keyword
MENU ▼
Read by QxMD icon Read
search

Gene network

keyword
https://www.readbyqxmd.com/read/28550410/different-exogenous-sugars-affect-the-hormone-signal-pathway-and-sugar-metabolism-in-red-globe-vitis-vinifera-l-plantlets-grown-in-vitro-as-shown-by-transcriptomic-analysis
#1
Juan Mao, Wenfang Li, Baoqin Mi, Mohammed Mujitaba Dawuda, Alejandro Calderón-Urrea, Zonghuan Ma, Yongmei Zhang, Baihong Chen
Exogenously applied 2% fructose is the most appropriate carbon source that enhances photosynthesis and growth of grape plantlets compared with the same concentrations of sucrose and glucose. The role of the sugars was regulated by the expression of key candidate genes related to hormones, key metabolic enzymes, and sugar metabolism of grape plantlets ( Vitis vinifera L.) grown in vitro. The addition of sugars including sucrose, glucose, and fructose is known to be very helpful for the development of grape (V...
May 26, 2017: Planta
https://www.readbyqxmd.com/read/28550109/chronic-%C3%AE-cell-depolarization-impairs-%C3%AE-cell-identity-by-disrupting-a-network-of-ca-2-regulated-genes
#2
Jennifer S Stancill, Jean-Philippe Cartailler, Hannah W Clayton, James T O'Connor, Matthew T Dickerson, Prasanna K Dadi, Anna B Osipovich, David A Jacobson, Mark A Magnuson
We used mice lacking Abcc8, a key component of the β-cell KATP-channel, to analyze the effects of a sustained elevation in the intracellular Ca(2+) concentration ([Ca(2+)]i) on β-cell identity and gene expression. Lineage tracing analysis revealed the conversion of β-cells lacking Abcc8 into PP-cells, but not to α- or δ-cells. RNA-Seq analysis of FACS-purified Abcc8(-/-) β-cells confirmed an increase in Ppy gene expression, and revealed altered expression of over 4,200 genes, many of which are involved in Ca(2+)-signaling, the maintenance of β-cell identity, and cell adhesion...
May 26, 2017: Diabetes
https://www.readbyqxmd.com/read/28549970/distinct-patterns-of-cellular-immune-response-elicited-by-influenza-non-adjuvanted-and-as03-adjuvanted-monovalent-h1n1-pdm09-vaccine
#3
Sarah Giarola-Silva, Jordana G A Coelho-Dos-Reis, Marina Moraes Mourão, Ana Carolina Campi-Azevedo, Erick E Nakagaki Silva, Maria Luiza-Silva, Marina Angela Martins, Amanda Cardoso de Oliveira Silveira Cassette, Maurício Azevedo Batista, Vanessa Peruhype-Magalhães, Lis Ribeiro do Valle Antonelli, José Geraldo Leite Ribeiro, Silvana Maria Elói-Santos, Alexandre Vieira Machado, Andréa Teixeira-Carvalho, Olindo Assis Martins-Filho, Márcio Sobreira Silva Araújo
The study aimed at identifying biomarkers of immune response elicited by non-adjuvanted-(NAV) and adjuvanted-(AV) H1N1(pdm09) vaccines. The results showed that despite both vaccines elicited similar levels of anti-H1N1 antibodies at day30 after vaccination, higher reactivity was observed in AV at day180. While AV induced early changes in cell-surface molecules on monocytes, CD4(+), CD8(+) T-cells and B-cells, NAV triggered minor changes, starting later on at day3. Furthermore, AV induced a late and persistent increase in TLR gene expression after day3, except for tlr4, while NAV displayed earlier but transient tlr3/4/7/9 up-regulation...
May 23, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28549619/a-mechanical-model-for-diversified-insect-wing-margin-shapes
#4
Yukitaka Ishimoto, Kaoru Sugimura
The wings in different insect species are morphologically distinct with regards to their size, outer contour (margin) shape, venation, and pigmentation. The basis of the diversity of wing margin shapes remains unknown, despite the fact that gene networks governing the Drosophila wing development have been well characterised. Among the different types of wing margin shapes, smoothly curved contour is the most frequently found and implies the existence of a highly organised, multicellular mechanical structure...
May 23, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28549481/late-onset-alzheimer-s-disease-genetics-implicates-microglial-pathways-in-disease-risk
#5
REVIEW
Anastasia G Efthymiou, Alison M Goate
Alzheimer's disease (AD) is a highly heritable complex disease with no current effective prevention or treatment. The majority of drugs developed for AD focus on the amyloid cascade hypothesis, which implicates Aß plaques as a causal factor in the disease. However, it is possible that other underexplored disease-associated pathways may be more fruitful targets for drug development. Findings from gene network analyses implicate immune networks as being enriched in AD; many of the genes in these networks fall within genomic regions that contain common and rare variants that are associated with increased risk of developing AD...
