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https://www.readbyqxmd.com/read/28330115/phylogenetic-and-metabolic-diversity-of-tunisian-forest-wood-degrading-fungi-a-wealth-of-novelties-and-opportunities-for-biotechnology
#1
Dalel Daâssi, Héla Zouari-Mechichi, Lassaad Belbahri, Jorge Barriuso, María Jesús Martínez, Moncef Nasri, Tahar Mechichi
In this study, 51 fungal strains were isolated from decaying wood samples collected from forests located in the Northwest of Tunisia in the vicinity of Bousalem, Ain Draham and Kef. Phylogenetic analysis based on the sequences of the internal transcribed spacers of the ribosomal DNA showed a high diversity among the 51 fungal isolates collection. Representatives of 25 genera and 29 species were identified, most of which were members of one of the following phyla (Ascomycota, Basidiomycota and Zygomycota). In addition to the phylogenetic diversity, a high diversity of secreted enzyme profiles was also detected among the fungal isolates...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330100/molecular-characterization-and-amplified-ribosomal-dna-restriction-analysis-of-entomopathogenic-bacteria-associated-with-rhabditis-oscheius-spp
#2
Balakrishnan Geetha Sangeetha, Cheruvandasseri Arumughan Jayaprakas, Jinachandrannair Vijayakumari Siji, Moochattil Rajitha, Basheerkutty Shyni, Chellappan Mohandas
Bacterial strains associated with entomopathogenic nematodes (EPNs) Rhabditis (Oscheius) spp. were isolated from infected cadavers of Galleria mellonella. The obtained 18 isolates were subdivided into nine phylogenetically different genera based on comparative sequence analysis of their 16S rRNA genes. The isolates were affiliated to three different class namely γ-proteobacteria (Enterobacter, Proteus, Providencia, Pseudomonas, Stenotrophomonas), β-proteobacteria (Alcaligenes) and Bacilli (Bacillus, Enterococcus, Lysinibacillus)...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329689/the-human-cchc-type-zinc-finger-nucleic-acid-binding-protein-binds-g-rich-elements-in-target-mrna-coding-sequences-and-promotes-translation
#3
Daniel Benhalevy, Sanjay K Gupta, Charles H Danan, Suman Ghosal, Hong-Wei Sun, Hinke G Kazemier, Katrin Paeschke, Markus Hafner, Stefan A Juranek
The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28328981/dysbiosis-and-compositional-alterations-with-aging-in-the-gut-microbiota-of-patients-with-heart-failure
#4
Takehiro Kamo, Hiroshi Akazawa, Wataru Suda, Akiko Saga-Kamo, Yu Shimizu, Hiroki Yagi, Qing Liu, Seitaro Nomura, Atsuhiko T Naito, Norifumi Takeda, Mutsuo Harada, Haruhiro Toko, Hidetoshi Kumagai, Yuichi Ikeda, Eiki Takimoto, Jun-Ichi Suzuki, Kenya Honda, Hidetoshi Morita, Masahira Hattori, Issei Komuro
Emerging evidence has suggested a potential impact of gut microbiota on the pathophysiology of heart failure (HF). However, it is still unknown whether HF is associated with dysbiosis in gut microbiota. We investigated the composition of gut microbiota in patients with HF to elucidate whether gut microbial dysbiosis is associated with HF. We performed 16S ribosomal RNA gene sequencing of fecal samples obtained from 12 HF patients and 12 age-matched healthy control (HC) subjects, and analyzed the differences in gut microbiota...
2017: PloS One
https://www.readbyqxmd.com/read/28328943/structurally-detailed-coarse-grained-model-for-sec-facilitated-co-translational-protein-translocation-and-membrane-integration
#5
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28328543/challenges-in-describing-ribosome-dynamics
#6
Kien Nguyen, Paul Charles Whitford
For decades, protein folding and functional dynamics have been described in terms of diffusive motion across an underlying energy landscape. With continued advances in structural biology and high-performance computing, the field is positioned to extend these approaches to large biomolecular assemblies. Through the application of energy landscape techniques to the ribosome, one may work towards establishing a comprehensive description of the dynamics, which will bridge theoretical concepts and experimental observations...
March 22, 2017: Physical Biology
https://www.readbyqxmd.com/read/28327156/mycobacterium-goodii-endocarditis-following-mitral-valve-ring-annuloplasty
#7
Rohan B Parikh, Matthew Grant
BACKGROUND: Mycobacterium goodii is an infrequent human pathogen which has been implicated in prosthesis related infections and penetrating injuries. It is often initially misidentified as a gram-positive rod by clinical microbiologic laboratories and should be considered in the differential diagnosis. CASE PRESENTATION: We describe here the second reported case of M. goodii endocarditis. Species level identification was performed by 16S rDNA (ribosomal deoxyribonucleic acid) gene sequencing...
