source Type: research
Correction to: Morphological Characterization and Gene Expression Patterns for Melanin Pigmentation in Rex Rabbit.
Abstract The original article has been published with an incorrect grant number in the Funding section. PMID: 31502072 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - September 9, 2019 Category: Genetics & Stem Cells Authors: Hu S, Zhai P, Chen Y, Zhao B, Yang N, Wang M, Xiao Y, Bao G, Wu X Tags: Biochem Genet Source Type: research
Genetic Diversity and Population Structure Analysis of Three Deep-Sea Amphipod Species from Geographically Isolated Hadal Trenches in the Pacific Ocean.
Abstract Amphipods of the superfamily Lysianassoidea that inhabit the hadal zone ( > 6000 m) have large bathymetric ranges and play a key role in deep ocean ecosystems. The endemism of these amphipod species makes them a good model for investigating potent natural selection and restricted dispersal in deep ocean trenches. Here, we describe genetic diversity and intraspecific population differentiation among three amphipod species from four Pacific trenches based on a mtDNA concatenated dataset (CO Ι and 16S rRNA genes) from 150 amphipod individuals. All amphipod populations had low genet...
Source: Biochemical Genetics - August 13, 2019 Category: Genetics & Stem Cells Authors: Chan J, Pan B, Geng D, Zhang Q, Zhang S, Guo J, Xu Q Tags: Biochem Genet Source Type: research
Expression of Concern: AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.
PMID: 31372808 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - August 1, 2019 Category: Genetics & Stem Cells Authors: Sorkheh K, Masaeli M, Chaleshtori MH, Adugna A, Ercisli S Tags: Biochem Genet Source Type: research
Biological Effects of Single-Nucleotide Polymorphisms in the Drosophila melanogaster Malic Enzyme Locus.
Abstract A pair of amino acid polymorphisms within the Drosophila melanogaster Malic enzyme (Men) locus presents an interesting case of genetic variation that appears to be under selection. The two alleles at each site are biochemically distinct, but their biological effects are unknown. One polymorphic site is near the active site and the other is buried within the protein. Strikingly, in twelve different populations, the first polymorphism is always found at approximately a 50:50 allelic frequency, whereas the second polymorphism is always found at approximately 90:10. The consistency of the frequencies between ...
Source: Biochemical Genetics - July 13, 2019 Category: Genetics & Stem Cells Authors: Baath S, Merritt TJS Tags: Biochem Genet Source Type: research
Morphological Characterization and Gene Expression Patterns for Melanin Pigmentation in Rex Rabbit.
Abstract Animal melanin has an important role in the formation of animal fur and skin, which is determined by its quantities, character, and distribution. To identify the effect of melanin on the formation of multi-colored Rex rabbits (Black, Chinchilla, Beaver, Protein cyan, Protein yellow, White), the structure of hair follicles and melanin content in multi-colored Rex rabbit skins were observed by Hematoxylin and Eosin (H&E) staining and melanin staining, respectively. The melanin granules were primarily found in the epidermis and hair follicle roots. The melanin content of skin was measured by extracting m...
Source: Biochemical Genetics - July 13, 2019 Category: Genetics & Stem Cells Authors: Hu S, Zhai P, Chen Y, Zhao B, Yang N, Wang M, Xiao Y, Bao G, Wu X Tags: Biochem Genet Source Type: research
Genome Wide Identification, Molecular Characterization, and Gene Expression Analyses of Grapevine NHX Antiporters Suggest Their Involvement in Growth, Ripening, Seed Dormancy, and Stress Response.
ana M Abstract Plant NHX antiporters are critical for cellular pH, Na+, and K+ homeostasis and salt tolerance. Even though their genomic and functional studies have been conducted in many species, the grapevine NHX family has not been described yet. Our work highlights the presence of six VvNHX genes whose phylogenetic analysis revealed their classification in two distinct groups: group I vacuolar (VvNHX1-5) and group II endosomal (VvNHX6). Several cis-acting regulatory elements related to tissue-specific expression, transcription factor binding, abiotic/biotic stresses response, and light regulation elements were...
