Effect of the traditional Chinese medicine Qi Teng Xiao Zhuo granules on chronic glomerulonephritis rats studied by using long noncoding RNAs expression profiling.
CONCLUSIONS: The ten lncRNAs might play important roles in the Qi Teng Xiao Zhuo granules treatment of CGN. Key genes, such as Ptprc (protein tyrosine phosphatase, receptor type, C), TOP2a, Fos (FBJ osteosarcoma oncogene), Myc (myelocytomatosis oncogene), etc, may be crucial biomarkers for Qi Teng Xiao Zhuo granules. PMID: 31821871 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - December 7, 2019 Category: Genetics & Stem Cells Authors: Wei LB, Gao JR, Gao YC, Liu XC, Jiang H, Qin XJ Tags: Gene Source Type: research

KLF2 protects BV2 microglial cells against oxygen and glucose deprivation injury by modulating BDNF/TrkB pathway.
Abstract Cerebral ischemia injury is common in cerebral ischemic disease, and treatment options remain limited. Krueppel-like factor 2 (KLF2) is reported to negatively regulate inflammation in several ischemic diseases. Our study aimed to investigate the effects and underlying mechanism of KLF2 in BV2 microglial cells exposed to oxygen and glucose deprivation (OGD). We first found decreased KLF2 and toll-like receptor 2 (TLR2)/TLR4 in these cells. OGD also led to decrease in cell viability and increase in LDH release, apoptosis, the Bax/Bcl-2 ratio, and caspase3/9 expression, as well as production of inflammatory ...
Source: Gene - December 7, 2019 Category: Genetics & Stem Cells Authors: Zhou J, Wang M, Deng D Tags: Gene Source Type: research

Genome-wide analysis of mammary gland shows modulation of transcriptome landscape with alternative splice variants in Staphylococcus aureus mastitis in mice.
Abstract Epidemiological mapping shows Staphylococcus aureus to be the leading mastitis causing pathogen in India with diverse genetic lineages circulating in the dairy cattle population. We previously reported that endemic clonal strains of S. aureus isolated from subclinical mastitis lead to specific alteration of epigenetic modulators resulting in deviating immune response in intramammary infection mouse model. However, the extent of transcriptome modulation and associated alternative splicing in S. aureus mastitis is poorly understood. Hence, to gain a deeper insight of the extent of modulation of transcriptom...
Source: Gene - December 7, 2019 Category: Genetics & Stem Cells Authors: Mitra SD, Ganaie F, Bankar K, Velu D, Mani B, Vasudevan M, Shome R, Rahman H, Kumar Ghosh S, Shome BR Tags: Gene Source Type: research

Role of Non-coding RNA in the Pathogenesis of Depression.
Abstract Depression is increasingly threatening human health as a serious psychological problem. However, it is remarkable that the precise mechanism underlying depression remains unelucidated. Recent studies have clarified that non-coding RNA, including but not limited to microRNA, long non-coding RNA, and circular RNA, plays an important role in the pathogenesis of depression. The research results cited in this paper reveal the origin, expression, distribution, function, and mechanism of microRNA in the nervous system. MicroRNA is involved in regulation of life activities, including growth, immune reaction, haem...
Source: Gene - December 6, 2019 Category: Genetics & Stem Cells Authors: Liu N, Wang ZZ, Zhao M, Zhang Y, Chen NH Tags: Gene Source Type: research

Restoring strategy of ethanolic extract of Moringa oleifera leaves against Tilmicosin-induced cardiac injury in rats: Targeting cell apoptosis-mediated pathways.
In this study, the ethanolic extract of Moringa oleifera (MO) leaves was investigated at two doses (400 and 800 mg/kg body weight [bw], orally) to determine its role in counteracting the effects of Til treatment (75 mg/kg bw) on the cardiac tissue in rats, exploring the oxidative stress-mediated damage and apoptosis. A high dose of MO ethanolic extract elicits considerable changes in the body weight, reduces the mortality rate, neutralizes the impaired cardiac injury markers, improves antioxidant endpoints (total antioxidant capacity, superoxide dismutase, catalase activity, and reduced glutathione level). Also it attenuat...
Source: Gene - December 5, 2019 Category: Genetics & Stem Cells Authors: Khalil SR, Abdel-Motal SM, Abd-Elsalam M, Abd El-Hameed NE, Awad A Tags: Gene Source Type: research

Small-cell variant renal oncocytoma: case report on its clinicopathological and genetic characteristics and literature review.
CONCLUSION: Small-cell variant of RO is considered benign renal neoplasms with good prognosis. A histochemical and immunohistochemical stains assist in diagnosis of this tumor. Definitive diagnosis can help avoid unnecessary total renal nephrectomy. The exact mechanism of Small-cell variant of RO remains to be further investigated. PMID: 31809837 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Li K, Wang C, Xiong X, Ma H, Qi Y, Hu W, Xiao S, Zhou X, Pang L, Zou H Tags: Gene Source Type: research

