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BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology

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https://read.qxmd.com/read/30734956/rna-binding-proteins-as-regulators-of-retrotransposon-induced-exonization
#1
John LaCava
No abstract text is available yet for this article.
February 8, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30734933/targeted-proteomics-comes-to-the-benchside-and-the-bedside-is-it-ready-for-us
#2
REVIEW
Anjali Arora, Kumaravel Somasundaram
While mass spectrometry (MS)-based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is the proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided...
February 8, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30730055/microtubule-plus-end-dynamics-do-we-know-how-microtubules-grow-cells-boost-microtubule-growth-by-promoting-distinct-structural-transitions-at-growing-microtubule-ends
#3
REVIEW
Jeffrey van Haren, Torsten Wittmann
Microtubules form a highly dynamic filament network in all eukaryotic cells. Individual microtubules grow by tubulin dimer subunit addition and frequently switch between phases of growth and shortening. These unique dynamics are powered by GTP hydrolysis and drive microtubule network remodeling, which is central to eukaryotic cell biology and morphogenesis. Yet, our knowledge of the molecular events at growing microtubule ends remains incomplete. Here, recent ultrastructural, biochemical and cell biological data are integrated to develop a realistic model of growing microtubule ends comprised of structurally distinct but biochemically overlapping zones...
February 7, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30730051/coordination-of-timers-and-sensors-in-cell-signaling
#4
Junbin Qian, Lendert Gelens, Mathieu Bollen
Timers and sensors are common devices that make our daily life safer, more convenient, and more efficient. In a cellular context, they arguably play an even more crucial role as they ensure the survival of cells in the presence of various extrinsic and intrinsic stresses. Biological timers and sensors generate distinct signaling profiles, enabling them to produce different types of cellular responses. Recent data suggest that they can work together to guarantee correct timing and responsiveness. By exploring examples of cellular stress signaling from mitosis, DNA damage, and hypoxia, the authors discuss the common architecture of timer-sensor integration, and how its added features contribute to the generation of desired signaling profiles when dealing with stresses of variable duration and strength...
February 7, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30714631/sentience-and-consciousness-in-single-cells-how-the-first-minds-emerged-in-unicellular-species
#5
REVIEW
František Baluška, Arthur Reber
A reductionistic, bottom-up, cellular-based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life-forms. All other varieties of mentation are the result of evolutionary mechanisms based on this singular event...
February 4, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30706966/ribosomal-proteins-control-tumor-suppressor-pathways-in-response-to-nucleolar-stress
#6
REVIEW
Frédéric Lessard, Léa Brakier-Gingras, Gerardo Ferbeyre
Ribosome biogenesis includes the making and processing of ribosomal RNAs, the biosynthesis of ribosomal proteins from their mRNAs in the cytosol and their transport to the nucleolus to assemble pre-ribosomal particles. Several stresses including cellular senescence reduce nucleolar rRNA synthesis and maturation increasing the availability of ribosome-free ribosomal proteins. Several ribosomal proteins can activate the p53 tumor suppressor pathway but cells without p53 can still arrest their proliferation in response to an imbalance between ribosomal proteins and mature rRNA production...
February 1, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30706963/back-from-the-brink-retrieval-of-membrane-proteins-from-terminal-compartments-unexpected-pathways-for-membrane-protein-retrieval-from-vacuoles-and-endolysosomes
#7
REVIEW
Matthew N J Seaman
It has long been believed that membrane proteins present in degradative compartments such as endolysosomes or vacuoles would be destined for destruction. Now however, it appears that mechanisms and machinery exist in simple eukaryotes such as yeast and more complex organisms such as mammals that can rescue potentially "doomed" membrane proteins by retrieving them from these "late" compartments and recycling them back to the Golgi complex. In yeast, a sorting nexin dimer containing Snx4p can recognize and retrieve the Atg27p membrane protein while in mammals, the AP5 complex (with SPG11 and SPG15) directs the recycling of Golgi-localized proteins along with the cation-independent mannose 6-phosphate receptor (CIMPR)...
February 1, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30706962/genomic-accumulation-of-retrotransposons-was-facilitated-by-repressive-rna-binding-proteins-a-hypothesis
#8
Jan Attig, Jernej Ule
Retrotransposon-derived elements (RDEs) can disrupt gene expression, but are nevertheless widespread in metazoan genomes. This review presents a hypothesis that repressive RNA-binding proteins (RBPs) facilitated the large-scale accumulation of RDEs. Many RBPs bind RDEs in pre-mRNAs to repress the effects of RDEs on RNA processing, or the formation of inverted repeat RNA structures. RDE-binding RBPs often assemble on extended, multivalent binding sites across the RDE, which ensures repression of cryptic splice or polyA sites...
February 1, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30614544/let-s-stop-the-sloppy-use-of-lamarckian
#9
EDITORIAL
Dave Speijer
No abstract text is available yet for this article.
January 7, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30614540/can-vestibular-stimulation-be-used-to-treat-obesity-vestibular-stimulation-targeting-the-otoliths-could-rebalance-energy-homeostasis-to-trigger-a-leaner-body-habitus-and-thus-treat-metabolic-syndrome
#10
REVIEW
Paul D McGeoch
It is hypothesized that repeated, non-invasive stimulation of the vestibular (balance) system, via a small electrical current to the skin behind the ears, will cause the brain centers that control energy homeostasis to shift the body toward a leaner physique. This is because these centers integrate multiple inputs to, in effect, fix a set-point for body fat, which though difficult to alter is not immutable. They will interpret repeated stimulation of the parts of the vestibular system that detect acceleration as a state of chronic activity...
