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https://www.readbyqxmd.com/read/29782536/fungal-type-carbohydrate-binding-modules-from-the-coccolithophore-emiliania-huxleyi-show-binding-affinity-to-cellulose-and-chitin
#1
Bart J M Rooijakkers, Martina S Ikonen, Markus B Linder
Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders...
2018: PloS One
https://www.readbyqxmd.com/read/29782003/collection-and-extraction-of-occupational-air-samples-for-analysis-of-fungal-dna
#2
Angela R Lemons, William G Lindsley, Brett J Green
Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several limitations that have resulted in the exclusion of many species. Advances in the field over the last two decades have led occupational health researchers to turn to molecular-based approaches for identifying fungal hazards. These methods have resulted in the detection of many species within indoor and occupational environments that have not been detected using traditional methods...
May 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781226/identification-of-an-hla-b-27-variant-b-27-120-by-sequence-based-typing-in-a-taiwanese-bone-marrow-stem-cell-donor
#3
K L Yang, P Y Lin
One nucleotide substitution at residue 577 of HLA-B*27:04:01 results in a novel allele, HLA-B*27:120. This article is protected by copyright. All rights reserved.
May 20, 2018: HLA
https://www.readbyqxmd.com/read/29780368/-salmonella-enterica-prophage-sequence-profiles-reflect-genome-diversity-and-can-be-used-for-high-discrimination-subtyping
#4
Walid Mottawea, Marc-Olivier Duceppe, Andrée A Dupras, Valentine Usongo, Julie Jeukens, Luca Freschi, Jean-Guillaume Emond-Rheault, Jeremie Hamel, Irena Kukavica-Ibrulj, Brian Boyle, Alexander Gill, Elton Burnett, Eelco Franz, Gitanjali Arya, Joel T Weadge, Samantha Gruenheid, Martin Wiedmann, Hongsheng Huang, France Daigle, Sylvain Moineau, Sadjia Bekal, Roger C Levesque, Lawrence D Goodridge, Dele Ogunremi
Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29780363/microbial-community-analyses-of-the-deteriorated-storeroom-objects-in-the-tianjin-museum-using-culture-independent-and-culture-dependent-approaches
#5
Zijun Liu, Yanhong Zhang, Fengyu Zhang, Cuiting Hu, Genliang Liu, Jiao Pan
In the storeroom C7 of the Tianjin Museum, one wooden desk and two leather luggages dated back to Qing dynasty (1644-1912 AD) presented viable microbial contamination. The aim of the present study was to investigate microbial communities responsible for the biodeterioration of storeroom objects using a combination of culture-independent and culture-dependent methods as well microscopic techniques. Scanning electron microscopy (SEM) revealed that the microflora on three storeroom objects were characterized by a marked presence of Eurotium halophilicum ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29779663/identification-of-enzymes-involved-in-sesterterpene-biosynthesis-in-marine-fungi
#6
Jingjing Yan, Jingjing Guo, Wei Yuan, Wanying Mai, Kui Hong
Diverse and bioactive terpene compounds are produced by marine fungi. The biosynthesis of sesterterpene molecules containing a C25 skeleton is catalyzed by chimeric enzymes that carry out both chain elongation and terpene cyclization reactions. These bifunctional characteristics facilitate using different chain length polyisoprenoid diphosphates as precursors to yield the geranylfarnesyl diphosphate intermediate, which is then converted to a sesterterpene in one step. In this chapter, we describe the identification of sesterterpene synthase enzymes, together with other related enzymes such as diterpene and farnesyl diphosphate synthases, in a single fungal strain...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29779136/genetic-mutation-analysis-of-the-malignant-transformation-of-sinonasal-inverted-papilloma-by-targeted-amplicon-sequencing
#7
Shinichiro Yasukawa, Satoshi Kano, Hiromitsu Hatakeyama, Yuji Nakamaru, Dai Takagi, Takatsugu Mizumachi, Masanobu Suzuki, Takayoshi Suzuki, Akira Nakazono, Shinya Tanaka, Hiroshi Nishihara, Akihiro Homma
BACKGROUND: The mechanism underlying the malignant transformation of inverted papilloma (IP) has not yet been elucidated. METHODS: To clarify the genes responsible for the malignant transformation, we analyzed 10 cases of IP, 8 of IP with dysplasia, and 11 of squamous cell carcinoma (SCC) by targeted amplicon sequencing. RESULTS: The number of mutant genes increased in the order of IP < dysplasia < SCC. Significant differences were observed in the mutation rates of three genes (KRAS, APC and STK11) in particular...