Association of the DRD4 Exon III and 5-HTTLPR VNTR Polymorphisms with Substance Abuse in Jordanian Arab population.
This study included 500 SUD patients and 500 healthy matched controls. The VNTR Genetic polymorphisms of DRD4 and SLC6A4 genes were genotyped using conventional polymerase chain reaction (PCR). While, the rs25531 SNP was genotyped using PCR-restriction fragment length polymorphism (PCR-RFLP) technique. The genetic association was analysed using different statistical analyses including chi-square, Fisher exact test and one way ANOVA test. The DRD4 exon III VNTR polymorphism was associated with SUD significantly in case of alleles 4, 7 and genotype 7/7 (P = 0.004, 0.0005 and 0.01, respectively). While, there was no genetic a...
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Al-Eitan LN, Alshudaifat KM, Anani JY Tags: Gene Source Type: research

Medaka oct4 is essential for gastrulation, central nervous system development and angiogenesis.
Abstract Gene oct4 (also called oct3/4 or pou5f1) encodes an octamer-binding transcription factor and is best known for its pluripotency-specific expression and pluripotency-maintaining role in early embryos and embryonic stem cells of mouse and human. Its fish paralog oct4 (also called pou2 or pou5f3) plays divergent roles in embryos and stem cells development. Here the expression and function of the medaka oct4 (Oloct4) during gastrulation and organogenesis were analysed. Oloct4 RNA was abundant in pluripotent cells and differentiated extraembryonic cells of blastula embryos. It was also detectable in primordial...
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Sun B, Gui L, Liu R, Hong Y, Li M Tags: Gene Source Type: research

What is the impact of BIRC5 gene polymorphisms on urinary cancer susceptibility? evidence from 9348 subjects.
Abstract As a member of apoptosis inhibition gene family, baculoviral IAP repeat containing 5 (BIRC5) protein acts as a survival factor in oncology through multiple ways. There are huge inconsistent results between urinary cancer risk and BIRC5 polymorphisms, so we searched and documented all eligible articles to clear up the mystery with the help of meta-analysis. According to the inclusion and exclusion criteria, we performed an overall search in Web of Science, PubMed, Google Scholar, Medline, CNKI and Wanfang database with pre-set search strategy up to November 2019. Z-test was performed to determine the stati...
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Xu M, Hu X, Zhang M, Ge Y Tags: Gene Source Type: research

Genetic diversity of Aoluguya Reindeer based on D-loop region of mtDNA and its conservation implications.
In this study, we identified the genetic diversity of Aoluguya Reindeer and the introduced reindeer, and provided a scientific basis for the conservation and breeding of Aoluguya Reindeer resources. PMID: 31809841 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Ju Y, Liu H, He J, Wang L, Xu J, Liu H, Dong Y, Zhang R, Zhao P, Xing X Tags: Gene Source Type: research

Overexpression of circular RNA hsa_circ_0001038 promotes cervical cancer cell progression by acting as a ceRNA for miR-337-3p to regulate cyclin-M3 and metastasis-associated in colon cancer 1 expression.
In conclusion, hsa_circ_0001038 plays an oncogenic role in CC cells partly by activating CNNM3 and MACC1. PMID: 31809842 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Wang Y, Wang L, Wang W, Guo X Tags: Gene Source Type: research

Genome-wide identification and expression analysis of major latex protein (MLP) family genes in the apple (Malus domestica Borkh.) genome.
Abstract Major latex protein/ripening-related proteins (MLP/RRP) subfamily are a class of proteins that play crucial roles in response to defense and stress response. However, their biological function is still not clear, the identification and characterization will provide essential information for understanding their roles. Here, we carried out a genome-wide evolutionary characteristics and gene expression analysis of the MLP family in apple (Malus domestica, Borkh.). A total of 36 MdMLP genes were screened in apple genome. They were uneven located on 5 chromosomes, where were mainly arranged in tandem clusters,...
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Yuan G, He S, Bian S, Han X, Liu K, Cong P, Zhang C Tags: Gene Source Type: research

Histone acetylation together with DNA demethylation empowers higher plasticity in adipocytes to differentiate into osteoblasts.
Abstract Bone regeneration has been a challenge for both researchers and clinicians. In the field of tissue engineering, much effort has been made to identify cell sources including stem cells. The present study aimed to induce trans-differentiation from adipocytes to osteoblasts using epigenetic modifiers; 5-aza-dC and/or trichostatin-A (TSA). 3T3-L1 preadipocytes were treated with TSA (100 nM) and then with Wnt3a (50 ng/ml). Microscopic observation showed trans-differentiated cell morphology. Methylation-specific PCR and immunoblotting were performed to analyze the DNA methylation and histone acetylation pattern...
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Cho YD, Kim BS, Kim WJ, Kim HJ, Baek JH, Woo KM, Seol YJ, Ku Y, Ryoo HM Tags: Gene Source Type: research

