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https://www.readbyqxmd.com/read/29792377/comparative-analysis-of-probiotic-bacteria-based-on-a-new-definition-of-core-genome
#1
Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes...
March 26, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29790275/suppressor-of-clathrin-deficiency-scd6-an-emerging-rgg-motif-translation-repressor
#2
REVIEW
Debadrita Roy, Purusharth I Rajyaguru
Translation control plays a key role in variety of cellular processes. Translation initiation factors augment translation, whereas translation repressor proteins inhibit translation. Different repressors act by distinct mechanisms to accomplish the repression process. Although messenger RNAs (mRNAs) can be repressed at various steps of translation, most repressors have been reported to target the initiation step. We focus on one such translation repressor, an Arginine-Glycine-Glycine (RGG)-motif containing protein Scd6...
May 22, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29789962/genome-based-identification-and-analysis-of-ionotropic-receptors-in-spodoptera-litura
#3
Jia-Ying Zhu, Zhi-Wen Xu, Xin-Min Zhang, Nai-Yong Liu
The ability to sense and recognize various classes of compounds is of particular importance for survival and reproduction of insects. Ionotropic receptor (IR), a sub-family of the ionotropic glutamate receptor family, has been identified as one of crucial chemoreceptor super-families, which mediates the sensing of odors and/or tastants, and serves as non-chemosensory functions. Yet, little is known about IR characteristics, evolution, and functions in Lepidoptera. Here, we identify the IR gene repertoire from a destructive polyphagous pest, Spodoptera litura...
May 22, 2018: Die Naturwissenschaften
https://www.readbyqxmd.com/read/29789638/human-carbonic-anhydrase-8-aav8-gene-therapy-inhibits-nerve-growth-factor-signaling-producing-prolonged-analgesia-and-anti-hyperalgesia-in-mice
#4
Gerald Z Zhuang, Udita Upadhyay, Xiaoying Tong, Yuan Kang, Diana M Erasso, Eugene S Fu, Konstantinos D Sarantopoulos, Eden R Martin, Tim Wiltshire, Luda Diatchenko, Shad B Smith, William Maixner, Roy C Levitt
Carbonic anhydrase-8 (Car8; murine gene symbol) is an allosteric inhibitor of inositol trisphosphate receptor-1 (ITPR1), which regulates neuronal intracellular calcium release. We previously reported that wild-type Car8 overexpression corrects the baseline allodynia and hyperalgesia associated with calcium dysregulation in the waddle (wdl) mouse due to a 19 bp deletion in exon 8 of the Car8 gene. In this report, we provide preliminary evidence that overexpression of the human wild-type ortholog of Car8 (CA8 WT ), but not the reported CA8 S100P loss-of-function mutation (CA8 MT ), inhibits nerve growth factor (NGF)-induced phosphorylation of ITPR1, TrkA (NGF high-affinity receptor), and ITPR1-mediated cytoplasmic free calcium release in vitro...
April 24, 2018: Gene Therapy
https://www.readbyqxmd.com/read/29789451/zebrafish-models-of-rare-hereditary-pediatric-diseases
#5
REVIEW
Máté Varga, Dorottya Ralbovszki, Eszter Balogh, Renáta Hamar, Magdolna Keszthelyi, Kálmán Tory
Recent advances in sequencing technologies have made it significantly easier to find the genetic roots of rare hereditary pediatric diseases. These novel methods are not panaceas, however, and they often give ambiguous results, highlighting multiple possible causative mutations in affected patients. Furthermore, even when the mapping results are unambiguous, the affected gene might be of unknown function. In these cases, understanding how a particular genotype can result in a phenotype also needs carefully designed experimental work...
May 22, 2018: Diseases (Basel)
https://www.readbyqxmd.com/read/29785177/characterization-of-new-microsatellite-markers-based-on-the-transcriptome-sequencing-of-clematis-finetiana
#6
Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye, Yongbao Shen
Background: Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the "Queen of the Vines". However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C...
