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https://www.readbyqxmd.com/read/28922909/evidence-of-correlation-between-tgfbr2-gene-expression-mediated-by-nf-kb-signaling-pathways-and-kawasaki-disease-in-children
#1
Qinling Gao, Shuhua Yuan, Dawei Yuan
BACKGROUND: We explored the correlation between the TGFBR2 gene that is mediated by NF-kb signaling pathways and the pathogenesis of Kawasaki disease in children. METHODS: In this study, 43 children with Kawasaki disease from April 2014 to January 2016 at our hospital were selected as the observation group, and 42 healthy children were selected as the control group. The mRNA expression levels of NF-kb gene and TGFBR2 gene in different groups were detected using fluorescence quantitative PCR...
September 15, 2017: Minerva Pediatrica
https://www.readbyqxmd.com/read/28922872/ancient-occasional-host-switching-of-maternally-transmitted-bacterial-symbionts-of-chemosynthetic-vesicomyid-clams
#2
Genki Ozawa, Shigeru Shimamura, Yoshihiro Takaki, Kiyotaka Takishita, Tetsuro Ikuta, James P Barry, Tadashi Maruyama, Katsunori Fujikura, Takao Yoshida
Vesicomyid clams in deep-sea chemosynthetic ecosystems harbor sulfur-oxidizing bacteria in their gill epithelial cells. These symbionts, which are vertically transmitted, are species-specific and thought to have cospeciated with their hosts. However, recent studies indicate incongruent phylogenies between some vesicomyid clams and their symbionts, suggesting that symbionts are horizontally transmitted. To more precisely understand the evolution of vesicomyid clams and their symbionts, we compared the evolution of vesicomyid clams and their symbionts through phylogenetic analyses using multi-gene data sets...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922871/divergence-of-the-venom-exogene-repertoire-in-two-sister-species-of-turriconus
#3
Qing Li, Neda Barghi, Aiping Lu, Alexander E Fedosov, Pradip K Bandyopadhyay, Arturo O Lluisma, Gisela P Concepcion, Mark Yandell, Baldomero M Olivera, Helena Safavi-Hemami
The genus Conus comprises approximately 700 species of venomous marine cone snails that are highly efficient predators of worms, snails, and fish. In evolutionary terms, cone snails are relatively young with the earliest fossil records occurring in the Lower Eocene, 55 Ma. The rapid radiation of cone snail species has been accompanied by remarkably high rates of toxin diversification. To shed light on the molecular mechanisms that accompany speciation, we investigated the toxin repertoire of two sister species, Conus andremenezi and Conus praecellens, that were until recently considered a single variable species...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922870/male-mutation-bias-is-the-main-force-shaping-chromosomal-substitution-rates-in-monotreme-mammals
#4
Vivian Link, Diana Aguilar-Gómez, Ciro Ramírez-Suástegui, Laurence D Hurst, Diego Cortez
In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922869/genome-organization-of-sphingobium-indicum-b90a-an-archetypal-hexachlorocyclohexane-hch-degrading-genotype
#5
Helianthous Verma, Abhay Bajaj, Roshan Kumar, Jasvinder Kaur, Shailly Anand, Namita Nayyar, Akshita Puri, Yogendra Singh, Jitendra P Khurana, Rup Lal
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922848/aggressive-behavior-in-silent-subtype-iii-pituitary-adenomas-may-depend-on-suppression-of-local-immune-response-a-whole-transcriptome-analysis
#6
Timothy E Richardson, Zhong-Jian Shen, Mohammed Kanchwala, Chao Xing, Alexander Filatenkov, Ping Shang, Samuel Barnett, Zahidur Abedin, James S Malter, Jack M Raisanen, Dennis K Burns, Charles L White, Kimmo J Hatanpaa
Silent subtype III pituitary adenomas (SS-3) are clinically nonfunctional adenomas that are more aggressive in terms of invasion and risk of recurrence than their conventional null cell counterparts. We previously showed that these tumors can be distinguished by immunohistochemistry based on the identification of a markedly enlarged and fragmented Golgi apparatus. To understand the molecular correlates of differential aggressiveness, we performed whole transcriptome sequencing (RNAseq) on 4 SS-3 and 4 conventional null cell adenomas...
October 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28922847/germline-msh6-mutation-in-a-patient-with-two-independent-primary-glioblastomas
#7
Linda M Forsström, Koichiro Sumi, Markus J Mäkinen, Ji Eun Oh, Riitta Herva, Paul Kleihues, Hiroko Ohgaki, Lauri A Aaltonen
We previously reported a patient who had developed 2 glioblastomas at the age of 54 and 64 years, respectively. The first glioblastoma in the right frontal lobe was treated with surgery and radiotherapy. Ten years later, the patient developed a second, left frontal glioblastoma. Discordant patterns of TP53 and PTEN mutations suggested that the second tumor was not a recurrence but an independently developed glioblastoma. To determine the molecular mechanism underlying this enigmatic case with 10-year survival, we performed whole-exome sequencing...
