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https://www.readbyqxmd.com/read/28747406/lncrnas-in-development-and-disease-from-functions-to-mechanisms
#1
REVIEW
M Joaquina Delás, Gregory J Hannon
Differential expression of long non-coding RNAs (lncRNAs) during differentiation and their misregulation in cancer highlight their potential as cell fate regulators. While some example lncRNAs have been characterized in great detail, the functional in vivo relevance of others has been called into question. Finding functional lncRNAs will most probably require a combination of complementary approaches that will greatly vary depending on their mode of action. In this review, we discuss the different tools available to dissect genetically lncRNA requirements and how each is best suited to studies in particular contexts...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28747405/nmda-receptor-dependent-presynaptic-inhibition-at-the-calyx-of-held-synapse-of-rat-pups
#2
Tomoko Oshima-Takago, Hideki Takago
N-Methyl-d-aspartate receptors (NMDARs) play diverse roles in synaptic transmission, synaptic plasticity, neuronal development and neurological diseases. In addition to their postsynaptic expression, NMDARs are also expressed in presynaptic terminals at some central synapses, and their activation modulates transmitter release. However, the regulatory mechanisms of NMDAR-dependent synaptic transmission remain largely unknown. In the present study, we demonstrated that activation of NMDARs in a nerve terminal at a central glutamatergic synapse inhibits presynaptic Ca(2+) currents (ICa) in a GluN2C/2D subunit-dependent manner, thereby decreasing nerve-evoked excitatory postsynaptic currents...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28724695/caryolan-1-ol-an-antifungal-volatile-produced-by-streptomyces-spp-inhibits-the-endomembrane-system-of-fungi
#3
Gyeongjun Cho, Junheon Kim, Chung Gyoo Park, Corey Nislow, David M Weller, Youn-Sig Kwak
Streptomyces spp. have the ability to produce a wide variety of secondary metabolites that interact with the environment. This study aimed to discover antifungal volatiles from the genus Streptomyces and to determine the mechanisms of inhibition. Volatiles identified from Streptomyces spp. included three major terpenes, geosmin, caryolan-1-ol and an unknown sesquiterpene. antiSMASH and KEGG predicted that the volatile terpene synthase gene clusters occur in the Streptomyces genome. Growth inhibition was observed when fungi were exposed to the volatiles...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28724694/role-of-long-chain-acyl-coas-in-the-regulation-of-mycolic-acid-biosynthesis-in-mycobacteria
#4
Yi Ting Tsai, Valentina Salzman, Matías Cabruja, Gabriela Gago, Hugo Gramajo
One of the dominant features of the biology of Mycobacterium tuberculosis, and other mycobacteria, is the mycobacterial cell envelope with its exceptional complex composition. Mycolic acids are major and very specific components of the cell envelope and play a key role in its architecture and impermeability. Biosynthesis of mycolic acid (MA) precursors requires two types of fatty acid synthases, FAS I and FAS II, which should work in concert in order to keep lipid homeostasis tightly regulated. Both FAS systems are regulated at their transcriptional level by specific regulatory proteins...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28701378/dictyostelium-ampk%C3%AE-regulates-aggregate-size-and-cell-type-patterning
#5
Ranjana Maurya, Rakesh Kumar, Shweta Saran
Starved Dictyostelium cells aggregate into groups of nearly 10(5) cells. AMPK is a highly conserved serine/threonine protein kinase consisting of a catalytic and two regulatory subunits. As multi-cellular development in Dictyostelium is initiated upon starvation, we explored the role of the energy sensor, AMPK, which shows significant similarity to human AMPK and is expressed throughout development. Deletion of the ampkα gene results in the formation of numerous small-sized aggregates that develop asynchronously to form few fruiting bodies with small sori and long stalks...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28701377/microrna-206-modulates-an-rtn4a-cxcr4a-thbs3a-axis-in-newly-forming-somites-to-maintain-and-stabilize-the-somite-boundary-formation-of-zebrafish-embryos
#6
Cheng-Yung Lin, Jun-Yu He, Chih-Wei Zeng, Moo-Rumg Loo, Wen-Yen Chang, Po-Hsiang Zhang, Huai-Jen Tsai
Although microRNA-206 (miR-206) is known to regulate proliferation and differentiation of muscle fibroblasts, the role of miR-206 in early-stage somite development is still unknown. During somitogenesis of zebrafish embryos, reticulon4a (rtn4a) is specifically repressed by miR-206. The somite boundary was defective, and actin filaments were crossing over the boundary in either miR-206-knockdown or rtn4a-overexpressed embryos. In these treated embryos, C-X-C motif chemokine receptor 4a (cxcr4a) was reduced, while thrombospondin 3a (thbs3a) was increased...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28679548/zebrafish-lipid-droplets-regulate-embryonic-atp-homeostasis-to-power-early-development
#7
Asmita Dutta, Deepak Kumar Sinha
