keyword
MENU ▼
Read by QxMD icon Read
search

rnaseq

keyword
https://www.readbyqxmd.com/read/29346549/transcriptome-and-functional-analysis-in-a-drosophila-model-of-ngly1-deficiency-provides-insight-into-therapeutic-approaches
#1
Katie G Owings, Joshua B Lowry, Yiling Bi, Matthew Might, Clement Y Chow
Autosomal recessive loss-of-function mutations in N-Glycanase 1 (NGLY1) cause NGLY1 deficiency, the only known human disease of deglycosylation. Patients present with developmental delay, movement disorder, seizures, liver dysfunction, and alacrima. NGLY1 is a conserved cytoplasmic component of the Endoplasmic Reticulum Associated Degradation (ERAD) pathway. ERAD clears misfolded proteins from the ER lumen. However, it is unclear how loss of NGLY1 function impacts ERAD and other cellular processes and results in the constellation of problems associated with NGLY1 deficiency...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29343494/uncovering-genomic-regions-associated-with-trypanosoma-infections-in-wild-populations-of-the-tsetse-fly-glossina-fuscipes
#2
Andrea Gloria-Soria, W Augustine Dunn, Xiaoqing Yu, Aurélien Vigneron, Kuang-Yao Lee, Mo Li, Brian L Weiss, Hongyu Zhao, Serap Aksoy, Adalgisa Caccone
Vector-borne diseases are responsible for more than one million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ~73,000 polymorphic sites distributed across the genome...
January 17, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29331591/brochosomins-and-other-novel-proteins-from-brochosomes-of-leafhoppers-insecta-hemiptera-cicadellidae
#3
Roman Rakitov, Alexander A Moysa, Arthur T Kopylov, Sergei A Moshkovskii, Ralph S Peters, Karen Meusemann, Bernhard Misof, Christopher H Dietrich, Kevin P Johnson, Lars Podsiadlowski, Kimberly K O Walden
Brochosomes (BS) are secretory granules resembling buckyballs, produced intracellularly in specialized glandular segments of the Malpighian tubules and forming superhydrophobic coatings on the integuments of leafhoppers (Hemiptera, Cicadellidae). Their composition is poorly known. Using a combination of SDS-PAGE, LC-MS/MS, next-generation sequencing (RNAseq) and bioinformatics we demonstrate that the major structural component of BS of the leafhopper Graphocephala fennahi Young is a novel family of 21-40-kDa secretory proteins, referred to herein as brochosomins (BSM), apparently cross-linked by disulfide bonds...
January 10, 2018: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29331210/to-roll-the-eyes-and-snap-a-bite-function-development-and-evolution-of-craniofacial-muscles
#4
REVIEW
Frank R Schubert, Arun J Singh, Oluwatomisin Afoyalan, Chrissa Kioussi, Susanne Dietrich
Craniofacial muscles, muscles that move the eyes, control facial expression and allow food uptake and speech, have long been regarded as a variation on the general body muscle scheme. However, evidence has accumulated that the function of head muscles, their developmental anatomy and the underlying regulatory cascades are distinct. This article reviews the key aspects of craniofacial muscle and muscle stem cell formation and discusses how this differs from the trunk programme of myogenesis; we show novel RNAseq data to support this notion...
