keyword
MENU ▼
Read by QxMD icon Read
search

Transcriptome

keyword
https://www.readbyqxmd.com/read/29166177/kinetic-behavior-of-campylobacter-jejuni-in-beef-tartare-at-cold-temperatures-and-transcriptomes-related-to-its-survival
#1
Sejeong Kim, Jiyeon Jeong, Heeyoung Lee, Jeeyeon Lee, Soomin Lee, Jimyeong Ha, Yukyoung Choi, Yohan Yoon, Kyoung-Hee Choi
This study was conducted to examine the kinetic behavior of Campylobacter jejuni in raw beef tartare by using mathematical models and to identify genes related to C. jejuni survival at cold temperatures. C. jejuni was inoculated onto beef tartare samples, stored at 4, 10, 15, 25, and 30°C, plated on modified charcoal-cefoperazone-deoxycholate agar, and enumerated. The survival data was fitted to the Weibull model to calculate delta (δ), which is the time required for the first 1-log reduction of the cells...
November 22, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/29165716/targeting-bcr-abl-independent-tki-resistance-in-chronic-myeloid-leukemia-by-mtor-and-autophagy-inhibition
#2
Rebecca Mitchell, Lisa E M Hopcroft, Pablo Baquero, Elaine K Allan, Kay Hewit, Daniel James, Graham Hamilton, Arunima Mukhopadhyay, Jim O'Prey, Alan Hair, Junia V Melo, Edmond Chan, Kevin M Ryan, Véronique Maguer-Satta, Brian J Druker, Richard E Clark, Subir Mitra, Pawel Herzyk, Franck E Nicolini, Paolo Salomoni, G Vignir Helgason
Background: Imatinib and second-generation tyrosine kinase inhibitors (TKIs) nilotinib and dasatinib have statistically significantly improved the life expectancy of chronic myeloid leukemia (CML) patients; however, resistance to TKIs remains a major clinical challenge. Although ponatinib, a third-generation TKI, improves outcomes for patients with BCR-ABL-dependent mechanisms of resistance, including the T315I mutation, a proportion of patients may have or develop BCR-ABL-independent resistance and fail ponatinib treatment...
November 20, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29165713/protein-complex-scaffolding-predicted-as-a-prevalent-function-of-long-non-coding-rnas
#3
Diogo M Ribeiro, Andreas Zanzoni, Andrea Cipriano, Riccardo Delli Ponti, Lionel Spinelli, Monica Ballarino, Irene Bozzoni, Gian Gaetano Tartaglia, Christine Brun
The human transcriptome contains thousands of long non-coding RNAs (lncRNAs). Characterizing their function is a current challenge. An emerging concept is that lncRNAs serve as protein scaffolds, forming ribonucleoproteins and bringing proteins in proximity. However, only few scaffolding lncRNAs have been characterized and the prevalence of this function is unknown. Here, we propose the first computational approach aimed at predicting scaffolding lncRNAs at large scale. We predicted the largest human lncRNA-protein interaction network to date using the catRAPID omics algorithm...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165597/gsta1-expression-is-correlated-with-aldosterone-level-in-kcnj5-mutated-adrenal-aldosterone-producing-adenoma
#4
Xintao Li, Baojun Wang, Lu Tang, Yu Zhang, Luyao Chen, Liangyou Gu, Fan Zhang, Jinzhi Ouyang, Xu Zhang
Context: KCNJ5 mutation is a major cause of aldosterone-producing adenoma (APA). The development of APA apart from KCNJ5 mutation is less investigated. Objective: To investigate other mechanisms affecting aldosterone secretion apart from KCNJ5. Patients and Methods: Six pairs of KCNJ5-mutated, high and low aldosterone-secreting APAs, five non-KCNJ5-mutated APAs and four normal adrenal glands were assayed by Affymetrix Genechip Human Transcriptome Array 2...
