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https://www.readbyqxmd.com/read/27915288/modification-of-orthogonal-trnas-unexpected-consequences-for-sense-codon-reassignment
#1
Wil Biddle, Margaret A Schmitt, John D Fisk
Breaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNA(Opt) We suspected a modification of the tRNA(Opt)AUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNA(Opt)AUG is converted to inosine...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27915250/importance-of-fumarate-and-nitrate-reduction-regulatory-protein-for-proliferation-for-intestinal-proliferation-of-vibrio-vulnificus
#2
Takehiro Kado, Takashige Kashimoto, Kohei Yamazaki, Shunji Ueno
The sepsis caused by Vibrio vulnificus is characterized by an average incubation period of 26 hours and a high mortality rate exceeding 50%. The fast growth and dissemination of V. vulnificus in vivo lead to poor clinical outcomes in patients. Therefore, elucidation of the proliferation mechanisms of this organism in vivo may lead to development of an effective therapeutic strategy. In this study, we focused on the low oxygen concentration in the intestinal milieu because of its drastic difference from that in the air...
December 2, 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27915153/room-temperature-structure-of-human-igg4-fc-from-crystals-analysed-in-situ
#3
Anna M Davies, Theo Rispens, Pleuni Ooijevaar-de Heer, Rob C Aalberse, Brian J Sutton
The Fc region of IgG antibodies (Cγ2 and Cγ3 domains) is responsible for effector functions such as antibody-dependent cell-mediated cytotoxicity and phagocytosis, through engagement with Fcγ receptors, although the ability to elicit these functions differs between the four human IgG subclasses. A key determinant of Fcγ receptor interactions is the FG loop in the Cγ2 domain. High resolution cryogenic IgG4-Fc crystal structures have revealed a unique conformation for this loop, which could contribute to the particular biological properties of this subclass...
December 1, 2016: Molecular Immunology
https://www.readbyqxmd.com/read/27914729/operative-team-communication-during-simulated-emergencies-too-busy-to-respond
#4
W Austin Davis, Seth Jones, Adrianna M Crowell-Kuhnberg, Dara O'Keeffe, Kelly M Boyle, Suzanne B Klainer, Douglas S Smink, Steven Yule
BACKGROUND: Ineffective communication among members of a multidisciplinary team is associated with operative error and failure to rescue. We sought to measure operative team communication in a simulated emergency using an established communication framework called "closed loop communication." We hypothesized that communication directed at a specific recipient would be more likely to elicit a check back or closed loop response and that this relationship would vary with changes in patients' clinical status...
November 30, 2016: Surgery
https://www.readbyqxmd.com/read/27914481/conserved-3-utr-stem-loop-structure-in-l1-and-alu-transposons-in-human-genome-possible-role-in-retrotransposition
#5
Daria Grechishnikova, Maria Poptsova
BACKGROUND: In the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27913791/circadian-transcription-factor-bmal1-regulates-innate-immunity-against-select-rna-viruses
#6
Tanmay Majumdar, Jayeeta Dhar, Sonal Patel, Roman Kondratov, Sailen Barik
BMAL1 (brain and muscle ARNT-like protein 1, also known as MOP3 or ARNT3) belongs to the family of the basic helix-loop-helix (bHLH)-PAS domain-containing transcription factors, and is a key component of the molecular oscillator that generates circadian rhythms. Here, we report that BMAL1-deficient cells are significantly more susceptible to infection by two major respiratory viruses of the Paramyxoviridae family, namely RSV and PIV3. Embryonic fibroblasts from Bmal1(-/-) mice produced nearly 10-fold more progeny virus than their wild type controls...
