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https://www.readbyqxmd.com/read/29142737/cloning-expression-and-identification-of-ktx-sp4-a-selective-kv1-3-peptidic-blocker-from-scorpiops-pococki
#1
Yan Zou, Feng Zhang, Yaxian Li, Yuanfang Wang, Yi Li, Zhengtao Long, Shujuan Shi, Li Shuai, Jiukai Liu, Zhiyong Di, Shijin Yin
Background: Specific and selective peptidic blockers of Kv1.3 channels can serve as a valuable drug lead for treating T cell-mediated autoimmune diseases, and scorpion venom is an important source of kv1.3 channel inhibitors. Through conducting transcriptomic sequencing for the venom gland of Scorpiops pococki from Xizang province of China, this research aims to discover a novel functional gene encoding peptidic blocker of Kv1.3, and identify its function. Results: We screened out a new peptide toxin KTX-Sp4 which had 43 amino acids including six cysteine residues...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/29141988/genotyping-by-sequencing-in-almond-snp-discovery-linkage-mapping-and-marker-design
#2
Shashi N Goonetilleke, Timothy J March, Michelle G Wirthensohn, Pere Arús, Amanda R Walker, Diane E Mather
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond [Prunus dulcis (Mill.) D.A. Webb], application of a double pseudo-testcross mapping approach to the F1 progeny of a bi-parental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping-by-sequencing to discover and map single-nucleotide polymorphisms in the almond cultivars 'Nonpareil' and 'Lauranne'...
November 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29141951/selector-genes-display-tumor-cooperation-and-inhibition-in-drosophila-epithelium-in-a-developmental-context-dependent-manner
#3
Ram Prakash Gupta, Anjali Bajpai, Pradip Sinha
During animal development, selector genes determine identities of body segments and those of individual organs. Selector genes are also misexpressed in cancers, although their contributions to tumor progression per se remain poorly understood. Using a model of cooperative tumorigenesis, we show that gain of selector genes results in tumor cooperation, but in only select developmental domains of the wing, haltere and eye-antennal imaginal discs of Drosophila larva. Thus, the field selector, Eyeless (Ey), and the segment selector, Ultrabithorax (Ubx), readily cooperate to bring about neoplastic transformation of cells displaying somatic loss of the tumor suppressor, Lgl, but in only those developmental domains that express the homeo-box protein, Homothorax (Hth), and/or the Zinc-finger protein, Teashirt (Tsh)...
November 15, 2017: Biology Open
https://www.readbyqxmd.com/read/29141946/age-related-clonal-hematopoiesis-arch
#4
Liran I Shlush
Age related alterations in the human blood system occur in B cells, T cells, cells of the innate system, as well as in hematopoietic stem and progenitor cells (HSPCs). Interestingly, age related, reduced genetic diversity can be identified both at the stem cell level, but also independently in B cells and T cells. This reduced diversity is most probably related to somatic mutations, or to changes in the micro-environmental niche. Either process can select for specific clones, or cause repeated evolutionary bottlenecks...
November 15, 2017: Blood
https://www.readbyqxmd.com/read/29141193/evolution-of-the-clock-and-bmal1-genes-in-a-subterranean-rodent-species-lasiopodomys-mandarinus
#5
Hong Sun, Yifeng Zhang, Yuhua Shi, Yangwei Li, Wei Li, Zhenlong Wang
Lasiopodomys mandarinus, a subterranean rodent, spends its entire life underground. To test whether the CLOCK and BMAL1 genes of L. mandarinus have undergone adaptive evolution to underground darkness, we cloned and analyzed their complete cDNA sequences, using Lasiopodomys brandtii as a control. The phylogenetic trees of the CLOCK and BMAL1 genes were similar to the trees of the conserved Cyt b gene,further, L. mandarinus clustered with L. brandtii and Microtus ochrogaster in the phylogenetic tree. The Q-rich region of the CLOCK gene in L...
November 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29138983/cloning-expression-analysis-and-enzyme-activity-assays-of-the-%C3%AE-carbonic-anhydrase-gene-from-chlamydomonas-sp-ice-l
#6
Changfeng Qu, Yingying He, Zhou Zheng, Meiling An, Lulu Li, Xixi Wang, Xiaodong He, Yibin Wang, Fangming Liu, Jinlai Miao
The α-carbonic anhydrase (α-CA) is a zinc ion-containing enzyme that catalyzes the hydration of carbon dioxide. In this paper, a full-length α-CA gene was cloned from Chlamydomonas sp. ICE-L using RT-PCR and RACE-PCR for bioinformatic analysis. The α-CA open reading frame obtained by PCR was cloned into a vector and transformed into Escherichia coli to generate α-CA-producing bacteria. The α-CA was highly expressed upon induction with isopropyl-β-d-thiogalactoside (IPTG) at a final concentration of 0...
