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https://www.readbyqxmd.com/read/29241086/practical-aspects-of-the-automated-preparation-of-aqueous-two-phase-systems-for-the-analysis-of-biological-macromolecules
#1
Rana Hameed, Jonathan Huddleston, Svetlana Ignatova
A robust strategy for the automated preparation of aqueous two-phase systems (ATPS) using a liquid handling sample processor was developed using gravimetric methods: to determine the accuracy of preparation. The major robotic control parameters requiring adjustment were; speed of aspiration and dispense; delay times following aspiration and dispense alongside measures to control cross-contamination during phase sampling. In general mixture compositions of both polymer/polymer and polymer/salt mixtures could be prepared with a target bias accuracy of less than 5%...
October 3, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29241042/the-adenovirus-e1a-c-terminus-suppresses-a-delayed-antiviral-response-and-modulates-ras-signaling
#2
Nathan R Zemke, Arnold J Berk
The N-terminal half of adenovirus e1a assembles multimeric complexes with host proteins that repress innate immune responses and force host cells into S-phase. In contrast, the functions of e1a's C-terminal interactions with FOXK, DCAF7, and CtBP are unknown. We found that these interactions modulate RAS signaling, and that a single e1a molecule must bind all three of these host proteins to suppress activation of a subset of IFN-stimulated genes (ISGs). These ISGs were otherwise induced in primary respiratory epithelial cells at 12 hr p...
December 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29240711/nad1-controls-defense-like-responses-in-medicago-truncatula-symbiotic-nitrogen-fixing-nodules-following-rhizobial-colonization-in-a-baca-independent-manner
#3
Ágota Domonkos, Szilárd Kovács, Anikó Gombár, Ernő Kiss, Beatrix Horváth, Gyöngyi Z Kováts, Attila Farkas, Mónika T Tóth, Ferhan Ayaydin, Károly Bóka, Lili Fodor, Pascal Ratet, Attila Kereszt, Gabriella Endre, Péter Kaló
Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules. Within symbiotic nodules, rhizobia are intracellularly accommodated in plant-derived membrane compartments, termed symbiosomes. In mature nodule, the massively colonized cells tolerate the existence of rhizobia without manifestation of visible defense responses, indicating the suppression of plant immunity in the nodule in the favur of the symbiotic partner. Medicago truncatulaDNF2 (defective in nitrogen fixation 2) and NAD1 (nodules with activated defense 1) genes are essential for the control of plant defense during the colonization of the nitrogen-fixing nodule and are required for bacteroid persistence...
December 14, 2017: Genes
https://www.readbyqxmd.com/read/29240668/heat-shock-proteins-in-vascular-diabetic-complications-review-and-future-perspective
#4
REVIEW
Stefania Bellini, Federica Barutta, Raffaella Mastrocola, Luigi Imperatore, Graziella Bruno, Gabriella Gruden
Heat shock proteins (HSPs) are a large family of proteins highly conserved throughout evolution because of their unique cytoprotective properties. Besides assisting protein refolding and regulating proteostasis under stressful conditions, HSPs also play an important role in protecting cells from oxidative stress, inflammation, and apoptosis. Therefore, HSPs are crucial in counteracting the deleterious effects of hyperglycemia in target organs of diabetes vascular complications. Changes in HSP expression have been demonstrated in diabetic complications and functionally related to hyperglycemia-induced cell injury...
December 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29240442/optical-antenna-based-fluorescence-correlation-spectroscopy-to-probe-the-nanoscale-dynamics-of-biological-membranes
#5
Pamina Martina Winkler, Raju Regmi, Valentin Flauraud, Juergen Brugger, Herve Rigneault, Jerome Wenger, Maria F Garcia-Parajo
The plasma membrane of living cells is compartmentalized at multiple spatial scales ranging from the nano- to the meso-scale. This non-random organization is crucial for a large number of cellular functions. At the nanoscale, cell membranes organize into dynamic nano-assemblies enriched by cholesterol, sphingolipids and certain types of proteins. Investigating these nano-assemblies known as lipid rafts is of paramount interest in fundamental cell biology. However, this goal requires simultaneous nanometer spatial precision and microsecond temporal resolution which is beyond the reach of common microscopes...