Investigation of the forensic GlobalFiler loci in the genetically isolated Circassian subpopulation in Jordan.
Abstract Circassians are a Caucasian ethnic group who make up a significant minority in Jordan. Although other ethnic groups have been the subject of forensic genetic analysis, no published study has investigated the forensic genetic efficiency of short tandem repeats (STRs) in Circassians, neither in Jordan nor in any other country. The main objective of the current study is to determine the allelic frequencies and evaluate the forensic efficiency parameters of 21 highly polymorphic autosomal STR loci among the Circassian subpopulation in Jordan. The GlobalFiler loci were amplified using DNA extracted from the wh...
Source: Gene - December 3, 2019 Category: Genetics & Stem Cells Authors: Al-Eitan LN, Darwish NN, Hakooz NM, Dajani RB Tags: Gene Source Type: research

5mC profiling characterized TET2 as an anti-adipogenic demethylase.
Abstract To explore its roles in adipogenesis, the levels of genomic 5mC methylation were examined across the adipocyte differentiation of 3T3-L1 cells. This led to the identification of an up-regulating 5mC profile during the process. To further explore the regulation, gene expression assay was performed with a set of 5mC metabolic enzymes. Among them, TET2 was found to be the most regulated 5mC demethylase, in addition to a well-investigated 5mC methylase DNMT1. In the process, the expression of Tet2 increased for over 16-fold, suggesting its implications in the differentiation. Therefore, loss-of-function and g...
Source: Gene - December 2, 2019 Category: Genetics & Stem Cells Authors: Hou Y, Zhang Z, Wang Y, Gao T, Liu X, Tang T, Du Q Tags: Gene Source Type: research

The Expression of Cysteine-Rich Secretory Protein 2 (CRISP2) and miR-582-5p in seminal plasma fluid and spermatozoa of infertile men.
Abstract Cysteine-Rich Secretory Protein 2 (CRISP2) plays an important role in the morphology and motion of male ejaculated spermatozoa. The association of its expression with some miRNAs is also well known. The aim of this study was to determine the expression of CRISP2 and mir-582 in the seminal plasma fluid and spermatozoa of three groups of infertile men and the possible association of their expressions. In this experimental study, the expression of CRISP2 in seminal plasma fluid and spermatozoa of 17 men with asthenozoospermia, 15 men with teratozoospermia, 17 men with teratoasthenozoospermia, and 18 infertil...
Source: Gene - November 25, 2019 Category: Genetics & Stem Cells Authors: Gholami D, Salman Yazdi R, Jami MS, Ghasemi S, Ali Sadighi Gilani M, Sadeghinia S, Teimori H Tags: Gene Source Type: research

Down-regulation of GLT25D1 inhibited collagen secretion and involved in liver fibrogenesis.
Abstract Collagen β (1-O) galactosyltransferase 1 (GLT25D1) has been reported to transfer galactose to hydroxylysine residues via β (1-O) linkages in collagen. However, the role of Glt25d1 in liver fibrogenesis is still unknow. Recently, we generated a Glt25d1 knockout mouse to elucidate the role of Glt25d1 in vivo. However, we found that complete deletion of the Glt25d1 gene resulted in embryonic lethality at E11.5. Histopathological analysis revealed that dysplasia in Glt25d1-/- labyrinth with defects of the vascular network. Immunohistochemical showed that the decrease in proliferation of Glt25d1-/- l...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: He L, Ye X, Gao M, Yang J, Ma J, Xiao F, Wei H Tags: Gene Source Type: research

The effect of foxo gene family variants and global dna metylation on rrms disease.
THE EFFECT OF FOXO GENE FAMILY VARIANTS AND GLOBAL DNA METYLATION ON RRMS DISEASE. Gene. 2019 Nov 21;:144172 Authors: Gökdoğan Edgünlü T, Ünal Y, Karakaş Çelik S, Genç Ö, Emre U, Kutlu G Abstract Multiple sclerosis is a chronic disease that usually occurs with exacerbations and remissions in young adults, affects the central nervous system white matter in multiple localization, and is thought to be the result of complex interactions of genetic and environmental factors, the most common form is relapsing-remitting MS. Forkhead transcription factors O class (FOXO...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Gökdoğan Edgünlü T, Ünal Y, Karakaş Çelik S, Genç Ö, Emre U, Kutlu G Tags: Gene Source Type: research

Evaluating the role of hsa-miR-200c in reversing the epithelial to mesenchymal transition in prostate cancer.
In this study, to identify key molecular principles of EMT pathway in prostate carcinogenesis, an elaborate gene expression profiling was conducted by qRT-PCR and Western blot analyses. A preponderance of mesenchymal trait was observed in the pathological samples of prostate cancer. To simulate an appropriate in vitro model, PC3 cell line was subjected to hypoxic stress, which resulted in elevated expression of vimentin along with EMT-mediating transcription factors Zeb1 and Slug. To conciliate this mesenchymal behavior of PC3 cells, hsa-miR-200c was deliberately overexpressed which led to a marked reduction of cell motili...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Basu S, Chaudhary A, Chowdhury P, Karmakar D, Basu K, Karmakar D, Chatterjee J, Sengupta S Tags: Gene Source Type: research