March 21, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/28326781/the-berkeleylactones-antibiotic-macrolides-from-fungal-coculture
#8
Andrea A Stierle, Donald B Stierle, Daniel Decato, Nigel D Priestley, Jeremy B Alverson, John Hoody, Kelly McGrath, Dorota Klepacki
A carefully timed coculture fermentation of Penicillium fuscum and P. camembertii/clavigerum yielded eight new 16-membered-ring macrolides, berkeleylactones A-H (1, 4, 6-9, 12, 13), as well as the known antibiotic macrolide A26771B (5), patulin, and citrinin. There was no evidence of the production of the berkeleylactones or A26771B (5) by either fungus when grown as axenic cultures. The structures were deduced from analyses of spectral data, and the absolute configurations of compounds 1 and 9 were determined by single-crystal X-ray crystallography...
March 22, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28326777/peptide-macrocyclization-inspired-by-non-ribosomal-imine-natural-products
#9
Lara R Malins, Justine Nicole deGruyter, Kevin J Robbins, Paul M Scola, Martin Eastgate, M Reza Ghadiri, Phil S Baran
A thermodynamic approach to peptide macrocyclization inspired by the cyclization of non-ribosomal peptide aldehydes is presented. The method provides access to structurally diverse macrocycles by exploiting the reactivity of transient macrocyclic peptide imines toward inter- and intramolecular nucleophiles. Reactions are performed in aqueous media, in the absence of side-chain protecting groups, and are tolerant of all proteinogenic functional groups. Macrocyclic products bearing non-native and rigidifying structural motifs, isotopic labels, and a variety of bioorthogonal handles are prepared, along with analogues of four distinct natural products...
March 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28324847/species-identification-in-forensic-samples-using-the-spindel-approach-a-ghep-isfg-inter-laboratory-collaborative-exercise
#10
Cíntia Alves, Rui Pereira, Lourdes Prieto, Mercedes Aler, Cesar R L Amaral, Cristina Arévalo, Gabriela Berardi, Florencia Di Rocco, Mariela Caputo, Cristian Hernandez Carmona, Laura Catelli, Heloísa Afonso Costa, Pavla Coufalova, Sandra Furfuro, Óscar García, Anibal Gaviria, Ana Goios, Juan José Builes Gómez, Alexis Hernández, Eva Del Carmen Betancor Hernández, Luís Miranda, David Parra, Susana Pedrosa, Maria João Anjos Porto, Maria de Lurdes Rebelo, Matteo Spirito, María Del Carmen Villalobos Torres, António Amorim, Filipe Pereira
DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis...
March 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28324166/redescription-of-chloromyxum-ellipticum-li-nie-1973-myxosporea-chloromyxidae-infecting-the-gall-bladder-of-grass-carp-ctenopharyngodon-idellus-valenciennes-1844-supplemented-by-morphological-and-molecular-characteristics
#11
J Y Zhang, Y L Zhao, M D Batueva, D Luo, Z F Xing, Q Q Zhang, X H Liu
The traditional taxonomy of the genus Chloromyxum Mingazzini, 1890 has been intensively challenged to be paraphyletic by recent ribosomal DNA (rDNA)-based phylogenetic analysis. Undersampling to get rich sequence data to infer more scientific phylogenetic relationships makes scientists conservatively assign all non-marine elasmobranch-infecting species as Chloromyxum sensu lato. Although complex ridge pattern on the spore surface observed by scanning electron microscopy was thought to be critical for the identification of Chloromyxum species, insufficient data also prevent this ultrastructural data to be a valid taxonomic feature for this genus...
March 21, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28323820/selective-stalling-of-human-translation-through-small-molecule-engagement-of-the-ribosome-nascent-chain
#12
Nathanael G Lintner, Kim F McClure, Donna Petersen, Allyn T Londregan, David W Piotrowski, Liuqing Wei, Jun Xiao, Michael Bolt, Paula M Loria, Bruce Maguire, Kieran F Geoghegan, Austin Huang, Tim Rolph, Spiros Liras, Jennifer A Doudna, Robert G Dullea, Jamie H D Cate
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a key role in regulating the levels of plasma low-density lipoprotein cholesterol (LDL-C). Here, we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28323150/systematic-expression-profiling-analysis-mines-dys-regulated-modules-in-active-tuberculosis-based-on-re-weighted-protein-protein-interaction-network-and-attract-algorithm
#13
Ying Sun, Yan Weng, Ying Zhang, Xiang Yan, Lei Guo, Jia Wang, Xin Song, Ying Yuan, Fu-Ye Chang, Chun-Ling Wang
About 90% of tuberculosis (TB) patients latently infected with Mycobacterium tuberculosis (Mtb) show no symptoms, yet have a 10% chance in lifetime to progress active TB. Nevertheless, current diagnosis approaches need improvement in efficiency and sensitivity. The objective of this work was to detect potential signatures for active TB to further improve the understanding of the biological roles of functional modules involved in this disease. First, targeted networks of active TB and control groups were established via re-weighting protein-protein interaction (PPI) networks using Pearson's correlation coefficient (PCC)...
March 17, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28322871/recurrent-emergence-of-structural-variants-of-ltr-retrotransposon-csrn1-evolving-novel-expression-strategy-and-their-selective-expansion-in-a-carcinogenic-liver-fluke-clonorchis-sinensis
#14
Seon-Hee Kim, Yoon Kong, Young-An Bae
Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups...
