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Affinity maturation

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https://www.readbyqxmd.com/read/27913890/performance-improvement-of-raw-water-pretreatment-process-with-pre-inoculation-biofilm-feasibility-and-limiting-factors
#1
Guang-Feng Yang, Li-Juan Feng, Cai-Rong Guo, Tian Xia, Xiang-Yang Xu, Liang Zhu
The initial formation of biofilm and the removal performance of pollutants in biological pretreatment process for polluted raw water were limited due to the oligotrophic niche in raw water. In this study, the feasibility of using pre-inoculation biofilm formed under nutrients enhanced condition for polluted raw water treatment was analyzed in nine batch reactors. Results showed that the pollutants removal performance of biofilm was improved under nutrients enhanced conditions. Ammonia oxidation rate (AOR) was exponentially increased with the increasing in NH4(+)-N levels, and organic matter removal rate (ORR) was positively related to the initial total organic carbon (TOC) concentration...
December 2, 2016: Biodegradation
https://www.readbyqxmd.com/read/27909922/production-of-biologically-active-recombinant-goose-fsh-in-a-single-chain-form-with-a-ctp-linker-sequence
#2
Hui Li, Huanxi Zhu, Qinming Qin, Mingming Lei, Zhendan Shi
FSH is a glycoprotein hormone secreted by the pituitary gland that is essential for gonadal development and reproductive function. In avian reproduction study, especially in avian reproduction hormone study, it is hindered by the lack of biologically active FSH. In order to overcome this shortcoming, we prepared recombinant goose FSH as a single chain molecule and tested its biological activities in the present study. Coding sequences for mature peptides of goose FSH α and β subunits were amplified from goose pituitary cDNA...
December 1, 2016: Molecular Biology Reports
https://www.readbyqxmd.com/read/27903913/functional-rnas-combined-assembly-and-packaging-in-vlps
#3
Po-Yu Fang, Lizzette M Gómez Ramos, Stefany Y Holguin, Chiaolong Hsiao, Jessica C Bowman, Hung-Wei Yang, Loren Dean Williams
We describe here a one pot RNA production, packaging and delivery system based on bacteriophage Qβ. We demonstrate a method for production of a novel RNAi scaffold, packaged within Qβ virus-like particles (VLPs). The RNAi scaffold is a general utility chimera that contains a functional RNA duplex with paired silencing and carrier sequences stabilized by a miR-30 stem-loop. The Qβ hairpin on the 5' end confers affinity for the Qβ coat protein (CP). Silencing sequences can include mature miRNAs and siRNAs, and can target essentially any desired mRNA...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27901020/structural-decoding-of-netrin-4-reveals-a-regulatory-function-towards-mature-basement-membranes
#4
Raphael Reuten, Trushar R Patel, Matthew McDougall, Nicolas Rama, Denise Nikodemus, Benjamin Gibert, Jean-Guy Delcros, Carina Prein, Markus Meier, Stéphanie Metzger, Zhigang Zhou, Jennifer Kaltenberg, Karen K McKee, Tobias Bald, Thomas Tüting, Paola Zigrino, Valentin Djonov, Wilhelm Bloch, Hauke Clausen-Schaumann, Ernst Poschl, Peter D Yurchenco, Martin Ehrbar, Patrick Mehlen, Jörg Stetefeld, Manuel Koch
Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies with netrin-1, netrin-4 was also proposed to play a role in neuronal outgrowth and developmental/pathological angiogenesis via interactions with netrin-1 receptors. Here, we present the high-resolution structure of netrin-4, which shows unique features in comparison with netrin-1, and show that it does not bind directly to any of the known netrin-1 receptors...