Genome Sequence comparison under a new form of tri-nucleotide representation based on bio-chemical properties of nucleotides.
Abstract Genetic sequence analysis, classification of genome sequence and evolutionary relationship between species using their biological sequences, are the emerging research domain in Bioinformatics. Several methods have already been applied to DNA sequence comparison under tri-nucleotide representation. In this paper, a new form of tri-nucleotide representation is proposed for sequence comparison. The comparison does not depend on the alignment of the sequences. In this representation, the bio-chemical properties of the nucleotides are considered. The novelty of this method is that the sequences of unequal leng...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Das S, Das A, Mondal B, Dey N, Bhattacharya DK, Tibarewala DN Tags: Gene Source Type: research

Transcriptome and methylome analysis of periodontitis and peri-implantitis with tobacco use.
Abstract Peri-implantitis is similar to periodontitis in both symptoms and treatment; however, their level of similarity remains controversial. Here, we compared multiple cases of periodontitis and peri-implantitis through transcriptome and methylome profiling, and analyzed the effects of smoking as a typical risk factor. Human gingival tissues were obtained from 20 patients with periodontitis or peri-implantitis via periodontal surgical procedures. Total RNA and genomic DNA were isolated, and transcriptome and methylome datasets were generated. Comprehensive analysis of differential gene expression, DNA methylati...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Cho YD, Kim PJ, Kim HG, Seol YJ, Lee YM, Ryoo HM, Ku Y Tags: Gene Source Type: research

Association study of long non-coding RNA HOTAIR rs920778 polymorphism with the risk of cancer in an elderly Japanese population.
Abstract The HOTAIR gene encodes a long noncoding RNA (lncRNA), which functions in development and tumorigenesis. A single nucleotide polymorphism (SNP) rs920778 in the HOTAIR gene, has been recurrently studied for susceptibility to many cancers including oesophageal cancer, gastric cancer, lung cancer, and hepatocellular carcinoma. Most of these studies were conducted in Chinese populations, and a few in Turkish, Iranian, and Portuguese populations. They mostly give rise to controversial results. It still remains largely unknown whether the cancer risk is conferred in a Japanese population. Here, we established a...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Ko Ko Minn A, Sato N, Naka Mieno M, Arai T, Muramatsu M Tags: Gene Source Type: research

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression.
Barh D, Ghosh P, Azevedo VAC, Dos Santos MA Abstract Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many aut...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh Tags: Gene Source Type: research

NRAS rs2273267 A > T polymorphism reduces neuroblastoma risk in Chinese children.
NRAS rs2273267 A>T polymorphism reduces neuroblastoma risk in Chinese children. Gene. 2019 Nov 21;:144262 Authors: Li S, Zhuo Z, Chang X, Ma Y, Zhou H, Zhang J, Cheng J, He J, Li Y Abstract Neuroblastoma is an extracranial solid tumor that mainly occurs in childhood. Mutations of NRAS gene have been described in several cancers. However, whether NRAS gene polymorphisms can predict the risk of neuroblastoma have not been investigated. We hypothesized that variations of NRAS gene contribute to neuroblastoma predisposition. Therefore, we conducted a multi-center case-control study using 263 cases and ...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Li S, Zhuo Z, Chang X, Ma Y, Zhou H, Zhang J, Cheng J, He J, Li Y Tags: Gene Source Type: research

Comparative transcriptomic analyses revealed genes and pathways responsive to heat stress in Diaphorina citri.
In this study, a large set of transcriptomic data derived from D. citri adults were generated and differentially expressed genes (DEGs) after heat stress were identified by RNA sequencing. A total of 118, 399 unigenes were obtained, from which 37, 665 were mapped to sequences from at least one database. Seven hundreds and twenty-two unigenes were affected by high temperature of 40 °C for 4 h, in which 486 up-regulated and 236 down-regulated, and part of heat shock proteins, antioxidant and detoxification genes and cathepsins were identified as the DEGs. KEGG pathway enrichment analysis demonstrated that part of genes i...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Shu B, Wu Y, Qu M, Pu X, Wu Z, Lin J Tags: Gene Source Type: research

