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

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https://www.readbyqxmd.com/read/29325207/developing-a-journal-s-influence-without-impact-factor-madness-quality-in-shape
#1
EDITORIAL
Andrew Moore
No abstract text is available yet for this article.
January 11, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29314107/single-pair-f%C3%A3-rster-resonance-energy-transfer-a-versatile-tool-to-investigate-protein-conformational-dynamics
#2
Lena Voith von Voithenberg, Don C Lamb
Conformational changes of proteins and other biomolecules play a fundamental role in their functional mechanism. Single pair Förster resonance energy transfer (spFRET) offers the possibility to detect these conformational changes and dynamics, and to characterize their underlying kinetics. Using spFRET on microscopes with different modes of detection, dynamic timescales ranging from nanoseconds to seconds can be quantified. Confocal microscopy can be used as a means to analyze dynamics in the range of nanoseconds to milliseconds, while total internal reflection fluorescence (TIRF) microscopy offers information about conformational changes on timescales of milliseconds to seconds...
January 5, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29286547/explaining-the-origin-of-three-membrane-bound-plastids-in-dinoflagellates-and-euglenophytes-kleptoplastidy-via-myzocytosis
#3
Daniel Moog, Uwe G Maier
No abstract text is available yet for this article.
December 29, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29283188/analyzing-horizontal-transfer-of-transposable-elements-on-a-large-scale-challenges-and-prospects
#4
Jean Peccoud, Richard Cordaux, Clément Gilbert
Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer (HT). Between multicellular organisms, the transferred material will likely turn out to be a transposable element (TE). Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs (HTT) profoundly impacts genome evolution...
December 28, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29283187/cell-size-control-via-an-unstable-accumulating-activator-and-the-phenomenon-of-excess-mitotic-delay
#5
Nicholas Rhind
Unstable Accumulating Activator models for cellular size control propose an activator that accumulates in a size-dependent manner and triggers cell cycle progression once it has reached a certain threshold. Having a short half life makes such an activator responsive to changes in cell size and makes specific predictions for how cells respond to perturbation. In particular, it explains the curious phenomenon of excess mitotic delay. Excess mitotic delay, first observed in Tetrahymena in the '50s, is a phenomenon in which a pulse of protein synthesis inhibition causes a delay in mitotic entry that is longer than the pulse and that gets longer the later in the cell cycle the pulse is delivered...
December 28, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29282758/noise-in-the-machine-alternative-pathway-sampling-is-the-rule-during-dna-replication
#6
REVIEW
Matthias J Scherr, Barbara Safaric, Karl E Duderstadt
The astonishing efficiency and accuracy of DNA replication has long suggested that refined rules enforce a single highly reproducible sequence of molecular events during the process. This view was solidified by early demonstrations that DNA unwinding and synthesis are coupled within a stable molecular factory, known as the replisome, which consists of conserved components that each play unique and complementary roles. However, recent single-molecule observations of replisome dynamics have begun to challenge this view, revealing that replication may not be defined by a uniform sequence of events...
December 28, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29280502/transmembrane-signal-transduction-in-two-component-systems-piston-scissoring-or-helical-rotation
#7
REVIEW
Ivan Gushchin, Valentin Gordeliy
Allosteric and transmembrane (TM) signaling are among the major questions of structural biology. Here, we review and discuss signal transduction in four-helical TM bundles, focusing on histidine kinases and chemoreceptors found in two-component systems. Previously, piston, scissors, and helical rotation have been proposed as the mechanisms of TM signaling. We discuss theoretically possible conformational changes and examine the available experimental data, including the recent crystallographic structures of nitrate/nitrite sensor histidine kinase NarQ and phototaxis system NpSRII:NpHtrII...
December 27, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29280160/when-micrornas-meet-rna-editing-in-cancer-a-nucleotide-change-can-make-a-difference
#8
Yumeng Wang, Han Liang
RNA editing is a major post-transcriptional mechanism that changes specific nucleotides at the RNA level. The most common RNA editing type in humans is adenosine (A) to inosine (I) editing, which is mediated by ADAR enzymes. RNA editing events can not only change amino acids in proteins, but also affect the functions of non-coding RNAs such as miRNAs. Recent studies have characterized thousands of miRNA RNA editing events across different cancer types. Importantly, individual cases of miRNA editing have been reported to play a role in cancer development...