October 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28922845/pot1-mediated-%C3%AE-integration-strategy-for-high-copy-stable-expression-of-heterologous-proteins-in-saccharomyces-cerevisiae
#8
Xiaofei Song, Quanli Liu, Jiwei Mao, Yuzhen Wu, Yuanzi Li, Kai Gao, Xiuming Zhang, Yanling Bai, Haijin Xu, Mingqiang Qiao
In biotechnological industry, increased expression cassette stability and copy number serve as important means of maintaining consistently high production levels of heterologous proteins in Saccharomyces cerevisiae. In this study, we combined δ sequences for site-specific integration with TPI1 gene from Schizosaccharomyces pombe (POT1) as a selection marker to realize high-copy integration and stable expression of heterologous proteins in S. cerevisiae. With the newly developed POT1 platform, a 32-copy integration of enhanced green fluorescent protein (EGFP) expression cassette was obtained in a single round and was stably maintained after 100 generations of growth in a rich complex medium...
September 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28922844/characterization-of-inulinase-promoter-from-kluyveromyces-marxianus-for-intensive-protein-expression-in-industrial-biotechnology
#9
Jiaoqi Gao, Wenjie Yuan, Yimin Li, Fengwu Bai, Yu Jiang
Inulinase from Kluyveromyces marxianus (KmINU1) has wide application in industrial biotechnology, and it is supposed that its expression is regulated at the transcriptional level via the promoter. Therefore, in this study, the KmINU1 promoter, fused to the reporter EGFP gene, was analyzed to determine its fundamental regulatory mechanisms in Saccharomyces cerevisiae S288C (ATCC 204508). Induction by inulin and repression by high glucose concentrations of KmINU1 promoters are reported, and the promoter with a length of 353 bp was shown to have the highest strength with the weakest responses to high glucose concentration...
September 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28922840/quantification-of-agrobacterium-tumefaciens-c58-attachment-to-arabidopsis-thaliana-roots
#10
Anna Petrovicheva, Jessica Joyner, Theodore R Muth
Agrobacterium tumefaciens is the causal agent of crown gall disease and is a vector for DNA transfer in transgenic plants. The transformation process by A. tumefaciens has been widely studied, but the attachment stage has not been well characterized. Most measurements of attachment have used microscopy and colony counting, both of which are labor and time intensive. To reduce the time and effort required to analyze bacteria attaching to plant tissues, we developed a quantitative real-time PCR (qPCR) assay to quantify attached A...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28922839/first-description-of-a-new-uncultured-epsilon-sulfur-bacterium-colonizing-marine-mangrove-sediment-in-the-caribbean-thiovulum-sp-strain-karukerense
#11
Olivier Gros
Here, the first description is reported of an epsilon sulfur-oxidizing bacterium from sulfide-rich sediments of marine mangrove in the Caribbean. By transition electron microscopy it was shown that this new strain contains intracytoplasmic large internal sulfur granules, which was confirmed by energy-dispersive X-ray spectroscopy analyses performed using an environmental scanning electron microscope. The sulfur distribution obtained for this sulfur-oxidizing bacterial strain allowed us to conclude that elemental sulfur is formed as an intermediate oxidation product and stored intracellularly...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#12
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28922833/the-knockout-of-synapsin-ii-in-mice-impairs-social-behavior-and-functional-connectivity-generating-an-asd-like-phenotype
#13
Caterina Michetti, Angela Caruso, Marco Pagani, Mara Sabbioni, Lucian Medrihan, Gergely David, Alberto Galbusera, Monica Morini, Alessandro Gozzi, Fabio Benfenati, Maria Luisa Scattoni
Autism spectrum disorders (ASD) and epilepsy are neurodevelopmental conditions that appear with high rate of co-occurrence, suggesting the possibility of a common genetic basis. Mutations in Synapsin (SYN) genes, particularly SYN1 and SYN2, have been recently associated with ASD and epilepsy in humans. Accordingly, mice lacking Syn1 or Syn2, but not Syn3, experience epileptic seizures and display autistic-like traits that precede the onset of seizures. Here, we analyzed social behavior and ultrasonic vocalizations emitted in 2 social contexts by SynI, SynII, or SynIII mutants and show that SynII mutants display the most severe ASD-like phenotype...
