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Fei Ji, Ruslan I Sadreyev
Quantitative analysis of gene expression is crucial for understanding the molecular mechanisms underlying genome regulation. RNA-seq is a powerful platform for comprehensive investigation of the transcriptome. In this unit, we present a general bioinformatics workflow for the quantitative analysis of RNA-seq data and describe a few current publicly available computational tools applicable at various steps of this workflow. These tools comprise a pipeline for quality assessment and quantitation of RNA-seq data that starts from raw sequencing files and is focused on the identification and analysis of genes that are differentially expressed between biological conditions...
September 17, 2018: Current Protocols in Molecular Biology
Wen-Jie Wang, Hong-Tao Li, Jian-Ping Yu, Yu-Min Li, Xiao-Peng Han, Peng Chen, Wen-Wen Yu, Wei-Kai Chen, Zuo-Yi Jiao, Hong-Bin Liu
Gastrointestinal stromal tumors (GISTs) are the most common type of mesenchymal tumor in the gastrointestinal tract. The present study aimed to identify the potential candidate biomarkers that may be involved in the pathogenesis and progression of v‑kit Hardy‑Zuckerman 4 feline sarcoma viral oncogene homolog (KIT)/platelet‑derived growth factor receptor α (PDGFRA) wild‑type GISTs. A joint bioinformatics analysis was performed to identify the differentially expressed genes (DEGs) in wild‑type GIST samples compared with KIT/PDGFRA mutant GIST samples...
September 5, 2018: Molecular Medicine Reports
Biao Ma, Yang Yang, Zhituo Li, Dali Zhao, Weihui Zhang, Yanfeng Jiang, Dongbo Xue
In recent years, an increasing number of studies on the roles of macrophages in tumors, immune responses and metabolism have been published, in which macrophage polarization has been an extensively discussed topic. In the present study, differentially expressed genes in various types of macrophages were analyzed using the Gene Expression Omnibus database. Cluster analysis of differentially expressed genes was conducted, and a protein‑protein interaction (PPI) network was constructed. Finally, modular analysis and functional enrichment analysis revealed that a Toll‑like receptor (TLR) signaling pathway is involved in the regulation of macrophage polarization...
September 14, 2018: Molecular Medicine Reports
Xiaotong Wang, Xiaopeng Cui, Chuanwu Zhu, Ming Li, Juan Zhao, Zhongyi Shen, Xiaohang Shan, Liang Wang, Han Wu, Yanting Shen, You Ni, Dongmei Zhang, Guoxiong Zhou
Endoplasmic reticulum (ER) stress in intestinal epithelial cells (IECs) has an important role in the pathogenesis of Crohn's disease (CD). FK506 binding protein 11 (FKBP11), a member of the peptidyl‑prolyl cis‑trans isomerase family, is involved in the unfolded protein response (UPR) and is closely associated with inflammation. Previous bioinformatics analysis revealed a potential association between FKBP11 and human CD. Thus, the present study aimed to investigate the potential significance of FKBP11 in IEC homeostasis and CD...
September 14, 2018: Molecular Medicine Reports
Zhu Wang, Jianwen Zhang, Ying Zhang, Qiong Deng, Hui Liang
Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) are the most well‑known genes linked to breast cancer and ovarian cancer, which are crucial in DNA repair and transcriptional regulation. The present study aimed to elucidate the expression profiles, mutations and interaction networks of BRCA1 and BRCA2, which may provide insights to reveal the mechanisms of BRCA genes ultimately leading to breast or ovarian tumorigenesis. Bioinformatics analyses were performed in the present study. The mRNA levels of BRCA1 and BRCA2 were evaluated using FIREHOSE analysis, SAGE Genie tools and Oncomine analysis...
