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https://www.readbyqxmd.com/read/28934318/identification-of-lag3-high-affinity-aptamers-by-ht-selex-and-conserved-motif-accumulation-cma
#1
Mario Martínez Soldevilla, Sandra Hervas, Helena Villanueva, Teresa Lozano, Obdulia Rabal, Julen Oyarzabal, Juan José Lasarte, Maurizio Bendandi, Susana Inoges, Ascensión López-Díaz de Cerio, Fernando Pastor
LAG3 receptor belongs to a family of immune-checkpoints expressed in T lymphocytes and other cells of the immune system. It plays an important role as a rheostat of the immune response. Focus on this receptor as a potential therapeutic target in cancer immunotherapy has been underscored after the success of other immune-checkpoint blockade strategies in clinical trials. LAG3 showcases the interest in the field of autoimmunity as several studies show that LAG3-targeting antibodies can also be used for the treatment of autoimmune diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28927835/evaluation-of-rice-tetraticopeptide-domain-containing-thioredoxin-as-a-novel-solubility-enhancing-fusion-tag-in-escherichia-coli
#2
Wenjun Xiao, Li Jiang, Weiyu Wang, Ruyue Wang, Jun Fan
Fusion of solubility-enhancing tag is frequently used for improving soluble production of target protein in Escherichia coli. The Arabidopsis tetraticopeptide domain-containing thioredoxin (TDX) has been documented to exhibit functions of disulfide reductase, foldase chaperone, and holdase chaperone. Here, we identified that fusion of rice TDX with the smaller size increased soluble expression levels of three fluorescent proteins with different fluorophores in the E. coli strain BL21(DE3) or the Rosetta (DE3) strain with coexpression of six rare tRNAs, but decreased conformational quality of certain fluorescent proteins, as comparison with the His6-tagged ones...
September 15, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28923896/experimental-and-theoretical-approaches-to-investigate-the-immunogenicity-of-taenia-solium-derived-ke7-antigen
#3
Raúl J Bobes, José Navarrete-Perea, Adrián Ochoa-Leyva, Víctor Hugo Anaya, Marisela Hernández, Jacquelynne Cervantes-Torres, Karel Estrada, Filiberto Sánchez-Lopez, Xavier Soberón, Gabriela Rosas, Cáris Maroni Nunes, Martín García-Varela, Rogerio Rafael Sotelo-Mundo, Alonso Alexis López-Zavala, Goar Gevorkian, Gonzalo Acero, Juan P Laclette, Gladis Fragoso, Edda Sciutto
Taenia solium cysticercosis, a parasitic disease that affects human health in various regions of the world, is preventable by vaccination. Both the 97-amino-acid-long KETc7 peptide and its carboxyl-terminal, 18-amino-acid-long sequence (GK-1) are found in Taenia crassiceps Both peptides, with proven protective capacity against cysticercosis, are part of the highly conserved, cestode-native, 264-amino-acid long protein KE7. KE7 belongs to a ubiquitously distributed family of proteins associated to membrane processes and may participate in several vital cell pathways...
September 18, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28922368/a-tree-of-life-based-on-ninety-eight-expressed-genes-conserved-across-diverse-eukaryotic-species
#4
Pawan Kumar Jayaswal, Vivek Dogra, Asheesh Shanker, Tilak Raj Sharma, Nagendra Kumar Singh
Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed...
2017: PloS One
https://www.readbyqxmd.com/read/28885157/conformational-space-sampling-method-using-multi-subpopulation-differential-evolution-for-de-novo-protein-structure-prediction
#5
Xiao-Hu Hao, Gui-Jun Zhang, Xiao-Gen Zhou
Protein structure prediction can be considered as a multimodal optimization problem for sampling the protein conformational space associated with an extremely complex energy landscape. To address this problem, a conformational space sampling method using multi-subpopulation differential evolution, MDE, is proposed. MDE first devotes to generate given numbers of concerned modal under the ultrafast shape recognition based modal identification protocol, which regards each individual as one modal at beginning. Then, differential evolution is used for keeping the preserved modal survival in the evolution process...
