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https://www.readbyqxmd.com/read/28731407/t-cell-receptor-repertoires-of-mice-and-humans-are-clustered-in-similarity-networks-around-conserved-public-cdr3-sequences
#1
Asaf Madi, Asaf Poran, Eric Shifrut, Shlomit Reich-Zeliger, Erez Greenstein, Irena Zaretsky, Tomer Arnon, Francois Van Laethem, Alfred Singer, Jinghua Lu, Peter D Sun, Irun R Cohen, Nir Friedman
Diversity of T cell receptor (TCR) repertoires, generated by somatic DNA rearrangements, is central to immune system function. However, the level of sequence similarity of TCR repertoires within and between species has not been characterized. Using network analysis of high-throughput TCR sequencing data, we found that abundant CDR3-TCRβ sequences were clustered within networks generated by sequence similarity. We discovered a substantial number of public CDR3-TCRβ segments that were identical in mice and humans...
July 21, 2017: ELife
https://www.readbyqxmd.com/read/28730513/element-repetition-rates-encode-functionally-distinct-information-in-pied-babbler-clucks-and-purrs
#2
Sabrina Engesser, Amanda R Ridley, Simon W Townsend
Human language is a recombinant system that achieves its productivity through the combination of a limited set of sounds. Research investigating the evolutionary origin of this generative capacity has generally focused on the capacity of non-human animals to combine different types of discrete sounds to encode new meaning, with less emphasis on meaning-differentiating mechanisms achieved through potentially simpler temporal modifications within a sequence of repeated sounds. Here we show that pied babblers (Turdoides bicolor) generate two functionally distinct vocalisations composed of the same sound type, which can only be distinguished by the number of repeated elements...
July 20, 2017: Animal Cognition
https://www.readbyqxmd.com/read/28729628/a-new-approach-for-ratiometric-in-vivo-calcium-imaging-of-microglia
#3
Bianca Brawek, Yajie Liang, Daria Savitska, Kaizhen Li, Natalie Fomin-Thunemann, Yury Kovalchuk, Elizabeta Zirdum, Johan Jakobsson, Olga Garaschuk
Microglia, resident immune cells of the brain, react to the presence of pathogens/danger signals with a large repertoire of functional responses including morphological changes, proliferation, chemotaxis, production/release of cytokines, and phagocytosis. In vitro studies suggest that many of these effector functions are Ca(2+)-dependent, but our knowledge about in vivo Ca(2+) signalling in microglia is rudimentary. This is mostly due to technical reasons, as microglia largely resisted all attempts of in vivo labelling with Ca(2+) indicators...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729274/genome-sequences-of-two-shewanella-spp-isolated-from-the-gut-of-the-sea-cucumber-apostichopus-japonicus-selenka-1867
#4
Hyun-Hee Hong, Hyunjun Choi, Seongmin Cheon, Hyun-Gwan Lee, Chungoo Park
In this study, we sequenced the genomes of two Shewanella spp., newly isolated from the gut of the sea cucumber Apostichopus japonicus (Selenka, 1867). The whole-genome sequences reported here will expand the repertoire of genomic information for the members of the genus Shewanella and will provide important insights into their roles within microbial communities.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28726771/rapid-elicitation-of-broadly-neutralizing-antibodies-to-hiv-by-immunization-in-cows
#5
Devin Sok, Khoa M Le, Melissa Vadnais, Karen Saye-Francisco, Joseph G Jardine, Jonathan Torres, Zachary T Berndsen, Leopold Kong, Robyn Stanfield, Jennifer Ruiz, Alejandra Ramos, Chi-Hui Liang, Patricia L Chen, Michael F Criscitiello, Waithaka Mwangi, Ian A Wilson, Andrew B Ward, Vaughn V Smider, Dennis R Burton
No immunogen to date has reliably elicited broadly neutralizing antibodies to HIV in humans or animal models. Advances in the design of immunogens (BG505 SOSIP) that antigenically mimic the HIV envelope glycoprotein (Env)(1) have improved the elicitation of potent isolate-specific antibody responses in rabbits(2) and macaques(3), but so far failed to induce broadly neutralizing antibodies. One possible contributor to this failure is that the relevant antibody repertoires are poorly suited to target somewhat occluded conserved epitope regions on Env relative to exposed variable epitopes...
July 20, 2017: Nature
https://www.readbyqxmd.com/read/28726211/genetic-engineering-of-native-chain-combinations-of-b-cell-repertoires-on-the-surface-of-methylotrophic-yeasts-pichia-pastoris
#6
T V Bobik, E M Shurdova, I V Smirnov, N A Ponomarenko, E N Khurs, V D Knorre, A G Gabibov
We designed genetic constructs for exposing Fab-fragment library of natively paired single cell B-cell receptors on the surface of Pichia pastoris yeast cells. We have previously obtained the A17 antibody in our laboratory [6]. In this study we showed that the newly designed genetic constructs provide a compatible level of A17 antibody Fab fragment on the surface of yeast cells as well as in the case of vectors containing DNA fragments corresponding to each chain of the antibody. The data suggest that the developed approach for constructing immunoglobulin gene libraries is adequate and fully convenient for studying properties of the real human B-lymphocyte repertoire...