In zebrafish embryos, the maternally supplied pool of ATP is insufficient to power even the earliest of developmental events (0-3 hpf) such as oocyte-to-embryo transition (OET). The embryos generate an additional pulse (2.5 h long) of ATP (1.25-4 hpf) to achieve the embryonic ATP homeostasis. We demonstrate that the additional pulse of ATP is needed for successful execution of OET. The maternally supplied yolk lipids play a crucial role in maintaining the embryonic ATP homeostasis. In this paper, we identify the source and trafficking routes of free fatty acids (FFAs) that feed the mitochondria for synthesis of ATP...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28659386/fate-predetermination-of-cardiac-myocytes-during-zebrafish-heart-regeneration
#8
Isil Tekeli, Anna Garcia-Puig, Mario Notari, Cristina García-Pastor, Isabelle Aujard, Ludovic Jullien, Angel Raya
Adult zebrafish have the remarkable ability to regenerate their heart upon injury, a process that involves limited dedifferentiation and proliferation of spared cardiomyocytes (CMs), and migration of their progeny. During regeneration, proliferating CMs are detected throughout the myocardium, including areas distant to the injury site, but whether all of them are able to contribute to the regenerated tissue remains unknown. Here, we developed a CM-specific, photoinducible genetic labelling system, and show that CMs labelled in embryonic hearts survive and contribute to all three (primordial, trabecular and cortical) layers of the adult zebrafish heart...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28659385/cep19-cooperates-with-fop-and-cep350-to-drive-early-steps-in-the-ciliogenesis-programme
#9
Bahareh A Mojarad, Gagan D Gupta, Monica Hasegan, Oumou Goudiam, Renata Basto, Anne-Claude Gingras, Laurence Pelletier
Primary cilia are microtubule-based sensory organelles necessary for efficient transduction of extracellular cues. To initiate cilia formation, ciliary vesicles (CVs) are transported to the vicinity of the centrosome where they dock to the distal end of the mother centriole and fuse to initiate cilium assembly. However, to this date, the early steps in cilia formation remain incompletely understood. Here, we demonstrate functional interplay between CEP19, FOP and CEP350 in ciliogenesis. Using three-dimensional structured-illumination microscopy (3D-SIM) imaging, we mapped the relative spatial distribution of these proteins at the distal end of the mother centriole and show that CEP350/FOP act upstream of CEP19 in their recruitment hierarchy...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28659384/cell-signalling-pathway-regulation-by-ranbpm-molecular-insights-and-disease-implications
#10
REVIEW
Louisa M Salemi, Matthew E R Maitland, Christina J McTavish, Caroline Schild-Poulter
RanBPM (Ran-binding protein M, also called RanBP9) is an evolutionarily conserved, ubiquitous protein which localizes to both nucleus and cytoplasm. RanBPM has been implicated in the regulation of a number of signalling pathways to regulate several cellular processes such as apoptosis, cell adhesion, migration as well as transcription, and plays a critical role during development. In addition, RanBPM has been shown to regulate pathways implicated in cancer and Alzheimer's disease, implying that RanBPM has important functions in both normal and pathological development...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28659383/recognition-of-a-glycosylation-substrate-by-the-o-glcnac-transferase-tpr-repeats
#11
Karim Rafie, Olawale Raimi, Andrew T Ferenbach, Vladimir S Borodkin, Vaibhav Kapuria, Daan M F van Aalten
O-linked N-acetylglucosamine (O-GlcNAc) is an essential and dynamic post-translational modification found on hundreds of nucleocytoplasmic proteins in metazoa. Although a single enzyme, O-GlcNAc transferase (OGT), generates the entire cytosolic O-GlcNAc proteome, it is not understood how it recognizes its protein substrates, targeting only a fraction of serines/threonines in the metazoan proteome for glycosylation. We describe a trapped complex of human OGT with the C-terminal domain of TAB1, a key innate immunity-signalling O-GlcNAc protein, revealing extensive interactions with the tetratricopeptide repeats of OGT...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28659382/domain-cell-theory-supports-the-independent-evolution-of-the-eukarya-bacteria-and-archaea-and-the-nuclear-compartment-commonality-hypothesis
#12
James T Staley
In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured 'Prokaryotes First' hypotheses and another addressed 'Eukaryotes First' hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28659381/sumoylation-pathway-alteration-coupled-with-downregulation-of-sumo-e2-enzyme-at-mucosal-epithelium-modulates-inflammation-in-inflammatory-bowel-disease
#13
Salman Ahmad Mustfa, Mukesh Singh, Aamir Suhail, Gayatree Mohapatra, Smriti Verma, Debangana Chakravorty, Sarika Rana, Ritika Rampal, Atika Dhar, Sudipto Saha, Vineet Ahuja, C V Srikanth
Post-translational modification pathways such as SUMOylation are integral to all cellular processes and tissue homeostasis. We investigated the possible involvement of SUMOylation in the epithelial signalling in Crohn's disease (CD) and ulcerative colitis (UC), the two major forms of inflammatory bowel disease (IBD). Initially in a murine model of IBD, induced by dextran-sulfate-sodium (DSS mice), we observed inflammation accompanied by a lowering of global SUMOylation of colonic epithelium. The observed SUMOylation alteration was due to a decrease in the sole SUMO E2 enzyme (Ubc9)...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28659380/deubiquitylation-of-deubiquitylases
