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https://www.readbyqxmd.com/read/28647433/targeted-release-of-transcription-factors-for-human-cell-reprogramming-by-zebra-cell-penetrating-peptide
#1
Benjamin Caulier, Lionel Berthoin, Helène Coradin, Frédéric Garban, Marie Claire Dagher, Benoît Polack, Bertrand Toussaint, Jean Luc Lenormand, David Laurin
Transcription factors (TFs) are key actors of the control of gene expression and consequently of every major process within cells, ranging from cell fate determination, cell cycle control and response to environment. Their ectopic expression has proven high potential in reprogramming cells for regenerative medicine; ontogenesis studies and cell based modelling. Direct delivery of proteins could represent an alternative to current reprogramming methods using gene transfer but still needs technological improvements...
June 21, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28647055/uncovering-gene-regulatory-networks-controlling-plant-cell-differentiation
#2
REVIEW
Colleen Drapek, Erin E Sparks, Philip N Benfey
The development of multicellular organisms relies on the precise regulation of cellular differentiation. As such, there has been significant effort invested to understand the process through which an immature cell undergoes differentiation. In this review, we highlight key discoveries and advances that have contributed to our understanding of the transcriptional networks underlying Arabidopsis root endodermal differentiation. To conclude, we propose perspectives on how advances in molecular biology, microscopy, and nucleotide sequencing will provide the tools to test the biological significance of these gene regulatory networks (GRN)...
June 21, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28646660/towards-understanding-transcriptional-networks-in-cellular-reprogramming
#3
REVIEW
Jaber Firas, Jose M Polo
Most of the knowledge we have on the molecular mechanisms of transcription factor mediated reprogramming comes from studies conducted in induced pluripotency. Recently however, a few studies investigated the mechanisms of cellular reprogramming in direct and indirect transdifferentiation, which allows us to explore whether shared parallel mechanisms can be drawn. Moreover, there are currently several computational tools that have been developed to predict and enhance the reprogramming process by reconstructing the transcriptional networks of reprogramming cells...
June 21, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28646136/recurrent-background-mutations-in-whi2-impair-proteostasis-and-degradation-of-misfolded-cytosolic-proteins-in-saccharomyces-cerevisiae
#4
Sophie A Comyn, Stéphane Flibotte, Thibault Mayor
Proteostasis promotes viability at both the cellular and organism levels by maintaining a functional proteome. This requires an intricate protein quality control (PQC) network that mediates protein folding by molecular chaperones and removes terminally misfolded proteins via the ubiquitin proteasome system and autophagy. How changes within the PQC network can perturb proteostasis and shift the balance between protein folding and proteolysis remain poorly understood. However, given that proteostasis is altered in a number of conditions such as cancer and ageing, it is critical that we identify the factors that mediate PQC and understand the interplay between members of the proteostatic network...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646090/cellular-functions-of-wasp-family-proteins-at-a-glance
#5
REVIEW
Olga Alekhina, Ezra Burstein, Daniel D Billadeau
Proteins of the Wiskott-Aldrich syndrome protein (WASP) family function as nucleation-promoting factors for the ubiquitously expressed Arp2/3 complex, which drives the generation of branched actin filaments. Arp2/3-generated actin regulates diverse cellular processes, including the formation of lamellipodia and filopodia, endocytosis and/or phagocytosis at the plasma membrane, and the generation of cargo-laden vesicles from organelles including the Golgi, endoplasmic reticulum (ER) and the endo-lysosomal network...