July 18, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28725665/data-on-haplotype-supported-immunoglobulin-germline-gene-inference
#7
Ufuk Kirik, Lennart Greiff, Fredrik Levander, Mats Ohlin
Data that defines IGHV (immunoglobulin heavy chain variable) germline gene inference using sequences of IgM-encoding transcriptomes obtained by Illumina MiSeq sequencing technology are described. Such inference is used to establish personalized germline gene sets for in-depth antibody repertoire studies and to detect new antibody germline genes from widely available immunoglobulin-encoding transcriptome data sets. Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28725035/systemic-lupus-erythematosus-a-repertoire-for-disaster
#8
Jessica McHugh
No abstract text is available yet for this article.
July 20, 2017: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/28724786/emergent-cortical-circuit-dynamics-contain-dense-interwoven-ensembles-of-spike-sequences
#9
Joseph B Dechery, Jason N MacLean
Temporal codes are theoretically powerful encoding schemes, but their precise form in neocortex remains unknown in part because of the large number of possible codes and the difficulty in disambiguating informative spikes from statistical noise. A biologically plausible and computationally powerful temporal coding scheme is the Hebbian assembly phase sequence (APS), which predicts reliable propagation of spikes between functionally related assemblies of neurons. Here, we sought to measure the inherent capacity of neocortical networks to produce reliable sequences of spikes, as would be predicted by an APS code...
July 19, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28724766/a-unique-t-cell-receptor-amino-acid-sequence-selected-by-htlv-i-tax301-309-specific-cytotoxic-t-cells-in-hla-a24-02-asymptomatic-carriers-and-adult-t-cell-leukemia-lymphoma-patients
#10
Yuko Ishihara, Yukie Tanaka, Seiichiro Kobayashi, Koji Kawamura, Hideki Nakasone, Ayumi Gomyo, Jin Hayakawa, Masaharu Tamaki, Yu Akahoshi, Naonori Harada, Machiko Kusuda, Kazuaki Kameda, Tomotaka Ugai, Hidenori Wada, Kana Sakamoto, Miki Sato, Kiriko Terasako-Saito, Misato Kikuchi, Shun-Ichi Kimura, Aki Tanihara, Shinichi Kako, Kaoru Uchimaru, Yoshinobu Kanda
We previously reported that the T-cell receptor (TCR) repertoire of HTLV-I Tax301-309-specific CD8(+) cytotoxic T-cells (Tax-CTLs) was highly restricted and a particular amino acid sequence motif, "PDR", was conserved among HLA-A*24:02(+) ATL patients who have undergone allogeneic hematopoietic cell transplantation (allo-HSCT). Furthermore, we found that donor-derived PDR+CTLs selectively expanded in ATL long-term HSCT survivors with strong CTL activity against HTLV-I. On the other hand, the TCR repertoires in Tax-CTL of asymptomatic HTLV-I carriers (ACs) remain unclear...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28724627/using-step-width-to-compare-locomotor-biomechanics-between-extinct-non-avian-theropod-dinosaurs-and-modern-obligate-bipeds
#11
P J Bishop, C J Clemente, R E Weems, D F Graham, L P Lamas, J R Hutchinson, J Rubenson, R S Wilson, S A Hocknull, R S Barrett, D G Lloyd
How extinct, non-avian theropod dinosaurs locomoted is a subject of considerable interest, as is the manner in which it evolved on the line leading to birds. Fossil footprints provide the most direct evidence for answering these questions. In this study, step width-the mediolateral (transverse) distance between successive footfalls-was investigated with respect to speed (stride length) in non-avian theropod trackways of Late Triassic age. Comparable kinematic data were also collected for humans and 11 species of ground-dwelling birds...