Source: Biochemical Genetics - July 8, 2019 Category: Genetics & Stem Cells Authors: Ayadi M, Martins V, Ben Ayed R, Jbir R, Feki M, Mzid R, Géros H, Aifa S, Hanana M Tags: Biochem Genet Source Type: research
Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies.
Abstract Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic inform...
Source: Biochemical Genetics - July 4, 2019 Category: Genetics & Stem Cells Authors: Ali MAM, Hassan AM, Saafan MA, Abdelmagid AA Tags: Biochem Genet Source Type: research
Upregulation of Pro-inflammatory Cytokine Genes by Parvovirus B19 in Human Bone Marrow Mesenchymal Stem Cells.
In this study, we hypothesized that BM-MSCs as the main cellular component of bone marrow niche may be induced to secret pro-inflammatory cytokines after B19V infection. BM-MSCs were cultured up to passage 3. The cells were then subjected to nucleofection to transfer a plasmid containing B19V genome. After 36 h, total RNA was extracted and the expression levels of IL-1β, IL-6, TNF-α and NF-κB genes were examined using qRT-PCR. Data analysis showed the significant increase in expression levels of all studied genes in the B19V-transfected cells (P
Source: Biochemical Genetics - June 27, 2019 Category: Genetics & Stem Cells Authors: Amiri S, Atashi A, Azad M, Elmi A, Abbaszade Dibavar M, Ajami M, Ajami M, Rassaei N, Mohammadihaji R, Gheibi N Tags: Biochem Genet Source Type: research
A Novel Method for Identifying the Potential Cancer Driver Genes Based on Molecular Data Integration.
Abstract The identification of the cancer driver genes is essential for personalized therapy. The mutation frequency of most driver genes is in the middle (2-20%) or even lower range, which makes it difficult to find the driver genes with low-frequency mutations. Other forms of genomic aberrations, such as copy number variations (CNVs) and epigenetic changes, may also reflect cancer progression. In this work, a method for identifying the potential cancer driver genes (iPDG) based on molecular data integration is proposed. DNA copy number variation, somatic mutation, and gene expression data of matched cancer sampl...
Source: Biochemical Genetics - May 21, 2019 Category: Genetics & Stem Cells Authors: Zhang W, Wang SL Tags: Biochem Genet Source Type: research
Complete Genome of Bacillus velezensis CMT-6 and Comparative Genome Analysis Reveals Lipopeptide Diversity.
Abstract The complete genome sequence of Bacillus velezensis type strain CMT-6 is presented for the first time. A comparative analysis between the genome sequences of CMT-6 with the genome of Bacillus amyloliquefaciens DSM7T, B. velezensis FZB42, and Bacillus subtilis 168 revealed major differences in the lipopeptide synthesis genes. Of the above, only the CMT-6 strain possessed an integrated synthetase gene for synthesizing surfactin, iturin, and fengycin. However, CMT-6 shared 14, 12, and 10 other lipopeptide-producing genes with FZB42, DSM7T, and 168 respectively. The largest numbers of non-synonymous mutations...
Source: Biochemical Genetics - May 17, 2019 Category: Genetics & Stem Cells Authors: Deng Q, Wang R, Sun D, Sun L, Wang Y, Pu Y, Fang Z, Xu D, Liu Y, Ye R, Yin S, Xie S, Gooneratne R Tags: Biochem Genet Source Type: research
NEMP1 Promotes Tamoxifen Resistance in Breast Cancer Cells.
In this study, we first established a tamoxifen-resistant BC cell line and then demonstrated the overexpression of nuclear envelope integral membrane protein 1 (NEMP1) in the tamoxifen-resistant BC cells. Moreover, through a cell viability assay combined with depletion or overexpression technology, we addressed the important role of NEMP1 for the tamoxifen resistance in BC cells. Importantly, we further revealed that NEMP1 modulated tamoxifen resistance by regulating nuclear receptor coactivator 1 (NCOA1). In general, NEMP1 shows responsibility for the resistance of tamoxifen through regulating NCOA1 in BC cells. These res...