2018: Hereditas
https://www.readbyqxmd.com/read/29784083/a-homozygous-loss-of-function-camk2a-mutation-causes-growth-delay-frequent-seizures-and-severe-intellectual-disability
#7
Poh Hui Chia, Franklin Lei Zhong, Shinsuke Niwa, Carine Bonnard, Kagistia Hana Utami, Ruizhu Zeng, Hane Lee, Ascia Eskin, Stanley F Nelson, William H Xie, Samah Al-Tawalbeh, Mohammad El-Khateeb, Mohammad Shboul, Mahmoud A Pouladi, Mohammed Al-Raqad, Bruno Reversade
Calcium/calmodulin-dependent protein kinase II (CAMK2) plays fundamental roles in synaptic plasticity that underlies learning and memory. Here, we describe a new recessive neurodevelopmental syndrome with global developmental delay, seizures and intellectual disability. Using linkage analysis and exome sequencing, we found that this disease maps to chromosome 5q31.1-q34 and is caused by a biallelic germline mutation in CAMK2A . The missense mutation, p.His477Tyr is located in the CAMK2A association domain that is critical for its function and localization...
May 22, 2018: ELife
https://www.readbyqxmd.com/read/29783865/flow-cytometry-based-epitope-binning-using-competitive-binding-profiles-for-the-characterization-of-monoclonal-antibodies-against-cellular-and-soluble-protein-targets
#8
Brian M Chan, Anita Badh, Kelly A Berry, Stephanie A Grauer, Chadwick T King
A key step in the therapeutic antibody drug discovery process is early identification of diverse candidate molecules. Information comparing antibody binding epitopes can be used to classify antibodies within a large panel, guiding rational lead molecule selection. We describe a novel epitope binning method utilizing high-throughput flow cytometry (HTFC) that leverages cellular barcoding or spectrally distinct beads to multiplex samples to characterize antibodies raised against cell membrane receptor or soluble protein targets...
May 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29779879/the-xmap215-ortholog-alp14-promotes-microtubule-nucleation-in-fission-yeast
#9
Ignacio Flor-Parra, Ana Belén Iglesias-Romero, Fred Chang
The organization and number of microtubules (MTs) in a cell depend on the proper regulation of MT nucleation. Currently, the mechanism of nucleation is the most poorly understood aspect of MT dynamics. XMAP215/chTOG/Alp14/Stu2 proteins are MT polymerases that stimulate MT polymerization at MT plus ends by binding and releasing tubulin dimers. Although these proteins also localize to MT organizing centers and have nucleating activity in vitro, it is not yet clear whether these proteins participate in MT nucleation in vivo...
May 10, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29778216/nitric-oxide-signalling-in-yeast
#10
Rika I Astuti, Ryo Nasuno, Hiroshi Takagi
Nitric oxide (NO) is a cellular signalling molecule widely conserved among organisms, including microorganisms such as bacteria, yeasts, and fungi, and higher eukaryotes such as plants and mammals. NO is mainly produced by the activities of NO synthase (NOS) or nitrite reductase (NIR). There are several NO detoxification systems, including NO dioxygenase (NOD) and S-nitrosoglutathione reductase (GSNOR). NO homeostasis, based on the balance between NO synthesis and degradation, is important for regulating its physiological functions, since an excess of NO causes nitrosative stress due to the high reactivity of NO and NO-derived compounds...
2018: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/29776340/the-developmental-transcriptomes-of-two-sea-biscuit-species-with-differing-larval-types
#11
Anne Frances Armstrong, Richard K Grosberg
BACKGROUND: Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776332/telnet-a-database-for-human-and-yeast-genes-involved-in-telomere-maintenance
#12
Delia M Braun, Inn Chung, Nick Kepper, Katharina I Deeg, Karsten Rippe
BACKGROUND: The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood...
May 18, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29775862/identification-and-functional-characterization-of-a-max2-ortholog-from-switchgrass-panicum-virgatum-l
#13
Tingting Cheng, Donghua Wang, Yongfeng Wang, Shumeng Zhang, Chao Zhang, Shudong Liu, Yajun Xi, Fengli Sun
Switchgrass (Panicum virgatum L.) is a sustainable cellulosic energy crop with high biomass yield on marginal soils. Tillering, an important agronomic characteristic related to biomass production in gramineous plants, is regulated by complex interacting factors, such as plant hormones. Strigolactones (SLs) comprise a novel class of plant hormones that inhibit shoot branching. The MORE AXILLARY GROWTH2 (MAX2)/DWARF 3 (D3)/RAMOSUS (RMS4) genes encode proteins involved in the SL signaling pathway in various plants...