December 1, 2016: Innate Immunity
https://www.readbyqxmd.com/read/27913679/modelling-gtpase-dynamics-to-understand-rhoa-driven-cancer-cell-invasion
#7
REVIEW
Joseph H R Hetmanski, Jean-Marc Schwartz, Patrick T Caswell
Metastasis, initially driven by cells migrating and invading through the local environment, leads to most cancer-associated deaths. Cells can use a variety of modes to move in vitro, all of which depend on Rho GTPases at some level. While traditionally it was thought that Rac1 activity drives protrusive lamellipodia at the leading edge of a polarised cell while RhoA drives rear retraction, more recent work in 3D microenvironments has revealed a much more complicated picture of GTPase dynamics. In particular, RhoA activity can dominate the leading edge polymerisation of actin to form filopodial actin-spike protrusions that drive more invasive cell migration...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913638/ms23-a-master-basic-helix-loop-helix-factor-regulates-the-specification-and-development-of-tapetum-in-maize
#8
Guo-Ling Nan, Jixian Zhai, Siwaret Arikit, Darren Morrow, John Fernandes, Lan Mai, Nhi Nguyen, Blake C Meyers, Virginia Walbot
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913625/absence-of-mir-146a-in-podocytes-increases-risk-of-diabetic-glomerulopathy-via-upregulation-of-erbb4-and-notch-1
#9
Ha Won Lee, Samia Q Khan, Shehryar Khaliqdina, Mehmet M Altintas, Florian Grahammer, Jimmy L Zhao, Kwihey Koh, Nicholas J Tardi, Mohd Hafeez Faridi, Terese Geraghty, David J Cimbaluk, Katalin Susztak, Luis F Moita, David Baltimore, Pierre-Louis Tharaux, Tobias B Huber, Matthias Kretzler, Markus Bitzer, Jochen Reiser, Vineet Gupta
Podocyte injury is an early event in diabetic kidney disease and is a hallmark of glomerulopathy. MicroRNA-146a (miR-146a) is highly expressed in many cell types under homeostatic conditions, and plays an important anti-inflammatory role in myeloid cells. However, its role in podocytes is unclear. Here, we show that miR-146a expression levels decrease in the glomeruli of patients with type 2 diabetes (T2D), which correlates with increased albuminuria and glomerular damage. MiR-146a levels are also significantly reduced in the glomeruli of albuminuric BTBR ob/ob mice, indicating its significant role in maintaining podocyte health...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913192/the-cellular-protein-nucleolin-preferentially-binds-long-looped-g-quadruplex-nucleic-acids
#10
Sara Lago, Elena Tosoni, Matteo Nadai, Manlio Palumbo, Sara N Richter
BACKGROUND: G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS: Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913141/acute-lung-injury-and-persistent-small-airway-disease-in-a-rabbit-model-of-chlorine-inhalation
#11
Sadiatu Musah, Connie F Schlueter, David M Humphrey, Karen S Powell, Andrew M Roberts, Gary W Hoyle
Chlorine is a pulmonary toxicant to which humans can be exposed through accidents or intentional releases. Acute effects of chlorine inhalation in humans and animal models have been well characterized, but less is known about persistent effects of acute, high-level chlorine exposures. In particular, animal models that reproduce the long-term effects suggested to occur in humans are lacking. Here, we report the development of a rabbit model in which both acute and persistent effects of chlorine inhalation can be assessed...
November 29, 2016: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/27913118/forces-controlling-organ-growth-and-size
#12
REVIEW
Dominik Eder, Christof Aegerter, Konrad Basler
One of the fundamental questions in developmental biology is what determines the final size and shape of an organ. Recent research strongly emphasizes that besides cell-cell communication, biophysical principals govern organ development. The architecture and mechanics of a tissue guide cellular processes such as movement, growth or differentiation. Furthermore, mechanical cues do not only regulate processes at a cellular level but also provide constant feedback about size and shape on a tissue scale. Here we review several models and experimental systems which are contributing to our understanding of the roles mechanical forces play during organ development...
November 29, 2016: Mechanisms of Development
https://www.readbyqxmd.com/read/27911788/near-atomic-structural-model-for-bacterial-dna-replication-initiation-complex-and-its-functional-insights
#13
Masahiro Shimizu, Yasunori Noguchi, Yukari Sakiyama, Hironori Kawakami, Tsutomu Katayama, Shoji Takada
Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911755/transformation-of-vestibular-signals-for-the-control-of-standing-in-humans
#14
Patrick A Forbes, Billy L Luu, H F Machiel Van der Loos, Elizabeth A Croft, J Timothy Inglis, Jean-Sébastien Blouin
: During standing balance, vestibular signals encode head movement and are transformed into coordinates that are relevant to maintaining upright posture of the whole body. This transformation must account for head-on-body orientation as well as the muscle actions generating the postural response. Here, we investigate whether this transformation is dependent upon a muscle's ability to stabilize the body along the direction of a vestibular disturbance. Subjects were braced on top of a robotic balance system that simulated the mechanics of standing while being exposed to an electrical vestibular stimulus that evoked a craniocentric vestibular error of head roll...
