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Transcriptome pathway

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https://www.readbyqxmd.com/read/29351308/skin-transcriptome-reveals-the-dynamic-changes-in-the-wnt-pathway-during-integument-morphogenesis-of-chick-embryos
#1
Husile Gong, Hong Wang, YueXing Wang, Xue Bai, Bin Liu, JinFeng He, JiangHong Wu, WangMei Qi, WenGuang Zhang
Avian species have a unique integument covered with feathers. Skin morphogenesis is a successive and complex process. To date, most studies have focused on a single developmental point or stage. Fewer studies have focused on whole transcriptomes based on the time-course of embryo integument development. To analyze the global changes in gene expression profiles, we sequenced the transcriptome of chicken embryo skin samples from day 6 to day 21 of incubation and identified 5830 differentially expressed genes (DEGs)...
2018: PloS One
https://www.readbyqxmd.com/read/29349926/extracellular-vesicles-from-early-stage-p-falciparum-infected-red-blood-cells-contain-pfemp1-and-induce-transcriptional-changes-in-human-monocytes
#2
Natália G Sampaio, Samantha Emery, Alexandra Garnham, Qiao Y Tan, Xavier Sisquella, Matthew A Pimentel, Neta Regev-Rudzki, Louis Schofield, Emily M Eriksson
Pathogens can release extracellular vesicles (EVs) for cell-cell communication and host modulation. EVs from Plasmodium falciparum, the deadliest malaria parasite species, can transfer drug resistance genes between parasites. EVs from late-stage parasite-infected RBC (iRBC-EVs) are immunostimulatory and affect endothelial cell permeability, but little is known about EVs from early-stage iRBC. We detected the parasite virulence factor PfEMP1, which is responsible for iRBC adherence and a major contributor to disease severity, in EVs only up to 12 hours-post RBC invasion...
January 18, 2018: Cellular Microbiology
https://www.readbyqxmd.com/read/29349709/the-host-response-in-critically-ill-sepsis-patients-on-statin-therapy-a-prospective-observational-study
#3
Maryse A Wiewel, Brendon P Scicluna, Lonneke A van Vught, Arie J Hoogendijk, Aeilko H Zwinderman, René Lutter, Janneke Horn, Olaf L Cremer, Marc J Bonten, Marcus J Schultz, Tom van der Poll
BACKGROUND: Statins can exert pleiotropic anti-inflammatory, vascular protective and anticoagulant effects, which in theory could improve the dysregulated host response during sepsis. We aimed to determine the association between prior statin use and host response characteristics in critically ill patients with sepsis. METHODS: We performed a prospective observational study in 1060 patients admitted with sepsis to the mixed intensive care units (ICUs) of two hospitals in the Netherlands between January 2011 and July 2013...
January 18, 2018: Annals of Intensive Care
https://www.readbyqxmd.com/read/29349608/comparative-transcriptomics-uncovers-differences-in-photoautotrophic-versus-photoheterotrophic-modes-of-nutrition-in-relation-to-secondary-metabolites-biosynthesis-in-swertia-chirayita
#4
Tarun Pal, Jibesh Kumar Padhan, Pawan Kumar, Hemant Sood, Rajinder S Chauhan
Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S...
