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https://www.readbyqxmd.com/read/28340427/identification-and-characterization-of-a-%C3%AE-defensin-gene-involved-in-the-immune-defense-response-of-channel-catfish-ictalurus-punctatus
#1
Jieyao Zhu, Hong Wang, Jun Wang, Xingli Wang, Shuang Peng, Yi Geng, Kaiyu Wang, Pin Ouyang, Zhiqiong Li, Xiaoli Huang, Defang Chen
Antimicrobial peptides are small peptides that play important roles in a host's innate immune response. As an important antimicrobial peptide, β-defensin widely distribute in mammals, insects and plants with broad-spectrum antimicrobial activity. In this study, the β-defensin gene of the channel catfish, Ictalurus punctatus, was cloned, sequenced, and subjected to a bioinformatic analysis. The β-defensin gene of the channel catfish contains three exons and two introns, and encodes a precursor peptide consisting of two domains: a signal peptide of 24 amino acid residues and a mature peptide of 43 amino acid residues...
March 21, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28340291/-head-to-head-prenyl-synthases-in-some-pathogenic-bacteria
#2
Christopher J Schwalen, Xinxin Feng, Weidong Liu, Bing O-Dowd, Tzu-Ping Ko, Christopher J Shin, Rey-Ting Guo, Douglas A Mitchell, Eric Oldfield
Many organisms contain "head-to-head" isoprenoid synthases and here, we investigate three types of such enzymes from the pathogens Neisseria meningitidis, N. gonorrhoeae, and Enterococcus hirae. The E. hirae enzyme was found to produce dehydrosqualene and we solved an inhibitor-bound structure which revealed a fold similar to that of CrtM from Staphylococcus aureus. In contrast, the homologous proteins from Neisseria spp. carried out only the "first half" reaction, yielding presqualene diphosphate (PSPP). Based on product analyses, bioinformatics, and mutagenesis we conclude that the Neisseria proteins are HpnDs (PSPP synthases)...
March 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28339862/a-new-insight-into-the-evolution-and-functional-divergence-of-sweet-transporters-in-chinese-white-pear-pyrus-bretschneideri
#3
Jiaming Li, Mengfan Qin, Xin Qiao, Yinsheng Cheng, Xiaolong Li, Huping Zhang, Jun Wu
SWEET genes are a recently identified plant gene family that play an indispensable role in sugar efflux. However, no systematic study has been performed in pear. In this research, 18 SWEET transporters identified in pear, almost twice the number found in woodland strawberry and Japanese apricot, were divided into four clades. Conserved motifs and six exons of the SWEET transporters were found in six species. SWEET transporters contained seven transmembrane segments (TMSs) that evolved from an internal duplication of an ancestral three-TMSs unit, connected by TMS4...
March 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#4
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28339176/identification-of-likely-associations-between-cerebral-folate-deficiency-and-complex-genetic-and-metabolic-pathogenesis-of-autism-spectrum-disorders-by-utilization-of-a-pilot-interaction-modeling-approach
#5
Daniel Krsička, Jan Geryk, Markéta Vlčková, Markéta Havlovicová, Milan Macek, Radka Pourová
Recently, cerebral folate deficiency (CFD) was suggested to be involved in the pathogenesis of autism spectrum disorders (ASD). However, the exact role of folate metabolism in the pathogenesis of ASD, identification of underlying pathogenic mechanisms and impaired metabolic pathways remain unexplained. The aim of our study was to develop and test a novel, unbiased, bioinformatics approach in order to identify links between ASD and disturbed cerebral metabolism by focusing on abnormal folate metabolism, which could foster patient stratification and novel therapeutic interventions...
