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https://www.readbyqxmd.com/read/29785012/multiplex-assessment-of-protein-variant-abundance-by-massively-parallel-sequencing
#1
Kenneth A Matreyek, Lea M Starita, Jason J Stephany, Beth Martin, Melissa A Chiasson, Vanessa E Gray, Martin Kircher, Arineh Khechaduri, Jennifer N Dines, Ronald J Hause, Smita Bhatia, William E Evans, Mary V Relling, Wenjian Yang, Jay Shendure, Douglas M Fowler
Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes requires generalizable, scalable assays. We describe variant abundance by massively parallel sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single-amino-acid variants of PTEN and TPMT, proteins in which functional variants are clinically actionable...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29782498/endoplasmic-reticulum-plasma-membrane-contact-sites-integrate-sterol-and-phospholipid-regulation
#2
Evan Quon, Yves Y Sere, Neha Chauhan, Jesper Johansen, David P Sullivan, Jeremy S Dittman, William J Rice, Robin B Chan, Gilbert di Paolo, Christopher T Beh, Anant K Menon
Tether proteins attach the endoplasmic reticulum (ER) to other cellular membranes, thereby creating contact sites that are proposed to form platforms for regulating lipid homeostasis and facilitating non-vesicular lipid exchange. Sterols are synthesized in the ER and transported by non-vesicular mechanisms to the plasma membrane (PM), where they represent almost half of all PM lipids and contribute critically to the barrier function of the PM. To determine whether contact sites are important for both sterol exchange between the ER and PM and intermembrane regulation of lipid metabolism, we generated Δ-super-tether (Δ-s-tether) yeast cells that lack six previously identified tethering proteins (yeast extended synatotagmin [E-Syt], vesicle-associated membrane protein [VAMP]-associated protein [VAP], and TMEM16-anoctamin homologues) as well as the presumptive tether Ice2...
May 21, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29751611/purification-and-characterization-of-recombinant-botulinum-neurotoxin-serotype-fa-also-known-as-serotype-h
#3
Gavin Hackett, Kevin Moore, David Burgin, Fraser Hornby, Bryony Gray, Mark Elliott, Imran Mir, Matthew Beard
We have purified and characterized recombinant botulinum neurotoxin serotype FA (BoNT/FA). This protein has also been named as a new serotype (serotype H), but the classification has been controversial. A lack of well-characterized, highly pure material has been a roadblock to study. Here we report purification and characterization of enzymatically active, and of inactive nontoxic, recombinant forms of BoNT/FA as tractable alternatives to purifying this neurotoxin from native Clostridium botulinum . BoNT/FA cleaves the same intracellular target proteins as BoNT/F1 and other F serotype BoNTs; the intracellular targets are vesicle associated membrane proteins (VAMP) 1, 2 and 3...
May 11, 2018: Toxins
https://www.readbyqxmd.com/read/29694296/situating-cyberzone-black-lesbian-identity-in-comics
#4
Sheena C Howard
Cyberzone is a fitting place to start any discussion around Black lesbian identity in comics, as it is the first comic book that this researcher could find which features a Black lesbian female lead superheroine. Cyberzone was self-published by Jimmie Robinson in 1994 and later re-vamped into a mini-comic series called Amanda and Gunn with Image Comics. First, this article deconstructs Cyberzone through the lens of Cultural Prism Theory (CPT). Second, this article situates Cyberzone within the framework of CPT to address Cyberzone's place within the comic book ecosystem...
April 25, 2018: Journal of Lesbian Studies
https://www.readbyqxmd.com/read/29688327/structural-and-biochemical-characterization-of-the-protease-domain-of-the-mosaic-botulinum-neurotoxin-type-ha
#5
Kwok-Ho Lam, Stefan Sikorra, Jasmin Weisemann, Hannah Maatsch, Kay Perry, Andreas Rummel, Thomas Binz, Rongsheng Jin
The extreme toxicity of botulinum neurotoxins (BoNTs) relies on their specific cleavage of SNARE proteins, which eventually leads to muscle paralysis. One newly identified mosaic toxin, BoNT/HA (aka H or FA), cleaves VAMP-2 at a unique position between residues L54 and E55, but the molecular basis underlying VAMP-2-recognition of BoNT/HA remains poorly characterized. Here, we report a ∼2.09 Å resolution crystal structure of the light chain protease domain of BoNT/HA (LC/HA). Structural comparison between LC/HA and LC of BoNT/F1 (LC/F1) reveals distinctive hydrophobic and electrostatic features near the active sites, which may explain their different VAMP-2 cleavage sites...