September 11, 2018: International Journal of Molecular Medicine
Xiaoqi Zhang, Hao Feng, Juan Du, Jing Sun, Dongfang Li, Tomoka Hasegawa, Norio Amizuka, Minqi Li
Rheumatoid arthritis (RA) is a commonly occurring autoimmune disease. Its defining pathological characteristic is the excessive proliferation of fibroblast‑like synoviocytes (FLS), which is similar to tumor cells and results in a range of clinical problems. As a commonly used antipyretic, analgesic and anti‑inflammatory drug, aspirin is the first‑line treatment for RA. However, its mechanism of action has not been well explained. The goal is to investigate the biological effects of aspirin on primary RA‑FLS and its underlying mechanisms...
September 17, 2018: International Journal of Molecular Medicine
Ying Zhou, Ling Li, Jun Qian, Haoyuan Jia, Yubao Cui
Aquaporins (AQPs), or water channel proteins, are highly conserved across species. These transmembrane proteins promote water and solute transport across cell membranes. No AQP‑related proteins have been identified in mites to date. The present study used transcriptomics (RNA‑sequencing) to identify potential AQPs in the mite species Blomia tropicalis. Molecular cloning techniques were then used to obtain the full‑length gene sequences encoding these AQP family members, and bioinformatics analyses were used to categorize them based on similarity to AQPs in other species...
September 13, 2018: International Journal of Molecular Medicine
Francisco Vargas-Albores, Luis R Martínez-Córdova, Marcel Martínez-Porchas, Kadiya Calderón, Asunción Lago-Lestón
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities...
September 17, 2018: Biotechnology & Genetic Engineering Reviews
Rolando Garcia-Milian, Denise Hersey, Milica Vukmirovic, Fanny Duprilot
Background: High-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor. Methods: A multimodal needs assessment analysis combined an online survey sent to 860 Yale-affiliated researchers (176 responded) and 15 in-depth one-on-one semi-structured interviews...
2018: PeerJ
Zhizhou Kuang, Ruochun Huang, Zhimin Yang, Zhiqiang Lv, Xinyan Chen, Fuping Xu, Yu-Hua Yi, Jian Wu, Ruo-Pan Huang
Screening biomarkers in serum samples for different diseases has always been of great interest because it presents an early, reliable, and, most importantly, noninvasive means of diagnosis and prognosis. Reverse phase protein arrays (RPPAs) are a high-throughput platform that can measure single or limited sets of proteins from thousands of patients' samples in parallel. They have been widely used for detection of signaling molecules involved in diseases, especially cancers, and related regulation pathways in cell lysates...
August 24, 2018: Oncotarget
Diego Robledo, Christos Palaiokostas, Luca Bargelloni, Paulino Martínez, Ross Houston
Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high-density single-nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date...
August 2018: Reviews in Aquaculture
Nelly R Hajizadeh, Joanna Pieprzyk, Petr Skopintsev, Ali Flayhan, Dmitri I Svergun, Christian Löw
The scaffolding protein PDZK1 has been associated with the regulation of membrane transporters. It contains four conserved PDZ domains, which typically recognize a 3-5-residue long motif at the C terminus of the binding partner. The atomic structures of the individual domains are available but their spatial arrangement in the full-length context influencing the binding properties remained elusive. Here we report a systematic study of full-length PDZK1 and deletion constructs using small-angle X-ray scattering, complemented with biochemical and functional studies on PDZK1 binding to known membrane protein partners...
August 16, 2018: Structure
Xuefeng An, Hong Quan, Jinhui Lv, Lingyu Meng, Cheng Wang, Zuoren Yu, Jing Han
AIM: The present study aimed to identify microRNA (miRNA) that can be used for not only detecting early-stage breast cancer (BC) but also diagnosing atypical hyperplasia (AH). MATERIALS & METHODS: RT-qPCR detected the expression levels of miRNAs and receiver operating characteristic curves were constructed to evaluate sensitivity and specificity of the assay. RESULTS: miR-24 and miR-103a were expressed in an upward trend in serum of benign proliferative tumor subjects, while they were downregulated significantly in serum of AH (p < 0...
