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apoptosis next generation sequencing

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https://www.readbyqxmd.com/read/29178829/encore-an-efficient-software-for-crispr-screens-identifies-new-players-in-extrinsic-apoptosis
#1
Dietrich Trümbach, Susanne Pfeiffer, Manuel Poppe, Hagen Scherb, Sebastian Doll, Wolfgang Wurst, Joel A Schick
BACKGROUND: As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight and efficient software to easily manipulate large raw next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include a simple graphical workflow, platform independence, local and fast multithreaded processing, data pre-processing and gene mapping with custom library import...
November 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29154802/microrna-profiling-in-mda-mb-231-human-breast-cancer-cell-exposed-to-the-phaleria-macrocarpa-boerl-fruit-ethyl-acetate-fraction-pmeaf-through-iilumina-hi-seq-technologies-and-various-in-silico-bioinformatics-tools
#2
Nowroji Kavitha, Soundararajan Vijayarathna, Shanmugapriya, Chern Ein Oon, Yeng Chen, Jagat R Kanwar, Vasu Punj, Sreenivasan Sasidharan
ETHNOPHARMACOLOGICAL RELEVANCE: Phaleria macrocarpa (Scheff) Boerl, is a famous traditional medicinal plant which exhibited cytotoxicity against various cancerous cells. Traditionally, P. macrocarpa has been used to control cancer, impotency, hemorrhoids, diabetes mellitus, allergies, liver and heart disease, kidney disorders, blood diseases, acne, stroke, migraine, and various skin diseases. AIM OF THE STUDY: Recent studies have demonstrated a potent anticancer potential of P...
November 14, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29138211/transcriptome-sequencing-of-the-naked-mole-rat-heterocephalus-glaber-and-identification-of-hypoxia-tolerance-genes
#3
Bang Xiao, Li Li, Chang Xu, Shanmin Zhao, Lifang Lin, Jishuai Cheng, Wenjing Yang, Wei Cong, Guanghan Kan, Shufang Cui
The naked mole rat (NMR; Heterocephalus glaber) is a small rodent species found in regions of Kenya, Ethiopia and Somalia. It has a high tolerance for hypoxia and is thus, considered one of the most important natural models for studying hypoxia tolerance mechanisms. The various mechanisms underlying the NMR's hypoxia tolerance are beginning to be understood at different levels of organization, and next-generation sequencing methods promise to expand this understanding to the level of gene expression. In this study, we examined the sequence and transcript abundance data of the muscle transcriptome of NMRs exposed to hypoxia using the Illumina HiSeq 2500 system to clarify the possible genomic adaptive responses to the hypoxic underground surroundings...
November 14, 2017: Biology Open
https://www.readbyqxmd.com/read/29137293/identification-of-novel-genetic-regulations-associated-with-airway-epithelial-homeostasis-using-next-generation-sequencing-data-and-bioinformatics-approaches
#4
Chau-Chyun Sheu, Ming-Ju Tsai, Feng-Wei Chen, Kuo-Feng Chang, Wei-An Chang, Inn-Wen Chong, Po-Lin Kuo, Ya-Ling Hsu
Airway epithelial cells play important roles in airway remodeling. Understanding gene regulations in airway epithelial homeostasis may provide new insights into pathogenesis and treatment of asthma. This study aimed to combine gene expression (GE) microarray, next generation sequencing (NGS), and bioinformatics to explore genetic regulations associated with airway epithelial homeostasis. We analyzed expression profiles of mRNAs (GE microarray) and microRNAs (NGS) in normal and asthmatic bronchial epithelial cells, and identified 9 genes with potential microRNA-mRNA interactions...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29058656/bursal-transcriptome-profiling-of-different-inbred-chicken-lines-reveals-key-differentially-expressed-genes-at-3-days-post-infection-with-very-virulent-infectious-bursal-disease-virus
#5
Mohd Isa Farhanah, Abd Rahaman Yasmin, Nurulfiza Mat Isa, Mohd Hair-Bejo, Aini Ideris, Claire Powers, Omobolanle Oladapo, Venugopal Nair, Jia-Shiun Khoo, Ahmad-Kamal Ghazali, Wai-Yan Yee, Abdul Rahman Omar
Infectious bursal disease is a highly contagious disease in the poultry industry and causes immunosuppression in chickens. Genome-wide regulations of immune response genes of inbred chickens with different genetic backgrounds, following very virulent infectious bursal disease virus (vvIBDV) infection are poorly characterized. Therefore, this study aims to analyse the bursal tissue transcriptome of six inbred chicken lines 6, 7, 15, N, O and P following infection with vvIBDV strain UK661 using strand-specific next-generation sequencing, by highlighting important genes and pathways involved in the infected chicken during peak infection at 3 days post-infection...