Source: Biochemical Genetics - May 11, 2019 Category: Genetics & Stem Cells Authors: Liu Y, Tong C, Cao J, Xiong M Tags: Biochem Genet Source Type: research
Tissue-Specific Monoallelic Expression of Bovine AXL is Associated with DNA Methylation of Promoter DMR.
Abstract The AXL protein is a receptor tyrosine kinase and is often implicated in proliferation, migration and therapy resistance in various cancers. The AXL gene in humans is maternally expressed and paternally imprinted with differentially methylated regions (DMR) surrounding the promoter region. However, the imprinting status and epigenetic regulation of AXL gene in cattle remain unclear. Therefore, we explored the molecular structure along with the patterns of allelic expression and DNA methylation of the bovine AXL gene. First, the complete cDNA sequence of bovine AXL was gathered by Sanger method, from trans...
Source: Biochemical Genetics - May 9, 2019 Category: Genetics & Stem Cells Authors: Xu D, Wang G, Li J, Zhang C, Chen W, Li D, Li S Tags: Biochem Genet Source Type: research
Genome-Wide Identification and Comparative Expression Profile Analysis of the Long-Chain Acyl-CoA synthetase (LACS) Gene Family in Two Different Oil Content Cultivars of Brassica napus.
Abstract Long-chain acyl-CoA synthetase (LACS) is one of the key enzymes involved in fatty acid metabolism, including phospholipid biosynthesis, triacylglycerol (TAG) biosynthesis, and fatty acid β-oxidation in plants. However, the characterization of LACSs family in seed oil biosynthesis of Brassica napus (B. napus) remains unknown. In the present study, we performed a comprehensive genome-wide analysis of this gene family in B. napus, and 34 B. napus LACS genes (BnaLACSs) were identified. Phylogenetic analysis classified the BnaLACS proteins into four groups (A, B, C, and D), which were supported by highly ...
Source: Biochemical Genetics - April 22, 2019 Category: Genetics & Stem Cells Authors: Xiao Z, Li N, Wang S, Sun J, Zhang L, Zhang C, Yang H, Zhao H, Yang B, Wei L, Du H, Qu C, Lu K, Li J Tags: Biochem Genet Source Type: research
Genome-Wide Identification of the Aux/IAA Family Genes (MdIAA) and Functional Analysis of MdIAA18 for Apple Tree Ideotype.
Abstract The Aux/IAA (auxin/indole-3-acetic acid) gene family is one of the early auxin-responsive gene families, which play a central role in auxin response. Few reports are involved in Aux/IAA genes in fruit trees, especially in apple (Malus × domestica Borkh.). A total of 33 MdIAA members were identified, of which 27 members contained four conserved domains, whereas the others lost one or two conserved domains. Several cis-elements in promoters of MdIAAs were predicted responsive to hormones and abiotic stress. Tissue-specific expression patterns of MdIAAs in different apple tree ideotypes w...
Source: Biochemical Genetics - April 17, 2019 Category: Genetics & Stem Cells Authors: Wang L, Xu K, Li Y, Cai W, Zhao Y, Yu B, Zhu Y Tags: Biochem Genet Source Type: research
Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation.
Abstract Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcr...
Source: Biochemical Genetics - April 17, 2019 Category: Genetics & Stem Cells Authors: Xanthopoulou A, Kissoudis C, Mellidou I, Manioudaki M, Bosmali I, Tsakonitis V, Kalivas A, Osathanunkul M, Tsaftaris A, Ganopoulos I, Madesis P Tags: Biochem Genet Source Type: research
Altered miR-21, miRNA-148a Expression in Relation to KRAS Mutation Status as Indicator of Adenoma-Carcinoma Transitional Pattern in Colorectal Adenoma and Carcinoma Lesions.
In this study, seventy-five archived FFPE CRC samples, including colorectal adenocarcinoma, adenomatous polyps (adenoma), and adjacent non-neoplastic mucosa were collected for the investigation by Sanger sequencing at the DNA level and by real-time PCR at the RNA level. The results of the KRAS mutational analysis have shown that the majority of somatic mutations in the KRAS affect only one codon, mainly codon 12(p.G12D) with low frequency in adenomas (13.3%) versus CRCs (36%). The results of dysregulated epigenetic changes of miR-21 clearly showed upregulation of expression in colorectal adenocarcinoma, compared to non-neo...
