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https://www.readbyqxmd.com/read/28541039/label-free-discrimination-of-rhizobial-bacteroids-and-mutants-by-single-cell-raman-microspectroscopy
#1
Jiabao Xu, Isabel Webb, Philip Poole, Wei E Huang
Symbiotic rhizobia in legume account for a large portion of nitrogen fixation in the biosphere. Nitrogen fixation is an energy-demanding process requiring tight control of metabolism and redox state. It is of great interest to understand the bacteroid differentiation process and the roles of energy storage molecules, such as glycogen and polyhydroxybutyrate (PHB), in maintaining the Rhizobium-legume symbioses. Traditional biochemical assays for checking phenotypic changes of mutants require a large volume of starting materials, which is difficult for unculturable, terminally differentiated bacteroids...
May 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28538703/metagenomic-approaches-to-assess-bacteriophages-in-various-environmental-niches
#2
REVIEW
Stephen Hayes, Jennifer Mahony, Arjen Nauta, Douwe van Sinderen
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral 'dark matter' of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research...
May 24, 2017: Viruses
https://www.readbyqxmd.com/read/28513579/electricity-from-methane-by-reversing-methanogenesis
#3
Michael J McAnulty, Venkata G Poosarla, Kyoung-Yeol Kim, Ricardo Jasso-Chávez, Bruce E Logan, Thomas K Wood
Given our vast methane reserves and the difficulty in transporting methane without substantial leaks, the conversion of methane directly into electricity would be beneficial. Microbial fuel cells harness electrical power from a wide variety of substrates through biological means; however, the greenhouse gas methane has not been used with much success previously as a substrate in microbial fuel cells to generate electrical current. Here we construct a synthetic consortium consisting of: (i) an engineered archaeal strain to produce methyl-coenzyme M reductase from unculturable anaerobic methanotrophs for capturing methane and secreting acetate; (ii) micro-organisms from methane-acclimated sludge (including Paracoccus denitrificans) to facilitate electron transfer by providing electron shuttles (confirmed by replacing the sludge with humic acids), and (iii) Geobacter sulfurreducens to produce electrons from acetate, to create a microbial fuel cell that converts methane directly into significant electrical current...
May 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28500915/a-comparison-of-denitrifying-bacterial-community-structures-and-abundance-in-acidic-soils-between-natural-forest-and-re-vegetated-forest-of-nanling-nature-reserve-in-southern-china
#4
Han Meng, Ruonan Wu, Yong-Feng Wang, Ji-Dong Gu
Denitrification plays a key role in converting reactive nitrogen species to dinitrogen gas back into the atmosphere to maintain the equilibrium of nitrogen cycling in ecosystems. In this study, functional genes of nirK and nosZ were used to detect the community structure and abundance of denitrifying microorganisms in acidic forest soils in southern China. Three sets of factors were considered for a comparison among 5 forests, including forest types (natural vs. re-vegetated), depths (surface layer vs. lower layer) and seasons (winter vs...
May 10, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28495852/high-throughput-mrna-sequencing-of-stromal-cells-from-endometriomas-and-endometrium
#5
Kadri Rekker, Merli Saare, Elo Eriste, Tõnis Tasa, Viktorija Kukuškina, Anne Mari Roost, Kristi Anderson, Külli Samuel, Helle Karro, Andres Salumets, Maire Peters
The aetiology of endometriosis is still unclear and to find mechanisms behind the disease development it is important to study each cell type from endometrium and ectopic lesions independently. The objective of this study was to uncover complete mRNA profiles in uncultured stromal cells from paired samples of endometriomas and eutopic endometrium. High-throughput mRNA sequencing revealed over 1,300 dysregulated genes in stromal cells from ectopic lesions, including several novel genes in the context of endometriosis...
May 11, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28493994/spatiotemporal-analysis-of-microbial-community-dynamics-during-seasonal-stratification-events-in-a-freshwater-lake-grand-lake-ok-usa
#6
Jessica M Morrison, Kristina D Baker, Richard M Zamor, Steve Nikolai, Mostafa S Elshahed, Noha H Youssef
Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column...
2017: PloS One
https://www.readbyqxmd.com/read/28487430/rna-dependent-cysteine-biosynthesis-in-bacteria-and-archaea
#7
Takahito Mukai, Ana Crnković, Takuya Umehara, Natalia N Ivanova, Nikos C Kyrpides, Dieter Söll
The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA(Cys) is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria ("Candidatus Parcubacteria" and Chloroflexi)...