January 18, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29348846/st6galnac1-plays-important-roles-in-enhancing-cancer-stem-phenotypes-of-colorectal-cancer-via-the-akt-pathway
#5
Tadashi Ogawa, Yoshihiko Hirohashi, Aiko Murai, Toshihiko Nishidate, Kenji Okita, Liming Wang, Yuzuru Ikehara, Tetsuta Satoyoshi, Akihiro Usui, Terufumi Kubo, Munehide Nakastugawa, Takayuki Kanaseki, Tomohide Tsukahara, Goro Kutomi, Tomohisa Furuhata, Koichi Hirata, Noriyuki Sato, Toru Mizuguchi, Ichiro Takemasa, Toshihiko Torigoe
Colorectal cancer (CRC) is a mortal disease due to treatment resistance, recurrence and distant metastasis. Emerging evidence has revealed that a small sub-population of cancer cells termed cancer stem cells (CSCs)/ cancer-initiating cells (CICs) is endowed with high levels of tumor-initiating ability, self-renewal ability and differentiation ability and is responsible for treatment resistance, recurrence and distant metastasis. Eradication of CSCs/CICs is essential to improve current treatments. However, the molecular mechanisms by which CSCs/CICs are maintained are still elusive...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348827/molecular-genetic-profiling-and-high-throughput-in-vitro-drug-screening-in-nut-midline-carcinoma-an-aggressive-and-fatal-disease
#6
Anja Stirnweiss, Joyce Oommen, Rishi S Kotecha, Ursula R Kees, Alex H Beesley
NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age. Genetically, NMC is defined by the chromosomal fusion of NUTM1 with a chromatin-binding partner, typically the bromodomain-containing protein BRD4. However, little is known about other genetic aberrations in this disease. In this study, we used a unique panel of cell lines to describe the molecular-genetic features of NMC. Next-generation sequencing identified a recurring high-impact mutation in the DNA-helicase gene RECQL5 in 75% of lines studied, and biological signals from mutation-signature and network analyses consistent with a general failure in DNA-repair...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348581/identifying-metabolic-pathways-for-production-of-extracellular-polymeric-substances-by-the-diatom-fragilariopsis-cylindrus-inhabiting-sea-ice
#7
Shazia N Aslam, Jan Strauss, David N Thomas, Thomas Mock, Graham J C Underwood
Diatoms are significant primary producers in sea ice, an ephemeral habitat with steep vertical gradients of temperature and salinity characterizing the ice matrix environment. To cope with the variable and challenging conditions, sea ice diatoms produce polysaccharide-rich extracellular polymeric substances (EPS) that play important roles in adhesion, cell protection, ligand binding and as organic carbon sources. Significant differences in EPS concentrations and chemical composition corresponding to temperature and salinity gradients were present in sea ice from the Weddell Sea and Eastern Antarctic regions of the Southern Ocean...
January 18, 2018: ISME Journal
https://www.readbyqxmd.com/read/29348435/macrophage-sensing-of-single-walled-carbon-nanotubes-via-toll-like-receptors
#8
Sourav P Mukherjee, Olesja Bondarenko, Pekka Kohonen, Fernando T Andón, Táňa Brzicová, Isabel Gessner, Sanjay Mathur, Massimo Bottini, Paolo Calligari, Lorenzo Stella, Elena Kisin, Anna Shvedova, Reija Autio, Heli Salminen-Mankonen, Riitta Lahesmaa, Bengt Fadeel
Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger inflammation. However, how these materials are 'sensed' by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348297/changes-in-macrophage-transcriptome-associate-with-systemic-sclerosis-and-mediate-gsdma-contribution-to-disease-risk
#9
Aida Moreno-Moral, Marta Bagnati, Surya Koturan, Jeong-Hun Ko, Carmen Fonseca, Nathan Harmston, Laurence Game, Javier Martin, Voon Ong, David J Abraham, Christopher P Denton, Jacques Behmoaras, Enrico Petretto
OBJECTIVES: Several common and rare risk variants have been reported for systemic sclerosis (SSc), but the effector cell(s) mediating the function of these genetic variants remains to be elucidated. While innate immune cells have been proposed as the critical targets to interfere with the disease process underlying SSc, no studies have comprehensively established their effector role. Here we investigated the contribution of monocyte-derived macrophages (MDMs) in mediating genetic susceptibility to SSc...
