keyword
MENU ▼
Read by QxMD icon Read
search

Gene network

keyword
https://www.readbyqxmd.com/read/29236255/identifying-mirna-targets-using-ago-ripseq
#1
Rebecca Petri, Johan Jakobsson
microRNAs (miRNA) are small, noncoding RNAs that bind to messenger RNAs (mRNAs) and regulate their activity. They are, therefore, important posttranscriptional regulators. In recent years it has become clear that miRNAs regulate large genetic networks, rather than single genes, and that one gene can be targeted by several miRNAs. To understand the role of miRNAs in cells or tissues, it is therefore important to analyze the targetome of miRNAs. Here, we present a technique called Argonaute-RNA Immunoprecipitation (AGO-RIP) which takes advantages of the fact that miRNAs and their targets are directly bound by the Argonaute protein family...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236054/genome-wide-profiling-of-small-rnas-and-degradome-revealed-conserved-regulations-of-mirnas-on-auxin-responsive-genes-during-fruit-enlargement-in-peaches
#2
Mengya Shi, Xiao Hu, Yu Wei, Xu Hou, Xue Yuan, Jun Liu, Yueping Liu
Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA)...
December 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29235467/in-situ-functional-dissection-of-rna-cis-regulatory-elements-by-multiplex-crispr-cas9-genome-engineering
#3
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29234933/micrornas-and-metastasis-small-rnas-play-big-roles
#4
Jongchan Kim, Fan Yao, Zhenna Xiao, Yutong Sun, Li Ma
MicroRNAs (miRNAs) are small non-coding RNAs regulating post-transcriptional gene expression. They play important roles in many biological processes under physiological or pathological conditions, including development, metabolism, tumorigenesis, metastasis, and immune response. Over the past 15 years, significant insights have been gained into the roles of miRNAs in cancer. Depending on the cancer type, miRNAs can act as oncogenes, tumor suppressors, or metastasis regulators. In this review, we focus on the role of miRNAs as components of molecular networks regulating metastasis...
December 12, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/29234668/a-genome-wide-screen-for-fty720-sensitive-mutants-reveals-genes-required-for-ros-homeostasis
#5
Kanako Hagihara, Kanako Kinoshita, Kouki Ishida, Shihomi Hojo, Yoshinori Kameoka, Ryosuke Satoh, Teruaki Takasaki, Reiko Sugiura
Fingolimod hydrochloride (FTY720), a sphingosine-1-phosphate (S1P) analogue, is an approved immune modulator for the treatment of multiple sclerosis (MS). Notably, in addition to its well-known mode of action as an S1P modulator, accumulating evidence suggests that FTY720 induces apoptosis in various cancer cells via reactive oxygen species (ROS) generation. Although the involvement of multiple signaling molecules, such as JNK (Jun N-terminal kinase), Akt (alpha serine/threonine-protein kinase) and Sphk has been reported, the exact mechanisms how FTY720 induces cell growth inhibition and the functional relationship between FTY720 and these signaling pathways remain elusive...
November 27, 2017: Microbial Cell
https://www.readbyqxmd.com/read/29234590/an-integrative-analysis-of-dna-methylation-in-osteosarcoma
#6
Jie Xu, Deng Li, Zhiqing Cai, Yingbin Zhang, Yulin Huang, Baohua Su, Ruofan Ma
Background: The study aimed to analyze aberrantly methylated genes, relevant pathways and transcription factors (TFs) in osteosarcoma (OS) development. Methods: Based on the DNA methylation microarray data GSE36002 that were downloaded from GEO database, the differentially methylated genes in promoter regions were identified between OS and normal samples. Pathway and function enrichment analyses of differentially methylated genes was performed. Subsequently, protein-protein interaction (PPI) network was constructed, followed by identification of cancer-associated differentially methylated genes and significant differentially methylated TFs...