Maya gene variants related to the risk of type 2 diabetes in a family-based association study.
This study also included the family-based association test (FBAT) statistic U to assess the genetic associations with T2D, and the multivariate statistical and haplotype analyses. A positive association with TD2 risk was found for WFS1 rs6446482 (p=0.046, Z=1.994) under an additive model, and SIRT1 rs7896005 (p= 0.038, Z=2.073) under the dominant model. Multivariate model analysis, including T2D status, age, and body mass index (BMI), displayed significant covariance in PPARGC-1α rs8192678; SIRT1 rs7896005; TCF7L2 rs7903146 and rs122243326; UCP3 rs3781907; and HHEX rs1111875 with a P
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Domínguez-Cruz MG, de Lourdes Muñoz M, Totomoch-Serra A, García-Escalante MG, Burgueño J, Valadez-González N, Pinto-Escalante D, Díaz-Badillo A Tags: Gene Source Type: research

Association between IL-1A (-889C/T) polymorphism and susceptibility of chronic periodontitis: a meta-analysis.
Abstract OBJECTIVE: The purpose of this study was to investigate the association between IL-1A (-889C/T, rs1800587) polymorphism and susceptibility of chronic periodontitis. METHODS: A systematic literature search was carried out in the databases updated on July 1, 2019, including PubMed, Embase, Cochrane Library and Web of Science. Through STATA 14.0 software, the association between IL-1A (-889C/T) polymorphism and susceptibility of chronic periodontitis was calculated by pooled odds rations (ORs) and 95% confidence intervals (CIs). Harbord test was used for the publication bias. RESULTS: The results o...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Feng X, Liu J Tags: Gene Source Type: research

Overexpression of microRNA-9 inhibits 3T3-L1 cell adipogenesis by targeting PNPLA3 via activation of AMPK.
Abstract Adipocyte differentiation, which plays an important role in the development of obesity, involves complex molecular networks in which microRNAs (miRNAs) are essential. Here, we show that miR-9 expression was upregulated during adipogenesis in 3T3-L1 cells. miR-9 overexpression reduced the accumulation of lipid droplets and the content of triglycerides by downregulating patatin-like phospholipase domain-containing protein 3 (PNPLA3). PNPLA3 knockdown or miR-9 overexpression downregulated the protein expression of peroxisome proliferator-activated receptor γ, oxidative tissue-enrichedPAT, and LC3, and ...
Source: Gene - November 21, 2019 Category: Genetics & Stem Cells Authors: Xu B, Shen J, Li D, Ning B, Guo L, Bing H, Chen J, Li Y Tags: Gene Source Type: research

MicroRNA expression profiling analysis in serum for nasopharyngeal carcinoma diagnosis.
CONCLUSION: A five-miRNA signature was identified in serum to be potential biomarkers for NPC detection. PMID: 31743768 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - November 16, 2019 Category: Genetics & Stem Cells Authors: Zou X, Zhu D, Zhang H, Zhang S, Zhou X, He X, Zhu J, Zhu W Tags: Gene Source Type: research

Downregulation of lncRNA SNHG12 reversed IGF1R-induced osteosarcoma metastasis and proliferation by targeting miR-195-5p.
Abstract Long non-coding RNA SNHG12 (lncSNHG12) plays important roles in the onset and progression of various cancers. However, the role of lncSNHG12 in osteosarcoma (OS) remains unclear. Therefore, the aim of the present study was to determine the function of lncSNHG12 in OS. A bioinformatics website was used to predict the downstream targets of lncSNHG12. In addition, qRT-PCR was employed to assess lncSNHG12 expression in OS cells. Cell migration and proliferation in vitro were verified using the transwell migration, clone formation, and CCK8 assays. Tumor metastasis and xenograft formation were monitored in nud...
Source: Gene - November 16, 2019 Category: Genetics & Stem Cells Authors: Xu N, Xu J, Zuo Z, Liu Y, Yan F, Han C Tags: Gene Source Type: research

Fgf21 Knockout Mice Generated Using CRISPR/Cas9 Reveal Genetic Alterations That May Affect Hair Growth.
Abstract OBJECTIVE: To investigate fibroblast growth factor 21 (Fgf21) alterations that may affect hair growth and the underlying molecular mechanisms by constructing Fgf21 global knockout (KO) mice using microinjection-mediated CRISPR/Cas9. RESULTS: Following genomic DNA sequencing, we identified 18 mice carrying Ffg21 mutations among the total 63 offspring mice obtained by injecting 340 embryos, which yielded a mutation rate of 28.6 percent. Of these 18 mice, three had both alleles knocked out and 15 were monoallelic KO mice. Compared with the wild-type (WT) mice, the phenotypic analysis showed that the lit...
Source: Gene - November 16, 2019 Category: Genetics & Stem Cells Authors: Liu X, Zhang P, Zhang X, Li X, Bai Y, Ao Y, Hexig B, Guo X, Liu D Tags: Gene Source Type: research