September 5, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28867285/mating-in-the-closest-living-relatives-of-animals-is-induced-by-a-bacterial-chondroitinase
#6
Arielle Woznica, Joseph P Gerdt, Ryan E Hulett, Jon Clardy, Nicole King
We serendipitously discovered that the marine bacterium Vibrio fischeri induces sexual reproduction in one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta. Although bacteria influence everything from nutrition and metabolism to cell biology and development in eukaryotes, bacterial regulation of eukaryotic mating was unexpected. Here, we show that a single V. fischeri protein, the previously uncharacterized EroS, fully recapitulates the aphrodisiac-like activity of live V...
September 7, 2017: Cell
https://www.readbyqxmd.com/read/28861634/novel-one-pot-atp-regeneration-system-based-on-three-enzyme-cascade-for-industrial-ctp-production
#7
Junzhi Wang, Cheng Zheng, Tianyi Zhang, Yingmiao Liu, Zhuopei Cheng, Dong Liu, Hanjie Ying, Huanqing Niu
OBJECTIVES: To develop a new one-pot polyphosphate kinase (PPK) system with low cost and high efficiency for ATP regeneration in industrial CTP production. RESULTS: We developed a new one-pot PPK system by applying a three-enzyme cascade (CMK, NDK and PPK) with an in vitro polyP-based ATP regeneration system. The PPK was selected from twenty sources, and was made solvable by fusion expressing with soluble protein and constructing polycistronic plasmids, or co-expressing with molecular chaperones GroES/EL...
August 31, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28860215/american-society-of-functional-neuroradiology-recommended-fmri-paradigm-algorithms-for-presurgical-language-assessment
#8
D F Black, B Vachha, A Mian, S H Faro, M Maheshwari, H I Sair, J R Petrella, J J Pillai, K Welker
INTRODUCTION: Functional MR imaging is increasingly being used for presurgical language assessment in the treatment of patients with brain tumors, epilepsy, vascular malformations, and other conditions. The inherent complexity of fMRI, which includes numerous processing steps and selective analyses, is compounded by institution-unique approaches to patient training, paradigm choice, and an eclectic array of postprocessing options from various vendors. Consequently, institutions perform fMRI in such markedly different manners that data sharing, comparison, and generalization of results are difficult...
August 31, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28851420/randomized-study-exploring-the-combination-of-radiotherapy-with-two-types-of-acupuncture-treatment-rosetta-study-protocol-for-a-randomized-controlled-trial
#9
Rebecca Asadpour, Kerstin A Kessel, Tom Bruckner, Serkan Sertel, Stephanie E Combs
BACKGROUND: Adverse effects such as fatigue, pain, erythema, nausea and vomiting are commonly known in patients undergoing irradiation (RT) alone or in combination with chemotherapy (RCHT). Patients suffering from these symptoms are limited in their daily life and their quality of life (QOL) is often reduced. As addressed in several trials, acupuncture can cause amelioration of these specific disorders. Especially for pain symptoms, several groups have shown efficacy of acupuncture. To what extent the difference between traditional acupuncture (verum acupuncture) and false acupuncture (sham acupuncture) is in reducing side effects and improvement of QOL is not clear...
August 29, 2017: Trials
https://www.readbyqxmd.com/read/28843817/a-novel-resistance-gene-lnu-h-confers-resistance-to-lincosamides-inriemerella-anatipestiferch-2
#10
Hong-Yan Luo, Ma-Feng Liu, Ming-Shu Wang, Xin-Xin Zhao, Ren-Yong Jia, Shun Chen, Kun-Feng Sun, Qiao Yang, Ying Wu, Xiao-Yue Chen, Francis Biville, Yuan-Feng Zou, Bo Jing, An-Chun Cheng, De-Kang Zhu
The Gram-negative bacteria Riemerella anatipestifer CH-2 is resistant to lincosamide (the MIC value of lincomycin is 128 µg/ml). The G148_1775 gene of R. anatipestifer CH-2, designated lnu(H), encodes a 260-amino-acid protein with ≤ 41% identity to other reported lincosamide nucleotidyltransferases. The E. coli Rosetta (DE3) containing pBAD24-lnu(H) plasmid showed 4- and 2-fold increases in lincomycin and clindamycin MICs, respectively. A kinetic assay of the purified Lnu(H) enzyme for lincomycin and clindamycin showed that the protein could inactive lincosamides...