November 2017: Journal of Bone Oncology
https://www.readbyqxmd.com/read/29234425/systems-pharmacological-approach-to-the-effect-of-bulsu-san-promoting-parturition
#7
Su Yeon Suh, Won G An
Bulsu-san (BSS) has been commonly used in oriental medicine for pregnant women in East Asia. The purpose of this research was to elucidate the effect of BSS on ease of parturition using a systems-level in silico analytic approach. Research results show that BSS is highly connected to the parturition related pathways, biological processes, and organs. There were numerous interactions between most compounds of BSS and multiple target genes, and this was confirmed using herb-compound-target network, target-pathway network, and gene ontology analysis...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/29234348/diurnal-transcriptome-and-gene-network-represented-through-sparse-modeling-in-brachypodium-distachyon
#8
Satoru Koda, Yoshihiko Onda, Hidetoshi Matsui, Kotaro Takahagi, Yukiko Yamaguchi-Uehara, Minami Shimizu, Komaki Inoue, Takuhiro Yoshida, Tetsuya Sakurai, Hiroshi Honda, Shinto Eguchi, Ryuei Nishii, Keiichi Mochida
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29234300/temporal-discrimination-mechanisms-and-relevance-to-adult-onset-dystonia
#9
REVIEW
Antonella Conte, Eavan M McGovern, Shruti Narasimham, Rebecca Beck, Owen Killian, Sean O'Riordan, Richard B Reilly, Michael Hutchinson
Temporal discrimination is the ability to determine that two sequential sensory stimuli are separated in time. For any individual, the temporal discrimination threshold (TDT) is the minimum interval at which paired sequential stimuli are perceived as being asynchronous; this can be assessed, with high test-retest and inter-rater reliability, using a simple psychophysical test. Temporal discrimination is disordered in a number of basal ganglia diseases including adult-onset dystonia, of which the two most common phenotypes are cervical dystonia and blepharospasm...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/29234286/identification-of-biomarkers-correlated-with-the-tnm-staging-and-overall-survival-of-patients-with-bladder-cancer
#10
Sheng Li, Xiaoping Liu, Tongzu Liu, Xiangyu Meng, Xiaohong Yin, Cheng Fang, Di Huang, Yue Cao, Hong Weng, Xiantao Zeng, Xinghuan Wang
Objective: To identify candidate biomarkers correlated with clinical prognosis of patients with bladder cancer (BC). Methods: Weighted gene co-expression network analysis was applied to build a co-expression network to identify hub genes correlated with tumor node metastasis (TNM) staging of BC patients. Functional enrichment analysis was conducted to functionally annotate the hub genes. Protein-protein interaction network analysis of hub genes was performed to identify the interactions among the hub genes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29234131/a-gene-expression-study-of-ornamental-fin-shape-in-neolamprologus-brichardi-an-african-cichlid-species
#11
Ehsan Pashay Ahi, Florian Richter, Kristina M Sefc
The diversity of fin morphology within and across fish taxa offers great, but still largely unexplored, opportunities to investigate the proximate mechanisms underlying fin shape variation. Relying on available genetic knowledge brought forth mainly by the comprehensive study of the zebrafish caudal fin, we explored candidate molecular mechanisms for the maintenance and formation of the conspicuously elongated filaments adorning the unpaired fins of the East African "princess cichlid" Neolamprologus brichardi...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29234095/enclaves-of-genetic-diversity-resisted-inca-impacts-on-population-history
#12
Chiara Barbieri, José R Sandoval, Jairo Valqui, Aviva Shimelman, Stefan Ziemendorff, Roland Schröder, Maria Geppert, Lutz Roewer, Russell Gray, Mark Stoneking, Ricardo Fujita, Paul Heggarty
The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233982/cacul1-reciprocally-regulates-sirt1-and-lsd1-to-repress-ppar%C3%AE-and-inhibit-adipogenesis
#13
Min Jun Jang, Ui-Hyun Park, Jeong Woo Kim, Hanbyeul Choi, Soo-Jong Um, Eun-Joo Kim
Peroxisome proliferator-activated receptor γ (PPARγ) is the master regulator of adipocyte differentiation and is closely linked to the development of obesity. Despite great progress in elucidating the transcriptional network of PPARγ, epigenetic regulation of this pathway by histone modification remains elusive. Here, we found that CDK2-associated cullin 1 (CACUL1), identified as a novel SIRT1 interacting protein, directly bound to PPARγ through the co-repressor nuclear receptor (CoRNR) box 2 and repressed the transcriptional activity and adipogenic potential of PPARγ...