January 7, 2019: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30537168/the-lkb1-ampk-and-mtorc1-metabolic-signaling-networks-in-schwann-cells-control-axon-integrity-and-myelination-assembling-and-upholding-nerves-by-metabolic-signaling-in-schwann-cells
#11
REVIEW
Bogdan Beirowski
The Liver kinase B1 with its downstream target AMP activated protein kinase (LKB1-AMPK), and the key nutrient sensor mammalian target of rapamycin complex 1 (mTORC1) form two signaling systems that coordinate metabolic and cellular activity with changes in the environment in order to preserve homeostasis. For example, nutritional fluctuations rapidly feed back on these signaling systems and thereby affect cell-specific functions. Recent studies have started to reveal important roles of these strategic metabolic regulators in Schwann cells for the trophic support and myelination of axons...
December 11, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30537007/hiv-disease-progression-overexpression-of-the-ectoenzyme-cd38-as-a-contributory-factor
#12
Juan C Rodríguez-Alba, Amayrani Abrego-Peredo, Carlos Gallardo-Hernández, Jocelyn Pérez-Lara, Wendolaine Santiago-Cruz, Wei Jiang, Enrique Espinosa
Despite abundant evidence associating CD38 overexpression and CD4 T cell depletion in HIV infection, no causal relation has been investigated. To address this issue, a series of mechanisms are proposed, supported by evidence from different fields, by which CD38 overexpression can facilitate CD4 T cell depletion in HIV infection. According to this model, increased catalytic activity of CD38 may reduce CD4 T cells' cytoplasmic nicotin-amide adenine dinucleotide (NAD), leading to a chronic Warburg effect. This will reduce mitochondrial function...
December 10, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30525212/can-all-major-ros-forming-sites-of-the-respiratory-chain-be-activated-by-high-fadh-2-nadh-ratios
#13
Peter Schönfeld
No abstract text is available yet for this article.
December 7, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30512221/can-all-major-ros-forming-sites-of-the-respiratory-chain-be-activated-by-high-fadh-2-nadh-ratios-ancient-evolutionary-constraints-determine-mitochondrial-ros-formation
#14
REVIEW
Dave Speijer
Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH2 /NADH (F/N) ratios (e.g., FAs) initiate ROS formation in Complex I due to insufficient availability of its electron acceptor (Q) and reverse electron transport from QH2 , e.g., during FAO or glycerol-3-phosphate shuttle use. Here it is proposed that the Q-cycle of Complex III contributes to enhanced ROS formation going from low F/N ratio substrates (glucose) to high F/N substrates...
December 4, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30507004/cura-x-ing-cancer-and-beyond
#15
Vassilis G Gorgoulis, Athanassios Kotsinas
No abstract text is available yet for this article.
December 3, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30506702/are-smc-complexes-loop-extruding-factors-linking-theory-with-fact
#16
REVIEW
Jonathan Baxter, Antony W Oliver, Stephanie A Schalbetter
The extreme length of chromosomal DNA requires organizing mechanisms to both promote functional genetic interactions and ensure faithful chromosome segregation when cells divide. Microscopy and genome-wide contact frequency analyses indicate that intra-chromosomal looping of DNA is a primary pathway of chromosomal organization during all stages of the cell cycle. DNA loop extrusion has emerged as a unifying model for how chromosome loops are formed in cis in different genomic contexts and cell cycle stages...
December 3, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30500085/a-perspective-on-the-potential-utility-of-a-viscosupplement-multifunctional-biotherapeutic-proteoglycan-4-from-mere-lubricant-to-regulator-of-tissue-homeostasis-and-inflammation
#17
James Melrose
No abstract text is available yet for this article.
November 30, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30500078/phase-separation-and-transcription-regulation-are-super-enhancers-and-locus-control-regions-primary-sites-of-transcription-complex-assembly
#18
REVIEW
Aishwarya Gurumurthy, Yong Shen, Eliot M Gunn, Jörg Bungert
It is proposed that the multiple enhancer elements associated with locus control regions and super-enhancers recruit RNA polymerase II and efficiently assemble elongation competent transcription complexes that are transferred to target genes by transcription termination and transient looping mechanisms. It is well established that transcription complexes are recruited not only to promoters but also to enhancers, where they generate enhancer RNAs. Transcription at enhancers is unstable and frequently aborted...
November 30, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30485469/proteoglycan-4-from-mere-lubricant-to-regulator-of-tissue-homeostasis-and-inflammation-does-proteoglycan-4-have-the-ability-to-buffer-the-inflammatory-response
#19
REVIEW
Nabangshu Das, Tannin A Schmidt, Roman J Krawetz, Antoine Dufour
Proteoglycan 4 (PRG4), first identified in synovial fluid, is an extracellular matrix structural protein in the joint implicated in reducing shear at the cartilage surface as well as controlling adhesion-dependent synovial growth and regulating bulk protein deposition onto the cartilage. However, recent evidence suggests that it can bind to and effect downstream signaling of a number of cell surface receptors implicated in regulating the inflammatory response. Therefore, we pose the hypothesis: Does PRG4 regulate the inflammatory response and maintain tissue homeostasis? Based on these novel findings implicating PRG4 as an inflammatory signaling molecule, we will present and discuss several hypotheses regarding potential mechanisms by which PRG4 may be able to regulate inflammation...
November 28, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/30485465/to-read-more-papers-or-to-read-papers-better-a-crucial-point-for-the-reproducibility-crisis
#20
Thiago F A França, José M Monserrat
The overflow of scientific literature stimulates poor reading habits which can aggravate science's reproducibility crisis. Thus, solving the reproducibility crisis demands not only methodological changes, but also changes in our relationship with the scientific literature, especially our reading habits. Importantly, this does not mean reading more, it means reading better.
November 28, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
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