December 14, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29240412/integration-of-on-column-chemical-reactions-in-protein-characterization-by-lc-ms-cross-path-reactive-chromatography
#6
Jake Pawlowski, Ian Carrick, Igor A Kaltashov
Profiling of complex proteins by means of mass spectrometry (MS) frequently requires that certain chemical modifications of their covalent structure (e.g., reduction of disulfide bonds) be carried out prior to the MS or MS/MS analysis. Traditionally, these chemical reactions take place in the off-line mode to allow the excess reagents (the majority of which interfere with the MS measurements and degrade the analytical signal) to be removed from the protein solution prior to MS measurements. In addition to a significant increase in the analysis time, chemical reactions may result in a partial or full loss of the protein if the modifications adversely affect its stability, e...
December 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29239719/live-cell-mapping-of-organelle-associated-rnas-via-proximity-biotinylation-combined-with-protein-rna-crosslinking
#7
Pornchai Kaewsapsak, David Michael Shechner, William Mallard, John L Rinn, Alice Y Ting
The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches...
December 14, 2017: ELife
https://www.readbyqxmd.com/read/29239314/taking-out-the-garbage-cathepsin-d-and-calcineurin-in-neurodegeneration
#8
REVIEW
Andreas Aufschnaiter, Verena Kohler, Sabrina Büttner
Cellular homeostasis requires a tightly controlled balance between protein synthesis, folding and degradation. Especially long-lived, post-mitotic cells such as neurons depend on an efficient proteostasis system to maintain cellular health over decades. Thus, a functional decline of processes contributing to protein degradation such as autophagy and general lysosomal proteolytic capacity is connected to several age-associated neurodegenerative disorders, including Parkinson's, Alzheimer's and Huntington's diseases...
November 2017: Neural Regeneration Research
https://www.readbyqxmd.com/read/29239171/thermoresponsive-arrays-patterned-via-photo-click-chemistry-smart-maldi-plate-for-protein-digest-enrichment-desalting-and-direct-ms-analysis
#9
Xiao Meng, Junjie Hu, Zhicong Chao, Ying Liu, Huangxian Ju, Quan Cheng
Sample desalting and concentrating is a crucial step prior to MALDI-MS analysis. Current sample pretreatment approaches require tedious fabrication and operation procedures, which are unamenable to high-throughput analysis and also result in sample loss. Here we report the development of a smart MALDI substrate for on-plate desalting, enrichment, and direct MS analysis of protein digests based on thermo-responsive, hydrophilic/hydrophobic transition of surface grafted poly(N-isopropylacrylamide) (PNIPAM) microarrays...
December 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29239106/er-stress-in-skeletal-muscle-remodeling-and-myopathies
#10
REVIEW
Dil Afroze, Ashok Kumar
Skeletal muscle is a highly plastic tissue in the human body that undergoes extensive adaptation in response to environmental cues, such as physical activity, metabolic perturbation, and disease conditions. The endoplasmic reticulum (ER) plays a pivotal role in protein folding and calcium homeostasis in many mammalian cell types including skeletal muscle. However, overload of misfolded or unfolded proteins in the ER lumen cause stress, which results in the activation of a signaling network called the unfolded protein response (UPR)...
December 14, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29238606/effects-of-amino-acid-composition-in-pig-diet-on-odorous-compounds-and-microbial-characteristics-of-swine-excreta
#11
Neeraja Recharla, Kihyun Kim, Juncheol Park, Jinyoung Jeong, Yongdae Jeong, Hyunjeong Lee, Okhwa Hwang, Jaehyoung Ryu, Youlchang Baek, Youngkyun Oh, Sungkwon Park
Background: Major amino acids in pig diets are Lys, Met, Thr, and Trp, but little is known about the requirements for the other essential amino acids, especially on odorous compounds and microbial characteristics in feces of growing-finishing pigs. To this end, different levels of amino acid composition added to diets to investigate the effects of amino acid composition on microbial characteristics and odorous compounds concentration. Methods: A total eight (n = 8) barrows (Landrace × Yorkshire × Duroc) with an average bodyweight of 89...
