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

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https://www.readbyqxmd.com/read/28098352/dna-repair-and-erasure-of-5-methylcytosine-in-vertebrates
#1
Lars Schomacher, Christof Niehrs
DNA methylation plays important roles in development and disease. Yet, only recently has the dynamic nature of this epigenetic mark via oxidation and DNA repair-mediated demethylation been recognized. A major conceptual challenge to the model that DNA methylation is reversible is the risk of genomic instability, which may come with widespread DNA repair activity. Here, we focus on recent advances in mechanisms of TET-TDG mediated demethylation and cellular strategies that avoid genomic instability. We highlight the recently discovered involvement of NEIL DNA glycosylases, which cooperate with TDG in oxidative demethylation to accelerate substrate turnover and promote the organized handover of harmful repair intermediates to maintain genome stability...
January 18, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28092121/hox-functional-diversity-novel-insights-from-flexible-motif-folding-and-plastic-protein-interaction
#2
Miguel Ortiz-Lombardia, Nicolas Foos, Corinne Maurel-Zaffran, Andrew J Saurin, Yacine Graba
How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins...
January 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28090662/adolescent-depression-linked-to-socioeconomic-status-molecular-approaches-for-revealing-premorbid-risk-factors
#3
Monica Uddin, Stefan Jansen, Eva H Telzer
The means by which social environmental exposures influence risk of mental disorders is a persistent and still open question. A key candidate mechanism for the biologic mediation of environmental effects involves epigenetic factors, which regulate gene function without altering underlying DNA sequence. Recent work has shown that environmental exposures such as childhood abuse, family history of mental disorder, and low socioeconomic status (SES) associate with differential DNA methylation (5mC) - a relatively stable, but modifiable, epigenetic factor...
January 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28083916/acetylated-tau-in-alzheimer-s-disease-an-instigator-of-synaptic-dysfunction-underlying-memory-loss-increased-levels-of-acetylated-tau-blocks-the-postsynaptic-signaling-required-for-plasticity-and-promotes-memory-deficits-associated-with-tauopathy
#4
Tara E Tracy, Li Gan
Pathogenesis in tauopathies involves the accumulation of tau in the brain and progressive synapse loss accompanied by cognitive decline. Pathological tau is found at synapses, and it promotes synaptic dysfunction and memory deficits. The specific role of toxic tau in disrupting the molecular networks that regulate synaptic strength has been elusive. A novel mechanistic link between tau toxicity and synaptic plasticity involves the acetylation of two lysines on tau, K274, and K281, which are associated with dementia in Alzheimer's disease (AD)...
January 13, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28083908/latitude-as-a-co-driver-of-human-gut-microbial-diversity
#5
Emma Dikongué, Laure Ségurel
The human gut microbial diversity has been reported to be lower in industrialized populations as compared to non-industrialized ones. Since it is also reduced in individuals with some metabolic and inflammatory diseases as compared to healthy ones, this "loss" of diversity in industrialized populations is currently considered to be a public health issue. However, little is known on the mechanisms that are causing this pattern. Is it due to differences in diet, sanitation, medication, host genetics, and/or other unidentified factors? In this review, we propose that part of this decrease in diversity is driven by latitude, as all studied industrialized countries are in higher latitudes than non-industrialized ones, and latitude is known to correlate with species diversity...
January 13, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28078683/worried-about-publishing-in-the-wrong-journal-%C3%A2
#6
EDITORIAL
Andrew Moore
No abstract text is available yet for this article.
January 12, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28054713/alternating-terminal-electron-acceptors-at-the-basis-of-symbiogenesis-how-oxygen-ignited-eukaryotic-evolution
#7
Dave Speijer
What kind of symbiosis between archaeon and bacterium gave rise to their eventual merger at the origin of the eukaryotes? I hypothesize that conditions favouring bacterial uptake were based on exchange of intermediate carbohydrate metabolites required by recurring changes in availability and use of the two different terminal electron chain acceptors, the bacterial one being oxygen. Oxygen won, and definitive loss of the archaeal membrane potential allowed permanent establishment of the bacterial partner as the proto-mitochondrion, further metabolic integration and highly efficient ATP production...