May 9, 2017: MBio
https://www.readbyqxmd.com/read/28458911/sequence-based-taxonomic-framework-for-the-classification-of-uncultured-single-stranded-dna-viruses-of-the-family-genomoviridae
#8
Arvind Varsani, Mart Krupovic
With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2-2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family...
January 2017: Virus Evolution
https://www.readbyqxmd.com/read/28457865/novel-abundant-oceanic-viruses-of-uncultured-marine-group-ii-euryarchaeota
#9
Alon Philosof, Natalya Yutin, José Flores-Uribe, Itai Sharon, Eugene V Koonin, Oded Béjà
Marine group II Euryarchaeota (MG-II) are among the most abundant microbes in oceanic surface waters [1-4]. So far, however, representatives of MG-II have not been cultivated, and no viruses infecting these organisms have been described. Here, we present complete genomes for three distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MG-II. These novel viruses, which we denote magroviruses, possess double-stranded DNA genomes of 65 to 100 kilobases in size that encode a structural module characteristic of head-tailed viruses and, unusually for archaeal and bacterial viruses, a nearly complete replication apparatus of apparent archaeal origin...
May 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28456990/prenatal-diagnosis-of-lysosomal-storage-disorders-using-chorionic-villi
#10
Jyotsna Verma, Sunita Bijarnia-Mahay, Ishwar C Verma
Prenatal enzymatic diagnosis for an array of lysosomal storage disorders (LSDs) can be performed accurately, provided that a confirmed diagnosis by biochemical/molecular study in the index case is available and a strict defined protocol, specific to each individual disorder is followed. The present chapter describes the protocols for reliable and accurate prenatal enzymatic diagnoses by fluorometric and spectrophotometric methods of lysosomal storage disorders: Gaucher, Fabry, Pompe, Niemann Pick A/B, Tay Sach, Sandhoff, GM1, Mucoplysaccharidoses, Wolman, Krabbe, Metachromatic leukodystrophy, and Batten diseases using uncultured chorionic villi samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28455588/a-diversity-study-of-saccharomycopsis-fibuligera-in-rice-wine-starter-nuruk-reveals-the-evolutionary-process-associated-with-its-interspecies-hybrid
#11
Mohamed El-Agamy Farh, Yunjoo Cho, Jae Yun Lim, Jeong-Ah Seo
The amylolytic yeast Saccharomycopsis fibuligera is the predominant yeast in the starter product, nuruk, which is utilized for rice wine production in South Korea. Latest molecular studies explore a recently developed interspecific hybridization among stains of S. fibuligera with a unique genetic feature. However, the origin of the natural hybridization occurrence is still unclear. Thus, to respectively distinguish parental and hybrid strains, specific primer sets were applied on 141 yeast strains isolated from different nuruk samples fermented in different provinces...
May 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28450499/draft-genome-sequence-of-uncultured-upland-soil-cluster-gammaproteobacteria-gives-molecular-insights-into-high-affinity-methanotrophy
#12
Collin R Edwards, Tullis C Onstott, Jennifer M Miller, Jessica B Wiggins, Wei Wang, Charles K Lee, S Craig Cary, Stephen B Pointing, Maggie C Y Lau
Aerated soils form the second largest sink for atmospheric CH4 A near-complete genome of uncultured upland soil cluster Gammaproteobacteria that oxidize CH4 at <2.5 ppmv was obtained from incubated Antarctic mineral cryosols. This first genome of high-affinity methanotrophs can help resolve the mysteries about their phylogenetic affiliation and metabolic potential.