July 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28723557/crystal-structure-of-the-human-ribosome-in-complex-with-denr-mct-1
#12
Ivan B Lomakin, Elena A Stolboushkina, Anand T Vaidya, Chenguang Zhao, Maria B Garber, Sergey E Dmitriev, Thomas A Steitz
The repertoire of the density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein was recently expanded to include translational control of a specific set of cancer-related mRNAs. DENR and MCT-1 form the heterodimer, which binds to the ribosome and operates at both translation initiation and reinitiation steps, though by a mechanism that is yet unclear. Here, we determined the crystal structure of the human small ribosomal subunit in complex with DENR-MCT-1. The structure reveals the location of the DENR-MCT-1 dimer bound to the small ribosomal subunit...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28722676/comparative-proteomic-analysis-of-virulent-and-avirulent-strains-of-toxoplasma-gondii-reveals-strain-specific-patterns
#13
Dong-Hui Zhou, Ze-Xiang Wang, Chun-Xue Zhou, Shuai He, Hany M Elsheikha, Xing-Quan Zhu
Research exploring the proteome of Toxoplasma gondii oocysts has gained momentum over the past few years. However, little is known about the oocyst's protein repertoires that contribute to differential virulence among T. gondii strains. Here, we used isobaric tag for relative and absolute quantitation-based proteomic analysis of oocysts of two T. gondii strains exhibiting the virulent PYS (ToxoDB#9) phenotype versus the less virulent PRU (Type II, ToxoDB#1) phenotype. Our aim was to determine protein expression patterns that contribute to the virulence of a particular phenotype...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28722545/trna-engineering-for-manipulating-genetic-code
#14
Takayuki Katoh, Yoshihiko Iwane, Hiroaki Suga
In ribosomal translation, only 20 kinds of proteinogenic amino acids (pAAs), namely 19 l-amino acids and glycine, are exclusively incorporated into polypeptide chain. To overcome this limitation, various methods to introduce non-proteinogenic amino acids (npAAs) other than the 20 pAAs have been developed to date. However, the repertoire of amino acids that can be simultaneously introduced is still limited. Moreover, the efficiency of npAA incorporation is not always sufficient depending on their structures...
July 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28721222/serological-evidence-of-francisella-tularensis-in-febrile-patients-seeking-treatment-at-remote-hospitals-northeastern-kenya-2014-2015
#15
J Njeru, H Tomaso, K Mertens, K Henning, G Wareth, R Heller, S Kariuki, E M Fèvre, H Neubauer, M W Pletz
Tularaemia is a highly contagious infectious zoonosis caused by the bacterial agent Francisella tularensis. The aim of this study was to investigate the presence of antibodies to F. tularensis in febrile patients in northeastern Kenya. During 2014-2015, 730 patients were screened for anti-F. tularensis antibodies using a combination of ELISA and Western blot. Twenty-seven (3.7%) individuals were positive for F. tularensis. Tularaemia was not suspected by the treating clinicians in any of them. Our results suggest that tularaemia may be present in Kenya but remain unreported, and emphasizes the need for local clinicians to broaden their diagnostic repertoire when evaluating patients with undifferentiated febrile illness...
September 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28720902/comparative-genomic-analysis-of-paenibacillus-sp-ssg-1-and-its-closely-related-strains-reveals-the-effect-of-glycometabolism-on-environmental-adaptation
#16
Hui Xu, Shishang Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dairong Qiao, Yu Cao, Yi Cao
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720884/molecular-tools-for-gabaa-receptors-high-affinity-ligands-for-%C3%AE-1-containing-subtypes
#17
Xenia Simeone, David C B Siebert, Konstantina Bampali, Zdravko Varagic, Marco Treven, Sabah Rehman, Jakob Pyszkowski, Raphael Holzinger, Friederike Steudle, Petra Scholze, Marko D Mihovilovic, Michael Schnürch, Margot Ernst
γ-Aminobutyric acid type A (GABAA) receptors are pentameric GABA-gated chloride channels that are, in mammalians, drawn from a repertoire of 19 different genes, namely α1-6, β1-3, γ1-3, δ, ε, θ, π and ρ1-3. The existence of this wide variety of subunits as well as their diverse assembly into different subunit compositions result in miscellaneous receptor subtypes. In combination with the large number of known and putative allosteric binding sites, this leads to a highly complex pharmacology. Recently, a novel binding site at extracellular α+/β- interfaces was described as the site of modulatory action of several pyrazoloquinolinones...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720874/knowledge-transfer-learning-for-prediction-of-matrix-metalloprotease-substrate-cleavage-sites
#18
Yanan Wang, Jiangning Song, Tatiana T Marquez-Lago, André Leier, Chen Li, Trevor Lithgow, Geoffrey I Webb, Hong-Bin Shen
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720401/multisensory-integration-induces-body-ownership-of-a-handtool-but-not-any-handtool
#19
Veronica Weser, Gianluca Finotti, Marcello Costantini, Dennis R Proffitt
Bodily boundaries are computed by integrating multisensory bodily signals and can be experimentally manipulated using bodily illusions. Research on tool use demonstrates that tools alter body representations motorically to account for changes in a user's action repertoire. The present experiment sought to unify perceptual and motoric accounts of tool embodiment using a modified Rubber Hand Illusion (RHI) that also addressed the skill and practice aspects of the tool use literature. In Experiment 1, synchronous multisensory stimulation induced perceptual embodiment of a tool, chopsticks...
July 16, 2017: Consciousness and Cognition
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#20
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
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