January 10, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29330722/location-of-low-copy-genes-in-chromosomes-of-brachiaria-spp
#5
Thaís Furtado Nani, James C Schnable, Jacob D Washburn, Patrice Albert, Welison Andrade Pereira, Fausto Souza Sobrinho, James A Birchler, Vânia Helena Techio
Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330289/brca1-through-its-e3-ligase-activity-regulates-the-transcription-factor-oct1-and-carbohydrate-metabolism
#6
Karina Vázquez-Arreguín, Jessica Maddox, Jinsuk Kang, Dongju Park, Reuben R Cano, Rachel E Factor, Thomas Ludwig, Dean Tantin
The tumor suppressor BRCA1 regulates the DNA damage response (DDR) and other processes that remain incompletely defined. Among these, BRCA1 heterodimerizes with BARD1 to ubiquitylate targets via its N-terminal E3 ligase activity. Here it is demonstrated that BRCA1 promotes oxidative metabolism by degrading Oct1 (POU2F1), a transcription factor with pro-glycolytic and tumorigenic effects. BRCA1 E3 ubiquitin ligase mutation skews cells towards a glycolytic metabolic profile while elevating Oct1 protein. CRISPR-mediated Oct1 deletion reverts the glycolytic phenotype...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29329637/transcriptomic-evidence-of-immune-activation-in-macroscopically-normal-appearing-and-scarred-lung-tissues-in-idiopathic-pulmonary-fibrosis
#7
Irina G Luzina, Mariah V Salcedo, Mónica L Rojas-Peña, Anne E Wyman, Jeffrey R Galvin, Ashutosh Sachdeva, Andrew Clerman, June Kim, Teri J Franks, Edward J Britt, Jeffrey D Hasday, Si M Pham, Allen P Burke, Nevins W Todd, Sergei P Atamas
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease manifested by overtly scarred peripheral and basilar regions and more normal-appearing central lung areas. Lung tissues from macroscopically normal-appearing (IPFn) and scarred (IPFs) areas of explanted IPF lungs were analyzed by RNASeq and compared with healthy control (HC) lung tissues. There were profound transcriptomic changes in IPFn compared with HC tissues, which included elevated expression of numerous immune-, inflammation-, and extracellular matrix-related mRNAs, and these changes were similar to those observed with IPFs compared to HC...
January 3, 2018: Cellular Immunology
https://www.readbyqxmd.com/read/29328463/construction-and-investigation-of-lncrna-associated-cerna-regulatory-network-in-papillary-thyroid-cancer
#8
Yangjing Zhao, Hui Wang, Chengjiang Wu, Meina Yan, Haojie Wu, Jingzhe Wang, Xinxin Yang, Qixiang Shao
Increasing evidence has experimentally proved the competitive endogenous RNA (ceRNA) hypothesis that long non-coding RNA (lncRNA) can affect the expression of RNA targets by competitively combining microRNA (miRNA) via miRNA response elements. However, an extensive ceRNA network of thyroid carcinoma in a large cohort has not been evaluated. We analyzed the RNAseq and miRNAseq data of 348 cases of primary papillary thyroid cancer (PTC) patients with clinical information downloaded from The Cancer Genome Atlas (TCGA) project to search for potential biomarkers or therapeutic targets...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29315949/transcriptome-based-analyses-of-phosphite-mediated-suppression-of-rust-pathogens-puccinia-emaculata-and-phakopsora-pachyrhizi-and-functional-characterization-of-selected-fungal-target-genes
#9
Upinder S Gill, Liang Sun, Sachin Rustgi, Yuhong Tang, Diter von Wettstein, Kirankumar S Mysore
Phosphite (Phi) is commercially used to manage diseases mainly caused by Oomycetes, primarily due to its low-cost compared to other fungicides, and persistent control of oomycetous pathogens. We explored the use of Phi in controlling fungal pathogens Puccinia emaculata and Phakopsora pachyrhizi the causal agents of the switchgrass rust and the Asian soybean rust, respectively. Phi primes host defenses and efficiently inhibits growth of P. emaculata, P. pachyrhizi, and several other fungal pathogens tested. To understand the Phi-mediated effects, a detailed molecular analysis was undertaken in both the host and the pathogen...
January 6, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29314727/molecular-processes-underlying-synergistic-linuron-mineralization-in-a-triple-species-bacterial-consortium-biofilm-revealed-by-differential-transcriptomics
#10
Pieter Albers, Bram Weytjens, René De Mot, Kathleen Marchal, Dirk Springael
The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple-species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis...
January 3, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29305708/identification-of-specific-feed-forward-apoptosis-mechanisms-and-associated-higher-survival-rates-for-low-grade-glioma-and-lung-squamous-cell-carcinoma
#11
Dhiraj Sikaria, Yaping N Tu, Diana A Fisler, James A Mauro, George Blanck
The mechanisms of cell proliferation due to the overexpression of certain transcription factors (TFs) have been well documented in the cancer setting. However, many of these same TFs have pro-apoptotic effects, particularly when expressed or activated at high levels, a process referred to as feed-forward apoptosis (FFA). To determine whether cancers could be stratified on the basis of specific FFA signatures, RNASeq data representing samples from the cancer genome atlas were analyzed, revealing that high expression of the pro-proliferative TFs, MYC and YY1, is associated with a favorable outcome in low-grade glioma (LGG) and lung squamous cell carcinoma (LUSC), respectively...