December 11, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29233811/dissecting-the-roles-of-the-calcineurin-pathway-in-unisexual-reproduction-stress-responses-and-virulence-in-cryptococcus-deneoformans
#14
Ci Fu, Nicholas Donadio, Maria E Cardenas, Joseph Heitman
The Ca2+/calmodulin-dependent protein phosphatase calcineurin orchestrates sexual reproduction, stress responses, and virulence via branched downstream pathways in the opportunistic human fungal pathogen, Cryptococcus neoformans The calcineurin binding protein Cbp1, the calcineurin temperature suppressor Cts1, the calcineurin responsive zinc finger transcription factor Crz1, and the calcineurin targets Pbp1, Tif3, and Puf4 all function downstream of calcineurin to orchestrate distinct cellular processes. To elucidate how the calcineurin pathway regulatory network governs unisexual reproduction, stress responses, and virulence, we have analyzed the self-filamentous C...
December 12, 2017: Genetics
https://www.readbyqxmd.com/read/29233120/prediction-of-5-year-overall-survival-in-cervical-cancer-patients-treated-with-radical-hysterectomy-using-computational-intelligence-methods
#15
Bogdan Obrzut, Maciej Kusy, Andrzej Semczuk, Marzanna Obrzut, Jacek Kluska
BACKGROUND: Computational intelligence methods, including non-linear classification algorithms, can be used in medical research and practice as a decision making tool. This study aimed to evaluate the usefulness of artificial intelligence models for 5-year overall survival prediction in patients with cervical cancer treated by radical hysterectomy. METHODS: The data set was collected from 102 patients with cervical cancer FIGO stage IA2-IIB, that underwent primary surgical treatment...
December 12, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29232879/the-alteration-of-nasopharyngeal-and-oropharyngeal-microbiota-in-children-with-mpp-and-non-mpp
#16
Zhiwei Lu, Wenkui Dai, Yanhong Liu, Qian Zhou, Heping Wang, Dongfang Li, Zhenyu Yang, Yinhu Li, Gan Xie, Shuaicheng Li, Yuejie Zheng
Background: In recent years, the morbidity of Mycoplasma pneumoniae pneumonia (MPP) has increased significantly in China. A growing number of studies indicate that imbalanced respiratory microbiota is associated with various respiratory diseases. Methods: We enrolled 119 children, including 60 pneumonia patients and 59 healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) sampling was performed for 16S ribosomal RNA (16S rRNA) gene analysis of all children. Sputum and OP swabs were obtained from patients for pathogen detection...
December 11, 2017: Genes
https://www.readbyqxmd.com/read/29231846/the-discrepant-and-similar-responses-of-genome-wide-transcriptional-profiles-between-drought-and-cold-stresses-in-cassava
#17
Changying Zeng, Zehong Ding, Fang Zhou, Yufei Zhou, Ruiju Yang, Zi Yang, Wenquan Wang, Ming Peng
Background: Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods: To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29231170/phenotypic-diversity-and-temporal-variability-in-a-bacterial-signaling-network-revealed-by-single-cell-fret
#18
Johannes M Keegstra, Keita Kamino, François Anquez, Milena D Lazova, Thierry Emonet, Thomas S Shimizu
We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations...
December 12, 2017: ELife
https://www.readbyqxmd.com/read/29231168/multiple-sources-of-slow-activity-fluctuations-in-a-bacterial-chemosensory-network
#19
Remy Colin, Christelle Rosazza, Ady Vaknin, Victor Sourjik
Cellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis of Escherichia coli provides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway...
December 12, 2017: ELife
https://www.readbyqxmd.com/read/29230433/proangiogenic-activity-of-endometrial-epithelial-and-stromal-cells-in-response-to-estradiol-in-gelatin-hydrogels
#20
Jacquelyn C Pence, Kathryn B H Clancy, Brendan A C Harley
Biomaterial vascularization remains a major focus in the field of tissue engineering. Biomaterial culture of endometrial cells is described as a platform to inform the design of proangiogenic biomaterials. The endometrium undergoes rapid growth and shedding of dense vascular networks during each menstrual cycle mediated via estradiol and progesterone in vivo. Cocultures of endometrial epithelial and stromal cells encapsulated within a methacrylamide-functionalized gelatin hydrogel are employed. It is reported that proangiogenic gene expression profiles and vascular endothelial growth factor production are hormone dependent in endometrial epithelial cells, but that hormone signals have no effect on human telomerase reverse transcriptase (hTERT)-immortalized endometrial stromal cells...
September 2017: Advanced Biosystems
keyword
keyword
43565
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"