2017: Journal of Animal Science and Technology
https://www.readbyqxmd.com/read/29238402/expressing-accessory-proteins-in-cellulolytic-yarrowia-lipolytica-to-improve-the-conversion-yield-of-recalcitrant-cellulose
#12
Zhong-Peng Guo, Sophie Duquesne, Sophie Bozonnet, Jean-Marc Nicaud, Alain Marty, Michael Joseph O'Donohue
Background: A recently constructed cellulolytic Yarrowia lipolytica is able to grow efficiently on an industrial organosolv cellulose pulp, but shows limited ability to degrade crystalline cellulose. In this work, we have further engineered this strain, adding accessory proteins xylanase II (XYNII), lytic polysaccharide monooxygenase (LPMO), and swollenin (SWO) from Trichoderma reesei in order to enhance the degradation of recalcitrant substrate. Results: The production of EG I was enhanced using a promoter engineering strategy...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29238378/association-of-macrophage-migration-inhibitory-factor-gene-polymorphisms-with-chronic-periodontitis-in-a-south-eastern-iranian-population
#13
Zahra Heidari, Hamidreza Mahmoudzadeh-Sagheb, Mohammad Hashemi, Somayeh Ansarimoghaddam, Bita Moudi, Nadia Sheibak
Background: Macrophage migration inhibitory factor (MIF) is a key proinflammatory mediator. It plays a vital role in immune response against the oral disease. MIF is a regulator of innate immunity, and bacterial antigens can stimulate serum level of this protein. In experimental gingivitis, the expression level of MIF increases and this increment positively correlates with oral plaque index. The single nucleotide polymorphisms in the gene encoding the MIF protein can control the function of MIF...
November 2017: Dental Research Journal
https://www.readbyqxmd.com/read/29238332/application-of-flp-frt-system-to-construct-unmarked-deletion-in-helicobacter-pylori-and-functional-study-of-gene-hp0788-in-pathogenesis
#14
Xiaofei Ji, Ying Wang, Jiaojiao Li, Qianyu Rong, Xingxing Chen, Ying Zhang, Xiaoning Liu, Boqing Li, Huilin Zhao
Helicobacter pylori is a Gram-negative, microaerophilic bacterium associated with human gastric diseases. Further investigations on virulence genes are still required to clarify the pathogenic mechanism of H. pylori and the heterogeneous problem of infection. In order to develop an efficient and accurate method to study gene functions in H. pylori pathogenesis, an unmarked deletion method for both a single gene and a large fragment was established based on the FLP-FRT recombination system. Using this method, the gene hp0788, encoding an outer membrane protein (HofF), was deleted...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29238070/the-interplay-between-mutant-p53-and-the-mevalonate-pathway
#15
REVIEW
Alejandro Parrales, Elizabeth Thoenen, Tomoo Iwakuma
Missense mutations in the TP53 gene lead to accumulation of dysfunctional TP53 proteins in tumors, showing oncogenic gain-of-function (GOF) activities. Stabilization of mutant TP53 (mutp53) is required for the GOF; however, the mechanisms by which mutp53 promotes cancer progression and how mutp53 stability is regulated are not completely understood. Recent work from our laboratory has identified statins, inhibitors of the mevalonate pathway, as degraders of conformational mutp53. Specific reduction of mevalonate-5-phosphate (MVP), a metabolic intermediate in the mevalonate pathway, by statins or mevalonate kinase (MVK) knockdown triggers CHIP ubiquitin ligase-mediated degradation of conformational mutp53 by inhibiting interaction between mutp53 and DNAJA1, a Hsp40 family member...
December 13, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29238068/microrna-105-is-involved-in-tnf-%C3%AE-related-tumor-microenvironment-enhanced-colorectal-cancer-progression
#16
Zetao Shen, Rui Zhou, Chen Liu, Yaofeng Wang, Wanqi Zhan, Ziyun Shao, Jian Liu, Feifei Zhang, Lijun Xu, Xinying Zhou, Lu Qi, Feng Bo, Yanqing Ding, Liang Zhao
TNF-α is a central proinflammatory cytokine contributing to malignant tumor progression in tumor microenvironment. In this study, we found the upregulation of miR-105 in colorectal cancer was associated with aggressive phenotype, and the enhanced expression of miR-105 was required for TNF-α-induced epithelial-mesenchymal transition (EMT). The expression of miR-105 was remarkably stimulated by TNF-α in a time-dependent manner using real-time qPCR analysis. Inhibition of miR-105 remarkably weakened the aggressive effects of TNF-α through preventing the activation of NF-κB signaling and the initiation of EMT...