June 23, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#6
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28645173/spatially-resolved-metabolic-analysis-reveals-a-central-role-for-transcriptional-control-in-carbon-allocation-to-wood
#7
Melissa Roach, Stéphanie Arrivault, Amir Mahboubi, Nicole Krohn, Ronan Sulpice, Mark Stitt, Totte Niittylä
The contribution of transcriptional and post-transcriptional regulation to modifying carbon allocation to developing wood of trees is not well defined. To clarify the role of transcriptional regulation, the enzyme activity patterns of eight central primary metabolism enzymes across phloem, cambium, and developing wood of aspen (Populus tremula L.) were compared with transcript levels obtained by RNA sequencing of sequential stem sections from the same trees. Enzymes were selected on the basis of their importance in sugar metabolism and in linking primary metabolism to lignin biosynthesis...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28644695/peer-supported-open-dialogue-a-thematic-analysis-of-trainee-perspectives-on-the-approach-and-training
#8
Tom Stockmann, Lisa Wood, Gabriela Enache, Frankie Withers, Lauren Gavaghan, Russell Razzaque
BACKGROUND: Open Dialogue (OD) is a Finnish social network based model of care, with practice and organisational aspects. Peer-supported Open Dialogue (POD) is a UK version involving peer workers, whose contributions include building on fragmented social networks. Fifty-four NHS staff undertook the first training in POD between 2014 and 2015. The training course was organised as four separate residential weeks, together with reflective sharing on an online platform. AIMS: This study aimed to explore the perspectives of the POD trainees on the training and the POD approach...
June 23, 2017: Journal of Mental Health
https://www.readbyqxmd.com/read/28644436/the-lats1-and-lats2-tumor-suppressors-beyond-the-hippo-pathway
#9
REVIEW
Noa Furth, Yael Aylon
Proper cellular functionality and homeostasis are maintained by the convergent integration of various signaling cascades, which enable cells to respond to internal and external changes. The Dbf2-related kinases LATS1 and LATS2 (LATS) have emerged as central regulators of cell fate, by modulating the functions of numerous oncogenic or tumor suppressive effectors, including the canonical Hippo effectors YAP/TAZ, the Aurora mitotic kinase family, estrogen signaling and the tumor suppressive transcription factor p53...
June 23, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28644004/the-intricate-effects-of-alpha-amino-and-lysine-modifications-on-arginine-methylation-on-the-n-terminal-tail-of-histone-h4
#10
Melody D Fulton, Jing Zhang, Maomao He, Meng-Chiao Ho, Y George Zheng
Chemical modifications on the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The "histone code" hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) on the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and over 450 histone PTMs discovered, and the PTMs on lysine and arginine residues account for a crucial part of the histone code. Although significant progress has been achieved in recent years, the molecular basis for the histone code is far from being fully understood...
June 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28642850/transcriptional-network-controlling-endochondral-ossification
#11
REVIEW
Kenji Hata, Yoshifumi Takahata, Tomohiko Murakami, Riko Nishimura
Endochondral ossification is the fundamental process of skeletal development in vertebrates. Chondrocytes undergo sequential steps of differentiation, including mesenchymal condensation, proliferation, hypertrophy, and mineralization. These steps, which are required for the morphological and functional changes in differentiating chondrocytes, are strictly regulated by a complex transcriptional network. Biochemical and mice genetic studies identified chondrogenic transcription factors critical for endochondral ossification...
May 2017: Journal of Bone Metabolism
https://www.readbyqxmd.com/read/28642593/transforming-growth-factor-%C3%AE-1-regulates-the-nascent-hematopoietic-stem-cell-niche-by-promoting-gluconeogenesis
#12
C-Y Zhang, H-M Yin, H Wang, D Su, Y Xia, L-F Yan, B Fang, W Liu, Y-M Wang, A-H Gu, Y Zhou
The understanding of hematopoietic stem cell (HSC) emergence is important to generate HSCs from pluripotent precursors. However, integrated signaling network that regulates the niche of nascent HSCs remains unclear. Herein, we uncovered a novel role of TGF-β1 in the metabolic niche of HSC emergence using the tgf-β1b(-/-) zebrafish. Our findings first showed that Tgf-β1 transcripts were enriched in the nascent HSCs. Loss of tgf-β1b caused a decrease of nascent HSCs within the aorta-gonad-mesonephros. Moreover, tgf-β1b(+) cells were runx1(+) HSCs and underwent an endothelial-to-hematopoietic-transition process...