October 23, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#6
REVIEW
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29026837/binding-site-analysis-of-the-caenorhabditis-elegans-nr4a-nuclear-receptor-nhr-6-during-development
#7
Brandon Praslicka, Jeremy S Harmson, Joohyun Kim, Vittobai Rashika Rangaraj, Aikseng Ooi, Chris R Gissendanner
Members of the NR4A subfamily of nuclear receptors make up a highly conserved, functionally diverse group of transcription factors implicated in a multitude of cellular processes such as proliferation, differentiation, apoptosis, metabolism and DNA repair. The gene nhr-6, which encodes the sole C. elegans NR4A nuclear receptor homolog, has a critical role in organogenesis and regulates the development of the spermatheca organ system. Our previous work revealed that nhr-6 is required for spermatheca cell divisions in late L3 and early L4 and spermatheca cell differentiation during the mid L4 stage...
2017: Nuclear Receptor Research
https://www.readbyqxmd.com/read/28938744/an-improved-ivm-method-for-cumulus-oocyte-complexes-from-small-follicles-in-polycystic-ovary-syndrome-patients-enhances-oocyte-competence-and-embryo-yield
#8
F Sánchez, F Lolicato, S Romero, M De Vos, H Van Ranst, G Verheyen, E Anckaert, J E J Smitz
STUDY QUESTION: Are meiotic and developmental competence of human oocytes from small (2-8 mm) antral follicles improved by applying an optimized IVM method involving a prematuration step in presence of C-Type Natriuretic Peptide (CNP) followed by a maturation step in presence of FSH and Amphiregulin (AREG)? SUMMARY ANSWER: A strategy involving prematuration culture (PMC) in the presence of CNP followed by IVM using FSH + AREG increases oocyte maturation potential leading to a higher availability of Day 3 embryos and good-quality blastocysts for single embryo transfer...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28935667/upregulation-of-human-endogenous-retrovirus-k-is-linked-to-immunity-and-inflammation-in-pulmonary-arterial-hypertension
#9
Toshie Saito, Kazuya Miyagawa, Shih-Yu Chen, Rasa Tamosiuniene, Lingli Wang, Orr Sharpe, Erik Samayoa, Daisuke Harada, Jan-Renier A J Moonen, Aiqin Cao, Pin-I Chen, Jan K Hennigs, Mingxia Gu, Caiyun G Li, Ryan D Leib, Dan Li, Christopher M Adams, Patricia A Del Rosario, Matthew Bill, Francois Haddad, Jose G Montoya, William H Robinson, Wendy J Fantl, Garry P Nolan, Roham T Zamanian, Mark R Nicolls, Charles Y Chiu, Maria E Ariza, Marlene Rabinovitch
BACKGROUND: Immune dysregulation has been linked to occlusive vascular remodeling in pulmonary arterial hypertension (PAH) that is hereditary, idiopathic, or associated with other conditions. Circulating autoantibodies, lung perivascular lymphoid tissue, and elevated cytokines have been related to PAH pathogenesis but without a clear understanding of how these abnormalities are initiated, perpetuated, and connected in the progression of disease. We therefore set out to identify specific target antigens in PAH lung immune complexes as a starting point toward resolving these issues to better inform future application of immunomodulatory therapies...
