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https://www.readbyqxmd.com/read/29224071/sequencing-of-genomes-from-environmental-single-cells
#1
Robert M Bowers, Janey Lee, Tanja Woyke
Sequencing of single bacterial and archaeal cells is an important methodology that provides access to the genetic makeup of uncultivated microorganisms. We here describe the high-throughput fluorescence-activated cell sorting-based isolation of single cells from the environment, their lysis and strand displacement-mediated whole genome amplification. We further outline 16S rRNA gene sequence-based screening of single-cell amplification products, their preparation for Illumina sequencing libraries, and finally propose computational methods for read and contig level quality control of the resulting sequence data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222754/template-assisted-metabolic-reconstruction-and-assembly-of-hybrid-bacterial-models
#2
Tiziano Vignolini, Alessio Mengoni, Marco Fondi
Intraspecific genomic exchanges happen frequently between bacteria living in the same natural environment and can also be performed artificially in the laboratory for basic research or genetic/metabolic engineering purposes. In silico metabolic reconstruction and simulation of the metabolism of the hybrid strains that result from these processes can be used to predict the phenotypic outcome of such genomic rearrangements; this can be especially helpful as a designing tool in the purview of synthetic biology...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222753/integration-of-comparative-genomics-with-genome-scale-metabolic-modeling-to-investigate-strain-specific-phenotypical-differences
#3
Jonathan Monk, Emanuele Bosi
Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222702/molecular-insights-into-the-non-recombining-nature-of-the-spinach-male-determining-region
#4
Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe, Atsushi Toyoda, Hideki Hirakawa, Yutaka Suzuki, Nobuko Ohmido, Yasuyuki Onodera
Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars...
December 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29222442/contrasting-patterns-of-genome-level-diversity-across-distinct-co-occurring-bacterial-populations
#5
Sarahi L Garcia, Sarah L R Stevens, Benjamin Crary, Manuel Martinez-Garcia, Ramunas Stepanauskas, Tanja Woyke, Susannah G Tringe, Siv G E Andersson, Stefan Bertilsson, Rex R Malmstrom, Katherine D McMahon
To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series...
December 8, 2017: ISME Journal
https://www.readbyqxmd.com/read/29222102/tracking-the-taxonomy-of-the-genus-bifidobacterium-based-on-a-phylogenomic-approach
#6
Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Francesca Turroni, Alice Viappiani, Douwe van Sinderen, Marco Ventura
For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species with reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29220644/structure-and-genetics-of-the-o-specific-polysaccharide-of-escherichia-coli-o27
#7
Andrei V Perepelov, Tingting Chen, Sofya N Senchenkova, Andrei V Filatov, Jingjie Song, Alexander S Shashkov, Bin Liu, Yuriy A Knirel
The O-specific polysaccharide (O-antigen) is a part of the lipopolysaccharide on the cell surface of Gram-negative bacteria. The O-polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O27 and studied by sugar analysis and Smith degradation along with 1H and 13C NMR spectroscopy. The following structure of the branched hexasaccharide repeating unit was established, which is unique among known structures of bacterial polysaccharides:where GlcA is non-stoichiometrically O-acetylated at position 3 (∼22%) or 4 (∼37%)...
December 2, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/29219107/molecular-methods-for-detection-of-antimicrobial-resistance
#8
Muna F Anjum, Ea Zankari, Henrik Hasman
The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR...