May 19, 2018: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/29778881/polymerase-chain-reaction-pcr-based-methods-promising-molecular-tools-in-dentistry
#8
REVIEW
Shahriar Shahi, Sepideh Zununi Vahed, Nazanin Fathi, Simin Sharifi
Polymerase chain reaction (PCR) has become a popular diagnosis and research technique in dentistry. Several studies show that its high sensitivity and specificity allow it as a precise, efficient, and rapid method for detection, identification, and quantification of microorganism. Several genetic polymorphisms can be determined along with detection of immune and inflammatory markers, therefore providing the more accurate perception into the mechanisms underlying the dental and periodontal disease. This review paper discusses the application of PCR as a diagnostic technique in periodontology, endodontic infections, implant-related, and peri-implantitis infection, immune and inflammatory markers identification and genetic polymorphism as well as application of next generation sequencing and gene microarray technology in dentistry mentioned...
May 17, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#9
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778427/genomics-driven-approach-for-identification-of-novel-therapeutic-targets-in-salmonella-enterica
#10
Priyanka Gawade, Payel Ghosh
Salmonella enterica is a causative agent of enteric and systemic salmonellosis that affects human and many other animal species. Due to the emergence of drug-resistant strains, available drugs against S. enterica infection are no more effective as before. Thus, there is an urgent need to develop new therapeutic strategies. The current study aims at prioritizing therapeutic targets by an in-silico genomics driven method. The method involves searching proteins of each Salmonella strain for essentiality, virulence and antibiotic-resistance and host-pathogen protein-protein interactions...
May 17, 2018: Gene
https://www.readbyqxmd.com/read/29778390/next-generation-sequencing-reveals-differentially-expressed-small-noncoding-rnas-in-uterine-leiomyoma
#11
Tsai-Der Chuang, Yeming Xie, Wei Yan, Omid Khorram
OBJECTIVE: To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN: Laboratory-based investigation. SETTING: Academic center. PATIENT(S): Women undergoing hysterectomy for benign indications. INTERVENTION(S): Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29778166/morphological-and-molecular-diversity-of-arbuscular-mycorrhizal-fungi-in-revegetated-iron-mining-site-has-the-same-magnitude-of-adjacent-pristine-ecosystems
#12
Caroline Krug Vieira, Matheus Nicoletti Marascalchi, Arthur Vinicius Rodrigues, Rafael Dutra de Armas, Sidney Luiz Stürmer
Arbuscular mycorrhizal fungi (AMF) are important during revegetation of mining sites, but few studies compared AMF community in revegetated sites with pristine adjacent ecosystems. The aim of this study was to assess AMF species richness in a revegetated iron-mining site and adjacent ecosystems and to relate AMF occurrence to soil chemical parameters. Soil samples were collected in dry and rainy seasons in a revegetated iron-mining site (RA) and compared with pristine ecosystems of forest (FL), canga (NG), and Cerrado (CE)...
May 2018: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29777822/effects-of-global-signal-regression-and-subtraction-methods-on-resting-state-functional-connectivity-using-arterial-spin-labeling-data
#13
João Paulo Santos Silva, Luciana da Mata Mônaco, André Monteiro Paschoal, Ícaro Agenor Ferreira de Oliveira, Renata Ferranti Leoni
BACKGROUND: Arterial spin labeling (ASL) is an established magnetic resonance imaging (MRI) technique that is finding broader applications in functional studies of the healthy and diseased brain. To promote improvement in cerebral blood flow (CBF) signal specificity, many algorithms and imaging procedures, such as subtraction methods, were proposed to eliminate or, at least, minimize noise sources. Therefore, this study addressed the main considerations of how CBF functional connectivity (FC) is changed, regarding resting brain network (RBN) identification and correlations between regions of interest (ROI), by different subtraction methods and removal of residual motion artifacts and global signal fluctuations (RMAGSF)...
May 16, 2018: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/29777592/early-identification-of-unusually-clustered-mutations-and-a-root-cause-in-therapeutic-antibody-development
#14
Yueming Qian, Zhiqiang Chen, Xin Huang, Xuning Wang, Xuankuo Xu, Stefan Kirov, Richard Ludwig, Nan-Xin Qian, Kandasamy Ravi, Li Tao, Michael C Borys, Zheng Jian Li
This study reports findings of an unusual cluster of mutations spanning 22 base pairs in a monoclonal antibody (mAb) expression vector. It was identified by two orthogonal methods: mass spectrometry on expressed protein and next-generation sequencing (NGS) on the plasmid DNA. While the initial NGS analysis confirmed the designed sequence modification, intact mass analysis detected an additional mass of the antibody molecule expressed in CHO cells. The extra mass was eventually found to be associated with unmatched nucleotides in a distal region by checking full-length sequence alignment plots...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777498/application-of-dirichlet-process-mixture-model-to-the-identification-of-spin-systems-in-protein-nmr-spectra
#15
Piotr Klukowski, Michał Augoff, Maciej Zamorski, Adam Gonczarek, Michał J Walczak
Analysis of structure, function and interactions of proteins by NMR spectroscopy usually requires the assignment of resonances to the corresponding nuclei in protein. This task, although automated by methods such as FLYA or PINE, is still frequently performed manually. To facilitate the manual sequence-specific chemical shift assignment of complex proteins, we propose a method based on Dirichlet process mixture model (DPMM) that performs automated matching of groups of signals observed in NMR spectra to corresponding nuclei in protein sequence...