April 23, 2018: Pathogens and Disease
https://www.readbyqxmd.com/read/29674253/involvement-of-snare-complex-in-the-hippocampus-and-prefrontal-cortex-of-offspring-with-depression-induced-by-prenatal-stress
#6
Yan Jun Cao, Qiong Wang, Xing Xing Zheng, Ying Cheng, Yan Zhang
BACKGROUND: Prenatal stress (PS) exposure can cause depression-like behavior in offspring, and maladaptive responses including physiological and neurobiological changes. Glutamate neurotransmission is implicated in effects of PS and in antidepressant mechanisms; however, the mechanisms underlying its involvement remain unclear. In the synapse, the formation of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is essential for vesicular docking and neurotransmitter release...
April 6, 2018: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29623065/-in-situ-proximity-ligation-assay-reveals-co-localization-of-alpha-synuclein-and-snare-proteins-in-murine-primary-neurons
#7
Leire Almandoz-Gil, Emma Persson, Veronica Lindström, Martin Ingelsson, Anna Erlandsson, Joakim Bergström
The aggregation of alpha-synuclein (αSyn) is the pathological hallmark of Parkinson's disease, dementia with Lewy bodies and related neurological disorders. However, the physiological function of the protein and how this function relates to its pathological effects remain poorly understood. One of the proposed roles of αSyn is to promote the soluble N -ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex assembly by binding to VAMP-2. The objective of this study was to visualize the co-localization between αSyn and the SNARE proteins (VAMP-2, SNAP-25, and syntaxin-1) for the first time using in situ proximity ligation assay (PLA)...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/29548989/snap-25a-and-snap-25b-differently-mediate-interactions-with-munc18-1-and-g%C3%AE-%C3%AE-subunits
#8
Teresa Daraio, Ismael Valladolid-Acebes, Kerstin Brismar, Christina Bark
SNAP-25 is a protein involved in regulated membrane fusion and part of the SNARE complex. It exists as two splicing variants, SNAP-25a and SNAP-25b, which differ in 9 out of 206 amino acids. SNAP-25 together with Syntaxin 1 and VAMP-2 forms the ternary SNARE complex essential for mediating activity-dependent release of hormones and neurotransmitters. The functional difference between SNAP-25a and SNAP-25b is poorly understood as both can participate in SNARE complexes and mediate membrane fusion. However, we recently demonstrated that SNAP-25b-deficiency results in metabolic disease and increased insulin secretion...
May 1, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29547901/molecular-partners-of-hnot-alg3-the-human-counterpart-of-the-drosophila-not-and-yeast-alg3-gene-suggest-its-involvement-in-distinct-cellular-processes-relevant-to-congenital-disorders-of-glycosylation-cancer-neurodegeneration-and-a-variety-of-further-pathologies
#9
Benedikt Hacker, Christoph Schultheiß, Michael Döring, Ursula Kurzik-Dumke
This study provides first insights into the involvement of hNOT/ALG3, the human counterpart of the Drosophila Neighbour of TID and yeast ALG3 gene, in various putative molecular networks. HNOT/ALG3 encodes two translated transcripts encoding precursor proteins differing in their N-terminus and showing 33% identity with the yeast asparagine-linked glycosylation 3 (ALG3) protein. Experimental evidence for the functional homology of the proteins of fly and man in the N-glycosylation has still to be provided. In this study, using the yeast two-hybrid technique we identify 17 molecular partners of hNOT-1/ALG3-1...