December 13, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29238067/alternative-nhej-pathway-proteins-as-components-of-mycn-oncogenic-activity-in-human-neural-crest-stem-cell-differentiation-implications-for-neuroblastoma-initiation
#17
Erika A Newman, Sahiti Chukkapalli, Daniela Bashllari, Tina T Thomas, Raelene A Van Noord, Elizabeth R Lawlor, Mark J Hoenerhoff, Anthony W Opipari, Valerie P Opipari
Neuroblastoma is a cancer of neural crest stem cell (NCSC) lineage. Signaling pathways that regulate NCSC differentiation have been implicated in neuroblastoma tumorigenesis. This is exemplified by MYCN oncogene targets that balance proliferation, differentiation, and cell death similarly in normal NCSC and in high-risk neuroblastoma. Our previous work discovered a survival mechanism by which MYCN-amplified neuroblastoma circumvents cell death by upregulating components of the error-prone non-canonical alternative nonhomologous end-joining (alt-NHEJ) DNA repair pathway...
December 13, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29238045/ripk3-promotes-adenovirus-type-5-activity
#18
Melanie Weigert, Alex Binks, Suzanne Dowson, Elaine Y L Leung, Dmitris Athineos, Xinzi Yu, Margaret Mullin, Josephine B Walton, Clare Orange, Darren Ennis, Karen Blyth, Stephen W G Tait, Iain A McNeish
Oncolytic adenoviral mutants infect human malignant cells and replicate selectively within them. This induces direct cytotoxicity that can also trigger profound innate and adaptive immune responses. However, the mechanism by which adenoviruses produce cell death remains uncertain. We previously suggested that type 5 adenoviruses, including the E1A CR2 deletion mutant dl922-947, might induce a novel form of programmed death resembling necroptosis. Here we have investigated the roles of core necrosis proteins RIPK1, RIPK3 and MLKL in the cytotoxicity of dl922-947 and other adenovirus serotypes...
December 13, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29237847/a-trimeric-hiv-1-envelope-gp120-immunogen-induces-potent-and-broad-anti-v1v2-loop-antibodies-against-hiv-1-in-rabbits-and-rhesus-macaques
#19
Andrew T Jones, Venkateswarlu Chamcha, Sannula Kesavardhana, Xiaoying Shen, David Beaumont, Raksha Das, Linda S Wyatt, Celia C LaBranche, Sherry Stanfield-Oakley, Guido Ferrari, David C Montefiori, Bernard Moss, Georgia D Tomaras, Raghavan Varadarajan, Rama Rao Amara
Trimeric HIV-1 envelope (Env) immunogens are attractive due to their ability to display quaternary epitopes targeted by broadly neutralizing antibodies while obscuring unfavorable epitopes. Results from the RV144 trial highlighted the importance of vaccine induced HIV-1 Env V1V2 directed antibodies, with key regions of the V2 loop as targets for vaccine-mediated protection. We recently reported that a trimeric JRFL-gp120 immunogen, generated by inserting a N-terminal trimerization domain in the V1 loop region of a cyclically permuted gp120 (cycP-gp120), induces neutralizing activity against multiple tier-2 HIV-1 isolates in guinea pigs in a DNA prime/protein boost approach...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29237845/human-cytomegalovirus-replication-is-inhibited-by-the-autophagy-inducing-compounds-trehalose-and-smer28-through-distinctively-different-mechanisms
#20
Alex E Clark, Maite Sabalza, Philip L S M Gordts, Deborah H Spector
Human Cytomegalovirus (HCMV) is the top viral cause of birth defects worldwide, and current therapies have high toxicity. We previously published that the mTOR-independent autophagy-inducing disaccharide trehalose inhibits HCMV replication in multiple cell types. Here, we examine the mechanism of inhibition and introduce the autophagy inducer SMER28 as an additional inhibitor of HCMV acting through a different mechanism. We find that trehalose induces vacuolation and acidification of vacuoles, and that debris, including debris consistent in appearance with abnormal virions, is present in multivesicular bodies...
December 13, 2017: Journal of Virology
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