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https://www.readbyqxmd.com/read/29040689/regulatory-dynamics-in-the-ternary-dnaa-complex-for-initiation-of-chromosomal-replication-in-escherichia-coli
#1
Yukari Sakiyama, Kazutoshi Kasho, Yasunori Noguchi, Hironori Kawakami, Tsutomu Katayama
In Escherichia coli, the level of the ATP-DnaA initiator is increased temporarily at the time of replication initiation. The replication origin, oriC, contains a duplex-unwinding element (DUE) flanking a DnaA-oligomerization region (DOR), which includes twelve DnaA-binding sites (DnaA boxes) and the DNA-bending protein IHF-binding site (IBS). Although complexes of IHF and ATP-DnaA assembly on the DOR unwind the DUE, the configuration of the crucial nucleoprotein complexes remains elusive. To resolve this, we analyzed individual DnaA protomers in the complex and here demonstrate that the DUE-DnaA-box-R1-IBS-DnaA-box-R5M region is essential for DUE unwinding...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040642/dynamic-dna-binding-junction-recognition-and-g4-melting-activity-underlie-the-telomeric-and-genome-wide-roles-of-human-cst
#2
Anukana Bhattacharjee, Yongyao Wang, Jiajie Diao, Carolyn M Price
Human CST (CTC1-STN1-TEN1) is a ssDNA-binding complex that helps resolve replication problems both at telomeres and genome-wide. CST resembles Replication Protein A (RPA) in that the two complexes harbor comparable arrays of OB-folds and have structurally similar small subunits. However, the overall architecture and functions of CST and RPA are distinct. Currently, the mechanism underlying CST action at diverse replication issues remains unclear. To clarify CST mechanism, we examined the capacity of CST to bind and resolve DNA structures found at sites of CST activity...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040563/ten-years-of-cazypedia-a-living-encyclopedia-of-carbohydrate-active-enzymes
#3
(no author information available yet)
CAZypeia was initiated in 2007 to create a comprehensive, living encyclopedia of the carbohydrate-active enzymes (CAZymes) and associated carbohydrate-binding modules involved in the synthesis, modification, and degradation of complex carbohydrates. CAZypedia is closely connected with the actively-curated CAZy database, which provides a sequence-based foundation for the biochemical, mechanistic, and structural characterization of these diverse proteins. Now celebrating its 10th anniversary online, CAZypedia is a successful example of dynamic, community-driven, and expert-based biocuration...
October 11, 2017: Glycobiology
https://www.readbyqxmd.com/read/29040533/hippocampal-phosphorylated-tau-induced-cognitive-decline-dendritic-spine-loss-and-mitochondrial-abnormalities-in-a-mouse-model-of-alzheimer-s-disease
#4
Ramesh Kandimalla, Maria Manczak, Xiangling Yin, Rui Wang, P Hemachandra Reddy
The purpose of our study was to understand the toxic effects of hippocampal phosphorylated tau in tau mice. Using rotarod and Morris Water Maze tests, immunoblotting & immunofluorescence, Golgi-cox staining and transmission electron microscopy, we assessed cognitive behavior, measured protein levels of mitochondrial dynamics, MAP2, total & phosphorylated tau, and quantified dendritic spines and mitochondrial number and length in 12-month-old tau mice with P301L mutation. Mitochondrial function was assessed by measuring the levels of H2O2, lipid peroxidation, cytochrome oxidase activity and mitochondrial ATP...
October 12, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29040448/male-brown-fat-specific-double-knockout-of-igfir-ir-atrophy-mitochondrial-fission-failure-impaired-thermogenesis-and-obesity
#5
Vanesa Viana-Huete, Carlos Guillén, Gema García, Silvia Fernández, Ana García-Aguilar, C R Kahn, Manuel Benito
It is unknown how the lack of IR (insulin receptor)/ IGFIR (insulin like growth factor receptor) in a tissue-specific manner does affect brown fat development and mitochondrial integrity and function and its impact on the redistribution of the adipose organ and the metabolic status. To address this important issue, we have developed the IR/IGFIR double knockout in brown adipose tissue-specific manner (DKO). Lack of those receptors caused a severe brown fat atrophy, an enhanced beige cell clusters in inguinal fat, loss of mitochondrial mass, mitochondrial damage related to cristae disruption, and the loss of proteins involved in autophagosome formation, mitophagy, mitochondrial quality control and dynamics and thermogenesis...