May 18, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29777484/identification-of-differentially-expressed-micrornas-in-sahiwal-bos-indicus-breed-of-cattle-during-thermal-stress
#16
Gyanendra Singh Sengar, Rajib Deb, Umesh Singh, Vivek Junghare, Saugata Hazra, T V Raja, Rani Alex, Ashish Kumar, R R Alyethodi, Rajiv Kant, Subhash Jakshara, C G Joshi
microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in post transcriptional gene regulation that influence various fundamental cellular processes, including the cellular responses during environmental stresses. However, perusal of literatures revealed few reports on the differential expression of miRNA during thermal stress in Indian native (Bos indicus) cattle breeds. The present investigation aimed to identify differentially expressed miRNAs during thermal stress in Sahiwal (Bos indicus) dairy cattle breed of India, adapted with tropical climate over a long period of time...
May 18, 2018: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/29777336/first-morphological-and-molecular-analysis-of-eucoleus-boehmi-like-eggs-in-dogs-from-argentina
#17
Carla Mariela Lavallén, Romina Sandra Petrigh, Martín Horacio Fugassa, Guillermo María Denegri, Marcela Cecilia Dopchiz
The canid parasites Eucoleus aerophilus (syn. Capillaria aerophila) and Eucoleus boehmi (syn. Capillaria boehmi) parasitize the lower and the upper respiratory tract, respectively. Reports and descriptions of these nematodes are scarce in Argentina, possibly due to misdiagnosis of morphologically similar trichuroids eggs, and the lack of knowledge about the species of Eucoleus in this geographical area. Scanning electron microscopy is a useful tool for identification of E. boehmi eggs based on the characteristics of the shell structure which differentiate between species...
May 18, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29777159/identification-of-mycobacterium-chimaera-in-heater-cooler-units-in-china
#18
Xiaoxia Zhang, Ji Lin, Yu Feng, Xiaohui Wang, Alan McNally, Zhiyong Zong
A global outbreak of infections due to Mycobacterium chimaera has been linked to the LivaNova (formerly Sorin) 3 T heater-cooler units (HCUs). We performed a study to investigate M. chimaera from HCUs in China. Water samples were collected from all 3 T HCUs (n = 5) at our hospital in May 2017. Mycobacteria isolates were subjected to genome sequencing using the HiSeq X10 Sequencer. Species were identified based on average nucleotide identity with M. chimaera type strain DSM 44623T . Paired-end reads of all M...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29777151/integrated-proteomics-genomics-metabolomics-approaches-reveal-oxalic-acid-as-pathogenicity-factor-in-tilletia-indica-inciting-karnal-bunt-disease-of-wheat
#19
Vishakha Pandey, Manoj Singh, Dinesh Pandey, Anil Kumar
Tilletia indica incites Karnal bunt (KB) disease in wheat. To date, no KB resistant wheat cultivar could be developed due to non-availability of potential biomarkers related to pathogenicity/virulence for screening of resistant wheat genotypes. The present study was carried out to compare the proteomes of T. indica highly (TiK) and low (TiP) virulent isolates. Twenty one protein spots consistently observed as up-regulated/differential in the TiK proteome were selected for identification by MALDI-TOF/TOF. Identified sequences showed homology with fungal proteins playing essential role in plant infection and pathogen survival, including stress response, adhesion, fungal penetration, invasion, colonization, degradation of host cell wall, signal transduction pathway...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776720/phylogenetic-analyses-of-bradyrhizobium-symbionts-associated-with-invasive-crotalaria-zanzibarica-and-its-coexisting-legumes-in-taiwan
#20
Cheng-Tai Huang, Kuan-Ting Hish, Chun-Neng Wang, Chi-Te Liu, Wen-Yuan Kao
In this study, the genetic diversity and identification of Bradyrhizobium symbionts of Crotalaria zanzibarica, the most widely-distributed invasive legume in Taiwan, and other sympatric legume species growing along riverbanks of Taiwan were evaluated for the first time. In total, 59 and 54 Bradyrhizobium isolates were obtained from C. zanzibarica and its coexisting legume species, respectively. Based on the multilocus sequence analysis (MLSA) of concatenated four housekeeping genes (dnaK-glnII-recA-rpoB gene sequences, 1901bp), the 113 isolates displayed 53 unique haplotypes and grouped into 21 clades...
May 7, 2018: Systematic and Applied Microbiology
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