January 17, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29348261/complement-receptor-c5ar1-plays-an-evolutionarily-conserved-role-in-successful-cardiac-regeneration
#10
Niranjana Natarajan, Yamen Abbas, Donald M Bryant, Juan Manuel Gonzalez-Rosa, Michka Sharpe, Aysu Uygur, Lucas H Cocco-Delgado, Nhi Ngoc Ho, Norma P Gerard, Craig J Gerard, Calum A Macrae, Caroline E Burns, C Geoffrey Burns, Jessica L Whited, Richard T Lee
Background -Defining conserved molecular pathways in animal models of successful cardiac regeneration could yield insight into why adult mammals have inadequate cardiac regeneration after injury. Insight into the transcriptomic landscape of early cardiac regeneration from model organisms will shed light on evolutionarily conserved pathways in successful cardiac regeneration. Methods -Here we describe a cross-species transcriptomic screen in three model organisms for cardiac regeneration -axolotl, neonatal mice and zebrafish...
January 18, 2018: Circulation
https://www.readbyqxmd.com/read/29348240/snf1-related-kinase1-controlled-c-s1-bzip-signaling-activates-alternative-mitochondrial-metabolic-pathways-to-ensure-plant-survival-in-extended-darkness
#11
Lorenzo Pedrotti, Christoph Weiste, Thomas Nägele, Elmar Wolf, Francesca Lorenzin, Katrin Dietrich, Andrea Mair, Wolfram Weckwerth, Markus Teige, Elena Baena-González, Wolfgang Dröge-Laser
Sustaining energy homeostasis is of pivotal importance for all living organisms. In Arabidopsis thaliana, evolutionarily conserved SnRK1 kinases (Snf1-RELATED KINASE1) control metabolic adaptation during low energy stress. To unravel starvation-induced transcriptional mechanisms, we performed transcriptome studies of inducible knock-down lines and found that S1-basic leucine Zipper transcription factors (S1-bZIPs) control a defined subset of genes downstream of SnRK1. For example, S1-bZIPs coordinate the expression of genes involved in branched-chain amino acid catabolism, which constitutes an alternative mitochondrial respiratory pathway that is crucial for plant survival during starvation...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29347945/microrna-transcriptome-analysis-of-porcine-vital-organ-responses-to-immunosuppressive-porcine-cytomegalovirus-infection
#12
Xiao Liu, Haoche Wei, Shan Liao, Jianheng Ye, Ling Zhu, Zhiwen Xu
BACKGROUND: Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits T-lymphocyte and macrophage immune functions; it has significantly damaged the farming industry. Although recent studies have shown that miRNAs play important roles in immune responses, the regulatory mechanisms of miRNAs during immunosuppressive virus infection remain unclear. METHODS: In this study, porcine small-RNA transcriptomes of PCMV-infected and uninfected vital organs were first characterised by high-throughput sequencing...
January 18, 2018: Virology Journal
https://www.readbyqxmd.com/read/29346762/transcriptome-and-dna-methylome-analysis-in-a-mouse-model-of-diet-induced-obesity-predicts-increased-risk-of-colorectal-cancer
#13
Ruifang Li, Sara A Grimm, Deepak Mav, Haiwei Gu, Danijel Djukovic, Ruchir Shah, B Alex Merrick, Daniel Raftery, Paul A Wade
Colorectal cancer (CRC) tends to occur at older age; however, CRC incidence rates have been rising sharply among young age groups. The increasing prevalence of obesity is recognized as a major risk, yet the mechanistic underpinnings remain poorly understood. Using a diet-induced obesity mouse model, we identified obesity-associated molecular changes in the colonic epithelium of young and aged mice, and we further investigated whether the changes were reversed after weight loss. Transcriptome analysis indicated that obesity-related colonic cellular metabolic switch favoring long-chain fatty acid oxidation happened in young mice, while obesity-associated downregulation of negative feedback regulators of pro-proliferative signaling pathways occurred in older mice...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346549/transcriptome-and-functional-analysis-in-a-drosophila-model-of-ngly1-deficiency-provides-insight-into-therapeutic-approaches
#14
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/29346386/histological-subtypes-of-mouse-mammary-tumors-reveal-conserved-relationships-to-human-cancers
#15
Daniel P Hollern, Matthew R Swiatnicki, Eran R Andrechek
Human breast cancer has been characterized by extensive transcriptional heterogeneity, with dominant patterns reflected in the intrinsic subtypes. Mouse models of breast cancer also have heterogeneous transcriptomes and we noted that specific histological subtypes were associated with particular subsets. We hypothesized that unique sets of genes define each tumor histological type across mouse models of breast cancer. Using mouse models that contained both gene expression data and expert pathologist classification of tumor histology on a sample by sample basis, we predicted and validated gene expression signatures for Papillary, EMT, Microacinar and other histological subtypes...