August 23, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28831399/new-frontiers-in-genetics-gut-microbiota-and-immunity-a-rosetta-stone-for-the-pathogenesis-of-inflammatory-bowel-disease
#11
REVIEW
Mingxia Zhou, Jing He, Yujie Shen, Cong Zhang, Jiazheng Wang, Yingwei Chen
Inflammatory bowel disease (IBD), which encompasses ulcerative colitis (UC) and Crohn's disease (CD), is a complicated, uncontrolled, and multifactorial disorder characterized by chronic, relapsing, or progressive inflammatory conditions that may involve the entire gastrointestinal tract. The protracted nature has imposed enormous economic burdens on patients with IBD, and the treatment is far from optimal due to the currently limited comprehension of IBD pathogenesis. In spite of the exact etiology still remaining an enigma, four identified components, including personal genetic susceptibility, external environment, internal gut microbiota, and the host immune response, are responsible for IBD pathogenesis, and compelling evidence has suggested that IBD may be triggered by aberrant and continuing immune responses to gut microbiota in genetically susceptibility individuals...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28827695/erratum-a-genome-wide-association-study-of-anorexia-nervosa-suggests-a-risk-locus-implicated-in-dysregulated-leptin-signaling
#12
Dong Li, Xiao Chang, John J Connolly, Lifeng Tian, Yichuan Liu, Elizabeth J Bhoj, Nora Robinson, Debra Abrams, Yun R Li, Jonathan P Bradfield, Cecilia E Kim, Jin Li, Fengxiang Wang, James Snyder, Maria Lemma, Cuiping Hou, Zhi Wei, Yiran Guo, Haijun Qiu, Frank D Mentch, Kelly A Thomas, Rosetta M Chiavacci, Roger Cone, Bingshan Li, Patrick A Sleiman, Hakon Hakonarson
A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28827102/shuffle%C3%A2-t7-strain-is-capable-of-producing-high-amount-of-recombinant-human-fibroblast-growth-factor-1-rhfgf-1-with-proper-physicochemical-and-biological-properties
#13
Marzieh Nasiri, Jalal Babaie, Samira Amiri, Ebrahim Azimi, Shiva Shamshiri, Vahid Khalaj, Majid Golkar, Pezhman Fard-Esfahani
BACKGROUND: Human fibroblast growth factor-1 (FGF-1) has powerful mitogenic activities in a variety of cell types and plays significant roles in many physiological processes e.g. angiogenesis and wound healing. There is increasing demand for large scale production of recombinant human FGF-1 (rhFGF-1), in order to investigate the potential medical use. In the present study, we explored SHuffle™ T7 strain for production of rhFGF-1. METHODS: A synthetic gene encoding Met-140 amino acid form of human FGF-1 was utilized for expression of the protein in three different E...
August 18, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28826489/acidic-c-terminal-domains-autoregulate-the-rna-chaperone-hfq
#14
Andrew Santiago-Frangos, Jeliazko R Jeliazkov, Jeffrey J Gray, Sarah A Woodson
The RNA chaperone Hfq is an Sm protein that facilitates base pairing between bacterial small RNAs (sRNAs) and mRNAs involved in stress response and pathogenesis. Hfq possesses an intrinsically disordered C-terminal domain (CTD) that may tune the function of the Sm domain in different organisms. In Escherichia coli, the Hfq CTD increases kinetic competition between sRNAs and recycles Hfq from the sRNA-mRNA duplex. Here, de novo Rosetta modeling and competitive binding experiments show that the acidic tip of the E...