January 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28054378/microrna-annotation-of-plant-genomes-do-it-right-or-not-at-all
#8
Richard S Taylor, James E Tarver, Alireza Foroozani, Philip C J Donoghue
MicroRNAs are non-coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts decisively to improve the accuracy of miRNAome annotations...
January 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28054372/what-explains-patterns-of-biodiversity-across-the-tree-of-life-new-research-is-revealing-the-causes-of-the-dramatic-variation-in-species-numbers-across-branches-of-the-tree-of-life
#9
John J Wiens
A major challenge in biology is to explain why some groups have thousands or millions of species whereas others have few. Here, I review the causes of this variation. New studies reveal that higher species numbers in many major groups are explained by higher diversification rates (and traits that accelerate these rates). These traits span most of biology (e.g. genomics, ecology, morphology). Rather than simply testing individual traits, research should now focus on comparing how much variation in diversification rates is explained by different types of traits...
January 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28054369/love-is-like-oxygen-comment-on-doi-10-1002-bies-201600174
#10
Neil W Blackstone
No abstract text is available yet for this article.
January 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28052353/temporal-and-spatial-regulation-of-mrna-export-single-particle-rna-imaging-provides-new-tools-and-insights
#11
Stephanie Heinrich, Carina Patrizia Derrer, Azra Lari, Karsten Weis, Ben Montpetit
The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export...
January 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28052345/open-complex-dna-scrunching-a-key-to-transcription-start-site-selection-and-promoter-escape
#12
Jared T Winkelman, Richard L Gourse
Bacterial RNA polymerase-promoter open complexes can exist in a range of states in which the leading edge of the enzyme moves but the trailing edge does not, a phenomenon we refer to as "open complex scrunching." Here we describe how open complex scrunching can determine the position of the transcription start site for some promoters, modulate the level of expression, and potentially could be targeted by factors to regulate transcription. We suggest that open complex scrunching at the extraordinarily active ribosomal RNA promoters might have evolved to initiate transcription at an unusual position relative to the core promoter elements in order to maximize the rate of promoter escape...
January 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28044359/mitochondria-in-complex-psychiatric-disorders-lessons-from-mouse-models-of-22q11-2-deletion-syndrome-hemizygous-deletion-of-several-mitochondrial-genes-in-the-22q11-2-genomic-region-can-lead-to-symptoms-associated-with-neuropsychiatric-disease
#13
Prakash Devaraju, Stanislav S Zakharenko
Mitochondrial ATP synthesis, calcium buffering, and trafficking affect neuronal function and survival. Several genes implicated in mitochondrial functions map within the genomic region associated with 22q11.2 deletion syndrome (22q11DS), which is a key genetic cause of neuropsychiatric diseases. Although neuropsychiatric diseases impose a serious health and economic burden, their etiology and pathogenesis remain largely unknown because of the dearth of valid animal models and the challenges in investigating the pathophysiology in neuronal circuits...