May 15, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29774234/the-fission-yeast-stn1-ten1-complex-limits-telomerase-activity-via-its-sumo-interacting-motif-and-promotes-telomeres-replication
#14
Samah Matmati, Mélina Vaurs, José M Escandell, Laetitia Maestroni, Toru M Nakamura, Miguel G Ferreira, Vincent Géli, Stéphane Coulon
Mammalian CST (CTC1-STN1-TEN1) complex fulfills numerous functions including rescue of the stalled replication forks and termination of telomerase action. In fission yeast lacking the CTC1 ortholog, the Stn1-Ten1 complex restricts telomerase action via its sumoylation-mediated interaction with Tpz1TPP1 . We identify a small ubiquitin-like modifier (SUMO)-interacting motif (SIM) in the carboxyl-terminal part of Stn1 and show that this domain is crucial for SUMO and Tpz1-SUMO interactions. Point mutations in the SIM (Stn1-226) lead to telomere elongation, impair Stn1-Ten1 recruitment to telomeres, and enhance telomerase binding, revealing that Stn1 SIM domain contributes to the inhibition of telomerase activity at chromosome ends...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29772240/identification-and-characterization-of-the-zinc-finger-protein-sjzf-in-schistosoma-japonicum
#15
Ruixiang Zhang, Jian Li, Manyu Xiang, Qinghua Hong, Bin Xu, Wei Hu
Schistosomiasis represents one of the most prevalent parasitic infections affecting over 249 million people worldwide. The pathological damage is mainly caused by the eggs laid by female schistosomes. Zinc finger proteins (ZFPs) usually play critical roles in many biological functions. In this study, we cloned, identified and characterized the zinc finger protein SjZF of Schistosoma japonicum. SjZF ortholog proteins were also identified in S. mansoni, S. haematobium, Opisthorchis viverrini and O. sinensis. Fluorescence localization showed that SjZF was particularly expressed in the worm gut of both genders and the vitelline glands of females...
May 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29770349/single-step-precision-genome-editing-in-yeast-using-crispr-cas9
#16
Azat Akhmetov, Jon M Laurent, Jimmy Gollihar, Elizabeth C Gardner, Riddhiman K Garge, Andrew D Ellington, Aashiq H Kachroo, Edward M Marcotte
Genome modification in budding yeast has been extremely successful largely due to its highly efficient homology-directed DNA repair machinery. Several methods for modifying the yeast genome have previously been described, many of them involving at least two-steps: insertion of a selectable marker and substitution of that marker for the intended modification. Here, we describe a CRISPR-Cas9 mediated genome editing protocol for modifying any yeast gene of interest (either essential or nonessential) in a single-step transformation without any selectable marker...
March 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29769315/characterization-of-additional-components-of-the-environmental-ph-sensing-complex-in-the-pathogenic-fungus-cryptococcus-neoformans
#17
Kaila M Pianalto, Kyla S Ost, Hannah E Brown, J Andrew Alspaugh
Pathogenic microorganisms must adapt to changes in their immediate surroundings, including alterations in pH, to survive the shift from the external environment to that of the infected host. In the basidiomycete fungal pathogen Cryptococcus neoformans , these pH changes are primarily sensed by the fungal-specific, alkaline pH-sensing Rim/Pal pathway. The C. neoformans Rim pathway has diverged significantly from that described in ascomycete fungi. We recently identified the C. neoformans putative pH sensor Rra1, which activates the Rim pathway in response to elevated pH...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29769272/original-ligand-for-lt%C3%AE-r-is-light-insight-into-evolution-of-the-lt-lt%C3%AE-r-system
#18
Tomoki Maeda, Hiroaki Suetake, Tomoyuki Odaka, Toshiaki Miyadai
The lymphotoxin (LT)/LTβ receptor (LTβR) axis is crucial for the regulation of immune responses and development of lymphoid tissues in mammals. Despite the importance of this pathway, the existence and function of LT and LTβR remain obscure for nonmammalian species. In this study, we report a nonmammalian LTβR and its ligand. We demonstrate that TNF-New (TNFN), which has been considered orthologous to mammalian LT, was expressed on the cell surface as a homomer in vitro. This different protein structure indicates that TNFN is not orthologous to mammalian LTα and LTβ...
May 16, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29769048/functional-insights-from-proteome-wide-structural-modeling-of-treponema-pallidum-subspecies-pallidum-the-causative-agent-of-syphilis
#19
Simon Houston, Karen Vivien Lithgow, Kara Krista Osbak, Chris Richard Kenyon, Caroline E Cameron
BACKGROUND: Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens...
May 16, 2018: BMC Structural Biology
https://www.readbyqxmd.com/read/29765069/de-novo-characterization-of-phenacoccus-solenopsis-transcriptome-and-analysis-of-gene-expression-profiling-during-development-and-hormone-biosynthesis
#20
Surjeet Kumar Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages...
May 15, 2018: Scientific Reports
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