January 5, 2018: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/29304737/rnaseq-analysis-of-%C3%AE-proteobacterium-gluconobacter-oxydans-621h
#12
Angela Kranz, Tobias Busche, Alexander Vogel, Björn Usadel, Jörn Kalinowski, Michael Bott, Tino Polen
BACKGROUND: The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium has been characterized to some extent, yet little is known about its transcriptomes and related data. In this study, we applied two different RNAseq approaches. Primary transcriptomes enriched for 5'-ends of transcripts were sequenced to detect transcription start sites, which allow subsequent analysis of promoter motifs, ribosome binding sites, and 5´-UTRs...
January 6, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29301788/cardiac-endothelial-cell-transcriptome
#13
Achim Lother, Stella Bergemann, Lisa Deng, Martin Moser, Christoph Bode, Lutz Hein
OBJECTIVE: Endothelial cells (ECs) are a highly specialized cell type with marked diversity between different organs or vascular beds. Cardiac ECs are an important player in cardiac physiology and pathophysiology but are not sufficiently characterized yet. Thus, the aim of the present study was to analyze the cardiac EC transcriptome. APPROACH AND RESULTS: We applied fluorescence-assisted cell sorting to isolate pure ECs from adult mouse hearts. RNAseq revealed 1288 genes predominantly expressed in cardiac ECs versus heart tissue including several transcription factors...
January 4, 2018: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29301509/assessment-of-pirna-biogenesis-and-function-in-testicular-germ-cell-tumors-and-their-precursor-germ-cell-neoplasia-in-situ
#14
Ildar V Gainetdinov, Yulia V Skvortsova, Sofia A Kondratieva, Alexey Klimov, Alexey A Tryakin, Tatyana L Azhikina
BACKGROUND: Aberrant overexpression of PIWI/piRNA pathway proteins is shown for many types of tumors. Interestingly, these proteins are downregulated in testicular germ cell tumors (TGCTs) compared to normal testis tissues. Here, we used germline and TGCT markers to assess the piRNA biogenesis and function in TGCTs and their precursor germ cell neoplasia in situ (GCNIS). METHODS: We used small RNA deep sequencing, qRT-PCR, and mining public RNAseq/small RNA-seq datasets to examine PIWI/piRNA gene expression and piRNA biogenesis at four stages of TGCT development: (i) germ cells in healthy testis tissues, (ii) germ cells in testis tissues adjacent to TGCTs, (iii) GCNIS cells and (iv) TGCT cells...
January 4, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29301198/regulation-of-cd4-receptor-and-hiv-1-entry-by-micrornas-221-and-222-during-differentiation-of-thp-1-cells
#15
Robert Lodge, Julian C Gilmore, Jérémy A Ferreira Barbosa, Félix Lombard-Vadnais, Éric A Cohen
Human immunodeficiency virus type-1 (HIV-1) infection of monocyte/macrophages is modulated by the levels of entry receptors cluster of differentiation 4 (CD4) and C-C chemokine receptor type 5 (CCR5), as well as by host antiviral restriction factors, which mediate several post-entry blocks. We recently identified two microRNAs, miR-221 and miR-222, which limit HIV-1 entry during infection of monocyte-derived macrophages (MDMs) by down-regulating CD4 expression. Interestingly, CD4 is also down-regulated during the differentiation of monocytes into macrophages...
December 30, 2017: Viruses
https://www.readbyqxmd.com/read/29300189/bcor-ccnb3-fusion-positive-sarcomas-a-clinicopathologic-and-molecular-analysis-of-36-cases-with-comparison-to-morphologic-spectrum-and-clinical-behavior-of-other-round-cell-sarcomas
#16
Yu-Chien Kao, Adepitan A Owosho, Yun-Shao Sung, Lei Zhang, Yumi Fujisawa, Jen-Chieh Lee, Leonard Wexler, Pedram Argani, David Swanson, Brendan C Dickson, Christopher D M Fletcher, Cristina R Antonescu
BCOR-CCNB3 sarcoma (BCS) is a recently defined genetic entity among undifferentiated round cell sarcomas, which was initially classified as and treated similarly to the Ewing sarcoma (ES) family of tumors. In contrast to ES, BCS shows consistent BCOR overexpression, and preliminary evidence suggests that these tumors share morphologic features with other tumors harboring BCOR genetic alterations, including BCOR internal tandem duplication (ITD) and BCOR-MAML3. To further investigate the pathologic features, clinical behavior, and their relationship to other round cell sarcomas, we collected 36 molecularly confirmed BCSs for a detailed histologic and immunohistochemical analysis...