May 26, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28549191/maintenance-of-phosphate-homeostasis-and-root-development-are-coordinately-regulated-by-myb1-an-r2r3-type-myb-transcription-factor-in-rice
#6
Mian Gu, Jun Zhang, Huanhuan Li, Daqian Meng, Ran Li, Xiaoli Dai, Shichao Wang, Wei Liu, Hongye Qu, Guohua Xu
The adaptive responses of plants to phosphate (Pi) starvation stress are fine-tuned by an elaborate regulatory network. In this study, we identified and characterized a novel Pi starvation-responsive gene, MYB1, encoding an R2R3-type transcription factor in rice. MYB1 was transcriptionally induced in leaf sheaths and old leaf blades. It was localized to the nucleus and expressed mainly in vascular tissues. Mutation of MYB1 led to an increase in Pi uptake and accumulation, accompanied by altered expression of a subset of Pi transporters and several genes involved in Pi starvation signaling...
May 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28549153/chippi-a-novel-method-for-mapping-chimeric-protein-protein-interactions-uncovers-selection-principles-of-protein-fusion-events-in-cancer
#7
Milana Frenkel-Morgenstern, Alessandro Gorohovski, Somnath Tagore, Vaishnovi Sekar, Miguel Vazquez, Alfonso Valencia
Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein-protein interactions (ChiPPI) that uses the domain-domain co-occurrence scores in order to identify preserved interactors of chimeric proteins...
May 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28549075/age-of-onset-in-huntington-s-disease-is-influenced-by-cag-repeat-variations-in-other-polyglutamine-disease-associated-genes
#8
Geerte Stuitje, Martine J van Belzen, Sarah L Gardiner, Willeke M C van Roon-Mom, Merel W Boogaard, Sarah J Tabrizi, Raymund A C Roos, N A Aziz
No abstract text is available yet for this article.
May 25, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28548604/quorum-sensing-systems-in-the-plant-growth-promoting-bacterium-paraburkholderia-phytofirmans-psjn-exhibit-cross-regulation-and-are-involved-in-biofilm-formation
#9
Ana Zúñiga, Raúl A Donoso, Daniela Ruiz, Gonzalo A Ruz, Bernardo González
Quorum-sensing systems play important roles in host colonization and host establishment of Burkholderiales species. Beneficial Paraburkholderia species share a conserved quorum-sensing (QS) system, designated BraI/R, that controls different phenotypes. In this context, the plant growth-promoting bacterium Paraburkholderia phytofirmans PsJN possesses two different homoserine lactone QS systems BpI.1/R.1 and BpI.2/R.2 (BraI/R-like QS system). The BpI.1/R.1 QS system was previously reported to be important to colonize and produce beneficial effects in Arabidopsis thaliana plants...
May 26, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28547568/biofertilizers-and-sustainable-agriculture-exploring-arbuscular-mycorrhizal-fungi
#10
REVIEW
Nicholas O Igiehon, Olubukola O Babalola
Worldwide agricultural food production has to double in 2050 so as to feed the global increasing population while reducing dependency on conventional chemical fertilizers plus pesticides. To accomplish this objective, there is the need to explore the several mutualistic interactions between plant roots and rhizosphere microbiome. Biofertilization is the process of boosting the abundance of microorganisms such as arbuscular mycorrhizal fungi (AMF) in the natural plant rhizosphere which depicts a beneficial alternative to chemical fertilization practices...
May 25, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28547343/msmir156-affects-global-gene-expression-and-promotes-root-regenerative-capacity-and-nitrogen-fixation-activity-in-alfalfa
#11
Banyar Aung, Ruimin Gao, Margaret Y Gruber, Ze-Chun Yuan, Mark Sumarah, Abdelali Hannoufa
MicroRNA156 (miR156) regulates a network of downstream genes to affect plant growth and development. We previously generated alfalfa (Medicago sativa) plants that overexpress homologous miR156 (MsmiR156OE), and identified three of its SPL target genes. These plants exhibited increased vegetative yield, delayed flowering and longer roots. In this study, we aimed to elucidate the effect of miR156 on the root system, including effect on nodulation and nitrogen fixation. We found that MsmiR156 overexpression increases root regeneration capacity in alfalfa, but with little effect on root biomass at the early stages of root development...
May 25, 2017: Transgenic Research
https://www.readbyqxmd.com/read/28546992/identification-of-transcription-factors-potentially-involved-in-human-adipogenesis-in%C3%A2-vitro
#12
Melvin Anyasi Ambele, Michael Sean Pepper
BACKGROUND: Increased adiposity in humans leads to obesity, which is a major risk factor for cardiovascular disease, type 2 diabetes, and cancer. We previously conducted an extensive unbiased in vitro transcriptomic analysis of adipogenesis, using human adipose-derived stromal cells (ASCs). Here, we have applied computational methods to these data to identify transcription factors (TFs) that constitute the upstream gene regulatory networks potentially, driving adipocyte formation in human ASCs...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546829/vinasse-fertirrigation-alters-soil-resistome-dynamics-an-analysis-based-on-metagenomic-profiles
#13
Lucas P P Braga, Rafael F Alves, Marina T F Dellias, Acacio A Navarrete, Thiago O Basso, Siu M Tsai
Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database...