November 14, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29138903/next-generation-sequencing-to-identify-candidate-genes-and-develop-diagnostic-markers-for-a-novel-phytophthora-resistance-gene-rpshc18-in-soybean
#7
Chao Zhong, Suli Sun, Yinping Li, Canxing Duan, Zhendong Zhu
A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates...
November 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29138790/high-efficiency-single-cell-encapsulation-and-size-selective-capture-of-cells-in-picoliter-droplets-based-on-hydrodynamic-micro-vortices
#8
Gopakumar Kamalakshakurup, Abraham P Lee
Single cell analysis has emerged as a paradigm shift in cell biology to understand the heterogeneity of individual cells in a clone for pathological interrogation. Microfluidic droplet technology is a compelling platform to perform single cell analysis by encapsulating single cells inside picoliter-nanoliter (pL-nL) volume droplets. However, one of the primary challenges for droplet based single cell assays is single cell encapsulation in droplets, currently achieved either randomly, dictated by Poisson statistics, or by hydrodynamic techniques...
November 15, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29138306/key-metabolites-and-mechanistic-changes-for-salt-tolerance-in-an-experimentally-evolved-sulfate-reducing-bacterium-desulfovibrio-vulgaris
#9
Aifen Zhou, Rebecca Lau, Richard Baran, Jincai Ma, Frederick von Netzer, Weiling Shi, Drew Gorman-Lewis, Megan L Kempher, Zhili He, Yujia Qin, Zhou Shi, Grant M Zane, Liyou Wu, Benjamin P Bowen, Trent R Northen, Kristina L Hillesland, David A Stahl, Judy D Wall, Adam P Arkin, Jizhong Zhou
Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29137976/proteomic-analysis-of-cho-cell-lines-producing-high-and-low-quantities-of-a-recombinant-antibody-before-and-after-selection-with-methotrexate
#10
Ruth Hausmann, Ivana Chudobová, Holger Spiegel, Stefan Schillberg
High levels of recombinant protein production in Chinese hamster ovary (CHO) cells can be achieved by amplification of transgenes using the dihydrofolate reductase/methotrexate (DHFR/MTX) system. With the aim to identify predictive markers enabling the preselection of suitable high producing clones we investigated the impact of MTX-based gene amplification on two CHO cells lines producing different levels of a human monoclonal antibody by carrying out a comparative proteome analysis. The difference in antibody yield between the high and low producer was 15-fold before and 245-fold after MTX selection...
November 11, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29136164/habitat-heterogeneity-host-population-structure-and-parasite-local-adaptation
#11
Curtis M Lively
Reciprocal-transplant experiments have proven to be a powerful tool for detecting local adaptation (LA). More recently, reciprocal cross-inoculation experiments have been used to evaluate adaptation by parasites to their local host populations. These experiments are conceptually similar to reciprocal-transplant experiments, except that the "environment" (the host population) may have evolved in response to changes in the parasite population. Here, I use analytical tools and computer simulations to determine when parasites would be expected to be more infective to their local host populations than to allopatric host populations...
November 9, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29133816/disruption-of-diphthamide-synthesis-genes-and-resulting-toxin-resistance-as-a-robust-technology-for-quantifying-and-optimizing-crispr-cas9-mediated-gene-editing
#12
Tobias Killian, Steffen Dickopf, Alexander K Haas, Claudia Kirstenpfad, Klaus Mayer, Ulrich Brinkmann
We have devised an effective and robust method for the characterization of gene-editing events. The efficacy of editing-mediated mono- and bi-allelic gene inactivation and integration events is quantified based on colony counts. The combination of diphtheria toxin (DT) and puromycin (PM) selection enables analyses of 10,000-100,000 individual cells, assessing hundreds of clones with inactivated genes per experiment. Mono- and bi-allelic gene inactivation is differentiated by DT resistance, which occurs only upon bi-allelic inactivation...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133557/a-novel-mechanism-of-inactivating-antibacterial-nitro-compounds-in-the-human-pathogen-staphylococcus-aureus-by-overexpression-of-a-nadh-dependent-flavin-nitroreductase
#13
Ebaa M El-Hossary, Konrad U Förstner, Patrice François, Damien Baud, Karin Streker, Jacques Schrenzel, Knut Ohlsen, Ulrike Holzgrabe
Recently, the nitro substituted bisquaternary bisnaphthalimides were reported to have substantial anti-infective activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Here, we selected resistant S. aureus clones by cultivation in increasing concentrations of the most active compound MT02. Interestingly, MT02 resistant variants induced a diffusible red color of the broth. Chromatographic and spectroscopic investigations revealed a stepwise reduction of the bisquaternary bisnaphthalimides̀ nitro groups to amino groups...