September 17, 2018: Future Oncology
A Fucic, A Aghajanyan, Z Culig, N Le Novere
Large investments by pharmaceutical companies in the development of new antineoplastic drugs have not been resulting in adequate advances of new therapies. Despite the introduction of new methods, technologies, translational medicine and bioinformatics, the usage of collected knowledge is unsatisfactory. In this paper, using examples of pancreatic ductal adenocarcinoma (PaC) and castrate-resistant prostate cancer (CRPC), we proposed a concept showing that, in order to improve applicability of current knowledge in oncology, the re-clustering of clinical and scientific data is crucial...
September 16, 2018: Pathology Oncology Research: POR
Jaroslav Budis, Juraj Gazdarica, Jan Radvanszky, Gabor Szucs, Marcel Kucharik, Lucia Strieskova, Iveta Gazdaricova, Maria Harsanyova, Frantisek Duris, Gabriel Minarik, Martina Sekelska, Balint Nagy, Jan Turna, Tomas Szemes
Motivation: Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test...
September 14, 2018: Bioinformatics
Albert Casanovas, Óscar Gallardo, Montserrat Carrascal, Joaquin Abian
Motivation: Protein function is regulated by post-translational modifications (PTMs) that may act individually or interact with others in a phenomenon termed PTM cross-talk. Multiple databases have been dedicated to PTMs, including recent initiatives oriented towards the in silico prediction of PTM interactions. The study of PTM cross-talk ultimately requires experimental evidence about whether certain PTMs co-exist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co-modified peptides...
September 13, 2018: Bioinformatics
Yan Wu, Liu Liu, Chunxiang Bian, Qingchun Diao, Muhammad Farrukh Nisar, Xuemei Jiang, Jörg W Bartsch, Maojiao Zhong, Xiangyu Hu, Julia Li Zhong
BACKGROUND: The extensive involvement of microRNA (miRNA) in the pathophysiology of psoriasis is well documented. However, in order for this information to be useful in therapeutic manipulation of miRNA levels, it is essential that detailed functional mechanisms are elucidated. This study aimed to explore the effects of IL-6 targeting by let-7b and ERK1/2 mediated signaling on keratinocyte differentiation in psoriasis. METHODS: Following imiquimod cream (IMQ) application to let-7bTG (keratinocyte-specific let-7b overexpression mouse) and control mice for 7 days, we analyzed erythema, scaling and thickening of skin...
September 15, 2018: Cell Communication and Signaling: CCS
Rohit Kongari, Manoj Rajaure, Jesse Cahill, Eric Rasche, Eleni Mijalis, Joel Berry, Ry Young
BACKGROUND: Spanins are phage lysis proteins required to disrupt the outer membrane. Phages employ either two-component spanins or unimolecular spanins in this final step of Gram-negative host lysis. Two-component spanins like Rz-Rz1 from phage lambda consist of an integral inner membrane protein: i-spanin, and an outer membrane lipoprotein: o-spanin, that form a complex spanning the periplasm. Two-component spanins exist in three different genetic architectures; embedded, overlapped and separated...
September 15, 2018: BMC Bioinformatics
Zhe Ju, Shi-Yun Wang
Lipoylation is a highly conserved post-translational modification which has been found to be involved in many biological processes and closely associated with various metabolic diseases. The accurate identification of lipoylation sites is necessary to elucidate the underlying molecular mechanisms of lipoylation. As the traditional experimental methods are time consuming and expensive, it is desired to develop computational methods to predict lipoylation sites. In this study, a novel predictor named LipoPred is proposed to predict lysine lipoylation sites...
September 12, 2018: Analytical Biochemistry
Bhavna Hurgobin, Emma de Jong, Anthony Bosco
Respiratory diseases such as asthma, chronic obstructive pulmonary disease and lung cancer represent a critical area for medical research as millions of people are affected globally. The development of new strategies for treatment and/or prevention, and the identification of biomarkers for patient stratification and early detection of disease inception are essential to reducing the impact of lung diseases. The successful translation of research into clinical practice requires a detailed understanding of the underlying biology...
September 14, 2018: Respirology: Official Journal of the Asian Pacific Society of Respirology
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