Source: Biochemical Genetics - April 17, 2019 Category: Genetics & Stem Cells Authors: Igder S, Mohammadiasl J, Mokarram P Tags: Biochem Genet Source Type: research
Association of the IL6 Gene Polymorphism with Component Features of Metabolic Syndrome in Obese Subjects.
Abstract Metabolic syndrome (MetS) is a risk factor for type 2 diabetes mellitus and cardiovascular disease. Obesity is a component of the metabolic syndrome. Several genetic variants are reported to be associated with obesity and hypo adiponectinemia, including ars1800796 polymorphism of the interleukin-6 (IL-6) gene. Since obesity is associated with inflammatory factors, the aim of this study was to investigate the association between this polymorphism and MetS and its related features. Obese patients with body mass index (BMI) ≥ 30 (n = 182) were recruited into this study and divi...
Source: Biochemical Genetics - April 15, 2019 Category: Genetics & Stem Cells Authors: Barati E, Ghazizadeh H, Sadabadi F, Kazemi E, Ferns GA, Avan A, Ghayour-Mobarhan M Tags: Biochem Genet Source Type: research
Combination of Simple Sequence Repeat, S-Locus Polymorphism and Phenotypic Data for Identification of Tunisian Plum Species (Prunus spp.).
In this study, single sequence repeat (SSR) markers allowed distinguishing between eighteen diploid accessions and five polyploid accessions, but SSR data alone precluded unambiguous ploidy estimation due to homozygosity. In contrast, S-allele markers were useful to identify the ploidy level between polyploid species, but they did not distinguish species with the same ploidy level. Seven out of 12 phenotypic traits were shown to be discriminant traits for plum species identification. Molecular and phenotypic traits were significantly correlated and revealed a powerful tool to draw taxonomic and genotypic keys. The results ...
Source: Biochemical Genetics - April 12, 2019 Category: Genetics & Stem Cells Authors: Baraket G, Abdallah D, Ben Mustapha S, Ben Tamarzizt H, Salhi-Hannachi A Tags: Biochem Genet Source Type: research
Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii.
In this study, 8121 EST-SSR markers were mined from D. hamiltonii transcriptome data. Among all, tri-repeats were most represented (52%), with the abundance of CCG/CGG repeat motif. A set of 114 polymorphic markers encompassing epigenetic regulators, transcription factors, cell cycle regulators, signaling, and cell wall biogenesis, detected polymorphism and interaction (in silico) with important genes, that might have role in bamboo growth and development. Genetic diversity and population structure of the three D. hamiltonii populations (72 individuals) revealed moderate to high-level genetic diversity (mean alleles per lo...
Source: Biochemical Genetics - April 5, 2019 Category: Genetics & Stem Cells Authors: Bhandawat A, Sharma V, Singh P, Seth R, Nag A, Kaur J, Sharma RK Tags: Biochem Genet Source Type: research
IGF2 is Deregulated During the Development of Uterine Cervical Carcinoma in Indian Patients.
Abstract Uterine cervical carcinoma (CACX) is one of the leading causes of deaths in Indian women. Chromosomal alterations including 11p15.5 locus were reported in CACX. Consequently, we strived for the first time to understand the molecular status of the candidate gene Insulin-like growth factor 2, IGF2 (11p15.5) in Indian CACX patients (n = 128). DNA copy number (CN) analysis using CGH-SNP analysis showed no genetic alteration and it was further validated by comparison with publicly available CN datasets. But promoter hypo-methylation during the progression of CACX was observed and also found to be...
Source: Biochemical Genetics - April 4, 2019 Category: Genetics & Stem Cells Authors: Roychowdhury A, Samadder S, Indra Mazumder D, Das P, Basu M, Mondal R, Roy A, Roychoudhury S, Panda CK Tags: Biochem Genet Source Type: research
Association of rs146292819 Polymorphism in ABCA1 Gene with the Risk of Coronary Artery Disease in Pakistani Population.