October 10, 2017: Endocrinology
https://www.readbyqxmd.com/read/29040313/premature-aortic-smooth-muscle-cell-differentiation-contributes-to-matrix-dysregulation-in-marfan-syndrome
#6
Matthew Dale, Matthew P Fitzgerald, Zhibo Liu, Trevor Meisinger, Andrew Karpisek, Laura N Purcell, Jeffrey S Carson, Paul Harding, Haili Lang, Panagiotis Koutakis, Rishi Batra, Constance J Mietus, George Casale, Iraklis Pipinos, B Timothy Baxter, Wanfen Xiong
Thoracic aortic aneurysm and dissection are life-threatening complications of Marfan syndrome (MFS). Studies of human and mouse aortic samples from late stage MFS demonstrate increased TGF-β activation/signaling and diffuse matrix changes. However, the role of the aortic smooth muscle cell (SMC) phenotype in early aneurysm formation in MFS has yet to be fully elucidated. As our objective, we investigated whether an altered aortic SMC phenotype plays a role in aneurysm formation in MFS. We describe previously unrecognized concordant findings in the aortas of a murine model of MFS, mgR, during a critical and dynamic phase of early development...
2017: PloS One
https://www.readbyqxmd.com/read/29040283/non-linear-min-protein-interactions-generate-harmonics-that-signal-mid-cell-division-in-escherichia-coli
#7
James C Walsh, Christopher N Angstmann, Iain G Duggin, Paul M G Curmi
The Min protein system creates a dynamic spatial pattern in Escherichia coli cells where the proteins MinD and MinE oscillate from pole to pole. MinD positions MinC, an inhibitor of FtsZ ring formation, contributing to the mid-cell localization of cell division. In this paper, Fourier analysis is used to decompose experimental and model MinD spatial distributions into time-dependent harmonic components. In both experiment and model, the second harmonic component is responsible for producing a mid-cell minimum in MinD concentration...
2017: PloS One
https://www.readbyqxmd.com/read/29039925/exosomes-secreted-by-hela-cells-shuttle-on-their-surface-the-plasma-membrane-associated-sialidase-neu3
#8
Lucia Paolini, Flavia Orizio, Sara Busatto, Annalisa Radeghieri, Roberto Bresciani, Paolo Bergese, Eugenio Monti
Sialidases are glycohydrolases that remove terminal sialic acid residues from oligosaccharides, glycolipids and glycoproteins. The plasma membrane-associated sialidase NEU3 is involved in the fine tuning of sialic acid containing glycans directly on the cell surface and plays relevant roles in important biological phenomena such as cell differentiation, molecular recognition and cancer transformation. Extracellular vesicles are membranous structures with a diameter of 0.03-1 m released by cells and detectable in blood, urine, as well as in culture media...
October 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/29039908/a-comprehensive-high-resolution-targeted-workflow-for-the-deep-profiling-of-sphingolipids
#9
Bing Peng, Susan T Weintraub, Cristina Coman, Srigayatri Ponnaiyan, Rakesh Sharma, Björn Tews, Dominic Winter, Robert Ahrends
Sphingolipids are a highly diverse group of biomolecules that are not only membrane components but are also involved in various cellular functions such as signaling and protein sorting. In order to obtain a quantitative view of the sphingolipidome, sensitive, accurate and comprehensive methods are needed. Here, we present a targeted reversed-phase liquid chromatography/high resolution mass spectrometry-based workflow that significantly increases the accuracy of measured sphingolipids by resolving nearly-isobaric and isobaric species; this is accomplished by a use of: i) an optimized extraction procedure, ii) a segmented gradient and iii) parallel reaction monitoring of a sphingolipid specific fragmentation pattern...
October 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29036903/resveratrol-and-amyloid-beta-mechanistic-insights
#10
REVIEW
Yongming Jia, Na Wang, Xuewei Liu
The amyloid-beta (Aβ) hypothesis that dyshomeostasis between Aβ production and clearance is a very early, key molecular factor in the etiology of Alzheimer's disease (AD) has been proposed and examined in the AD research field. Scientists have focused on seeking natural products or drugs to influence the dynamic equilibrium of Aβ, targeting production and clearance of Aβ. There is emerging evidence that resveratrol (Res), a naturally occurring polyphenol mainly found in grapes and red wine, acts on AD in numerous in vivo and in vitro models...
October 14, 2017: Nutrients
https://www.readbyqxmd.com/read/29036702/a-hyperdynamic-h3-3-nucleosome-marks-promoter-regions-in-pluripotent-embryonic-stem-cells
#11
Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D Aguilera, Divya M Sivaraman, Tommy Kaplan, Eran Meshorer
Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#12
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036326/circular-rnas-are-abundant-and-dynamically-expressed-during-embryonic-muscle-development-in-chickens
#13
Hongjia Ouyang, Xiaolan Chen, Zhijun Wang, Jiao Yu, Xinzheng Jia, Zhenhui Li, Wei Luo, Bahareldin Ali Abdalla, Endashaw Jebessa, Qinghua Nie, Xiquan Zhang
The growth and development of skeletal muscle is regulated by proteins as well as non-coding RNAs. Circular RNAs (circRNAs) are universally expressed in various tissues and cell types, and regulate gene expression in eukaryotes. To identify the circRNAs during chicken embryonic skeletal muscle development, leg muscles of female Xinghua (XH) chicken at three developmental time points 11 embryo age (E11), 16 embryo age (E16) and 1 day post hatch (P1) were performed RNA sequencing. We identified 13,377 circRNAs with 3,036 abundantly expressed and most were derived from coding exons...