April 27, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28446901/anaerobic-methanotrophic-archaea-of-the-anme-2d-cluster-are-active-in-a-low-sulfate-iron-rich-freshwater-sediment
#13
Hannah S Weber, Kirsten S Habicht, Bo Thamdrup
ANaerobic MEthanotrophic (ANME) archaea remove the greenhouse gas methane from anoxic environments and diminish its flux to the atmosphere. High methane removal efficiencies are well documented in marine environments, whereas anaerobic oxidation of methane (AOM) was only recently indicated as an important methane sink in freshwater systems. Freshwater AOM-mediating microorganisms lack taxonomic identification and only little is known about metabolic adaptions to prevailing biogeochemical conditions. One of the first study sites providing information about AOM activity in freshwater sediment is Lake Ørn, a low-sulfate, iron-rich Danish lake...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28443069/long-term-enrichment-of-stress-tolerant-cellulolytic-soil-populations-following-timber-harvesting-evidenced-by-multi-omic-stable-isotope-probing
#14
Roland C Wilhelm, Erick Cardenas, Hilary Leung, András Szeitz, Lionel D Jensen, William W Mohn
Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28442730/exploration-of-the-relationship-between-biogas-production-and-microbial-community-under-high-salinity-conditions
#15
Shaojie Wang, Xiaocong Hou, Haijia Su
High salinity frequently causes inhibition and even failure in anaerobic digestion. To explore the impact of increasing NaCl concentrations on biogas production, and reveal the microbial community variations in response to high salinity stress, the Illumina high-throughput sequencing technology was employed. The results showed that a NaCl concentration of 20 g/L (H group) exhibited a similar level of VFAs and specific CO2 production rate with that in the blank group, thus indicating that the bacterial activity in acidogenesis might not be inhibited...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28426403/pcr-denaturing-gradient-gel-electrophoresis-as-a-useful-method-to-identify-of-intestinal-bacteria-flora-in-haemaphysalis-flava-ticks
#16
Tian-Yin Cheng, Guo-Hua Liu
Ticks are blood-sucking ectoparasites of great medical and veterinary significance that can transmit bacteria, protozoa, fungi and viruses, causing a variety of human and animal diseases worldwide. In the present study, the intestinal bacterial flora associated with Haemaphysalis flava ticks in different developmental stages were analyzed using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). Eleven distinct DGGE bands were found using PCR-DGGE method. Sequences analyses indicated that they belonged to Bacillus cereus, Candidatus rickettsia, Erwinia sp...
June 1, 2017: Acta Parasitologica
https://www.readbyqxmd.com/read/28420516/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of%C3%A2-low-level-mosaic-trisomy-12-at-amniocentesis-associated-with%C3%A2-a%C3%A2-favorable-pregnancy-outcome
#17
Chih-Ping Chen, Chen-Ju Lin, Schu-Rern Chern, Peih-Shan Wu, Yen-Ni Chen, Shin-Wen Chen, Chen-Wen Pan, Chien-Wen Yang, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis of low-level mosaic trisomy 12. CASE REPORT: A 40-year-old woman underwent amniocentesis at 18 weeks of gestation because of advanced maternal age, which revealed a karyotype of 47,XX,+12[5]/46,XX[24] consistent with 17.2% (5/29) mosaicism for trisomy 12. Repeat amniocentesis performed at 21 weeks of gestation revealed a karyotype of 47,XX,+12[4]/46,XX[6] consistent with 40% (4/10) mosaicism for trisomy 12. Interphase fluorescence in situ hybridization (FISH) on 112 uncultured amniocytes detected 23 cells with trisomy 12 consistent with 20...
April 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28420511/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of-concomitant-familial-small-supernumerary-marker-chromosome-derived-from-chromosome-4q-4q11-1-q13-2-and-5q13-2-microdeletion-with-no-apparent-phenotypic-abnormality
#18
Chih-Ping Chen, Schu-Rern Chern, Yen-Ni Chen, Shin-Wen Chen, Peih-Shan Wu, Chien-Wen Yang, Chen-Chi Lee, Meng-Shan Lee, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis and molecular cytogenetic characterization of concomitant familial small supernumerary marker chromosome 4 [sSMC(4)] derived from 4q11.1-q12 and q13.2, and 5q13.2 microdeletion with no apparent phenotypic abnormality. MATERIALS AND METHODS: A 32-year-old woman underwent amniocentesis at 21 weeks of gestation because of absent nasal bone on fetal ultrasound. Amniocentesis revealed a karyotype of 47,XX,+mar[13]/46,XX[3]. Array comparative genomic hybridization analysis on the cultured amniocytes revealed a 2...
April 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28394321/the-role-of-angiopoietin-2-in-nucleus-pulposus-cells-during-human-intervertebral-disc-degeneration
#19
Kun Wang, Wei Liu, Yu Song, Xinghuo Wu, Yukun Zhang, Shuai Li, Yong Gao, Ji Tu, Yingle Liu, Cao Yang
Although evidence shows that intervertebral disc degeneration is generally characterized by angiogenesis, the role of angiopoietin has not been investigated. This study examined the presence of angiopoietin-1 (Ang-1) and angiopoietin-2 (Ang-2) within the native intervertebral disc (IVD) and elucidated their functions in the regulation of nucleus pulposus (NP) cells. Initial investigation of uncultured NP tissue revealed that Ang-1 and Ang-2 were expressed by native NP cells. Ang-2 expression was significantly increased in infiltrated and degenerate samples relative to normal samples...
April 10, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28393681/characterization-of-bacterial-community-structure-in-a-hydrocarbon-contaminated-tropical-african-soil
#20
Lateef B Salam, Mathew O Ilori, Olukayode O Amund, Yee LiiMien, Hideaki Nojiri
Bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty seven clones cutting across thirteen bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria...
April 10, 2017: Environmental Technology
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