Polyamine Homeostasis in Tomato Biotic/Abiotic Stress Cross-Tolerance.
Abstract Adverse conditions and biotic strain can lead to significant losses and impose limitations on plant yield. Polyamines (PAs) serve as regulatory molecules for both abiotic/biotic stress responses and cell protection in unfavourable environments. In this work, the transcription pattern of 24 genes orchestrating PA metabolism was investigated in Cucumber Mosaic Virus or Potato Virus Y infected and cold stressed tomato plants. Expression analysis revealed a differential/pleiotropic pattern of gene regulation in PA homeostasis upon biotic, abiotic or combined stress stimuli, thus revealing a discrete response ...
Source: Gene - November 16, 2019 Category: Genetics & Stem Cells Authors: Tsaniklidis G, Pappi P, Tsafouros A, Charova SN, Nikoloudakis N, Roussos PA, Paschalidis KA, Delis C Tags: Gene Source Type: research

Determining the Polymorphism Information Content of a Molecular Marker.
Abstract This review was carried out with the purpose of contributing to the discussion on the equations used in calculating the Polymorphism Information Content (PIC) of molecular markers. PIC measures the ability of a marker to detect polymorphisms, and therefore has enormous importance in selecting markers for genetic studies. We perform a summary analysis of PIC and its difference in relation to heterozygosity, another parameter used to evaluate the quality of a marker, presenting and discussing the several equations registered in the literature for both dominant and codominant markers. Finally, we present a b...
Source: Gene - November 11, 2019 Category: Genetics & Stem Cells Authors: Lemos SCM, Lia Rejane Silveira R, Karol Buuron S, Silvia Machado Dos Santos R, Charlene Moro S Tags: Gene Source Type: research

Celiac disease associated snp rs17810546 is located in a gene silencing region.
Abstract GWAS studies have identified variant rs17810546 in a non-coding region on chromosome 3 as a risk factor for several auto-immune diseases, including Celiac Disease. In silico analysis reveals that this variant is located in a transcription regulatory site. By means of reporter constructs we show that this region can override the expression rate of a gene as determined by its native promoter and that this modulation is influenced by the genetic composition of the haplotype which rs17810546 forms with a nearby other variant, rs761008. Secondly, we present data that this genetically imprinted modulation could...
Source: Gene - November 11, 2019 Category: Genetics & Stem Cells Authors: Zwiers A, Wanrooij RLJV, Dieckman T, Nijeboer P, Kraal G, Bouma G Tags: Gene Source Type: research

Identification of the circRNA-miRNA-mRNA regulatory network of Hsp90 inhibitor-induced cell death in colorectal cancer by integrated analysis.
In this study, Caco-2 cells were treated with 0.25 μM SNX-2112, an Hsp90 inhibitor, for 48 h; subsequently, whole-transcriptome sequencing was performed. At the mRNA level in SNX-2112-treated Caco-2 cells, 1588 genes were upregulated, and 433 genes were downregulated. Six genes were found to be associated with necroptosis and apoptosis, and these 6 upregulated genes were validated by RT-qPCR. Hundred and six miRNAs were upregulated, and 48 miRNAs were downregulated in SNX-2112-treated Caco-2 cells. Eleven downregulated miRNAs were found to interact with the 6 upregulated genes. Moreover, 676 circRNAs were upregulated, a...
Source: Gene - November 9, 2019 Category: Genetics & Stem Cells Authors: Liu K, Guo Y, Zheng K, Zou C, Wu H, Wang S, Ou L, Wang Y, Huang B, Wang X Tags: Gene Source Type: research

p53 Regulates Katanin-p60 Promoter in HCT 116 Cells.
bay A Abstract Tumor suppressor protein p53, which functions in the cell cycle, apoptosis and neuronal differentiation via transcriptional regulations of target genes or interactions with several proteins, has been associated with neurite outgrowth through microtubule re-organization. We previously demonstrated in neurons that upon p53 induction, the level of microtubule severing protein Katanin-p60 increases, indicating that p53 might be a transcriptional regulator of the KATNA1 gene encoding Katanin-p60. In this context, we firstly elucidated the activity of KATNA1 regulatory regions and endogenous KATNA1 mRNA l...
Source: Gene - November 9, 2019 Category: Genetics & Stem Cells Authors: Kırımtay K, Selçuk E, Kelle D, Erman B, Karabay A Tags: Gene Source Type: research

The silencing of DEK reduced disease resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 based on virus-induced gene silencing analysis in tomato.
Abstract DEK involves in the modulation of cell proliferation, differentiation, apoptosis, migration and cell senescence. However, direct genetic evidence proving the functions of DEK in disease resistance against pathogens is still deficient. In the present study, four DEKs were identified in tomato genome and their roles in disease resistance in tomato were analyzed. The expression levels of DEKs were differently induced by Botrytis cinerea, Pseudomonas syringae pv. tomato (Pst) DC3000 and defense-related signaling molecules (such as jasmonic acid, aethylene precursor and salicylic acid). The DEKs' silencing by ...
Source: Gene - November 9, 2019 Category: Genetics & Stem Cells Authors: Zhang H, Yan M, Deng R, Song F, Jiang M Tags: Gene Source Type: research