November 20, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29165363/identification-and-initial-characterization-of-the-effectors-of-an-anther-smut-fungus-and-potential-host-target-proteins
#5
Venkata S Kuppireddy, Vladimir N Uversky, Su San Toh, Ming-Chang Tsai, William C Beckerson, Catarina Cahill, Brittany Carman, Michael H Perlin
(1) Background: Plant pathogenic fungi often display high levels of host specificity and biotrophic fungi; in particular, they must manipulate their hosts to avoid detection and to complete their obligate pathogenic lifecycles. One important strategy of such fungi is the secretion of small proteins that serve as effectors in this process. Microbotryum violaceum is a species complex whose members infect members of the Caryophyllaceae; M. lychnidis-dioicae, a parasite on Silene latifolia, is one of the best studied interactions...
November 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29165344/high-throughput-identification-of-antimicrobial-peptides-from-amphibious-mudskippers
#6
Yunhai Yi, Xinxin You, Chao Bian, Shixi Chen, Zhao Lv, Limei Qiu, Qiong Shi
Widespread existence of antimicrobial peptides (AMPs) has been reported in various animals with comprehensive biological activities, which is consistent with the important roles of AMPs as the first line of host defense system. However, no big-data-based analysis on AMPs from any fish species is available. In this study, we identified 507 AMP transcripts on the basis of our previously reported genomes and transcriptomes of two representative amphibious mudskippers, Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM)...
November 22, 2017: Marine Drugs
https://www.readbyqxmd.com/read/29165046/phytophthora-parasitica-effector-pprxlr2-suppresses-nicotiana-benthamiana-immunity
#7
Ronaldo J D Dalio, Heros José Máximo, Tiago Silva Oliveira, Renata Dias, Michele Breton, Henrique Leme Felizatti, Marcos Antonio Antonio Machado
Phytophthora species secrete several classes of effector proteins during interaction with their hosts. These proteins can have multiple functions including modulation of host physiology and immunity. The RxLR effectors have the ability to enter plant cells using the plant machinery. Some of these effectors have been characterized as immunity suppressors; however, very little is known about their functions in the interaction between Phytophthora parasitica and its hosts. Using a bioinformatics pipeline, we have identified 172 candidate RxLR effectors (CREs) in the isolate IAC 01_95 of P...
November 22, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29164972/molecular-subtyping-of-breast-cancer-improves-identification-of-both-high-and-low-risk-patients
#8
Maria Rossing, Olga Østrup, Wiktor W Majewski, Savvas Kinalis, Maj-Britt Jensen, Ann Knoop, Niels Kroman, Maj-Lis Talman, Thomas V O Hansen, Bent Ejlertsen, Finn C Nielsen
BACKGROUND: Transcriptome analysis enables classification of breast tumors into molecular subtypes that correlate with prognosis and effect of therapy. We evaluated the clinical benefits of molecular subtyping compared to our current diagnostic practice. MATERIALS AND METHODS: Molecular subtyping was performed on a consecutive and unselected series of 524 tumors from women with primary breast cancer (n = 508). Tumors were classified by the 256 gene expression signature (CIT) and compared to conventional immunohistochemistry (IHC) procedures...
November 22, 2017: Acta Oncologica
https://www.readbyqxmd.com/read/29164968/characterization-of-basal-like-subtype-in-a-danish-consecutive-primary-breast-cancer-cohort
#9
Savvas Kinalis, Finn Cilius Nielsen, Maj-Lis Talman, Bent Ejlertsen, Maria Rossing
BACKGROUND: Transcriptome analysis enables classification of breast tumors into molecular subtypes. BRCA1/2 predisposed patients are more likely to suffer from a basal-like subtype and this group of patients displays a more distinct phenotype and genotype. Hence, in-depth characterization of this separate entity is needed. MATERIAL AND METHODS: Molecular subtyping was performed on a consecutive and unselected series of 1560 tumors from patients with primary breast cancer...
November 22, 2017: Acta Oncologica
https://www.readbyqxmd.com/read/29164594/rna-sequencing-study-of-peripheral-blood-mononuclear-cells-in-sporadic-meniere-s-disease-patients-possible-contribution-of-immunologic-dysfunction-to-the-development-of-this-disorder
#10
Ying Sun, Daogong Zhang, Gaoying Sun, Yafeng Lv, Yawei Li, Xiaofei Li, Yongdong Song, Jianfeng Li, Zhaomin Fan, Haibo Wang
To date, the pathogenesis of Meniere's disease (MD) remains unclear. This study aims to investigate the possible relationship between potential immune system related genes and sporadic Meniere's disease. The whole RNA-sequencing (RNA-seq) technology was used to analyze the transcriptome of peripheral blood mononuclear cells of 3 MD patients and 3 control individuals. Of 366 differentially expressed genes (DEGs), 154 genes were up-regulated and 212 genes were down-regulated (|log2Foldchange| >1 and p <0...