October 3, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29035839/insights-into-protein-misfolding-and-aggregation-enabled-by-solid-state-nmr-spectroscopy
#14
REVIEW
Patrick C A van der Wel
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation...
October 4, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/29035747/studies-on-the-adsorption-and-desorption-of-mitoxantrone-to-lauric-acid-albumin-coated-iron-oxide-nanoparticles
#15
Jan Zaloga, Artem Feoktystov, Vasil M Garamus, Weronika Karawacka, Alexander Ioffe, Thomas Brückel, Rainer Tietze, Christoph Alexiou, Stefan Lyer
A rational use of superparamagnetic iron oxide nanoparticles (SPIONs) in drug delivery, diagnostics, and other biomedical applications requires deep understanding of the molecular drug adsorption/desorption mechanisms for proper design of new pharmaceutical formulations. The adsorption and desorption of the cytostatic Mitoxantrone (MTO) to lauric acid-albumin hybrid coated particles SPIONs (SEON(LA-HSA)) was studied by Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), surface titration, release experiments and small-angle neutron and X-ray scattering...
September 28, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29035686/the-human-odontoblast-cell-layer-and-dental-pulp-proteomes-and-n-terminomes
#16
S R Abbey, U Eckhard, N Solis, G Marino, I Matthew, C M Overall
The proteome and N-terminome of the human odontoblast cell layer were identified for the first time by shotgun proteomic and terminal amine isotopic labeling of substrates (TAILS) N-terminomic analyses, respectively, and compared with that of human dental pulp stroma from 26 third molar teeth. After reverse-phase liquid chromatography-tandem mass spectrometry, >170,000 spectra from the shotgun and TAILS analyses were matched by 4 search engines to 4,888 and 12,063 peptides in the odontoblast cell layer and pulp stroma, respectively...
October 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/29035562/quantification-of-membrane-protein-detergent-complex-interactions
#17
Aaron John Wolfe, Wei Si, Zhengqi Zhang, Adam R Blanden, Yi-Ching Hsueh, Jack Fredrick Gugel, Bach Pham, Min Chen, Stewart N Loh, Sharon Rozovsky, Aleksei Aksimentiev, Liviu Movileanu
Although fundamentally significant in structural, chemical, and membrane biology, the interfacial protein-detergent complex (PDC) interactions have been modestly examined because of the complicated behavior of both detergents and membrane proteins in aqueous phase. Membrane proteins are prone to unproductive aggregation resulting from poor detergent solvation, but the participating forces in this phenomenon remain ambiguous. Here, we show that using rational membrane protein design, targeted chemical modification, and steady-state fluorescence polarization spectroscopy, the detergent desolvation of membrane proteins can be quantitatively evaluated...
October 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29035554/star-polymers-reduce-iapp-toxicity-via-accelerated-amyloid-aggregation
#18
Emily H Pilkington, May Lai, Xinwei Ge, William J Stanley, Bo Wang, Miaoyi Wang, Aleksandr Kakinen, Marc-Antoine Sani, Michael R Whittaker, Esteban N Gurzov, Feng Ding, John F Quinn, Thomas P Davis, Pu Chun Ke
Protein aggregation into amyloid fibrils is a ubiquitous phenomenon across the spectrum of neurodegenerative disorders and type 2 diabetes. A common strategy against amyloidogenesis is to minimize the populations of toxic oligomers and protofibrils by inhibiting protein aggregation with small molecules or nanoparticles. However, melanin synthesis in nature is realized by accelerated protein fibrillation to circumvent accumulation of toxic intermediates. Accordingly, we designed and demonstrated the use of star-shaped poly(2-hydroxyethyl acrylate) (PHEA) nanostructures for promoting the aggregation while ameliorating the toxicity of human islet amyloid polypeptide (IAPP), the peptide involved in glycemic control and the pathology of type 2 diabetes...
October 16, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/29035497/conformational-dynamics-of-dna-binding-and-cas3-recruitment-by-the-crispr-rna-guide-cascade-complex
#19
Paul B G van Erp, Angela Patterson, Ravi Kant, Luke Berry, Sarah M Golden, Brittney L Forsman, Joshua Carter, Ryan N Jackson, Brian Bothner, Blake Wiedenheft
Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for sequence specific elimination of foreign nucleic acids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble with Cas (CRISPR-associated) proteins into a 405-kilodalton multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade binds foreign DNA complementary to the crRNA guide and recruits Cas3, a trans-acting nuclease-helicase required for target degradation...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29035272/binding-stability-of-peptides-on-major-histocompatibility-complex-class-i-proteins-role-of-entropy-and-dynamics
#20
Ahmet Gul, Burak Erman
Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: Peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies...
October 16, 2017: Physical Biology
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