Comparative transcriptome profiling of tuberous roots of two sweetpotato lines with contrasting low temperature tolerance during storage.
Abstract Sweetpotato (Ipomoea batatas [L.] Lam) is considered an economically important crop worldwide and is used as a source of food, feed, and biomaterials. However, its origin in tropical regions makes it vulnerable to chilling injury during postharvest storage at low temperature. To gain further insight into the molecular mechanism of chilling response, we performed comparative transcriptome analysis of two sweetpotato lines, Xushu 15-1 and Xushu 15-4, with high and low cold storage ability, respectively. Tuberous roots of these lines were stored at 4°C for 0, 2, and 6 weeks. RNA-Seq data of both lines we...
Source: Gene - November 9, 2019 Category: Genetics & Stem Cells Authors: Yoon Ji C, Soo Kim H, Lee CJ, Kim SE, Lee HU, Nam SS, Li Q, Ma DF, Kwak SS Tags: Gene Source Type: research

Novel Splice Site and Nonsense Variants in INVS Cause Infantile Nephronophthisis.
We report a child with bilateral enlarged, echogenic, polycystic kidneys with end-stage renal disease, anemia and metabolic acidosis caused by biallelic novel pathogenic variants, c.796+5G>A and c.1789C>T in INVS. We show that the variant, c.796+5G>A disrupts the canonical splicing and nonsense variant, c.1789C>T results in nonsense mediated decay. PMID: 31706999 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - November 7, 2019 Category: Genetics & Stem Cells Authors: Somashekar PH, Upadhyai P, Shula A, Girisha KM Tags: Gene Source Type: research

Molecular evolution of autophagy rate-limiting factor LAMP2 in placental mammals.
Abstract Autophagy is the cellular process of removal of misfolded or damaged macromolecules and organelles. Experimental studies have demonstrated autophagy as a major mechanism of lifespan extension in long-lived mammals such as bats and mole rat rodents. Moreover, the role of this biological process has been well documented in protection against age-associated diseases and viral infection. However, studies on the molecular adaptive changes of autophagy factors during evolution are scarce. Here, we conducted a bioinformatics study of the molecular evolution of the Lysosomal Associated Membrane Protein 2 (LAMP2),...
Source: Gene - November 7, 2019 Category: Genetics & Stem Cells Authors: Jalali Z, Parvaz N Tags: Gene Source Type: research

Epigenetic inheritance and intergenerational effects in mollusks.
Abstract Recent insights in evolutionary biology have shed light on epigenetic variation that interacts with genetic variation to convey heritable information. An important characteristic of epigenetic changes is that they can be produced in response to environmental cues and passed on to later generations, potentially facilitating later genetic adaptation. While our understanding of epigenetic mechanisms in vertebrates is rapidly growing, our knowledge about invertebrates remains lower, or is restricted to model organisms. Mollusks in particular, are a large group of invertebrates, with several species important ...
Source: Gene - October 30, 2019 Category: Genetics & Stem Cells Authors: Fallet M, Luquet E, David P, Cosseau C Tags: Gene Source Type: research

The in silico characterization of neutral alpha-glucosidase C (GANC) and its evolution from GANAB.
;ko M Abstract In the Carbohydrate-Active enZymes database (CAZy) glycoside hydrolases (GHs) are classified presently into 156 GH families. In human, there are five known enzymes from the family GH31. Two (MGAM and SI) are intestinal glucosidases involved in saccharide digestion, the acidic glucosidase (GAA) is responsible for glycogen degradation in lysosomes and GANAB (glucosidase II) plays a role in the control of a proper protein folding in the endoplasmic reticulum. The fifth protein is called GANC. It is an α-glucosidase, which is able to release the terminal glucose from maltotriose and glycogen at ne...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Gabriško M Tags: Gene Source Type: research

RNA-Seq comparative analysis reveals the response of Enterococcus faecalis TV4 under fluoride exposure.
In this study, a strain of E. faecalis (named TV4), which is a symbiotic bacteria of silkworm, was isolated and characterized. Inhibition assay showed that fluoride could significantly inhibit the growth of the TV4 strain (P
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Li G, Shi M, Zhao S, Li D, Long Y, Yang C, Zhu Y Tags: Gene Source Type: research

Whole Exome Sequencing identified two homozygous ALMS1 Mutations in an Iranian Family with Alstr öm Syndrome.
This study aimed to identify pathogenic mutations in a consanguineous Iranian family with AS. Next-generation sequencing was performed on the genomic DNA obtained from a 12 years old girl with AS. According to the bioinformatics analysis, computational modelling and segregation of variants, we identified two homozygous mutations close together in exon 8 of ALMS1 in the patient, including c.7262 G>T and c.7303-7305delAG. The clinically normal parents were heterozygous for both mutations. These mutations have a very rare frequency and only reported in the heterozygous state in the public genomic databases. Overall, due to...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Torkamandi S, Rezaei S, Mirfakhraei R, Askari M, Piltan S, Gholami M Tags: Gene Source Type: research