December 27, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29280156/the-many-roles-of-type-ii-phosphatidylinositol-4-kinases-in-membrane-trafficking-new-tricks-for-old-dogs
#9
Shane Minogue
The type II phosphatidylinositol 4-kinases (PI4KIIs) produce the lipid phosphatidylinositol 4-phosphate (PtdIns4P) and participate in a confusing variety of membrane trafficking and signaling roles. This review argues that both historical and contemporary evidence supports the function of the PI4KIIs in numerous trafficking pathways, and that the key to understanding the enzymatic regulation is through membrane interaction and the intrinsic membrane environment. By summarizing new research and examining the trafficking roles of the PI4KIIs in the context of recently solved molecular structures, I highlight how mechanisms of PI4KII function and regulation are providing insights into the development of cancer and in neurological disease...
December 27, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29266341/microbiome-germline-interactions-and-their-transgenerational-implications
#10
REVIEW
Michael Elgart, Yoav Soen
It is becoming increasingly clear that most, if not all, animals and plants are associated with a diverse array of resident gut microbiota. This symbiosis is regulated by host-microbiome interactions which influence the development, homeostasis, adaptation and evolution of the host. Recent evidence indicated that these interactions can also affect the host germline and have a potential of supporting transgenerational effects, including inheritance of acquired characteristics. Taken together, the influence of gut bacteria on the host soma and germline could potentially give rise to emergent phenotypes, which may be partially inherited by three distinguishable modes of transgenerational influence of gut bacteria: 1) "soma-to-soma" 2) "soma-to-germline" and 3) "soma-germline-soma"...
December 21, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29266287/rnase-iii-nucleases-and-the-evolution-of-antiviral-systems
#11
REVIEW
Lauren C Aguado, Benjamin R tenOever
Every living entity requires the capacity to defend against viruses in some form. From bacteria to plants to arthropods, cells retain the capacity to capture genetic material, process it in a variety of ways, and subsequently use it to generate pathogen-specific small RNAs. These small RNAs can then be used to provide specificity to an otherwise non-specific nuclease, generating a potent antiviral system. While small RNA-based defenses in chordates are less utilized, the protein-based antiviral invention in this phylum appears to have derived from components of the same ancestral small RNA machinery...
December 21, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29251357/epigenetic-and-transcriptional-variability-shape-phenotypic-plasticity
#12
REVIEW
Simone Ecker, Vera Pancaldi, Alfonso Valencia, Stephan Beck, Dirk S Paul
Epigenetic and transcriptional variability contribute to the vast diversity of cellular and organismal phenotypes and are key in human health and disease. In this review, we describe different types, sources, and determinants of epigenetic and transcriptional variability, enabling cells and organisms to adapt and evolve to a changing environment. We highlight the latest research and hypotheses on how chromatin structure and the epigenome influence gene expression variability. Further, we provide an overview of challenges in the analysis of biological variability...
December 18, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29250807/the-wnt-transcriptional-switch-tle-removal-or-inactivation
#13
REVIEW
Aravinda-Bharathi Ramakrishnan, Abhishek Sinha, Vinson B Fan, Ken M Cadigan
Many targets of the Wnt/β-catenin signaling pathway are regulated by TCF transcription factors, which play important roles in animal development, stem cell biology, and oncogenesis. TCFs can regulate Wnt targets through a "transcriptional switch," repressing gene expression in unstimulated cells and promoting transcription upon Wnt signaling. However, it is not clear whether this switch mechanism is a general feature of Wnt gene regulation or limited to a subset of Wnt targets. Co-repressors of the TLE family are known to contribute to the repression of Wnt targets in the absence of signaling, but how they are inactivated or displaced by Wnt signaling is poorly understood...