November 22, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/29164313/genome-wide-analysis-of-a-recently-active-retrotransposon-au-sine-in-wheat-content-distribution-within-subgenomes-and-chromosomes-and-gene-associations
#11
Danielle Keidar, Chen Doron, Khalil Kashkush
Here, we show that Au SINE elements have strong associations with protein-coding genes in wheat. Most importantly Au SINE insertion within introns causes allelic variation and might induce intron retention. The impact of transposable elements (TEs) on genome structure and function is intensively studied in eukaryotes, especially in plants where TEs can reach up to 90% of the genome in some cases, such as in wheat. Here, we have performed a genome-wide in-silico analysis using the updated publicly available genome draft of bread wheat (T...
November 21, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29164142/pathogenesis-molecular-genetics-and-genomics-of-mycobacterium-avium-subsp-paratuberculosis-the-etiologic-agent-of-johne-s-disease
#12
REVIEW
Govardhan Rathnaiah, Denise K Zinniel, John P Bannantine, Judith R Stabel, Yrjö T Gröhn, Michael T Collins, Raúl G Barletta
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's disease in ruminants causing chronic diarrhea, malnutrition, and muscular wasting. Neonates and young animals are infected primarily by the fecal-oral route. MAP attaches to, translocates via the intestinal mucosa, and is phagocytosed by macrophages. The ensuing host cellular immune response leads to granulomatous enteritis characterized by a thick and corrugated intestinal wall. We review various tissue culture systems, ileal loops, and mice, goats, and cattle used to study MAP pathogenesis...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29163636/a-pipeline-for-high-throughput-concentration-response-modeling-of-gene-expression-for-toxicogenomics
#13
John S House, Fabian A Grimm, Dereje D Jima, Yi-Hui Zhou, Ivan Rusyn, Fred A Wright
Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29163622/transcriptome-and-metabolome-analyses-provide-insights-into-the-occurrence-of-peel-roughing-disorder-on-satsuma-mandarin-citrus-unshiu-marc-fruit
#14
Xiao-Peng Lu, Fei-Fei Li, Jiang Xiong, Xiong-Jun Cao, Xiao-Chuan Ma, Zi-Mu Zhang, Shang-Yin Cao, Shen-Xi Xie
Roughing disorder (RD) is a significant quality barrier in citrus fruit, prevalent on easy-peeling mandarins. As RD is not yet well-understood, this study aimed to examine the changes and synergic molecular processes involved in peel RD. Peel with RD was induced by severely defruiting Satsuma mandarin trees. Morphology observations, RNA-sequencing, and targeted and untargeted metabolic analyses were conducted. The results showed that the primary metabolites of sugars, organic acids and amino acids are dramatically changed in RD peel...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163601/genome-wide-constitutively-expressed-gene-analysis-and-new-reference-gene-selection-based-on-transcriptome-data-a-case-study-from-poplar-canker-disease-interaction
#15
Jiaping Zhao, Fan Yang, Jinxia Feng, Yanli Wang, Barbara Lachenbruch, Jiange Wang, Xianchong Wan
A number of transcriptome datasets for differential expression (DE) genes have been widely used for understanding organismal biology, but these datasets also contain untapped information that can be used to develop more precise analytical tools. With the use of transcriptome data generated from poplar/canker disease interaction system, we describe a methodology to identify candidate reference genes from high-throughput sequencing data. This methodology will improve the accuracy of RT-qPCR and will lead to better standards for the normalization of expression data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163598/an-rna-sequencing-transcriptome-analysis-of-grasspea-lathyrus-sativus-l-and-development-of-ssr-and-kasp-markers
#16
Xiaopeng Hao, Tao Yang, Rong Liu, Jinguo Hu, Yang Yao, Marina Burlyaeva, Yan Wang, Guixing Ren, Hongyan Zhang, Dong Wang, Jianwu Chang, Xuxiao Zong
Grasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeq(TM) 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163591/transcriptomic-and-hormonal-analyses-reveal-that-yuc-mediated-auxin-biogenesis-is-involved-in-shoot-regeneration-from-rhizome-in-cymbidium
#17
Yang Liu, Hai-Liang Zhang, He-Rong Guo, Li Xie, Rui-Zhen Zeng, Xiang-Qian Zhang, Zhi-Sheng Zhang
Cymbidium, one of the most important orchid genera in horticulture, can be classified into epiphytic and terrestrial species. Generally, epiphytic Cymbidium seedlings can be easily propagated by tissue culture, but terrestrial seedlings are difficult to propagate. To date, the molecular mechanisms underlying the differences in the ease with which terrestrial and epiphytic cymbidiums can be propagated are largely unknown. Using RNA-sequencing, quantitative reverse transcription PCR and enzyme-linked immunosorbent assay, Cymbidium 'Xiaofeng' (CXF), which can be efficiently micropropagated, and terrestrial Cymbidium sinense 'Qijianbaimo' (CSQ), which has a low regeneration ability, were used to explore the molecular mechanisms underlying the micropropagation ability of Cymbidium species...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163564/non-replicative-integral-membrane-proteins-encoded-by-plant-alpha-like-viruses-emergence-of-diverse-orphan-orfs-and-movement-protein-genes
#18
Andrey G Solovyev, Sergey Y Morozov
Fast accumulation of sequencing data on plant virus genomes and plant transcriptomes demands periodic re-evaluation of current views on the genome evolution of viruses. Here, we substantiate and further detail our previously mostly speculative model on the origin and evolution of triple gene block (TGB) encoding plant virus movement proteins TGB1, TGB2, and TGB3. Recent experimental data on functional competence of transport gene modules consisting of two proteins related to TGB1 and TGB2, as well as sequence analysis data on similarity of TGB2 and TGB3 encoded by a viral genome and virus-like RNAs identified in a plant transcriptomes, suggest that TGB evolution involved events of gene duplication and gene transfer between viruses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163495/human-cd141-dendritic-cell-and-cd1c-dendritic-cell-undergo-concordant-early-genetic-programming-after-activation-in-humanized-mice-in-vivo
#19
Yoshihito Minoda, Isaac Virshup, Ingrid Leal Rojas, Oscar Haigh, Yide Wong, John J Miles, Christine A Wells, Kristen J Radford
Human immune cell subsets develop in immunodeficient mice following reconstitution with human CD34(+) hematopoietic stem cells. These "humanized" mice are useful models to study human immunology and human-tropic infections, autoimmunity, and cancer. However, some human immune cell subsets are unable to fully develop or acquire full functional capacity due to a lack of cross-reactivity of many growth factors and cytokines between species. Conventional dendritic cells (cDCs) in mice are categorized into cDC1, which mediate T helper (Th)1 and CD8(+) T cell responses, and cDC2, which mediate Th2 and Th17 responses...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29163426/sugar-metabolism-of-the-first-thermophilic-planctomycete-thermogutta-terrifontis-comparative-genomic-and-transcriptomic-approaches
#20
Alexander G Elcheninov, Peter Menzel, Soley R Gudbergsdottir, Alexei I Slesarev, Vitaly V Kadnikov, Anders Krogh, Elizaveta A Bonch-Osmolovskaya, Xu Peng, Ilya V Kublanov
Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic acid residues, is involved in numerous biotechnological applications in cosmetics, agriculture, pharmaceuticals, food and petroleum industries. Additionally, its oligosaccharides were shown to possess antimicrobial, antioxidant, and few other properties. Yet, despite its extensive usage, little is known about xanthan gum degradation pathways and mechanisms. Thermogutta terrifontis, isolated from a sample of microbial mat developed in a terrestrial hot spring of Kunashir island (Far-East of Russia), was described as the first thermophilic representative of the Planctomycetes phylum...
2017: Frontiers in Microbiology
keyword
keyword
13493
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"