Integrated analysis of competing endogenous RNA (ceRNA) networks in subacute stage of spinal cord injury.
This study aims to investigate the genetic and epigenetic mechanisms involved in the pathogenesis of subacute stage of spinal cord injury (SCI). Gene-expression datasets associated with SCI were downloaded from the Gene Expression Omnibus (GEO) database, and differential expression analyses were performed in order to identify differentially expressed genes (DEGs). Multiple network types were constructed and analyzed , including protein-protein-interaction (PPI) network, miRNA-target network, lncRNA-associated competing endogenous RNA (ceRNA) network, and miRNA-transcription factor (TF)-target network. Cluster analyses were...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Wang N, He L, Yang Y, Li S, Chen Y, Tian Z, Ji Y, Wang Y, Pang M, Wang Y, Liu B, Rong L Tags: Gene Source Type: research

Associated of rs895819 with risk of stomach neoplasms.
Abstract A recent study published in GENE performed a meta-analysis on the relationship between genetic variant rs895819 in microRNA-27a and risk of stomach neoplasms, and the results indicated an association of rs895819 with increased risk of stomach neoplasms in heterogenous model among Chinese. However, the meta-analysis did not include one large sample size of study that met inclusion criteria. When including all related studies, our meta-analysis showed no significant association of rs895819 with stomach neoplasms risk in each different model in all population, Chinese and Europeans. Thus, pooling all related...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Weng Y, Wang D, Bai R Tags: Gene Source Type: research

A novel splice site variant in ANOS1 gene leads to Kallmann syndrome in three siblings.
Abstract Idiopathic hypogonadotropic hypogonadism (IHH) is a rare genetic disease caused by low doses of hypothalamic gonadotropin-releasing hormone (GnRH), leading to absence or delayed sexual development. Kallmann syndrome (KS) is characterized by IHH with anosmia or hyposmia. Here, we identified a novel splice site variant (c. 726+2T>G) of ANOS1 gene in three siblings with KS from a Chinese Han family by whole-exome sequencing (WES). In this family, KS is classified as an X-linked recessive inheritance pattern. This mutation was inherited from the mother by Sanger sequencing. An in vitro functional experimen...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Jiang X, Li D, Gao Y, Zhang X, Wang X, Yang Y, Shen Y Tags: Gene Source Type: research

Next-generation sequencing reveals hsa_circ_0058092 being a potential oncogene candidate involved in gastric cancer.
Abstract Gastric cancer is a serious problem for human health. As part of noncoding RNA, circular RNA (circRNA) plays a key role in the occurrence and development of malignant tumor. We used next generation sequencing technology to detect circRNA expression profiles in 5 paired human gastric cancer tissues. Then, bioinformatics analysis was carried out to analyze the function of dysregulated circRNAs. Hsa_circ_0058092 was selected as the object of follow-up analysis. After using the Cistrome DB dataset the data was used to predict specific transcription factors of hsa_circ_0058092. The relationship between hsa_cir...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Bu X, Zhang X, Luan W, Zhang R, Zhang Y, Zhang A, Yan Y Tags: Gene Source Type: research

Long non-coding RNA AFAP1-AS1 promotes proliferation and invasion in prostate cancer via targeting miR-512-3p.
CONCLUSION: AFAP1-AS1 regulates miR-512-3p, so as to realize the regulation effect on the proliferation, invasion and migration of prostate cancer cells, and thereby promote the occurrence and development of prostate cancer, so as to provide the corresponding program for the treatment of prostate cancer. Abberivation: ADPC, androgen-dependent prostate cancer; CRPC, castrated prostate cancer; RNA1 AFAP1-Asl, Actin fiber-associated protein 1-anti-RNA1; miRNAs, MicroRNAs. PMID: 31669642 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Wang K, Sun H, Sun T, Qu H, Xie Q, Lv H, Hu B Tags: Gene Source Type: research

Role of the NF- κB signaling pathway in the pathogenesis of colorectal cancer.
Role of the NF-κB signaling pathway in the pathogenesis of colorectal cancer. Gene. 2019 Oct 26;:144132 Authors: Soleimani A, Rahmani F, Ferns GA, Ryzhikov M, Avan A, Hassanian SM Abstract The NF-κB signaling pathway is a key regulator of CRC cell proliferation, apoptosis, angiogenesis, inflammation, metastasis, and drug resistance. Over-activation of the NF-κB pathway is a feature of colorectal cancer (CRC). While new combinatorial treatments have improved overall patient outcome; quality of life, cost of care, and patient survival rate have seen little improvement. Suppression of t...
Source: Gene - October 26, 2019 Category: Genetics & Stem Cells Authors: Soleimani A, Rahmani F, Ferns GA, Ryzhikov M, Avan A, Hassanian SM Tags: Gene Source Type: research