November 9, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27911565/radiative-screening-of-fifth-forces
#15
Clare Burrage, Edmund J Copeland, Peter Millington
We describe a symmetron model in which the screening of fifth forces arises at the one-loop level through the Coleman-Weinberg mechanism of spontaneous symmetry breaking. We show that such a theory can avoid current constraints on the existence of fifth forces but still has the potential to give rise to observable deviations from general relativity, which could be seen in cold atom experiments.
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911542/higher-loop-amplitude-monodromy-relations-in-string-and-gauge-theory
#16
Piotr Tourkine, Pierre Vanhove
The monodromy relations in string theory provide a powerful and elegant formalism to understand some of the deepest properties of tree-level field theory amplitudes, like the color-kinematics duality. This duality has been instrumental in tremendous progress on the computations of loop amplitudes in quantum field theory, but a higher-loop generalization of the monodromy construction was lacking. In this Letter, we extend the monodromy relations to higher loops in open string theory. Our construction, based on a contour deformation argument of the open string diagram integrands, leads to new identities that relate planar and nonplanar topologies in string theory...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911528/berry-curvature-in-magnon-phonon-hybrid-systems
#17
Ryuji Takahashi, Naoto Nagaosa
We study theoretically the Berry curvature of the magnon induced by the hybridization with the acoustic phonons via the spin-orbit and dipolar interactions. We first discuss the magnon-phonon hybridization via the dipolar interaction, and show that the dispersions have gapless points in momentum space, some of which form a loop. Next, when both spin-orbit and dipolar interactions are considered, we show anisotropic texture of the Berry curvature and its divergence with and without gap closing. Realistic evaluation of the consequent anomalous velocity is given for yttrium iron garnet...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911064/-intestinal-stomas-are-they-as-simple-as-they-seem
#18
P Bragagnini Rodríguez, Y González Ruiz, R Fernández Atuán, N González Martínez-Pardo, P Burgués Prado, J Elías Pollina
OBJECTIVES: To examine the morbidity and mortality of the formation and closure of enterostomies. METHODS: Retrospective study between 2000-2014 of patients younger than 14 years old who underwent an enterostomy. We evaluated: surgical technique, underlying pathology, general and stoma complications, sex, age and weight at the time of formation. At the closure we evaluated: surgical technique, age, weight, hemoglobin, hematocrit and albumin, as well as complications...
January 25, 2016: Cirugía Pediátrica: Organo Oficial de la Sociedad Española de Cirugía Pediátrica
https://www.readbyqxmd.com/read/27911005/adsorption-as-a-contributor-for-inflammatory-mediators-removal-by-different-hemofiltration-membranes-a-pilot-study
#19
Benjamin Malard, Nans Florens, Corine Lambert, Laurent Juillard
Atherosclerosis is an important predictor of mortality in patients with chronic kidney disease (CKD) and is associated with a wide inflammatory response. The aim of this study is to evaluate in vitro how different membranes can remove mediators associated with this pathology in a closed loop dialysis model. We performed experimental hemofiltration in vitro using three different membrane materials. Human plasma was preliminarily incubated with various inflammatory mediators and filtered in a closed loop circulation model for 240 min...
December 2, 2016: Artificial Organs
https://www.readbyqxmd.com/read/27910949/ascl3-transcription-factor-marks-a-distinct-progenitor-lineage-for-non-neuronal-support-cells-in-the-olfactory-epithelium
#20
Pei-Lun Weng, Mridula Vinjamuri, Catherine E Ovitt
The olfactory epithelium (OE) is composed of olfactory sensory neurons (OSNs), sustentacular supporting cells, and several types of non-neuronal cells. Stem and progenitor cells are located basally, and are the source of all cell types needed to maintain OE homeostasis. Here, we report that Ascl3, a basic helix-loop-helix transcription factor, is expressed in the developing OE. Lineage tracing experiments demonstrate that the non-neuronal microvillar cells and Bowman's glands are exclusively derived from Ascl3(+) progenitor cells in the OE during development...
December 2, 2016: Scientific Reports
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