November 30, 2016: Nature Communications
https://www.readbyqxmd.com/read/27895641/pneumococcal-polysaccharide-vaccination-elicits-igg-anti-a-b-blood-group-antibodies-in-healthy-individuals-and-patients-with-type-i-diabetes-mellitus
#5
Wendelin Wolfram, Kai M T Sauerwein, Christoph J Binder, Nicole Eibl-Musil, Hermann M Wolf, Michael B Fischer
HYPOTHESIS: Blood group antibodies are natural antibodies that develop early in life in response to cross-reactive environmental antigens in the absence of antigen encounter. Even later in life structural similarities in saccharide composition between environmental antigens such as bacterial polysaccharides and blood group A/B antigens could lead to changes in serum levels, IgM/IgG isotype, and affinity maturation of blood group anti-A/B antibodies. We addressed the question whether immunization with pneumococcal polysaccharide (PnP) vaccine Pneumo 23 Vaccine "Pasteur Merieux" (Pn23) could have such an effect in patients with type I diabetes mellitus (DM I), an autoimmune disease where an aberrant immune response to microbial antigens likely plays a role...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27893830/mechanistic-studies-and-modeling-reveal-the-origin-of-differential-inhibition-of-gag-polymorphic-viruses-by-hiv-1-maturation-inhibitors
#6
Zeyu Lin, Joseph Cantone, Hao Lu, Beata Nowicka-Sans, Tricia Protack, Tian Yuan, Hong Yang, Zheng Liu, Dieter Drexler, Alicia Regueiro-Ren, Nicholas A Meanwell, Mark Cockett, Mark Krystal, Max Lataillade, Ira B Dicker
HIV-1 maturation inhibitors (MIs) disrupt the final step in the HIV-1 protease-mediated cleavage of the Gag polyprotein between capsid p24 capsid (CA) and spacer peptide 1 (SP1), leading to the production of infectious virus. BMS-955176 is a second generation MI with improved antiviral activity toward polymorphic Gag variants compared to a first generation MI bevirimat (BVM). The underlying mechanistic reasons for the differences in polymorphic coverage were studied using antiviral assays, an LC/MS assay that quantitatively characterizes CA/SP1 cleavage kinetics of virus like particles (VLPs) and a radiolabel binding assay to determine VLP/MI affinities and dissociation kinetics...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27891132/impact-of-chronic-hiv-siv-infection-on-t-follicular-helper-cell-subsets-and-germinal-center-homeostasis
#7
REVIEW
Stéphanie Graff-Dubois, Angeline Rouers, Arnaud Moris
The discovery of broad and potent HIV-1 neutralizing antibodies (bNAbs) has renewed optimism for developing an effective vaccine against HIV-1. The generation of most bNAbs requires multiple rounds of B cell receptor affinity maturation, suggesting a crucial role of follicular helper T (Tfh) cells in their production. However, less than 1% of HIV-infected patients develop bNAbs that arise late in the course of infection, indicating probable Tfh and B cell dysfunctions in this context. Since the last few years, many studies have characterized Tfh cells from lymph nodes and spleen of HIV-infected individuals and SIV-infected macaques...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27883180/mitochondrial-reactive-oxygen-species-suppress-humoral-immune-response-through-reduction-of-cd19-expression-in-b-cells-in-mice
#8
Masato Ogura, Takeshi Inoue, Junko Yamaki, Miwako K Homma, Tomohiro Kurosaki, Yoshimi Homma
Reactive oxygen species (ROS) are implicated in the modulation of diverse processes including immune responses. To evaluate the effects of metabolic ROS produced by mitochondria on B-cell function and development, we created transgenic (Tg) mice expressing a phosphorylation-defective mutant of succinate dehydrogenase A (SDHA(Y215F) ) in B cells (bSDHA(Y215F) ). Splenic B cells in male, but not female, bSDHA(Y215F) mice produced three times more ROS than those in the control mice, and had decreased production of IgM, IgG1 , and IgG3 , and affinity maturation of IgG1 against T-cell-dependent antigens...
November 24, 2016: European Journal of Immunology
https://www.readbyqxmd.com/read/27878965/a-simplified-procedure-for-antibody-engineering-by-yeast-surface-display-coupling-display-levels-and-target-binding-by-ribosomal-skipping
#9
Julius Grzeschik, Steffen C Hinz, Doreen Könning, Thomas Pirzer, Stefan Becker, Stefan Zielonka, Harald Kolmar
Yeast surface display is a valuable, widely used method for protein engineering. However, current yeast display applications rely on the staining of epitope tags in order to verify full-length presentation of the protein of interest on the cell surface. We aimed at developing a modified yeast display approach that relies on ribosomal skipping, thereby enabling the translation of two proteins from one open reading frame and, in that manner, generating an intracellular fluorescence signal. This improved setup is based on a 2A sequence that is encoded between the protein to be displayed and a gene for green fluorescent protein (GFP)...