March 24, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28339095/expression-of-yes-associated-protein%C3%A2-1-and-its-clinical-significance-in-ovarian-serous-cystadenocarcinoma
#6
Sang Yeon Cho, Kwanghun Kim, Min Soo Park, Mi Young Jang, Young Hwan Choi, Suyeon Han, Hyun Mo Shin, Chaeuk Chung, Hye Young Han, Jung Bo Yang, Young Bok Ko, Heon Jong Yoo
Yes-associated protein 1 (YAP1) is a key transcriptional regulator in the Hippo signaling pathway that plays a critical role in the development and progression of several types of malignancies, including ovarian cancer. Herein, we investigated the expression of YAP1 and its clinical significance in a large population of patients with ovarian serous cystadenocarcinoma (OSC), which is the most common form of epithelial ovarian neoplasm, using the TCGA database. Surprisingly, cross-cancer mRNA expression and alterations in YAP1 were higher in OSC than in those of other types of cancers in the TCGA database...
March 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28339092/macc1-decreases-the-chemosensitivity-of-gastric-cancer-cells-to-oxaliplatin-by-regulating-fasn-expression
#7
Jiangman Duan, Lishan Chen, Minyu Zhou, Jingwen Zhang, Li Sun, Na Huang, Jianping Bin, Yulin Liao, Wangjun Liao
The effect of chemotherapeutic agents is limited as a result of drug resistance, which demands prompt solutions provided by clinical studies. To date, the underlying mechanisms of chemotherapy resistance are relatively unknown. Metastasis-associated in colon cancer 1 (MACC1) is an oncogene associated with the progression and prognosis of gastric cancer (GC). Bioinformatic analysis revealed that MACC1 is positively associated with fatty acid synthase (FASN), a major enzyme of lipogenesis, and drives chemoresistance to oxaliplatin in GC...
March 22, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28339061/identification-of-two-novel-mutations-in-the-slco2a1-prostaglandin-transporter-gene-in-a-chinese-patient-with-primary-hypertrophic-osteoarthropathy
#8
Ting Guo, Kai Yang, Lv Liu, Zhi-Ping Tan, Hong Luo
Primary hypertrophic osteoarthropathy (PHO), which is a rare multi‑organic disease characterized by digital clubbing, pachydermia and periosteal reaction, typically begins during childhood or adolescence and progresses gradually over years prior to disease stabilization. To date, only two genes have been reported to be associated with PHO, 15‑hydroxyprostaglandin dehydrogenase and solute carrier organic anion transporter family, member 2A1 (SLCO2A1). However, the pathogenesis and the functions of the underlying genes remain to be fully elucidated...
March 24, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28339011/reduction-of-mir%C3%A2-132%C3%A2-3p-contributes-to-gastric-cancer-proliferation-by-targeting-muc13
#9
Liang He, Linlin Qu, Lijing Wei, Yan Chen, Jian Suo
Abnormal expression of epidermal growth factor receptor (EGFR) signaling and microRNAs (miRNAs) has been widely seen in gastric cancer. The present study focused on the miRNAs that regulate human epidermal growth factor receptor (HER) activation through mucin 13 (MUC13). The protein level of MUC13 was demonstrated to be significantly increased in gastric cancer tissues compared with normal tissues by western blot analysis and immunohistochemistry. TargetScan bioinformatic predictions indicated that miRNA (miR)‑212‑3p and miR‑132‑3p may bind to the 3'‑untranslated region of MUC13...
March 22, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28338718/identification-and-characterization-of-gra6-gra7-of-neospora-caninum-in-mdbk-cells
#10
Jingquan Dong, Jianhua Li, Jinpeng Wang, Fei Li, Ju Yang, Pengtao Gong, He Li, Xichen Zhang
Neospora caninum, an apicomplexan parasite, is recognized as a major bovine abortifacient. Dense granule antigens (GRAs) play important roles in the formation and modification of parasitophorous vacuoles (PVs) in Toxoplasma gondii. However, a few studies investigating GRAs have been reported in N. caninum. The aim of the present study was to characterize the dense GRA6/GRA7 of N. caninum in PVs using MDBK cells as a host cell model. Neospora caninum was inoculated into MDBK cells, and changes were observed using a transmission electron microscope (TEM)...
