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https://www.readbyqxmd.com/read/29770421/quantitative-proteomics-and-systems-analysis-of-cultured-h9c2-cardiomyoblasts-during-differentiation-over-time-supports-a-function-follows-form-model-of-differentiation
#1
Cynthia Kankeu, Kylie Clarke, Delphi Van Haver, Kris Gevaert, Francis Impens, Anna Dittrich, H Llewelyn Roderick, Egle Passante, Heinrich J Huber
The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis...
May 17, 2018: Molecular omics
https://www.readbyqxmd.com/read/29769718/ankrd16-prevents-neuron-loss-caused-by-an-editing-defective-trna-synthetase
#2
My-Nuong Vo, Markus Terrey, Jeong Woong Lee, Bappaditya Roy, James J Moresco, Litao Sun, Hongjun Fu, Qi Liu, Thomas G Weber, John R Yates, Kurt Fredrick, Paul Schimmel, Susan L Ackerman
Editing domains of aminoacyl tRNA synthetases correct tRNA charging errors to maintain translational fidelity. A mutation in the editing domain of alanyl tRNA synthetase (AlaRS) in Aars sti mutant mice results in an increase in the production of serine-mischarged tRNAAla and the degeneration of cerebellar Purkinje cells. Here, using positional cloning, we identified Ankrd16, a gene that acts epistatically with the Aars sti mutation to attenuate neurodegeneration. ANKRD16, a vertebrate-specific protein that contains ankyrin repeats, binds directly to the catalytic domain of AlaRS...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29768346/abnormally-high-expression-of-pold1-mcm2-and-plk4-promotes-relapse-of-acute-lymphoblastic-leukemia
#3
Sheng Li, Chengzhong Wang, Weikai Wang, Weidong Liu, Guiqin Zhang
This study aimed to explore the underlying mechanism of relapsed acute lymphoblastic leukemia (ALL).Datasets of GSE28460 and GSE18497 were downloaded from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) between diagnostic and relapsed ALL samples were identified using Limma package in R, and a Venn diagram was drawn. Next, functional enrichment analyses of co-regulated DEGs were performed. Based on the String database, protein-protein interaction network and module analyses were also conducted...
May 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29766767/neural-architecture-from-cells-to-circuits
#4
Sarah E V Richards, Stephen D Van Hooser
Circuit operations are determined jointly by the properties of the circuit elements and the properties of the connections among these elements. In the nervous system, neurons exhibit diverse morphologies and branching patterns, allowing rich compartmentalization within individual cells, and complex synaptic interactions among groups of cells. Here, we summarize work detailing how neuronal morphology impacts neural circuit function. In particular, we consider example neurons in the retina, cerebral cortex, and the stomatogastric ganglion of crustaceans...
May 16, 2018: Journal of Neurophysiology
https://www.readbyqxmd.com/read/29763523/role-of-basic-pentacysteiene-transcription-factors-in-a-sub-set-of-cytokinin-signaling-responses
#5
Carly M Shanks, Andreas Hecker, Chia-Yi Cheng, Luise Brand, Silvio Collani, Markus Schmid, G Eric Schaller, Dierk Wanke, Klaus Harter, Joseph J Kieber
Cytokinin plays diverse roles in plant growth and development, generally acting by modulating gene transcription in target tissues. The type-B ARR transcription factors have emerged as primary targets of cytokinin signaling and are required for essentially all cytokinin-mediated changes in gene expression. The diversity of cytokinin function is likely imparted by the activity of various transcription factors working with the type-B ARRs to alter specific sets of target genes. One potential set of co-regulators modulating the cytokinin response are the BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family of plant-specific transcription factors...
May 15, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29761061/transcriptomic-studies-reveal-a-key-metabolic-pathway-contributing-to-a-well-maintained-photosynthetic-system-under-drought-stress-in-foxtail-millet-setaria-italica-l
#6
Weiping Shi, Jingye Cheng, Xiaojie Wen, Jixiang Wang, Guanyan Shi, Jiayan Yao, Liyuan Hou, Qian Sun, Peng Xiang, Xiangyang Yuan, Shuqi Dong, Pingyi Guo, Jie Guo
Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet ( Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents...