March 16, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28322844/a-harmine-derived-beta-carboline-displays-anti-cancer-effects-in-vitro-by-targeting-protein-synthesis
#15
Annelise Carvalho, Jennifer Chu, Céline Meinguet, Robert Kiss, Guy Vandenbussche, Bernard Masereel, Johan Wouters, Alexander Kornienko, Jerry Pelletier, Véronique Mathieu
Growing evidence indicates that protein synthesis is deregulated in cancer onset and progression and targeting this process might be a selective way to combat cancers. While harmine is known to inhibit DYRK1A and intercalate into the DNA, tri-substitution was shown previously to modify its activity profile in favor of protein synthesis inhibition. In this study, we thus evaluated the optimized derivative CM16 in vitro anti-cancer effects unfolding its protein synthesis inhibition activity. Indeed, the growth inhibitory profile of CM16 in the NCI 60-cancer-cell-line-panel correlated with those of other compounds described as protein synthesis inhibitors...
March 16, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28322208/prevalence-and-pathogen-load-estimates-for-the-fungus-batrachochytrium-dendrobatidis-are-impacted-by-its-dna-copy-number-variation
#16
Eria A Rebollar, Douglas C Woodhams, Brandon LaBumbard, Jos Kielgast, Reid N Harris
The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses of organisms from all 3 domains of life. In fungi, the copy number of the internal transcribed spacer (ITS) is used to detect abundance of pathogens causing diseases such as chytridiomycosis in amphibians and white nose syndrome in bats. Chytridiomycosis is caused by the fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), and is responsible for declines and extinctions of amphibians worldwide...
March 21, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28322160/an-efficient-transient-expression-system-for-enhancing-generation-of-monoclonal-antibodies-in-293-suspension-cells
#17
Guoquan Zhang, Jie Liu, Wanting Fan, Qianyi Chen, Bin Shi
BACKGROUND: Recombinant monoclonal antibodies (mAbs) are useful in research, diagnosis, and therapy. The increased demands of recombinant mAbs require efficient production systems. A variety of expression vectors have been developed for stable or transient production of mAb in mammalian cells. However, though a few commercial expression systems of mAbs can be listened, the high expense often impedes academia researches. METHODS: In this study, we described the development of a transient mammalian system based on a bicistronic vector, which contains internal ribosome entry site (IRES) and enhancer elements to express IgG1 light chain (LC) and heavy chain (HC) in one transcript...
March 20, 2017: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/28322147/molecular-characterization-and-antioxidant-potential-of-three-wild-culinary-medicinal-mushrooms-from-tripura-northeast-india
#18
Aparajita Roy Das, Madhusmita Borthakur, Ajay Krishna Saha, Santa Ram Joshi, Panna Das
The aim of this study was to characterize 3 wild culinary-medicinal mushrooms using molecular tools and to analyze their antioxidant activity. Antioxidant properties were studied by evaluating free radical scavenging, reducing power, and chelating effect. The mushrooms were identified as Lentinus squarrosulus, L. tuber-regium, and Macrocybe gigantean by amplifying internal transcribed spacer regions of ribosomal DNA. The results demonstrated that the methanolic extract of M. gigantean has the highest free radical scavenging effect and chelating effect, whereas the methanolic extract of L...
2017: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/28321920/xanthothecium-peruvianum-isolated-from-human-stratum-corneum-a-case-report-characterisation-and-short-review-that-suggest-emendation-of-arachnomyces-peruvianus
#19
REVIEW
Jochen Brasch, Vera Beck-Jendroscheck, Karin Voss, Andrey Yurkov, Alberto Miguel Stchigel, Yvonne Gräser
From stratum corneum samples of a palmar eczema, a fungus was isolated that developed white colonies with a yellowish dark reverse, suggestive of dermatophytes. The isolate produced numerous chlamydospores and sparse aleuroconidia, was resistant to cycloheximide, grew well on human stratum corneum samples and was positive in tests for urease production and hair perforation, but no dermatophyte could be identified. After several weeks, cleistothecia with delicate asci and disc-shaped ascospores were formed, suggesting Arachnomyces spp...
March 20, 2017: Mycoses
https://www.readbyqxmd.com/read/28321788/characteristics-of-aerococcus-viridans-isolated-from-bovine-subclinical-mastitis-and-its-effect-on-milk-scc-yield-and-composition
#20
Meng Sun, Jian Gao, Tariq Ali, Dan Yu, Shiyao Zhang, Saeed U Khan, Séamus Fanning, Bo Han
Aerococcus viridians (A. viridans), an environmental Gram-positive bacterium, has been documented to be associated with bovine mastitis. However, its exact role in bovine mastitis and the changes it brings about in milk characteristics are not yet known. The objectives of the current study were to describe the antibiotic resistance of A. viridans from bovine mastitis as well as the correlation between existence of this pathogen in udders and the somatic cell counts (SCC), daily milk yield, and composition of individual cow...
March 20, 2017: Tropical Animal Health and Production
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