October 25, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29296973/high-throughput-sequencing-of-the-b-cell-receptor-in-african-burkitt-lymphoma-reveals-clues-to-pathogenesis
#17
Katharine A Lombardo, David G Coffey, Alicia J Morales, Christopher S Carlson, Andrea M H Towlerton, Sarah E Gerdts, Francis K Nkrumah, Janet Neequaye, Robert J Biggar, Jackson Orem, Corey Casper, Sam M Mbulaiteye, Kishor G Bhatia, Edus H Warren
Burkitt lymphoma (BL), the most common pediatric cancer in sub-Saharan Africa, is a malignancy of antigen-experienced B lymphocytes. High-throughput sequencing (HTS) of the immunoglobulin heavy (IGH) and light chain (IGK/IGL) loci was performed on genomic DNA from 51 primary BL tumors: 19 from Uganda and 32 from Ghana. Reverse transcription polymerase chain reaction analysis and tumor RNA sequencing (RNAseq) was performed on the Ugandan tumors to confirm and extend the findings from the HTS of tumor DNA. Clonal IGH and IGK/IGL rearrangements were identified in 41 and 46 tumors, respectively...
March 28, 2017: Blood Advances
https://www.readbyqxmd.com/read/29288462/primary-characterization-of-small-rnas-in-symbiotic-nitrogen-fixing-bacteria
#18
Marta Robledo, Natalia I García-Tomsig, José I Jiménez-Zurdo
High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. A large fraction of sRNAs are differentially regulated and rely on protein-assisted antisense interactions to trans-encoded target mRNAs to fine-tune posttranscriptional reprogramming of gene expression in response to external cues. However, annotation and function of sRNAs are still largely overlooked in nonmodel bacteria with complex lifestyles...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29288237/genomics-driven-precision-medicine-for-advanced-pancreatic-cancer-early-results-from-the-compass-trial
#19
Kyaw Lwin Aung, Sandra E Fischer, Robert E Denroche, Gun-Ho Jang, Anna Dodd, Sean Creighton, Bernadette Southwood, Sheng-Ben Liang, Dianne Chadwick, Amy Zhang, Grainne M O'Kane, Hamzeh Adel Amin Albaba, Shari Moura, Robert C Grant, Jessica K Miller, Faridah Mbabaali, Danielle Pasternack, Ilinca M Lungu, John M S Bartlett, Sangeet Ghai, Mathieu Lemire, Spring Holter, Ashton A Connor, Richard A Moffitt, Jen Jen Yeh, Lee Timms, Paul M Krzyzanowski, Neesha C Dhani, David W Hedley, Faiyaz Notta, Julie M Wilson, Malcolm J Moore, Steven Gallinger, Jennifer J Knox
PURPOSE: To perform real time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for better treatment selection.  Experimental Design: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases...
December 29, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29285317/altered-expression-of-differential-gene-and-lncrna-in-the-lower-thoracic-spinal-cord-on-different-time-courses-of-experimental-obstructive-jaundice-model-accompanied-with-altered-peripheral-nociception-in-rats
#20
Qian Wang, Zhi-Xiao Li, Bao-Wen Liu, Zhi-Gang He, Cheng Liu, Min Chen, San-Guang Liu, Wei-Zhong Wu, Hong-Bing Xiang
The spinal origin of jaundice-induced altered peripheral nociceptive response poorly understood. In the current study, we aimed to first validate rats with bile duct ligation (BDL) as a jaundice model accompanied by altered peripheral nociceptive response, and then to analyze differential gene and lncRNA expression patterns in the lower thoracic spinal cord on different time courses after BDL operation by using high-throughput RNA sequencing. The differentially expressed genes (DEGs) identified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, followed by clustering analysis, Gene Ontology analysis and pathway analysis...
December 1, 2017: Oncotarget
keyword
keyword
44655
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"