In this study, genotype frequencies of rs146292819 polymorphism in CAD patients were GG (43%), GT (27%), TT (30%) as compared to GG (25%), GT (31%), TT (44%) in healthy subjects. GG genotype increased the risk of developing CAD by 2.2326 times (OR 2.2326; 95% CI 1.5775-3.1597) and caused decrease in HDL-C levels by 2.6348 times. GT genotype was neither associated with CAD development (OR 0.8504; 95% CI 0.5974-1.2106) nor HDL-C levels. TT genotype lowered the risk of CAD development by 0.5381 times (OR 0.5381; 95% CI 0.3846-0.753) and protected from drop in HDL-C levels by 0.5086 times (OR 0.5086; 95% CI 0.3429-0.7544). It ...
Source: Biochemical Genetics - April 3, 2019 Category: Genetics & Stem Cells Authors: Sameem M, Rani A, Arshad M Tags: Biochem Genet Source Type: research
De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry.
Abstract Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla). To date, few molecular markers have been reported for this plant. RNA sequencing provides a relatively fast and low-cost approach for large-scale detection of simple sequence repeats (SSRs). In the present study, we profiled the transcriptome of red-flowered strawberry by Illumina HiSeq 2500 to identify SSRs related to petal color. Based on 2 million clean reads of red and white flowers from red-flowered strawberry hybrids, we assembled 91,835 unigenes with an average len...
Source: Biochemical Genetics - March 1, 2019 Category: Genetics & Stem Cells Authors: Ding Y, Xue L, Guo RX, Luo GJ, Song YT, Lei JJ Tags: Biochem Genet Source Type: research
Genetic Polymorphisms of CCDC26 rs891835, rs6470745, and rs55705857 in Glioma Risk: A Systematic Review and Meta-analysis.
artínez-Magaña JJ, Rodríguez-Pérez JM Abstract A genetic component is accepted in the etiology of the glioma. Evidence from candidate genes studies and GWAS reveal that CCDC26 gene could increase the risk of glioma. We performed a systematic review and up-to-date meta-analysis to explore if polymorphisms of CCDC26 gene (rs891835, rs6470745, and rs55705857) may be a susceptibility factor in developing glioma. An online search in PubMed, Web of Science, and SCOPUS up to September 2018 was performed. The pooled odds ratios were evaluated by fixed effects model and random effects model. Ana...
Source: Biochemical Genetics - February 18, 2019 Category: Genetics & Stem Cells Authors: González-Castro TB, Juárez-Rojop IE, López-Narváez ML, Tovilla-Zárate CA, Genis-Mendoza AD, Pérez-Hernández N, Martínez-Magaña JJ, Rodríguez-Pérez JM Tags: Biochem Genet Source Type: research
Variant Ionotropic Receptors are Expressed in the Antennae of Anopheles sinensis (Diptera: Culicidae).
Abstract Mosquitoes transmit many harmful diseases that seriously threaten public health. The mosquito's olfactory system is of great significance for host selection. Inotropic receptors (IRs) and olfactory receptors (ORs) have been demonstrated to be capable of odorant molecular recognition. Analyzing the molecular principles of mosquito olfaction facilitates the development of prevention and therapy techniques. Advances in the understanding of IRs have been seriously inadequate compared to those of ORs. Here, we provide evidence that 35 Anopheles sinensis IR (AsIR) genes are expressed, 7 of which are in the ante...
Source: Biochemical Genetics - February 8, 2019 Category: Genetics & Stem Cells Authors: Li J, Chen Q, Man Y, Pei D, Wu W Tags: Biochem Genet Source Type: research
Analysis of Genetic Diversity and Development of a SCAR Marker for Green Tea (Camellia sinensis) Cultivars in Zhejiang Province: The Most Famous Green Tea-Producing Area in China.