December 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/29218845/probiotic-consortia-are-not-uniformly-effective-against-different-amphibian-chytrid-pathogen-isolates
#9
Rachael E Antwis, Xavier A Harrison
Symbiotic bacterial communities can protect their hosts from infection by pathogens. Treatment of wild individuals with protective bacteria (probiotics) isolated from hosts can combat the spread of emerging infectious diseases. However, it is unclear whether candidate probiotic bacteria can offer consistent protection across multiple isolates of globally-distributed pathogens. Here we use the lethal amphibian fungal pathogen Batrachochytrium dendrobatidis to investigate whether probiotic richness (number of bacteria) or genetic distance among consortia members influences broad-scale in vitro inhibitory capabilities of probiotics across multiple isolates of the pathogen...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29218377/genetic-mapping-of-a-major-gene-in-triticale-conferring-resistance-to-bacterial-leaf-streak
#10
Aimin Wen, Malini Jayawardana, Jason Fiedler, Suraj Sapkota, Gongjun Shi, Zhao Peng, Sanzhen Liu, Frank F White, Adam J Bogdanove, Xuehui Li, Zhaohui Liu
A major gene conferring resistance to bacterial leaf streak was mapped to chromosome 5R in triticale. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), is an important disease of wheat and triticale around the world. Although resistance to BLS is limited in wheat, several triticale accessions have high levels of resistance. To characterize the genetic basis of this resistance, we developed triticale mapping populations using a resistant accession (Siskiyou) and two susceptible accessions (UC38 and Villax St...
December 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29218035/characterization-of-two-cryptic-plasmids-isolated-in-haiti-from-clinical-vibrio-cholerae-non-o1-non-o139
#11
Daniela Ceccarelli, Geneviève Garriss, Seon Y Choi, Nur A Hasan, Ramunas Stepanauskas, Mihai Pop, Anwar Huq, Rita R Colwell
We report the complete sequence of two novel plasmids, pSDH-1 and pSDH-2, isolated from clinical Vibrio cholerae non-O1/non-O139 during the early phase of the 2010 Haitian cholera epidemic. Plasmids were revealed by employing single-cell genomics and their genome content suggests self-mobilization and, for pSDH-2, a toxin-antitoxin (TA) system for plasmid stabilization was identified. The putative origin of replication of pSDH-2 was mapped suggesting it replicates following the ColE1 model of plasmid replication...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29218034/replication-of-staphylococcal-resistance-plasmids
#12
REVIEW
Stephen M Kwong, Joshua P Ramsay, Slade O Jensen, Neville Firth
The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transmission to other bacteria in their surroundings, allowing extraordinarily rapid adaptation of bacterial populations. Once the resistance plasmids have been spread, they are often perpetually maintained in the new host, even in the absence of selective pressure...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29217567/plant-rubisco-assembly-in-e-coli-with-five-chloroplast-chaperones-including-bsd2
#13
H Aigner, R H Wilson, A Bracher, L Calisse, J Y Bhat, F U Hartl, M Hayer-Hartl
Plant RuBisCo, a complex of eight large and eight small subunits, catalyzes the fixation of CO2 in photosynthesis. The low catalytic efficiency of RuBisCo provides strong motivation to reengineer the enzyme with the goal of increasing crop yields. However, genetic manipulation has been hampered by the failure to express plant RuBisCo in a bacterial host. We achieved the functional expression of Arabidopsis thaliana RuBisCo in Escherichia coli by coexpressing multiple chloroplast chaperones. These include the chaperonins Cpn60/Cpn20, RuBisCo accumulation factors 1 and 2, RbcX, and bundle-sheath defective-2 (BSD2)...
December 8, 2017: Science
https://www.readbyqxmd.com/read/29216926/pro-inflammatory-adjuvant-properties-of-pigment-grade-titanium-dioxide-particles-are-augmented-by-a-genotype-that-potentiates-interleukin-1%C3%AE-processing
#14
Sebastian Riedle, Laetitia C Pele, Don E Otter, Rachel E Hewitt, Harjinder Singh, Nicole C Roy, Jonathan J Powell
BACKGROUND: Pigment-grade titanium dioxide (TiO2) particles are an additive to some foods (E171 on ingredients lists), toothpastes, and pharma-/nutraceuticals and are absorbed, to some extent, in the human intestinal tract. TiO2 can act as a modest adjuvant in the secretion of the pro-inflammatory cytokine interleukin 1β (IL-1β) when triggered by common intestinal bacterial fragments, such as lipopolysaccharide (LPS) and/or peptidoglycan. Given the variance in human genotypes, which includes variance in genes related to IL-1β secretion, we investigated whether TiO2 particles might, in fact, be more potent pro-inflammatory adjuvants in cells that are genetically susceptible to IL-1β-related inflammation...