January 3, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28026052/trna-biology-in-the-omics-era-stress-signalling-dynamics-and-cancer-progression
#14
Andrea Orioli
Recent years have seen a burst in the number of studies investigating tRNA biology. With the transition from a gene-centred to a genome-centred perspective, tRNAs and other RNA polymerase III transcripts surfaced as active regulators of normal cell physiology and disease. Novel strategies removing some of the hurdles that prevent quantitative tRNA profiling revealed that the differential exploitation of the tRNA pool critically affects the ability of the cell to balance protein homeostasis during normal and stress conditions...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28026040/forces-positioning-the-mitotic-spindle-theories-and-now-experiments
#15
Hai-Yin Wu, Ehssan Nazockdast, Michael J Shelley, Daniel J Needleman
The position of the spindle determines the position of the cleavage plane, and is thus crucial for cell division. Although spindle positioning has been extensively studied, the underlying forces ultimately responsible for moving the spindle remain poorly understood. A recent pioneering study by Garzon-Coral et al. uses magnetic tweezers to perform the first direct measurements of the forces involved in positioning the mitotic spindle. Combining this with molecular perturbations and geometrical effects, they use their data to argue that the forces that keep the spindle in its proper position for cell division arise from astral microtubules growing and pushing against the cell's cortex...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28026036/the-re-emerging-arboviral-threat-hidden-enemies-the-emergence-of-obscure-arboviral-diseases-and-the-potential-use-of-wolbachia-in-their-control
#16
Heverton Leandro Carneiro Dutra, Eric Pearce Caragata, Luciano Andrade Moreira
Mayaro, Oropouche, and O'Nyong-Nyong share many traits with more prominent arboviruses, like dengue and yellow fever, chikungunya, and Zika. These include severe clinical symptoms, multiple animal hosts, and widespread vector species living in close proximity to human habitats, all of which constitute significant risk factors for more frequent outbreaks in the future, greatly increasing the potential of these hidden enemies to follow Zika and become the next wave of global arboviral threats. Critically, the current dearth of knowledge on these arboviruses might impede the success of future control efforts, including the potential application of Wolbachia pipientis...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28026028/chromatin-priming-elements-establish-immunological-memory-in-t-cells-without-activating-transcription-t-cell-memory-is-maintained-by-dna-elements-which-stably-prime-inducible-genes-without-activating-steady-state-transcription
#17
Sarah L Bevington, Pierre Cauchy, Peter N Cockerill
We have identified a simple epigenetic mechanism underlying the establishment and maintenance of immunological memory in T cells. By studying the transcriptional regulation of inducible genes we found that a single cycle of activation of inducible factors is sufficient to initiate stable binding of pre-existing transcription factors to thousands of newly activated distal regulatory elements within inducible genes. These events lead to the creation of islands of active chromatin encompassing nearby enhancers, thereby supporting the accelerated activation of inducible genes, without changing steady state levels of transcription in memory T cells...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28026026/mams-are-attractive-targets-for-bacterial-repurposing-of-the-host-cell-mam-functions-might-be-key-for-undermining-an-infected-cell
#18
Pedro Escoll, Monica Rolando, Carmen Buchrieser
Pathogenic bacteria frequently target the endoplasmic reticulum (ER) and mitochondria in order to exploit host functions. ER-mitochondria inter-organelle communication is topologically sub-compartmentalized at mitochondria-associated ER membranes (MAMs). MAMs are specific membranous microdomains with unique regulatory functions such as lipid synthesis and trafficking, calcium homeostasis, mitochondrial morphology, inflammasome activation, autophagosome formation, and apoptosis. These important cellular processes are all modulated by pathogens to subvert host functions and promote infection, thus it is tempting to assume that pathogenic bacteria target MAMs to subvert these different pathways in their hosts...
December 27, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28009453/reassigning-stop-codons-via-translation-termination-how-a-few-eukaryotes-broke-the-dogma
#19
Elena Alkalaeva, Tatiana Mikhailova
The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes...
December 23, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28009057/indole-an-evolutionarily-conserved-influencer-of-behavior-across-kingdoms
#20
Jeffery K Tomberlin, Tawni L Crippen, Guoyao Wu, Ashleigh S Griffin, Thomas K Wood, Rebecca M Kilner
Indole is a key environmental cue that is used by many organisms. Based on its biochemistry, we suggest indole is used so universally, and by such different organisms, because it derives from the metabolism of tryptophan, a resource essential for many species yet rare in nature. These properties make it a valuable, environmental cue for resources almost universally important for promoting fitness. We then describe how indole is used to coordinate actions within organisms, to influence the behavior of conspecifics and can even be used to change the behavior of species that belong to other kingdoms...
December 23, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
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