October 1, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28922823/de-novo-genome-assembly-of-camptotheca-acuminata-a-natural-source-of-the-anti-cancer-compound-camptothecin
#14
Dongyan Zhao, John P Hamilton, Gina M Pham, Emily Crisovan, Krystle Wiegert-Rininger, Brieanne Vaillancourt, Dean DellaPenna, C Robin Buell
Camptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28922804/hunting-for-agile-prey-trophic-specialisation-in-leptophryid-amoebae-vampyrellida-rhizaria-revealed-by-two-novel-predators-of-planktonic-algae
#15
Sebastian Hess
Vampyrellid amoebae (Vampyrellida, Rhizaria) are widespread in freshwater, marine and terrestrial ecosystems and consume a wide range of eukaryotes, e.g. algae, fungi and micrometazoa. Environmental sequences indicate that only a small fraction of their genetic diversity is phenotypically characterised, emphasising the need to further explore unknown vampyrellids and their interactions with prey organisms. This study tests the prey range specificity of three vampyrellid amoebae with 49 strains of three common groups of freshwater algae (Zygnematophyceae, Euglenophyceae and Volvocales), and documents specific interactions by time-lapse microscopy...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28922802/succession-of-arbuscular-mycorrhizal-fungi-along-a-52-year-agricultural-recultivation-chronosequence
#16
Julien Roy, Rüdiger Reichel, Nicolas Brüggemann, Stefan Hempel, Matthias C Rillig
Arbuscular mycorrhizal (AM) fungi provide a range of functions in natural and managed ecosystems. However, the trajectory of AM fungal diversity after land degradation is poorly known. We studied the succession of AM fungi along an agricultural recultivation chronosequence after open-cast mining near Cologne, Germany. We used high-throughput sequencing of the large-subunit ribosomal RNA genes to characterize the soil AM fungal communities of 10 agricultural fields spanning 52 years of recultivation. During three years, soils are recultivated with a legume, and then converted to agriculture to be later returned to local farmers implementing conventional agriculture...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28922801/effect-of-severe-weather-events-on-the-shedding-of-shiga-toxigenic-escherichia-coli-in-slaughter-cattle-and-phenotype-of-serogroup-o157-isolates
#17
Kim Stanford, Tim Reuter, Susan J Bach, Linda Chui, Angela Ma, Cheyenne C Conrad, Renata Tostes, Tim A McAllister
High-event periods (HEPs) occur sporadically when beef carcasses and meat have episodes of acute contamination with Shiga toxin-producing Escherichia coli (STEC). In this study, severe weather events were investigated as catalysts for HEPs based on PCR and isolate prevalence of seven E. coli serogroups in slaughter cattle feces. Winter ambient temperatures with daily means 10.5oC warmer or 12.3°C colder than seasonal norms (-10.4°C) most altered STEC shedding. Fecal samples yielded increased proportions (P < 0...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28922794/genome-wide-variation-patterns-uncover-the-origin-and-selection-in-cultivated-ginseng-panax-ginseng-meyer
#18
Ming-Rui Li, Feng-Xue Shi, Ya-Ling Li, Peng Jiang, Lili Jiao, Bao Liu, Lin-Feng Li
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922793/diurnal-cycling-transcription-factors-of-pineapple-revealed-by-genome-wide-annotation-and-global-transcriptomic-analysis
#19
Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Circadian clock provides fitness advantage by coordinating internal metabolic and physiological processes to external cyclic environments. Core clock components exhibit daily rhythmic changes in gene expression, and the majority of them are transcription factors (TFs) and transcription coregulators (TCs). We annotated 1,398 TFs from 67 TF families and 80 TCs from 20 TC families in pineapple, and analyzed their tissue-specific and diurnal expression patterns. Approximately 42% of TFs and 45% of TCs displayed diel rhythmic expression, including 177 TF/TCs cycling only in the nonphotosynthetic leaf tissue, 247 cycling only in the photosynthetic leaf tissue, and 201 cycling in both...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922790/the-balance-between-cytotoxic-t-cell-lymphocytes-and-immune-checkpoint-expression-in-the-prognosis-of-colon-tumors
#20
Laetitia Marisa, Magali Svrcek, Ada Collura, Etienne Becht, Pascale Cervera, Kristell Wanherdrick, Olivier Buhard, Anastasia Goloudina, Vincent Jonchère, Janick Selves, Gerard Milano, Dominique Guenot, Romain Cohen, Chrystelle Colas, Pierre Laurent-Puig, Sylviane Olschwang, Jérémie H Lefèvre, Yann Parc, Valérie Boige, Côme Lepage, Thierry André, Jean-François Fléjou, Valentin Dérangère, François Ghiringhelli, Aurélien de Reynies, Alex Duval
Background: Immune checkpoint (ICK) expression might represent a surrogate measure of tumor-infiltrating T cell (CTL) exhaustion and therefore be a more accurate prognostic biomarker for colorectal cancer (CRC) patients than CTL enumeration as measured by the Immunoscore. Methods: The expression of ICKs, Th1, CTLs, cytotoxicity-related genes, and metagenes, including Immunoscore-like metagenes, were evaluated in three independent cohorts of CRC samples (260 microsatellite instable [MSI], 971 non-MSI)...
January 1, 2018: Journal of the National Cancer Institute
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