December 8, 2017: Particle and Fibre Toxicology
https://www.readbyqxmd.com/read/29216826/6s-rna-plays-a-role-in-recovery-from-nitrogen-depletion-in-synechocystis-sp-pcc-6803
#15
Beate Heilmann, Kaisa Hakkila, Jens Georg, Taina Tyystjärvi, Wolfgang R Hess, Ilka M Axmann, Dennis Dienst
BACKGROUND: The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. RESULTS: Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation...
December 8, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/29216777/the-long-and-winding-road-stem-cells-for-cystic-fibrosis
#16
Massimo Conese, Elisa Beccia, Stefano Castellani, Sante Di Gioia, Carla Colombo, Antonella Angiolillo, Annalucia Carbone
Cystic fibrosis (CF) is a genetic syndrome with a high mortality rate due to severe lung disease. Despite having several drugs targeting specific mutated CFTR proteins already in clinical trials, new therapies, based on stem cells, are also emerging to treat those patients. Areas covered: The authors review the main sources of stem cells, including embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), gestational stem cells, and adult stem cells, such as mesenchymal stem cells (MSCs) in the context of CF...
December 8, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/29216488/microbial-community-composition-and-pahs-removal-potential-of-indigenous-bacteria-in-oil-contaminated-sediment-of-taean-coast-korea
#17
Dong Wan Lee, Hanbyul Lee, Aslan Hwanhwi Lee, Bong-Oh Kwon, Jong Seong Khim, Un Hyuk Yim, Beom Seok Kim, Jae-Jin Kim
The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons...
December 4, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/29216085/hybrid-artificial-bee-colony-algorithm-for-parameter-optimization-of-five-parameter-bidirectional-reflectance-distribution-function-model
#18
Qianqian Wang, Jing Zhao, Yong Gong, Qun Hao, Zhong Peng
A hybrid artificial bee colony (ABC) algorithm inspired by the best-so-far solution and bacterial chemotaxis was introduced to optimize the parameters of the five-parameter bidirectional reflectance distribution function (BRDF) model. To verify the performance of the hybrid ABC algorithm, we measured BRDF of three kinds of samples and simulated the undetermined parameters of the five-parameter BRDF model using the hybrid ABC algorithm and the genetic algorithm, respectively. The experimental results demonstrate that the hybrid ABC algorithm outperforms the genetic algorithm in convergence speed, accuracy, and time efficiency under the same conditions...
November 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/29215550/poly-%C3%AE-glutamic-acid-synthesis-gene-regulation-phylogenetic-relationships-and-role-in-fermentation
#19
REVIEW
Yi-Huang Hsueh, Kai-Yao Huang, Sikhumbuzo Charles Kunene, Tzong-Yi Lee
Poly-γ-glutamic acid (γ-PGA) is a biodegradable biopolymer produced by several bacteria, including Bacillus subtilis and other Bacillus species; it has good biocompatibility, is non-toxic, and has various potential biological applications in the food, pharmaceutical, cosmetic, and other industries. In this review, we have described the mechanisms of γ-PGA synthesis and gene regulation, its role in fermentation, and the phylogenetic relationships among various pgsBCAE, a biosynthesis gene cluster of γ-PGA, and pgdS, a degradation gene of γ-PGA...
December 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29215086/genetic-predisposition-to-infection-in-a-case-of-atypical-hemolytic-uremic-syndrome
#20
Lambertus van den Heuvel, Kristian Riesbeck, Omaima El Tahir, Valentina Gracchi, Mariann Kremlitzka, Servaas A Morré, A Marceline van Furth, Birendra Singh, Marcin Okrój, Nicole van de Kar, Anna M Blom, Elena Volokhina
Most cases of hemolytic uremic syndrome (HUS) are caused by infection with enterohemorrhagic Escherichia coli (EHEC). Genetic defects causing uncontrolled complement activation are associated with the more severe atypical HUS (aHUS). Non-EHEC infections can trigger the disease, however, complement defects predisposing to such infections have not yet been studied. We describe a 2-month-old patient infected with different Gram-negative bacterial species resulting in aHUS. Serum analysis revealed slow complement activation kinetics...
November 13, 2017: Journal of Human Genetics
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