August 9, 2017: ELife
https://www.readbyqxmd.com/read/28811664/structure-based-cross-docking-analysis-of-antibody-antigen-interactions
#15
Krishna Praneeth Kilambi, Jeffrey J Gray
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody-antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody-antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808001/two-transmembrane-dimers-of-the-bovine-papillomavirus-e5-oncoprotein-clamp-the-pdgf-%C3%AE-receptor-in-an-active-dimeric-conformation
#16
Alexander G Karabadzhak, Lisa M Petti, Francisco N Barrera, Anne P B Edwards, Andrés Moya-Rodríguez, Yury S Polikanov, J Alfredo Freites, Douglas J Tobias, Donald M Engelman, Daniel DiMaio
The dimeric 44-residue E5 protein of bovine papillomavirus is the smallest known naturally occurring oncoprotein. This transmembrane protein binds to the transmembrane domain (TMD) of the platelet-derived growth factor β receptor (PDGFβR), causing dimerization and activation of the receptor. Here, we use Rosetta membrane modeling and all-atom molecular dynamics simulations in a membrane environment to develop a chemically detailed model of the E5 protein/PDGFβR complex. In this model, an active dimer of the PDGFβR TMD is sandwiched between two dimers of the E5 protein...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28792967/aminophosphinates-against-helicobacter-pylori-ureolysis-biochemical-and-whole-cell-inhibition-characteristics
#17
Katarzyna Macegoniuk, Ewa Grela, Monika Biernat, Mateusz Psurski, Grażyna Gościniak, Anna Dziełak, Artur Mucha, Joanna Wietrzyk, Łukasz Berlicki, Agnieszka Grabowiecka
Urease is an important virulence factor from Helicobacter pylori that enables bacterial colonization of human gastric mucosa. Specific inhibition of urease activity can be regarded as a promising adjuvant strategy for eradication of this pathogen. A group of organophosphorus inhibitors of urease, namely, aminophosphinic acid and aminophosphonic acid derivatives, were evaluated in vitro against H. pylori urease. The kinetic characteristics of recombinant enzyme activity demonstrated a competitive reversible mode of inhibition with Ki values ranging from 0...
2017: PloS One
https://www.readbyqxmd.com/read/28791861/in-vivo-multienzyme-complex-coconstruction-of-n-acetylneuraminic-acid-lyase-and-n-acetylglucosamine-2-epimerase-for-biosynthesis-of-n-acetylneuraminic-acid
#18
Zhenfu Wang, Wei Zhuang, Jian Cheng, Wujin Sun, Jinglan Wu, Yong Chen, Hanjie Ying
Metabolic channeling enables efficient transfer of the intermediates by forming a multienzyme complex. To leverage the metabolic channeling for improved biosynthesis, we coexpressed N-acetylneuraminic acid lyase from C. glutamicum ATCC 13032 (CgNal) and N-acetylglucosamine-2-epimerase from Anabaena sp. CH1 (anAGE) in Escherichia coli and used the whole cell to synthesize N-acetylneuraminic acid (Neu5Ac) from N-acetylglucosamine (GlcNAc) and pyruvate. To get the multienzyme complex, polycistronic plasmid with high levels of CgNal and anAGE expression was constructed by tuning the orders of the genes...
August 30, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#19
Dorota Latek
BACKGROUND: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28763012/performance-of-a-rt-pcr-assay-in-comparison-to-fish-and-immunohistochemistry-for-the-detection-of-alk-in-non-small-cell-lung-cancer
#20
David R Hout, Brock L Schweitzer, Kasey Lawrence, Stephan W Morris, Tracy Tucker, Rosetta Mazzola, Rachel Skelton, Frank McMahon, John Handshoe, Mary Lesperance, Aly Karsan, David L Saltman
Patients with lung cancers harboring an activating anaplastic lymphoma kinase (ALK) rearrangement respond favorably to ALK inhibitor therapy. Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are validated and widely used screening tests for ALK rearrangements but both methods have limitations. The ALK RGQ RT-PCR Kit (RT-PCR) is a single tube quantitative real-time PCR assay for high throughput and automated interpretation of ALK expression. In this study, we performed a direct comparison of formalin-fixed paraffin-embedded (FFPE) lung cancer specimens using all three ALK detection methods...
August 1, 2017: Cancers
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