November 23, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27876862/in-silico-exploration-for-novel-type-i-inhibitors-of-tie-2-tek-the-performance-of-different-selection-strategy-in-selecting-virtual-screening-candidates
#10
Peichen Pan, Huiyong Sun, Hui Liu, Dan Li, Wenfang Zhou, Xiaotian Kong, Youyong Li, Huidong Yu, Tingjun Hou
The receptor tyrosine kinase Tie-2 is involved in vessel remodeling and maturation, and has been regarded as a potential target for the treatment of various solid tumors. The absence of novel, potent and selective inhibitors severely hampers the understanding of the therapeutic potential of Tie-2. In the present work, we describe the discovery of novel type-I inhibitors of Tie-2 by structure-based virtual screening. Preliminary SAR was also performed based on one active compound, and several novel inhibitors with low micro-molar affinity were discovered...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27867055/heterologous-expression-and-functional-characterization-of-phytaspase-a-caspase-like-plant-protease
#11
Sharmila Narayanan, Pallab Sanpui, Lingaraj Sahoo, Siddhartha Sankar Ghosh
Following the cloning and expression of tobacco (Nicotiana tabacum) phytaspase gene in Escherichia coli BL21, the recombinant protease was purified by affinity chromatography for further characterization. Circular dichroism (CD) spectroscopy and in silico analysis revealed structural similarities of recombinant phytaspase with other plant serine-proteases. Molecular docking studies showed favourable binding of synthetic peptide substrate for caspase 8 (Ac-VETD-AMC) to the reactive pocket of recombinant phytaspase indicating its potential in assessing functional activity of recombinant phytaspase...
November 17, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27865780/rasins-genetically-encoded-intrabodies-of-activated-ras-proteins
#12
Mehmet Cetin, William E Evenson, Garret G Gross, Farzad Jalali-Yazdi, Daniel Krieger, Don Arnold, Terry T Takahashi, Richard W Roberts
K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10th domain of human fibronectin as their scaffold, are stable inside cells and when fused with a fluorescent protein label constitutively active G12V mutant H-Ras. Primary selection of ligands against Ras with mRNA display resulted in an intrabody (termed RasIn1) that binds with a KD of 2...
November 16, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27863842/development-of-t-follicular-helper-cells-and-their-role-in-disease-and-immune-system
#13
REVIEW
Sadegh Eivazi, Salman Bagheri, Mohammad Sadegh Hashemzadeh, Majdedin Ghalavand, Elmira Safaie Qamsari, Ruhollah Dorostkar, Maryam Yasemi
The T follicular helper cells (TFH) are a subset of CD4+ T cells specialized to regulate antibody responses. The production of these cells is associated with the dendritic cells (DCs) and B cells. TFH cells help B cells form germinal centers (GC) differentiate into memory and plasma cells (antibody-secreting cells) as humoral responses. In addition, there is strong evidence that TFH cells play a pivotal role in the development of long-lived humoral immunity. Molecular factors such as transcription factors, surface receptors, cytokine and micro RNAs are involved in the formation of TFH cells...
November 15, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27862752/improving-the-binding-affinity-of-in-vitro-evolved-cyclic-peptides-by-inserting-atoms-into-the-macrocycle-backbone
#14
Jonas Wilbs, Simon J Middendorp, Christian Heinis
Cyclic peptides binding to targets of interest can be generated efficiently with powerful in vitro display techniques, such as phage display or mRNA display. The cyclic peptide libraries screened with these methods are generated by altering in a combinatorial fashion the amino acid sequence of the peptides, the number of amino acids in the macrocycle rings, and the cyclization chemistry. A structural element that cannot easily be varied in the cyclic peptides is the backbone, which is built from amino acids, each of which contributes three atoms to the macrocyclic ring structure...
November 11, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27858788/valorization-of-romanian-silver-fir-tree-bark-abies-alba-mill-wastes-as-low-cost-sorbent-of-cu-ii-ions-from-polluted-waters
#15
Lavinia Tofan, Carmen Paduraru, Roxana Laura Mihailescu Amalinei, Ion Bunia, Anca Miron
Considering recycling as the first option in the hierarchy of sustainable waste management, and also the demand for efficient processes for wastewater treatment with reduced costs, the potential applicability of Romanian Abies alba bark, the main waste from the industrial processing of the wood of mature silver fir trees, as sorbent for Cu(II) has been studied in batch conditions. It was observed that the extent of Cu(II) sorption is strongly dependent on initial solution pH, sorbent dose, initial Cu(II) ion concentration, temperature and contact time...