#14
REVIEW
Saba Haq, Suresh Ramakrishna
Deubiquitylating enzymes (DUBs) reverse the ubiquitylation of target proteins, thereby regulating diverse cellular functions. In contrast to the plethora of research being conducted on the ability of DUBs to counter the degradation of cellular proteins or auto-ubiquitylated E3 ligases, very little is known about the mechanisms of DUB regulation. In this review paper, we summarize a novel possible mechanism of DUB deubiquitylation by other DUBs. The available data suggest the need for further experiments to validate and characterize this notion of 'Dubbing DUBs'...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28615474/regulation-of-expression-of-human-rna-polymerase-ii-transcribed-snrna-genes
#15
REVIEW
Joana Guiro, Shona Murphy
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3' end formation of the transcripts...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28615473/forkhead-box-transcription-factor-l2-activates-fcp3c-to-regulate-insect-chorion-formation
#16
Yu-Xuan Ye, Peng-Lu Pan, Ji-Yu Xu, Zhang-Fei Shen, Dong Kang, Jia-Bao Lu, Qing-Lin Hu, Hai-Jian Huang, Yi-Han Lou, Nai-Ming Zhou, Chuan-Xi Zhang
Most animals are oviparous. However, the genes regulating egg shell formation remain not very clear. In this study, we found that Nilaparvata lugens Forkhead box transcription factor L2 (NlFoxL2) directly activated follicle cell protein 3C (NlFcp3C) to regulate chorion formation. NlFoxL2 and NlFcp3C had a similar expression pattern, both highly expressed in the follicular cells of female adults. Knockdown of NlFoxL2 or NlFcp3C also resulted in the same phenotypes: obesity and female infertility. RNA interference (RNAi) results suggested that NlFcp3C is a downstream gene of NlFoxL2 Furthermore, transient expression showed that NlFoxL2 could directly activate the NlFcp3C promoter...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28615472/neuronal-circadian-clock-protein-oscillations-are-similar-in-behaviourally-rhythmic-forager-honeybees-and-in-arrhythmic-nurses
#17
T Fuchikawa, K Beer, C Linke-Winnebeck, R Ben-David, A Kotowoy, V W K Tsang, G R Warman, E C Winnebeck, C Helfrich-Förster, G Bloch
Internal clocks driving rhythms of about a day (circadian) are ubiquitous in animals, allowing them to anticipate environmental changes. Genetic or environmental disturbances to circadian clocks or the rhythms they produce are commonly associated with illness, compromised performance or reduced survival. Nevertheless, some animals including Arctic mammals, open sea fish and social insects such as honeybees are active around-the-clock with no apparent ill effects. The mechanisms allowing this remarkable natural plasticity are unknown...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28592509/comparative-functional-genomic-screens-of-three-yeast-deletion-collections-reveal-unexpected-effects-of-genotype-in-response-to-diverse-stress
#18
Erica Acton, Amy Huei-Yi Lee, Pei Jun Zhao, Stephane Flibotte, Mauricio Neira, Sunita Sinha, Jennifer Chiang, Patrick Flaherty, Corey Nislow, Guri Giaever
The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, 'prototrophic' versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PBprot) or by backcrossing (Backcrossed, BCprot) to a wild-type strain...
June 2017: Open Biology
https://www.readbyqxmd.com/read/28566301/understanding-rna-modifications-the-promises-and-technological-bottlenecks-of-the-epitranscriptome
#19
REVIEW
Matthias Schaefer, Utkarsh Kapoor, Michael F Jantsch
The discovery of mechanisms that alter genetic information via RNA editing or introducing covalent RNA modifications points towards a complexity in gene expression that challenges long-standing concepts. Understanding the biology of RNA modifications represents one of the next frontiers in molecular biology. To this date, over 130 different RNA modifications have been identified, and improved mass spectrometry approaches are still adding to this list. However, only recently has it been possible to map selected RNA modifications at single-nucleotide resolution, which has created a number of exciting hypotheses about the biological function of RNA modifications, culminating in the proposition of the 'epitranscriptome'...
May 2017: Open Biology
https://www.readbyqxmd.com/read/28566300/sphingolipids-membrane-microdomains-in-brain-development-function-and-neurological-diseases
#20
REVIEW
Anne S B Olsen, Nils J Færgeman
Sphingolipids are highly enriched in the nervous system where they are pivotal constituents of the plasma membranes and are important for proper brain development and functions. Sphingolipids are not merely structural elements, but are also recognized as regulators of cellular events by their ability to form microdomains in the plasma membrane. The significance of such compartmentalization spans broadly from being involved in differentiation of neurons and synaptic transmission to neuronal-glial interactions and myelin stability...
May 2017: Open Biology
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