February 24, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28338236/hsa-mir-3199-2-and-hsa-mir-1293-as-novel-prognostic-biomarkers-of-papillary-renal-cell-carcinoma-by-cox-ratio-risk-regression-model-screening
#11
Wen Luo, Lei Wang, Mao-Hua Luo, Yu-Zhu Huang, Hua Yang, Yu Zhou, Hong-Tao Jia, Xiu-Xin Wang
Papillary renal cell carcinoma(PRCC) is the second most common and aggressive renal cell carcinoma. Identification of novel microRNA biomarkers could be beneficial for the diagnosis and prognosis of PRCCpatients.We aimed to screen differentially expressed miRNAs that can act as prognostic factors and to predict the survival of PRCC patients. High-throughput data of miRNAs of 274 PRCC samples were downloaded from TCGA(The Cancer Genome Atlas) dataset and interested miRNAs were identified. Hierarchical clustering and principal component analysis (PCA) were performed on these miRNAs...
March 24, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28338203/mir-155-regulates-oral-squamous-cell-carcinoma-tca8113-cell-proliferation-cycle-and-apoptosis-via-regulating-p27kip1
#12
S Fu, H-H Chen, P Cheng, C-B Zhang, Y Wu
OBJECTIVE: P27Kip1 is the one of the negative regulators of the cell cycle that plays an important role in regulating cell cycle and inhibiting cell proliferation by restraining cell in G1 phase. P27Kip1 downregulation maybe related to the occurrence of oral squamous cell carcinoma (OSCC). It was found that miR-155 significantly upregulated in OSCC tissue. Bioinformatics analysis revealed that miR-155 may bind with the 3'-UTR of p27Kip1. This study investigated the role of miR-155 in regulating p27Kip1 and affecting Tca8113 cell proliferation, cycle, and apoptosis...
March 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28337402/a-brief-review-of-bioinformatics-tools-for-glycosylation-analysis-by-mass-spectrometry
#13
Pei-Lun Tsai, Sung-Fang Chen
The purpose of this review is to provide updated information regarding bioinformatic software for the use in the characterization of glycosylated structures since 2013. A comprehensive review by Woodin et al.Analyst 138: 2793-2803, 2013 (ref. 1) described two main approaches that are introduced for starting researchers in this area; analysis of released glycans and the identification of glycopeptide in enzymatic digests, respectively. Complementary to that report, this review focuses on mass spectrometry related bioinformatics tools for the characterization of N-linked and O-linked glycopeptides...
2017: Mass Spectrometry
https://www.readbyqxmd.com/read/28337390/an-rbcl-reference-library-to-aid-in-the-identification-of-plant-species-mixtures-by-dna-metabarcoding
#14
Karen L Bell, Virginia M Loeffler, Berry J Brosi
PREMISE OF THE STUDY: DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS: Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337302/different-impairment-of-immune-and-inflammation-functions-in-short-and-long-term-after-ischemic-stroke
#15
Wen-Xing Li, Fei Qi, Jia-Qian Liu, Gong-Hua Li, Shao-Xing Dai, Tao Zhang, Fei Cheng, Dahai Liu, Song Guo Zheng
Ischemic stroke therapy and prognosis outcomes largely depend on the time periods after symptom onset. This study aims to explore the difference of global gene expression profiles and impairment of biological functions between short-term and long-term after stroke onset. We compared three short-term (3 h, 5 h and 24 h) and a long-term (6-month) gene expression levels by a multi-platform microarray data integration method. RankProd was used to calculate the differentially expressed genes between stroke patients and controls...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337293/mir-146b-protects-cardiomyocytes-injury-in-myocardial-ischemia-reperfusion-by-targeting-smad4
#16
Yun-Feng Di, De-Cai Li, Yan-Qing Shen, Chun-Lei Wang, Da-Yong Zhang, An-Quan Shang, Teng Hu