November 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/27856750/substrate-recognition-and-catalysis-by-gh47-%C3%AE-mannosidases-involved-in-asn-linked-glycan-maturation-in-the-mammalian-secretory-pathway
#16
Yong Xiang, Khanita Karaveg, Kelley W Moremen
Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation...
November 17, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27853434/expression-of-steroid-receptors-in-ameloblasts-during-amelogenesis-in-rat-incisors
#17
Sophia Houari, Sophia Loiodice, Katia Jedeon, Ariane Berdal, Sylvie Babajko
Endocrine disrupting chemicals (EDCs) play a part in the modern burst of diseases and interfere with the steroid hormone axis. Bisphenol A (BPA), one of the most active and widely used EDCs, affects ameloblast functions, leading to an enamel hypomineralization pattern similar to that of Molar Incisor Hypomineralization (MIH). In order to explore the molecular pathways stimulated by BPA during amelogenesis, we thoroughly investigated the receptors known to directly or indirectly mediate the effects of BPA. The expression patterns of high affinity BPA receptors (ERRγ, GPR30), of ketosteroid receptors (ERs, AR, PGR, GR, MR), of the retinoid receptor RXRα, and PPARγ were established using RT-qPCR analysis of RNAs extracted from microdissected enamel organ of adult rats...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27849172/novel-e2-glycoprotein-tetramer-detects-hepatitis-c-virus-specific-memory-b-cells
#18
Maude Boisvert, Wanrui Zhang, Elizabeth J Elrod, Nicole F Bernard, Jean-Pierre Villeneuve, Julie Bruneau, Joseph Marcotrigiano, Naglaa H Shoukry, Arash Grakoui
Acute hepatitis C virus (HCV) infection culminates in viral persistence in the majority of cases. Abs that recognize the envelope glycoproteins E1 and E2 are generated during the late stages of acute infection, yet their contribution to spontaneous viral clearance remains controversial. Investigation of the humoral responses during acute HCV infection have been limited by the inability to directly identify and characterize HCV-specific B cells. In this study we describe the development of a novel tetramer of the E2 glycoprotein ectodomain (J6, genotype 2a strain), which allowed us to visualize E2-specific B cells longitudinally in the peripheral blood of HCV-infected individuals...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27845226/enhancement-of-solubility-purification-and-inclusion-bodies-refolding-of-an-active-pectin-lyase-from-penicillium-occitanis-expressed-in-escherichia-coli
#19
Azza Hadj Sassi, Hèla Trigui-Lahiani, Salma Abdeljalil, Ali Gargouri
Pectin lyase (pnl) is the only pectinase able to hydrolyze directly the highly methylated pectin without liberating the toxic methanol and without disturbing ester content responsible for specific aroma of juices. The cDNA of Penicillium occitanis pnl (mature form) was cloned into pET-21a as expression vector and over-expressed into Esherichia coli. Most of recombinant pnl was expressed as inclusion bodies. Pnl activity was confirmed by colorimetric assay. To enhance the solubility yield of the expressed pnl, the effects of induction temperature, host strain and expression level were optimized...
November 11, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27843891/establishment-and-maintenance-of-the-human-na%C3%A3-ve-cd4-t-cell-compartment
#20
REVIEW
Susana L Silva, Ana E Sousa
The naïve CD4(+) T-cell compartment is considered essential to guarantee immune competence throughout life. Its replenishment with naïve cells with broad diverse receptor repertoire, albeit with reduced self-reactivity, is ensured by the thymus. Nevertheless, cumulative data support a major requirement of post-thymic proliferation both for the establishment of the human peripheral naïve compartment during the accelerated somatic growth of childhood, as well as for its lifelong maintenance. Additionally, a dynamic equilibrium is operating at the cell level to fine-tune the T-cell receptor threshold to activation and survival cues, in order to counteract the continuous naïve cell loss by death or conversion into memory/effector cells...
2016: Frontiers in Pediatrics
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