November 14, 2017: Circulation
https://www.readbyqxmd.com/read/28928862/discovering-the-mir-26a-5p-targetome-in-prostate-cancer-cells
#10
Milena Rizzo, Gabriele Berti, Francesco Russo, Sofia Fazio, Monica Evangelista, Romina D'Aurizio, Marco Pellegrini, Giuseppe Rainaldi
Purpose. miR-26a-5p is a tumor suppressor (TS) miRNA often downregulated in several tumor tissues and tumor cell lines. In this work, we performed the re-expression of the miR-26a-5p in DU-145 prostate cancer cells to collect genes interacting with miR-26a-5p and analyzed their integration in the tumorigenesis related pathways. Methods. The transfection of DU-145 prostate cancer cells with miR-26a-5p was done using nucleofection. The biological effects induced by miR-26a-5p re-expression were detected with routine assays for cell proliferation, cell cycle, survival, apoptosis and cell migration...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28884089/splenic-microrna-expression-profiles-and-integration-analyses-involved-in-host-responses-to-salmonella-enteritidis-infection-in-chickens
#11
Peng Li, Wenlei Fan, Qinghe Li, Jie Wang, Ranran Liu, Nadia Everaert, Jie Liu, Yonghong Zhang, Maiqing Zheng, Huanxian Cui, Guiping Zhao, Jie Wen
To understand the role of miRNAs in regulating genes involved in the host response to Salmonella enteritidis (SE) infection, next generation sequencing was applied to explore the altered splenic expression of microRNAs (miRNAs) and deregulated genes in specific-pathogen-free chickens. Birds were either infected or not (controls, C) and those challenged with SE were evaluated 24 h later and separated into two groups on the basis of the severity of clinical symptoms and blood load of SE: resistant (R, SE challenged-slight clinical symptoms and <10(5) cfu / 10 μL), and susceptible (S, SE challenged-severe clinical symptoms and >10(7) cfu/10 μL)...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28832170/-novel-findings-in-follicular-lymphoma-pathogenesis-and-the-concepts-of-targeted-therapy
#12
J Deván, K Musilová, A Janíková, M Mráz
The molecular pathogenesis of follicular lymphoma (FL) was partially revealed by the discovery of BCL2 translocations to the region encoding the immunoglobulin heavy chain, which accompany the vast majority of cases. This aberration leads to the ectopic and constitutive expression of anti-apoptotic BCL2 protein in B-cells. Nevertheless, the aberration alone is not sufficient for FL development, which suggests necessity of further genetic aberrations acquisition for neoplastic transformation to FL. Their discovery has been enabled by recent progress in the field of massive parallel sequencing (next generation sequencing), which revealed high number of genetic aberrations connected with onset and progression of FL...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28830922/deletion-of-11q-in-neuroblastomas-drives-sensitivity-to-parp-inhibition
#13
Elena Sanmartín, Lisandra Muñoz, Marta Piqueras, J Antoni Sirerol, Pablo Berlanga, Adela Cañete, Victoria Castel, Jaime Font de Mora
Purpose: Despite advances in multimodal therapy, neuroblastomas with hemizygous deletion in chromosome 11q (20%-30%) undergo consecutive recurrences with poor outcome. We hypothesized that patients with 11q-loss may share a druggable molecular target(s) that can be exploited for a precision medicine strategy to improve treatment outcome.Experimental Design: SNP arrays were combined with next-generation sequencing (NGS) to precisely define the deleted region in 17 primary 11q-loss neuroblastomas and identify allelic variants in genes relevant for neuroblastoma etiology...
August 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28827396/genetic-diagnosis-of-polycystic-kidney-disease-alport-syndrome-and-thalassemia-minor-in-a-large-chinese-family
#14
Yun Miao, Jun Xiong, Xuelian Zhang, Huajie Huang, Lixin Yu, Jianfan Chen, Wenfeng Deng, Huiling Xu, Rumin Liu, Chenglin Xiang, Xiangmin Xu, Fu Xiong
Polycystic kidney disease (PKD) and Alport syndrome (AS) are serious inherited disorders associated with renal disease, and thalassemia is a hereditary blood disease with a high prevalence in south China. Here, we report an exceptional PKD coincidence of thalassemia minor and AS (diagnosed genetically) in a large Chinese family. Whole genome next-generation sequencing (NGS) was performed on the proband, and all family members underwent clinical evaluation. Sanger sequencing was used to validate the mutations distinguished by NGS...
October 1, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28748849/a-novel-missense-mutation-in-peripheral-myelin-protein-22-causes-charcot-marie-tooth-disease
#15
Li-Xi Li, Hai-Lin Dong, Bao-Guo Xiao, Zhi-Ying Wu
BACKGROUND: Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. A great number of causative genes have been described in CMT, and among them, the heterozygous duplication of peripheral myelin protein-22 (PMP22) is the major cause. Although the missense mutation in PMP22 is rarely reported, it has been demonstrated to be associated with CMT. This study described a novel missense mutation of PMP22 in a Chinese family with CMT phenotype. METHODS: Targeted next-generation sequencing (NGS) was used to screen the causative genes in a family featured with an autosomal dominant demyelinating form of CMT...