The objectives of this study were to assess the genetic diversity of the eighteen main green tea cultivars in Zhejiang Province-the most famous green tea-producing area of China-using start codon-targeted (SCoT) markers and to develop a specific sequence-characterized amplified region (SCAR) marker for application in cultivar diagnosis. Thirty-one SCoT primers produced 264 loci, 226 of which were polymorphic. The genetic similarity coefficients among these green tea cultivars ranged from 0.587 to 0.814, indicating that a high level of genetic diversity was present. Both a UPGMA dendrogram and a PCoA plot grouped the tea cu...
Source: Biochemical Genetics - February 8, 2019 Category: Genetics & Stem Cells Authors: Xu YX, Shen SY, Chen W, Chen L Tags: Biochem Genet Source Type: research
Population Genetics of Calotropis gigantea, a Medicinal and Fiber Resource Plant, as Inferred from Microsatellite Marker Variation in two Native Countries.
Abstract Calotropis gigantea is well known for its aesthetic, medicinal, pharmacological, fodder, fuel, and fiber production potential. Unfortunately, this plant species is still undomesticated, and the genetic information available for crop improvement is limited. For this study, we sampled 21 natural populations of C. gigantea from two key areas of its natural distribution range (Bangladesh and China) and genotyped 379 individuals using nine nuclear microsatellite markers. Population genetic diversity was higher in Bangladesh than that observed in Chinese populations. Overall, a moderate level of genetic diversi...
Source: Biochemical Genetics - February 7, 2019 Category: Genetics & Stem Cells Authors: Islam MR, Li ZZ, Gichira AW, Alam MN, Fu PC, Hu GW, Wang QF, Chen LY Tags: Biochem Genet Source Type: research
Down-Regulation of SIRT1 Expression by mir-23b Contributes to Lipid Accumulation in HepG2 Cells.
Abstract Non-alcoholic fatty liver disease is one of the main causes of chronic liver disease and therefore is currently considered a major public health problem. Sirtuin 1 (SIRT1) is an NAD-dependent deacetylase enzyme that contributes in the regulation of metabolic processes and protects against lipid accumulation in hepatocytes. Its expression is potentially regulated by microRNAs which attach to the 3' untranslated region (3'-UTR) of their target mRNA. HepG2 cells were incubated by glucose to induce lipid accumulation and were subsequently transfected with mir-23b mimic and inhibitor. Real-time PCR was used fo...
Source: Biochemical Genetics - January 29, 2019 Category: Genetics & Stem Cells Authors: Borji M, Nourbakhsh M, Shafiee SM, Owji AA, Abdolvahabi Z, Hesari Z, Ilbeigi D, Seiri P, Yousefi Z Tags: Biochem Genet Source Type: research
A Novel CNGA1 Gene Mutation (c.G622A) of Autosomal Recessive Retinitis Pigmentosa Leads to the CNGA1 Protein Reduction on Membrane.
Abstract CNGA1 encodes a membrane protein on rod photoreceptor related to phototransduction. The present study was to identify a novel mutation of CNGA1 associated with autosomal recessive retinitis pigmentosa by using next generation sequencing of a Chinese family. Next generation sequencing and Sanger sequencing has identified a compound heterozygous mutation in CNGA1 gene, c0.472 del C (reported) and c0.829G>A (novel mutation, same as c0.622G>A according to NM_000087.3) of the proband. SIFT and Polyphen-2 predicted the CNGA1 G622A site to be possibly deleterious. Evolutionary conservation analysis of amin...
Source: Biochemical Genetics - January 16, 2019 Category: Genetics & Stem Cells Authors: Gao Q, Liu Y, Lei X, Deng Q, Tong Y, Du L, Shen Y Tags: Biochem Genet Source Type: research
Omega-3 PUFA Alters the Expression Level but Not the Methylation Pattern of the WIF1 Gene Promoter in a Pancreatic Cancer Cell Line (MIA PaCa-2).
Abstract Pancreatic cancer is the fourth leading cause of death in both males and females, with a 5-year relative survival rate of 8%. The Wnt signaling pathway has a significant role in the pathogenesis of many tumors, including those of pancreatic cancer. Hypermethylation of the Wnt inhibitory Factor-1 (WIF1) gene promoter have been detected in different types of cancer. In contrast, the anticancer effects of long-chain omega-3 PUFA (ALA) have been reported. Regarding its anticancer effects, in this study, we investigated the effects of various concentrations of omega-3 PUFA on expression level and promoter meth...