2018: PeerJ
https://www.readbyqxmd.com/read/29755654/mycn-acts-as-a-direct-co-regulator-of-p53-in-mycn-amplified-neuroblastoma
#7
Saurabh Agarwal, Giorgio Milazzo, Kimal Rajapakshe, Ronald Bernardi, Zaowen Chen, Eveline Barberi, Jan Koster, Giovanni Perini, Cristian Coarfa, Jason M Shohet
The MYC oncogenes and p53 have opposing yet interrelated roles in normal development and tumorigenesis. How MYCN expression alters the biology and clinical responsiveness of pediatric neuroblastoma remains poorly defined. Neuroblastoma is p53 wild type at diagnosis and repression of p53 signaling is required for tumorigenesis. Here, we tested the hypothesis that MYCN amplification alters p53 transcriptional activity in neuroblastoma. Interestingly, we found that MYCN directly binds to the tetrameric form of p53 at its C-terminal domain, and this interaction is independent of MYCN/MAX heterodimer formation...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29753912/biomimetic-soft-fibrous-hydrogels-for-contractile-and-pharmacologically-responsive-smooth-muscle
#8
Yonghui Ding, Xin Xu, Sadhana Sharma, Michael Floren, Kurt Stenmark, Stephanie J Bryant, Corey P Neu, Wei Tan
The ability to assess changes in smooth muscle contractility and pharmacological responsiveness in normal or pathological-relevant vascular tissue environments is critical to enable vascular drug discovery. However, major challenges remain in both capturing the complexity of in vivo vascular remodeling and evaluating cell contractility in complex, tissue-like environments. Herein, we developed a biomimetic fibrous hydrogel with tunable structure, stiffness, and composition to resemble the native vascular tissue environment...
May 10, 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/29751738/transcriptomic-and-metabolomic-analyses-reveal-that-bacteria-promote-plant-defense-during-infection-of-soybean-cyst-nematode-in-soybean
#9
Wenshu Kang, Xiaofeng Zhu, Yuanyuan Wang, Lijie Chen, Yuxi Duan
BACKGROUND: Soybean cyst nematode (SCN) is the most devastating pathogen of soybean. Our previous study showed that the plant growth-promoting rhizobacterium Bacillus simplex strain Sneb545 promotes soybean resistance to SCN. Here, we conducted a combined metabolomic and transcriptomic analysis to gain information regarding the biological mechanism of defence enhancement against SCN in Sneb545-treated soybean. To this end, we compared the transcriptome and metabolome of Sneb545-treated and non-treated soybeans under SCN infection...
May 11, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29743619/co-regulation-of-photosynthetic-capacity-by-nitrogen-phosphorus-and-magnesium-in-a-subtropical-karst-forest-in-china
#10
Jing Wang, Xuefa Wen, Xinyu Zhang, Shenggong Li, Da-Yong Zhang
Leaf photosynthetic capacity is mainly constrained by nitrogen (N) and phosphorus (P). Little attention has been given to the photosynthetic capacity of mature forests with high calcium (Ca) and magnesium (Mg) in the Karst critical zone. We measured light-saturated net photosynthesis (Asat ), photosynthetic capacity (maximum carboxylation rate [Vcmax ], and maximum electron transport rate [Jmax ]) as well as leaf nutrient contents (N, P, Ca, Mg, potassium [K], and sodium [Na]), leaf mass per area (LMA), and leaf thickness (LT) in 63 dominant plants in a mature subtropical forest in the Karst critical zone in southwestern China...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29739818/spermiogenesis-and-male-fertility-require-the-function-of-suppressor-of-hairy-wing-in-somatic-cyst-cells-of-drosophila
#11
Tingting Duan, Pamela K Geyer
Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is an example of a multivalent transcription factor. Although best known for its role in establishing the chromatin insulator of the gypsy retrotransposon, Su(Hw) functions as an activator and repressor at non- gypsy genomic sites. It remains unclear how the different regulatory activities of Su(Hw) are utilized during development. Motivated from observations of spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis to advance an understanding of its developmental contributions as an insulator, repressor and activator protein...
May 8, 2018: Genetics
https://www.readbyqxmd.com/read/29738528/network-inference-reveals-novel-connections-in-pathways-regulating-growth-and-defense-in-the-yeast-salt-response
#12
Matthew E MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J Coon, Audrey P Gasch
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress...
May 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29735765/characterization-of-flagellar-and-toxin-phase-variation-in-clostridiodes-difficile-ribotype-012-isolates
#13
Brandon R Anjuwon-Foster, Natalia Maldonado-Vazquez, Rita Tamayo
Clostridiodes difficile causes diarrheal diseases mediated in part by the secreted toxins TcdA and TcdB. C. difficile produces flagella that also contribute to motility and bacterial adherence to intestinal cells during infection. Flagellum and toxin gene expression are linked via the flagellar alternative sigma factor, SigD. Recently, we identified a "flagellar switch" upstream of the early flagellar biosynthesis operon that mediates phase variation of both flagellum and toxin production in C. difficile strain R20291...
May 7, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29730294/live-imaging-reveals-a-conserved-role-of-fatty-acid-%C3%AE-oxidation-in-early-lymphatic-development-in-zebrafish
#14
Annalisa Zecchin, Brian Wong, Bieke Tembuyser, Joris Souffreau, An Van Nuffelen, Sabine Wyns, Stefan Vinckier, Peter Carmeliet, Mieke Dewerchin
During embryonic development, lymphatic endothelial cells (LECs) differentiate from venous endothelial cells (VECs), a process that is tightly regulated by several genetic signals. While the aquatic zebrafish model is regularly used for studying lymphangiogenesis and offers the unique advantage of time-lapse video-imaging of lymphatic development, some aspects of lymphatic development in this model differ from those in the mouse. It therefore remained to be determined whether fatty acid β-oxidation (FAO), which we showed to regulate lymphatic formation in the mouse, also co-determines lymphatic development in this aquatic model...