June 23, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28642487/hypoxia-is-a-key-driver-of-alternative-splicing-in-human-breast-cancer-cells
#13
Jian Han, Jia Li, Jolene Caifeng Ho, Grace Sushin Chia, Hiroyuki Kato, Sudhakar Jha, Henry Yang, Lorenz Poellinger, Kian Leong Lee
Adaptation to hypoxia, a hallmark feature of many tumors, is an important driver of cancer cell survival, proliferation and the development of resistance to chemotherapy. Hypoxia-induced stabilization of hypoxia-inducible factors (HIFs) leads to transcriptional activation of a network of hypoxia target genes involved in angiogenesis, cell growth, glycolysis, DNA damage repair and apoptosis. Although the transcriptional targets of hypoxia have been characterized, the alternative splicing of transcripts that occurs during hypoxia and the roles they play in oncogenesis are much less understood...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#14
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28640975/nac-transcription-factor-jungbrunnen1-enhances-drought-tolerance-in-tomato
#15
Venkatesh P Thirumalaikumar, Vikas Devkar, Nikolay Mehterov, Shawkat Ali, Rengin Ozgur, Ismail Turkan, Bernd Mueller-Roeber, Salma Balazadeh
Water deficit (drought stress) massively restricts plant growth and the yield of crops; reducing the deleterious effects of drought is therefore of high agricultural relevance. Drought triggers diverse cellular processes including the inhibition of photosynthesis, the accumulation of cell-damaging reactive oxygen species, and gene expression reprogramming, besides others. Transcription factors (TF) are central regulators of transcriptional reprogramming and expression of many TF genes is affected by drought, including members of the NAC family...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#16
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#17
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640249/mybl2-b-myb-a-central-regulator-of-cell-proliferation-cell-survival-and-differentiation-involved-in-tumorigenesis
#18
REVIEW
Julian Musa, Marie-Ming Aynaud, Olivier Mirabeau, Olivier Delattre, Thomas Gp Grünewald
Limitless cell proliferation, evasion from apoptosis, dedifferentiation, metastatic spread and therapy resistance: all these properties of a cancer cell contribute to its malignant phenotype and affect patient outcome. MYBL2 (alias B-Myb) is a transcription factor of the MYB transcription factor family and a physiological regulator of cell cycle progression, cell survival and cell differentiation. When deregulated in cancer cells, MYBL2 mediates the deregulation of these properties. In fact, MYBL2 is overexpressed and associated with poor patient outcome in numerous cancer entities...
June 22, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28639619/long-noncoding-rna-lnchifcar-mir31hg-is-a-hif-1%C3%AE-co-activator-driving-oral-cancer-progression
#19
Jing-Wen Shih, Wei-Fan Chiang, Alexander T H Wu, Ming-Heng Wu, Ling-Yu Wang, Yen-Ling Yu, Yu-Wen Hung, Wen-Chang Wang, Cheng-Ying Chu, Chiu-Lien Hung, Chun A Changou, Yun Yen, Hsing-Jien Kung
Long noncoding RNAs (lncRNAs) have been implicated in hypoxia/HIF-1-associated cancer progression through largely unknown mechanisms. Here we identify MIR31HG as a hypoxia-inducible lncRNA and therefore we name it LncHIFCAR (long noncoding HIF-1α co-activating RNA); we describe its oncogenic role as a HIF-1α co-activator that regulates the HIF-1 transcriptional network, crucial for cancer development. Extensive analyses of clinical data indicate LncHIFCAR level is substantially upregulated in oral carcinoma, significantly associated with poor clinical outcomes and representing an independent prognostic predictor...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28639116/integration-of-transcriptomic-and-metabolic-data-reveals-hub-transcription-factors-involved-in-drought-stress-response-in-sunflower-helianthus-annuus-l
#20
Sebastián Moschen, Julio A Di Rienzo, Janet Higgins, Takayuki Tohge, Mutsumi Watanabe, Sergio González, Máximo Rivarola, Francisco García-García, Joaquin Dopazo, H Esteban Hopp, Rainer Hoefgen, Alisdair R Fernie, Norma Paniego, Paula Fernández, Ruth A Heinz
By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach...
June 21, 2017: Plant Molecular Biology
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