2017: BioData Mining
https://www.readbyqxmd.com/read/28546527/effect-of-necrosis-on-the-mirna-mrna-regulatory-network-in-crt-mg-human-astroglioma-cells
#14
So-Hee Ahn, Jung-Hyuck Ahn, Dong-Ryeol Ryu, Jisoo Lee, Min-Sun Cho, Youn-Hee Choi
Purpose: Glioblastoma multiforme (GBM) is the most common adult primary intracranial tumor. The remarkable features of GBM include central necrosis. MicroRNAs (miRNAs) have been considered as diagnostic/prognostic biomarkers for many cancers, including glioblastoma. However, the effect of necrosis on the miRNA expression profile and predicted miRNA-mRNA regulatory information remain unclear. The purpose of this study is to examine the effect of necrotic cells on the modulation of miRNA and mRNA expression profiles and miRNA-mRNA network in CRT-MG cells...
May 22, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28546318/an-environment-dependent-transcriptional-network-specifies-human-microglia-identity
#15
David Gosselin, Dylan Skola, Nicole G Coufal, Inge R Holtman, Johannes C M Schlachetzki, Eniko Sajti, Baptiste N Jaeger, Carolyn O'Connor, Conor Fitzpatrick, Martina P Pasillas, Monique Pena, Amy Adair, David G Gonda, Michael L Levy, Richard M Ransohoff, Fred H Gage, Christopher K Glass
Microglia play essential roles in central nervous system (CNS) homeostasis and influence diverse aspects of neuronal function. However, the transcriptional mechanisms that specify human microglia phenotypes are largely unknown. We examined the transcriptomes and epigenetic landscapes of human microglia isolated from surgically resected brain tissue ex vivo and following transition to an in vitro environment. Transfer to a tissue culture environment results in rapid and extensive downregulation of microglia-specific genes that are induced in primitive mouse macrophages following migration into the fetal brain...
May 25, 2017: Science
https://www.readbyqxmd.com/read/28545973/evolutionary-and-ecological-forces-influencing-population-diversification-in-bornean-montane-passerines
#16
Vivien L Chua, Brian Tilston Smith, Ryan C Burner, Mustafa Abdul Rahman, Maklarin Lakim, Dewi M Prawiradilaga, Robert G Moyle, Frederick H Sheldon
The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal...
May 22, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28545612/drug-repositioning-based-on-triangularly-balanced-structure-for-tissue-specific-diseases-in-incomplete-interactome
#17
Liang Yu, Jin Zhao, Lin Gao
Finding new uses for existing drugs has become a new strategy for decades to treat more patients. Few traditional approaches consider the tissue specificities of diseases. Moreover, disease genes, drug targets and protein interaction (PPI) networks remain largely incomplete and the relationships between drugs and diseases conform to the triangularly balanced structure. Therefore, based on tissue specificities of diseases, we apply the triangularly balanced theory and the module distance defined for incomplete interaction networks to build drug-disease associations...
March 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28545608/differential-regulation-analysis-reveals-dysfunctional-regulatory-mechanism-involving-transcription-factors-and-micrornas-in-gastric-carcinogenesis
#18
Quanxue Li, Junyi Li, Wentao Dai, Yi-Xue Li, Yuan-Yuan Li
Gastric cancer (GC) is one of the most incident malignancies in the world. Although lots of featured genes and microRNAs (miRNAs) have been identified to be associated with gastric carcinogenesis, underlying regulatory mechanisms still remain unclear. In order to explore the dysfunctional mechanisms of GC, we developed a novel approach to identify carcinogenesis relevant regulatory relationships, which is characterized by quantifying the difference of regulatory relationships between stages. Firstly, we applied the strategy of differential coexpression analysis (DCEA) to transcriptomic datasets including paired mRNA and miRNA of gastric samples to identify a set of genes/miRNAs related to gastric cancer progression...
March 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28545587/type-2-diabetes-and-obesity-induce-similar-transcriptional-reprogramming-in-human-myocytes
#19
Leif Väremo, Tora Ida Henriksen, Camilla Scheele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
BACKGROUND: Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity. METHODS: We generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription...
May 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28545550/genetic-variation-in-neurodegenerative-diseases-and-its-accessibility-in-the-model-organism-caenorhabditis-elegans
#20
REVIEW
Yiru Anning Wang, Jan Edward Kammenga, Simon Crawford Harvey
BACKGROUND: Neurodegenerative diseases (NGDs) such as Alzheimer's and Parkinson's are debilitating and largely untreatable conditions strongly linked to age. The clinical, neuropathological, and genetic components of NGDs indicate that neurodegeneration is a complex trait determined by multiple genes and by the environment. MAIN BODY: The symptoms of NGDs differ among individuals due to their genetic background, and this variation affects the onset and progression of NGD and NGD-like states...
May 25, 2017: Human Genomics
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"