August 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28731464/trophoblast-survival-signaling-during-human-placentation-requires-hsp70-activation-of-mmp2-mediated-hbegf-shedding
#16
Chandni V Jain, Philip Jessmon, Charbel T Barrak, Alan D Bolnick, Brian A Kilburn, Michael Hertz, D Randall Armant
Survival of trophoblast cells in the low oxygen environment of human placentation requires metalloproteinase-mediated shedding of HBEGF and downstream signaling. A matrix metalloproteinase (MMP) antibody array and quantitative RT-PCR revealed upregulation of MMP2 post-transcriptionally in human first trimester HTR-8/SVneo trophoblast cells and placental villous explants exposed to 2% O2. Specific MMP inhibitors established the requirement for MMP2 in HBEGF shedding and upregulation. Because α-amanitin inhibited the upregulation of HBEGF, differentially expressed genes were identified by next-generation sequencing of RNA from trophoblast cells cultured at 2% O2 for 0, 1, 2 and 4 h...
October 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28667769/resistance-to-rhd-virus-in-wild-australian-rabbits-comparison-of-susceptible-and-resistant-individuals-using-a-genomewide-approach
#17
Nina I Schwensow, Harald Detering, Stephen Pederson, Camila Mazzoni, Ron Sinclair, David Peacock, John Kovaliski, Brian Cooke, Jörns Fickel, Simone Sommer
Deciphering the genes involved in disease resistance is essential if we are to understand host-pathogen coevolutionary processes. The rabbit haemorrhagic disease virus (RHDV) was imported into Australia in 1995 as a biocontrol agent to manage one of the most successful and devastating invasive species, the European rabbit (Oryctolagus cuniculus). During the first outbreaks of the disease, RHDV caused mortality rates of up to 97%. Recently, however, increased genetic resistance to RHDV has been reported. Here, we have aimed to identify genomic differences between rabbits that survived a natural infection with RHDV and those that died in the field using a genomewide next-generation sequencing (NGS) approach...
July 1, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28647693/recognition-investigation-and-management-of-mitochondrial-disease
#18
REVIEW
James E Davison, Shamima Rahman
Mitochondria are dynamic organelles present in virtually all human cells that are needed for a multitude of cellular functions, including energy production, control of cell apoptosis and numerous biochemical catabolic and synthetic pathways that are critical for cellular health. Primary mitochondrial disorders are a group of greater than 200 single gene defects arising from two genomes (nuclear and mitochondrial) leading to mitochondrial dysfunction, and are associated with extremely heterogeneous phenotypes...
November 2017: Archives of Disease in Childhood
https://www.readbyqxmd.com/read/28646916/prc1-contributes-to-tumorigenesis-of-lung-adenocarcinoma-in-association-with-the-wnt-%C3%AE-catenin-signaling-pathway
#19
Ping Zhan, Bin Zhang, Guang-Min Xi, Ying Wu, Hong-Bing Liu, Ya-Fang Liu, Wu-Jian Xu, Qing-Qing Zhu, Feng Cai, Ze-Jun Zhou, Ying-Ying Miu, Xiao-Xia Wang, Jia-Jia Jin, Qian Li, Li-Ping Qian, Tang-Feng Lv, Yong Song
BACKGROUND: Protein regulator of cytokinesis-1 (PRC1) belongs to the microtubule-associated proteins (MAPs) family, and is involved in cytokinesis. Recent investigations suggest PRC1 involvement in human carcinogenesis, including breast carcinoma, hepatocellular carcinoma and etc. However, whether PRC1 contributes to lung adenocarcinoma tumorigenesis remains unknown. METHODS: Quantitative reverse-transcription polymerase chain reaction (qRT-PCR), Western blotting and Immunohistochemical staining (IHC) were used to evaluate and contrast the PRC1 expression profile in lung adenocarcinoma and adjacent normal lung tissues...
June 24, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28641578/methylome-analysis-of-extreme-chemoresponsive-patients-identifies-novel-markers-of-platinum-sensitivity-in-high-grade-serous-ovarian-cancer
#20
Tushar Tomar, Nicolette G Alkema, Leroy Schreuder, Gert Jan Meersma, Tim de Meyer, Wim van Criekinge, Harry G Klip, Heidi Fiegl, Els van Nieuwenhuysen, Ignace Vergote, Martin Widschwendter, Ed Schuuring, Ate G J van der Zee, Steven de Jong, G Bea A Wisman
BACKGROUND: Despite an early response to platinum-based chemotherapy in advanced stage high-grade serous ovarian cancer (HGSOC), the majority of patients will relapse with drug-resistant disease. Aberrant epigenetic alterations like DNA methylation are common in HGSOC. Differences in DNA methylation are associated with chemoresponse in these patients. The objective of this study was to identify and validate novel epigenetic markers of chemoresponse using genome-wide analysis of DNA methylation in extreme chemoresponsive HGSOC patients...
June 23, 2017: BMC Medicine
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