Source: Biochemical Genetics - January 16, 2019 Category: Genetics & Stem Cells Authors: Rahmani B, Hamedi Asl D, Naserpour Farivar T, Azad M, Sahmani M, Gheibi N Tags: Biochem Genet Source Type: research
Genome-Wide Identification and Characterization of DIR Genes in Medicago truncatula.
This study will facilitate further studies on DIR family and provide useful clues for functional validation of DIR genes in higher plants. PMID: 30649641 [PubMed - as supplied by publisher] (Source: Biochemical Genetics)
Source: Biochemical Genetics - January 16, 2019 Category: Genetics & Stem Cells Authors: Song M, Peng X Tags: Biochem Genet Source Type: research
PTPN22 +788 G > A (R263Q) Polymorphism is Associated with mRNA Expression but it is not a Susceptibility Marker for Rheumatoid Arthritis Patients from Western Mexico.
PTPN22 +788 G>A (R263Q) Polymorphism is Associated with mRNA Expression but it is not a Susceptibility Marker for Rheumatoid Arthritis Patients from Western Mexico. Biochem Genet. 2019 Jan 14;: Authors: Ramírez-Pérez S, Sánchez-Zuno GA, Chavarría-Buenrostro LE, Montoya-Buelna M, Reyes-Pérez IV, Ramírez-Dueñas MG, Palafox-Sánchez CA, Martínez-Bonilla GE, Muñoz-Valle JF Abstract PTPN22 represents an important non-HLA gene that has been strongly associated with rheumatoid arthritis (RA) pathogenesis. Several studies have repo...
Source: Biochemical Genetics - January 14, 2019 Category: Genetics & Stem Cells Authors: Ramírez-Pérez S, Sánchez-Zuno GA, Chavarría-Buenrostro LE, Montoya-Buelna M, Reyes-Pérez IV, Ramírez-Dueñas MG, Palafox-Sánchez CA, Martínez-Bonilla GE, Muñoz-Valle JF Tags: Biochem Genet Source Type: research
Engineering Corynebacterium glutamicum Mutants for 3-Methyl-1-butanol Production.
Abstract 3-Methyl-1-butanol (3MB) is a promising biofuel that can be produced from 2-ketoisocaproate via the common L-leucine biosynthesis pathway. Corynebacterium glutamicum was chosen as a host bacterium because of its strong resistance to isobutanol. In the current study, several strategies were designed to overproduce 3MB in C. glutamicum through a non-fermentation pathway. The engineered C. glutamicum mutant was obtained by silencing the pyruvate dehydrogenase gene complex (aceE) and deleting the lactic dehydrogenase gene (ldh), followed by mutagenesis with diethyl sulfate (DES) and selection with Fmoc-3-4-th...
Source: Biochemical Genetics - January 14, 2019 Category: Genetics & Stem Cells Authors: Zhang Y, Zhang X, Xiao S, Qi W, Xu J, Yuan Z, Wang Z Tags: Biochem Genet Source Type: research
Genetic Diversity and Population Structure in Upland Rice (Oryza sativa L.) of Mizoram, North East India as Revealed by Morphological, Biochemical and Molecular Markers.
Abstract Upland rice landraces from different villages of Mizoram, Northeast India were analyzed for seed morphology, amylose content, aromatic characteristic, seed storage protein profiling and genetic diversity. Results revealed variation in grain length, width, weight and shape. Protein profiling showed polypeptide bands ranging from 7 to 10 with similarity coefficient from 0.556 to 1.000 in the studied populations. Population genetic analysis using simple sequence repeats markers revealed a total of 63 alleles with a high level of gene diversity at 0.6468. High values of Fst and PIC estimates were found at 0.7...
Source: Biochemical Genetics - January 2, 2019 Category: Genetics & Stem Cells Authors: Vanlalsanga, Singh YT Tags: Biochem Genet Source Type: research