January 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29345255/pure-mechanistic-analysis-of-additive-neuroprotective-effects-between-baicalin-and-jasminoidin-in-ischemic-stroke-mice
#16
Peng-Qian Wang, Qiong Liu, Wen-Juan Xu, Ya-Nan Yu, Ying-Ying Zhang, Bing Li, Jun Liu, Zhong Wang
Both baicalin (BA) and jasminoidin (JA) are active ingredients in Chinese herb medicine Scutellaria baicalensis and Fructus gardeniae, respectively. They have been shown to exert additive neuroprotective action in ischemic stroke models. In this study we used transcriptome analysis to explore the pure therapeutic mechanisms of BA, JA and their combination (BJ) contributing to phenotype variation and reversal of pathological processes. Mice with middle cerebral artery obstruction were treated with BA, JA, their combination (BJ), or concha margaritifera (CM)...
January 18, 2018: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29345219/transcriptional-changes-when-myxococcus-xanthus-preys-on-escherichia-coli-suggest-myxobacterial-predators-are-constitutively-toxic-but-regulate-their-feeding
#17
Paul G Livingstone, Andrew D Millard, Martin T Swain, David E Whitworth
Predation is a fundamental ecological process, but within most microbial ecosystems the molecular mechanisms of predation remain poorly understood. We investigated transcriptome changes associated with the predation of Escherichia coli by the myxobacterium Myxococcus xanthus using mRNA sequencing. Exposure to pre-killed prey significantly altered expression of 1319 predator genes. However, the transcriptional response to living prey was minimal, with only 12 genes being significantly up-regulated. The genes most induced by prey presence (kdpA and kdpB, members of the kdp regulon) were confirmed by reverse transcriptase quantitative PCR to be regulated by osmotic shock in M...
January 18, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29345059/microrna-networks-associated-with-active-systemic-juvenile-idiopathic-arthritis-regulate-cd163-expression-and-anti-inflammatory-functions-in-macrophages-through-two-distinct-mechanisms
#18
Thuy Do, Rachel Tan, Mark Bennett, Mario Medvedovic, Alexei A Grom, Nan Shen, Sherry Thornton, Grant S Schulert
Systemic juvenile idiopathic arthritis (SJIA) is a severe childhood arthropathy with features of autoinflammation. Monocytes and macrophages in SJIA have a complex phenotype with both pro- and anti-inflammatory properties that combine features of several well characterized in vitro conditions used to activate macrophages. An important anti-inflammatory phenotype is expression of CD163, a scavenger receptor that sequesters toxic pro-inflammatory complexes that is highly expressed in both active SJIA and macrophage activation syndrome (MAS)...
January 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29344683/the-root-transcriptome-of-achyranthes-bidentata-and-the-identification-of-the-genes-involved-in-the-replanting-benefit
#19
Yan Hui Yang, Ming Jie Li, Yan Jie Yi, Rui Fang Li, Cheng Dong, Zhong Yi Zhang
The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit...
January 17, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29343235/comparison-of-three-assembly-strategies-for-a-heterozygous-seedless-grapevine-genome-assembly
#20
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
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