May 3, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29728618/defining-a-conformational-ensemble-that-directs-activation-of-ppar%C3%AE
#15
Ian M Chrisman, Michelle D Nemetchek, Ian Mitchelle S de Vera, Jinsai Shang, Zahra Heidari, Yanan Long, Hermes Reyes-Caballero, Rodrigo Galindo-Murillo, Thomas E Cheatham, Anne-Laure Blayo, Youseung Shin, Jakob Fuhrmann, Patrick R Griffin, Theodore M Kamenecka, Douglas J Kojetin, Travis S Hughes
The nuclear receptor ligand-binding domain (LBD) is a highly dynamic entity. Crystal structures have defined multiple low-energy LBD structural conformations of the activation function-2 (AF-2) co-regulator-binding surface, yet it remains unclear how ligand binding influences the number and population of conformations within the AF-2 structural ensemble. Here, we present a nuclear receptor co-regulator-binding surface structural ensemble in solution, viewed through the lens of fluorine-19 (19 F) nuclear magnetic resonance (NMR) and molecular simulations, and the response of this ensemble to ligands, co-regulator peptides and heterodimerization...
May 4, 2018: Nature Communications
https://www.readbyqxmd.com/read/29720972/spot-mediated-regulation-and-amino-acid-prototrophy-are-essential-for-pyocyanin-production-during-parasitic-growth-of-pseudomonas-aeruginosa-in-a-co-culture-model-system-with-aeromonas-hydrophila
#16
Nina Jagmann, Bodo Philipp
The opportunistic pathogen Pseudomonas aeruginosa employs its complex quorum sensing (QS) network to regulate the expression of virulence factors such as pyocyanin. Besides cell density, QS in this bacterium is co-regulated by environmental cues. In this study, we employed a previously established co-culture model system to identify metabolic influences that are involved in the regulation of pyocyanin production in P. aeruginosa . In this co-culture consisting of P. aeruginosa and the chitinolytic bacterium Aeromonas hydrophila , parasitic growth of P...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29718163/profiling-of-3696-nuclear-receptor-coregulator-interactions-a-resource-for-biological-and-clinical-discovery
#17
Marjoleine F Broekema, Danielle A A Hollman, Arjen Koppen, Henk-Jan van den Ham, Diana Melchers, Dirk Pijnenburg, Rob Ruijtenbeek, Saskia W C van Mil, René Houtman, Eric Kalkhoven
Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction and physiology, and, as a consequence, are implicated in a broad-range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including co-activators and co-repressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding...
April 30, 2018: Endocrinology
https://www.readbyqxmd.com/read/29709641/transcriptome-profiling-analysis-revealed-co-regulation-of-multiple-pathways-in-jujube-during-infection-by-candidatus-phytoplasma-ziziphi
#18
Huiyu Wang, Xia Ye, Jidong Li, Bin Tan, Peng Chen, Jun Cheng, Wei Wang, Xianbo Zheng, Jiancan Feng
BACKGROUND: Jujube witches' broom (JWB), caused by a phytoplasma, devastates jujube tree (Ziziphus jujuba) growth and production in Asia. Although host responses to phytoplasmas are studied at the phenotypic, physiological, biochemical and molecular levels, it remains unclear how a host plant responds at the molecular level during the primary stage of infection. METHODS: To understand the response of the jujube tree to JWB infection, leaves were sampled at different times during the phytoplasma infection...
April 27, 2018: Gene
https://www.readbyqxmd.com/read/29706654/the-essential-role-of-wd-repeat-domain-77-in-prostate-tumor-initiation-induced-by-pten-loss
#19
Deon O'Bryant, Zhengxin Wang
Prostate cancer is the most commonly diagnosed malignancy among men, but few genetic factors that drive prostate cancer initiation have been identified. The WD repeat domain 77 (Wdr77) protein is essential for cellular proliferation when localizes in the cytoplasm of epithelial cells at the early stage of prostate development. In the adult prostate, it is transported into the nucleus and functions as a co-regulator of the androgen receptor to promote cellular differentiation and prostate function. This developmental process is reversed during prostate tumorigenesis, i...
April 30, 2018: Oncogene
https://www.readbyqxmd.com/read/29704232/prognostic-and-microrna-profile-analysis-for-cd44-positive-expression-pediatric-posterior-fossa-ependymoma
#20
C Shu, Q Wang, X Yan, J Wang
BACKGROUND: Ependymoma is the third most common pediatric brain tumor and occurs most frequently in the posterior fossa. However, the lack of immortalized cell lines, xenografts, or animal models has significantly hindered the study of pediatric posterior fossa ependymoma (P-PF-EPN) pathogenesis. This prompted us to use clinical big data to study this rare disease. METHODS: Application of the robust rank aggregation method revealed CD44 as a reliable biomarker in P-PF-EPN...
April 27, 2018: Clinical & Translational Oncology
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