June 1, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29540745/structural-characterisation-of-the-catalytic-domain-of-botulinum-neurotoxin-x-high-activity-and-unique-substrate-specificity
#10
Geoffrey Masuyer, Sicai Zhang, Sulyman Barkho, Yi Shen, Linda Henriksson, Sara Košenina, Min Dong, Pål Stenmark
Botulinum neurotoxins (BoNTs) are among the most potent toxins known and are also used to treat an increasing number of medical disorders. There are seven well-established serotypes (BoNT/A-G), which all act as zinc-dependent endopeptidases targeting specific members of the SNARE proteins required for synaptic vesicle exocytosis in neurons. A new toxin serotype, BoNT/X, was recently identified. It cleaves not only the canonical targets, vesicle associated membrane proteins (VAMP) 1/2/3 at a unique site, but also has the unique ability to cleave VAMP4/5 and Ykt6...
March 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29511299/synaptic-loss-in-schizophrenia-a-meta-analysis-and-systematic-review-of-synaptic-protein-and-mrna-measures
#11
REVIEW
Emanuele Felice Osimo, Katherine Beck, Tiago Reis Marques, Oliver D Howes
Although synaptic loss is thought to be core to the pathophysiology of schizophrenia, the nature, consistency and magnitude of synaptic protein and mRNA changes has not been systematically appraised. Our objective was thus to systematically review and meta-analyse findings. The entire PubMed database was searched for studies from inception date to the 1st of July 2017. We selected case-control postmortem studies in schizophrenia quantifying synaptic protein or mRNA levels in brain tissue. The difference in protein and mRNA levels between cases and controls was extracted and meta-analysis conducted...
March 6, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29496544/frontotemporal-dysregulation-of-the-snare-protein-interactome-is-associated-with-faster-cognitive-decline-in-old-age
#12
Alfredo Ramos-Miguel, Andrea A Jones, Ken Sawada, Alasdair M Barr, Thomas A Bayer, Peter Falkai, Sue E Leurgans, Julie A Schneider, David A Bennett, William G Honer
The molecular underpinnings associated with cognitive reserve remain poorly understood. Because animal models fail to fully recapitulate the complexity of human brain aging, postmortem studies from well-designed cohorts are crucial to unmask mechanisms conferring cognitive resistance against cumulative neuropathologies. We tested the hypothesis that functionality of the SNARE protein interactome might be an important resilience factor preserving cognitive abilities in old age. Cognition was assessed annually in participants from the Rush "Memory and Aging Project" (MAP), a community-dwelling cohort representative of the overall aging population...
June 2018: Neurobiology of Disease
https://www.readbyqxmd.com/read/29373835/the-in-vitro-detection-of-botulinum-neurotoxin-cleaved-endogenous-vamp-is-epitope-dependent
#13
B Gray, V Cadd, M Elliott, M Beard
The in vitro potency of botulinum neurotoxin (BoNT) serotypes is often measured by monitoring cleavage of their soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein substrates. A frequently used method is Western blot, whereby the full-length protein and cleaved form migrate at different molecular weights. Until now, it has been extremely difficult to detect the cleaved cellular form of the SNARE protein vesicle associated membrane protein 1, 2 or 3 (VAMP1, 2 or 3) by Western blot...
April 2018: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29358308/%C3%AE-adrenoceptor-activation-increased-vamp-2-and-syntaxin-4-in-secretory-granules-are-involved-in-protein-secretion-of-submandibular-gland-through-the-pka-f-actin-pathway
#14
Chong Ding, Xin Cong, Yan Zhang, Sheng-Lin Li, Li-Ling Wu, Guang-Yan Yu
Autologous submandibular gland transplantation is an effective treatment for severe dry eye syndrome. However, the protein secretion in transplanted gland is altered by a mechanism that remains to be elucidated. In the present study, we found that β1-adrenoceptor (β1-AR) and β2-AR expression and the phosphorylation of the downstream molecule protein kinase A (PKA) were elevated in transplanted submandibular glands obtained from epiphora patients. Synaptobrevin/vesicle-associated membrane protein 2 (VAMP-2) interacted with syntaxin-4 and actin in human submandibular gland...