MicroRNAs, a class of small and non-encoding RNAs that transcriptionally or post-transcriptionally modulate the expression of their target genes, have been implicated as critical regulatory molecules in many cardiovascular diseases, including ischemia-/reperfusion-induced cardiac injury. In the present study, we report on the role of miR-146b in myocardial I/R injury and the underlying cardio-protective mechanism. Antagomir-146b was used to explore the effects of miR-146b on cardiac ischemia/reperfusion injury (30 min ischemia followed by 180 min reperfusion)...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337286/lps-induces-huvec-angiogenesis-in-vitro-through-mir-146a-mediated-tgf-%C3%AE-1-inhibition
#17
Yize Li, Huayu Zhu, Xu Wei, Heng Li, Zhicao Yu, Hongmei Zhang, Wenchao Liu
Angiogenesis is an essential process for tissue growth and embryo development. However, inflammation, abnormal wound healing, vascular diseases, and tumor development and progression can result from inappropriate angiogenesis. Lipopolysaccharide (LPS) can activate various cells and alter endothelium function and angiogenesis. This study investigated the underlying molecular events involved in LPS-induced angiogenesis and revealed a novel strategy for controlling abnormal angiogenesis. LPS treatment promoted wound healing and tube formation in human umbilical vein endothelial cell (HUVEC) cultures and induced their expression of miR-146a...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337280/mir-15a-suppresses-hepatocarcinoma-cell-migration-and-invasion-by-directly-targeting-cmyb
#18
Bo Liu, Ting Sun, Gang Wu, Hui Shang-Guan, Zhao-Jin Jiang, Ji-Ren Zhang, Yan-Fang Zheng
PURPOSE: This study aimed to determine the function of miR-15a in HCC, and identify cMyb as a target of miR-15a. METHODS: RNA expression was evaluated by quantitative real-time PCR (qRT-PCR). The effects of miR-15a or cMyb on HCC cells were evaluated by transwell migration assay and western blot analysis. CMyb, the predicted target, has been frequently verified by luciferase assay. RESULTS: MiR-15a was markedly downregulated in sphere culture HCC cells by qRT-PCR...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337276/microrna-9-regulates-non-small-cell-lung-cancer-cell-invasion-and-migration-by-targeting-eukaryotic-translation-initiation-factor-5a2
#19
Guodong Xu, Guofeng Shao, Qiaoling Pan, Lebo Sun, Dawei Zheng, Minghui Li, Ni Li, Huoshun Shi, Yiming Ni
MicroRNAs (miRNAs) play a critical role in cancer development and progression. Bioinformatics analyses has identified eukaryotic translation initiation factor 5A2 (eIF5A2) as a target of miR-9. In this study, we attempted to determine whether miR-9 regulates non-small cell lung cancer (NSCLC) cell invasion and migration by targeting eIF5A2 We examined eIF5A2 expression using reverse transcription-quantitative PCR (RT-qPCR) and subsequently transfected A549 and NCI-H1299 NSCLC cells with a miR-9 mimic or miR-9 inhibitor to determine the migration and invasive capability of the cells via wound healing assay and Transwell invasion assay, respectively...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337273/t-box-family-of-transcription-factor-tbx5-insights-in-development-and-disease
#20
Ting Zhu, Longwei Qiao, Qian Wang, Rui Mi, Jinnan Chen, Yaojuan Lu, Junxia Gu, Qiping Zheng
The T-box gene family refers to a group of transcription factors that share a highly conserved, sequence-specific DNA-binding domain (T-box) containing around 180-amino acids. According to HUGO gene nomenclature committee (HGNC), there are 18 T-box family members. These T-box genes have been implicated essential roles during embryogenesis and cardiac development, given their specific expression pattern in developing mammalian heart for several T-box genes, including TBX5. TBX5 is consisted of three transcriptional variants which cover 9 exons and encode two distinct isoforms that differ in N-terminus...
2017: American Journal of Translational Research
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