November 13, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29132331/adaptation-of-the-goldenbraid-modular-cloning-system-and-creation-of-a-toolkit-for-the-expression-of-heterologous-proteins-in-yeast-mitochondria
#14
Ana Pérez-González, Ryan Kniewel, Marcel Veldhuizen, Hemant K Verma, Mónica Navarro-Rodríguez, Luis M Rubio, Elena Caro
BACKGROUND: There is a need for the development of synthetic biology methods and tools to facilitate rapid and efficient engineering of yeast that accommodates the needs of specific biotechnology projects. In particular, the manipulation of the mitochondrial proteome has interesting potential applications due to its compartmentalized nature. One of these advantages resides in the fact that metalation occurs after protein import into mitochondria, which contains pools of iron, zinc, copper and manganese ions that can be utilized in recombinant metalloprotein metalation reactions...
November 13, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/29132146/identification-of-unique-neoantigen-qualities-in-long-term-survivors-of-pancreatic-cancer
#15
Vinod P Balachandran, Marta Łuksza, Julia N Zhao, Vladimir Makarov, John Alec Moral, Romain Remark, Brian Herbst, Gokce Askan, Umesh Bhanot, Yasin Senbabaoglu, Daniel K Wells, Charles Ian Ormsby Cary, Olivera Grbovic-Huezo, Marc Attiyeh, Benjamin Medina, Jennifer Zhang, Jennifer Loo, Joseph Saglimbeni, Mohsen Abu-Akeel, Roberta Zappasodi, Nadeem Riaz, Martin Smoragiewicz, Z Larkin Kelley, Olca Basturk, Mithat Gönen, Arnold J Levine, Peter J Allen, Douglas T Fearon, Miriam Merad, Sacha Gnjatic, Christine A Iacobuzio-Donahue, Jedd D Wolchok, Ronald P DeMatteo, Timothy A Chan, Benjamin D Greenbaum, Taha Merghoub, Steven D Leach
Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8(+) T-cell infiltrates, but neither alone, stratified patients with the longest survival...
November 8, 2017: Nature
https://www.readbyqxmd.com/read/29132030/capture-and-detection-of-staphylococcus-aureus-with-dual-labeled-aptamers-to-cell-surface-components
#16
Shylaja Ramlal, Bhairab Mondal, Padma Sudharani Lavu, Bhavanashri N, Joseph Kingston
In the present study, a high throughput whole cell SELEX method has been applied successfully in selecting specific aptamers against whole cells of Staphylococcus aureus, a potent food poisoning bacterium. A total ten rounds of SELEX and three rounds of intermittent counter SELEX, was performed to obtain specific aptamers. Obtained oligonucleotide pool were cloned, sequenced and then grouped into different families based on their primary sequence homology and secondary structure similarity. FITC labeled sequences from different families were selected for further characterization via flow cytometry analysis...
November 7, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29127500/distinct-communities-of-poplar-endophytes-on-an-unpolluted-and-a-risk-element-polluted-site-and-their-plant-growth-promoting-potential-in-vitro
#17
C S Schmidt, P Lovecká, L Mrnka, A Vychodilová, M Strejček, M Fenclová, K Demnerová
Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts' fitness both in nutrient-limited and polluted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests...
November 10, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/29127429/a-high-density-consensus-linkage-map-of-white-lupin-highlights-synteny-with-narrow-leafed-lupin-and-provides-markers-tagging-key-agronomic-traits
#18
Michał Książkiewicz, Nelson Nazzicari, Hua'an Yang, Matthew N Nelson, Daniel Renshaw, Sandra Rychel, Barbara Ferrari, Maria Carelli, Magdalena Tomaszewska, Stanisław Stawiński, Barbara Naganowska, Bogdan Wolko, Paolo Annicchiarico
White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29118748/remarkable-diversity-of-escherichia-coli-carrying-mcr-1-from-hospital-sewage-with-the-identification-of-two-new-mcr-1-variants
#19
Feifei Zhao, Yu Feng, Xiaoju Lü, Alan McNally, Zhiyong Zong
The plasmid-borne colistin-resistant gene mcr-1 has rapidly become a worldwide public health concern. This study aims to determine the host bacterial strains, plasmids, and genetic contexts of mcr-1 in hospital sewage. A 1-ml hospital sewage sample was cultured. Colistin-resistant bacterial colonies were selected on agar plates and were subjected to whole genome sequencing and subsequent analysis. The transfer of mcr-1 between bacterial strains was tested using conjugation. New variants of mcr-1 were cloned to test the impact of variations on the function of mcr-1...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29116523/orfeome-phage-display
#20
Jonas Zantow, Gustavo Marçal Schmidt Garcia Moreira, Stefan Dübel, Michael Hust
ORFeome phage display allows the efficient functional screening of entire proteomes or even metaproteomes to identify immunogenic proteins. For this purpose, randomly fragmented, whole genomes or metagenomes are cloned into a phage-display vector allowing positive selection for open reading frames (ORF) to improve the library quality. These libraries display all possible proteins encoded by a pathogen or a microbiome on the phage surface. Consequently, immunogenic proteins can be selected from these libraries using disease-related immunoglobulins from patient serum...
2018: Methods in Molecular Biology
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