December 18, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29236296/rna-decay-factor-upf1-promotes-protein-decay-a-hidden-talent
#14
REVIEW
Terra-Dawn M Plank, Miles F Wilkinson
The RNA-binding protein, UPF1, is best known for its central role in the nonsense-mediated RNA decay (NMD) pathway. Feng et al. now report a new function for UPF1-it is an E3 ubiquitin ligase that specifically promotes the decay of a key pro-muscle transcription factor: MYOD. UPF1 achieves this through its RING-like domain, which confers ubiquitin E3 ligase activity. Feng et al. provide evidence that the ability of UPF1 to destabilize MYOD represses myogenesis. In the future, it will be important to define other protein substrates of UPF1-driven ubiquitination and to determine whether this biochemical activity is responsible for some of UPF1's previously defined biological functions, including in development and stress responses...
December 13, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29236295/supporting-behaviour-not-sex-the-women-in-science-debate-re-framed%C3%A2
#15
EDITORIAL
Andrew Moore
No abstract text is available yet for this article.
December 13, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29226983/combing-chromosomal-dna-mediated-by-the-smc-complex-structure-and-mechanisms
#16
REVIEW
Katsuhiko Kamada, Daniela Barillà
Genome maintenance requires various nucleoid-associated factors in prokaryotes. Among them, the SMC (Structural Maintenance of Chromosomes) protein has been thought to play a static role in the organization and segregation of the chromosome during cell division. However, recent studies have shown that the bacterial SMC is required to align left and right arms of the emerging chromosome and that the protein dynamically travels from origin to Ter region. A rod form of the SMC complex mediates DNA bridging and has been recognized as a machinery responsible for DNA loop extrusion, like eukaryotic condensin or cohesin complexes, which act as chromosome organizers...
December 11, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29226979/it-is-time-to-re-evaluate-the-peer-review-process-for-preclinical-research
#17
Rajat Bhattacharya, Lee M Ellis
Problems in peer review, the backbone of maintaining high standards in scientific publishing, have led to wide spread discontent within the scientific community. Training in the peer review process and a simpler format to assist in decision making are possible courses to improve and expedite the process of peer review and scientific publishing.
December 11, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29210086/evolution-is-linear-debunking-life-s-little-joke
#18
Ronald A Jenner
Linear depictions of the evolutionary process are ubiquitous in popular culture, but linear evolutionary imagery is strongly rejected by scientists who argue that evolution branches. This point is frequently illustrated by saying that we didn't evolve from monkeys, but that we are related to them as collateral relatives. Yet, we did evolve from monkeys, but our monkey ancestors are extinct, not extant. Influential voices, such as the late Stephen Jay Gould, have misled audiences for decades by falsely portraying the linear and branching aspects of evolution to be in conflict, and by failing to distinguish between the legitimate linearity of evolutionary descent, and the branching relationships among collateral relatives that result when lineages of ancestors diverge...
December 6, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29206283/transposable-element-mediated-innovation-in-gene-regulatory-landscapes-of-cells-re-visiting-the-gene-battery-model
#19
REVIEW
Vasavi Sundaram, Ting Wang
Transposable elements (TEs) are no longer considered to be "junk" DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten and EH Davidson hypothesized that TEs can integrate the function of various transcriptional regulators into gene regulatory networks. Uniquely TEs can deposit regulatory sites across the genome when they transpose, and thereby bring multiple genes under control of the same regulatory logic...
December 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29205437/mrna-traffic-control-reviewed-n6-methyladenosine-m6-a-takes-the-driver-s-seat
#20
REVIEW
Abhirami Visvanathan, Kumaravel Somasundaram
Messenger RNA is a flexible tool box that plays a key role in the dynamic regulation of gene expression. RNA modifications variegate the message conveyed by the mRNA. Similar to DNA and histone modifications, mRNA modifications are reversible and play a key role in the regulation of molecular events. Our understanding about the landscape of RNA modifications is still rudimentary in contrast to DNA and histone modifications. The major obstacle has been the lack of sensitive detection methods since they are non-editing events...
December 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
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