February 28, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29351997/spatiotemporal-organization-of-exocytosis-emerges-during-neuronal-shape-change
#15
Fabio L Urbina, Shawn M Gomez, Stephanie L Gupton
Neurite elongation and branching in developing neurons requires plasmalemma expansion, hypothesized to occur primarily via exocytosis. We posited that exocytosis in developing neurons and nonneuronal cells would exhibit distinct spatiotemporal organization. We exploited total internal reflection fluorescence microscopy to image vesicle-associated membrane protein (VAMP)-pHluorin-mediated exocytosis in mouse embryonic cortical neurons and interphase melanoma cells, and developed computer-vision software and statistical tools to uncover spatiotemporal aspects of exocytosis...
March 5, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29340032/c3g-promotes-a-selective-release-of-angiogenic-factors-from-activated-mouse-platelets-to-regulate-angiogenesis-and-tumor-metastasis
#16
Víctor Martín-Granado, Sara Ortiz-Rivero, Rita Carmona, Sara Gutiérrez-Herrero, Mario Barrera, Laura San-Segundo, Celia Sequera, Pedro Perdiguero, Francisco Lozano, Francisco Martín-Herrero, José Ramón González-Porras, Ramón Muñoz-Chápuli, Almudena Porras, Carmen Guerrero
Previous observations indicated that C3G (RAPGEF1) promotes α-granule release, evidenced by the increase in P-selectin exposure on the platelet surface following its activation. The goal of the present study is to further characterize the potential function of C3G as a modulator of the platelet releasate and its implication in the regulation of angiogenesis. Proteomic analysis revealed a decreased secretion of anti-angiogenic factors from activated transgenic C3G and C3G∆Cat platelets. Accordingly, the secretome from both transgenic platelets had an overall pro-angiogenic effect as evidenced by an in vitro capillary-tube formation assay with HUVECs (human umbilical vein endothelial cells) and by two in vivo models of heterotopic tumor growth...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29328362/microrna-493-5p-promotes-apoptosis-and-suppresses-proliferation-and-invasion-in-liver-cancer-cells-by-targeting-vamp2
#17
Guannan Wang, Xiaosan Fang, Meng Han, Xiaoming Wang, Qiang Huang
The aim of the present study was to explore the role of miR‑493-5p in liver cancer tissues and cell lines, and its effect on cell behavioral characteristics. The expression of miR-493-5p was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in liver cancer tissues and cell lines (hepatic cell line HL-7702 and the liver cancer cell lines HCCC-9810, HuH-7 and HepG2). In addition, the mechanism by which miR-493-5p mediates its effects was analyzed via the transfection of miR-493-5p mimic and negative control miRNA into HepG2 cells...
March 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29295994/vampnets-for-deep-learning-of-molecular-kinetics
#18
Andreas Mardt, Luca Pasquali, Hao Wu, Frank Noé
There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated coordinates into structural features, dimension reduction, clustering the dimension-reduced data, and estimation of a Markov state model or related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial amount of modeling expertise, as poor decisions at any step will lead to large modeling errors...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29284612/vamp-3-mediates-platelet-endocytosis
#19
COMMENT
Charles J Lowenstein
No abstract text is available yet for this article.
December 28, 2017: Blood
https://www.readbyqxmd.com/read/29189100/a-soft-tube-climbing-robot
#20
Mohit S Verma, Alar Ainla, Dian Yang, Daniel Harburg, George M Whitesides
This article demonstrates a pneumatically actuated soft robot capable of navigating the inside of a tube. This robot was built using buckling pneumatic actuators (vacuum-actuated muscle-inspired pneumatic structures, or VAMPs). The tube climber can navigate through a tube with turns, inclines, and varying diameters. The robot is also able to remove obstacles (of more than 10 times its own weight) from tubes to perform a clearing function. It maintains climbing and clearing performance in wet conditions and under water...
November 30, 2017: Soft Robotics
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