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https://www.readbyqxmd.com/read/30102276/combining-analysis-of-dna-in-a-crude-virion-extraction-with-the-analysis-of-rna-from-infected-leaves-to-discover-new-virus-genomes
#1
Jeanmarie Verchot, Aastha Thapa, Dulanjani Wijayasekara, Peter R Hoyt
This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components...
July 27, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29492893/metagenomic-analyses-of-the-viruses-detected-in-mycorrhizal-fungi-and-their-host-orchid
#2
Hanako Shimura, Chikara Masuta, Yasunori Koda
In nature, mycorrhizal association with soilborne fungi is indispensable for orchid families. Fungal structures from compatible endo-mycorrhizal fungi in orchid cells are digested in cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until shoots develop (leaves) and become photoautotrophic. Seeds of all orchid species surely geminate with the help of their own fungal partners, and this specific partnership has been acquired for a long evolutional history between orchids and fungi...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29385846/unraveling-uncultivable-pesticide-degraders-via-stable-isotope-probing-sip
#3
Bo Jiang, Naifu Jin, Yi Xing, Yuping Su, Dayi Zhang
Uncultivable microorganisms account for over 99% of all species on earth, playing essential roles in ecological processes such as carbon/nitrogen cycle and chemical mineralization. Their functions remain unclear in ecosystems and natural habitats, requiring cutting-edge biotechnologies for a deeper understanding. Stable isotope probing (SIP) incorporates isotope-labeled elements, e.g. 13  C, 18  O or 15  N, into the cellular components of active microorganisms, serving as a powerful tool to link phylogenetic identities to their ecological functions in situ...
February 1, 2018: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29353803/metagenome-enrichment-approach-used-for-selection-of-oil-degrading-bacteria-consortia-for-drill-cutting-residue-bioremediation
#4
Alaine B Guerra, Jorge S Oliveira, Rita C B Silva-Portela, Wydemberg Araújo, Aline C Carlos, Ana Tereza R Vasconcelos, Ana Teresa Freitas, Yldeney Silva Domingos, Mirna Ferreira de Farias, Glauber José Turolla Fernandes, Lucymara F Agnez-Lima
Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform...
April 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29088131/the-trajectory-of-microbial-single-cell-sequencing
#5
REVIEW
Tanja Woyke, Devin F R Doud, Frederik Schulz
Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future...
October 31, 2017: Nature Methods
https://www.readbyqxmd.com/read/29029724/new-leaves-in-the-growing-tree-of-pestiviruses
#6
Sandra Blome, Martin Beer, Kerstin Wernike
Pestiviruses are a group of viruses of veterinary importance infecting livestock animals like pigs, cattle, and sheep, and also wildlife animals like wild boar and different deer species. While for decades only four classical species (Classical swine fever virus, Bovine viral diarrhea virus types 1 and 2, Border disease virus), and a few so-called atypical pestiviruses were known (e.g., Giraffe virus, Pronghorn virus, HoBi virus), a series of novel pestiviruses was identified in the last years (Bungowannah virus, Bat pestivirus, Norway rat pestivirus, Atypical porcine pestivirus, LINDA virus)...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/29016661/modified-rna-seq-method-for-microbial-community-and-diversity-analysis-using-rrna-in-different-types-of-environmental-samples
#7
Yong-Wei Yan, Bin Zou, Ting Zhu, Wael N Hozzein, Zhe-Xue Quan
RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step...
2017: PloS One
https://www.readbyqxmd.com/read/28943629/an-integrated-outlook-on-the-metagenome-and-metabolome-of-intestinal-diseases
#8
REVIEW
Wanping Aw, Shinji Fukuda
Recently, metagenomics and metabolomics are the two most rapidly advancing "omics" technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites) that specific cellular processes leave behind. Remarkable progress in DNA sequencing and mass spectrometry technologies has enabled the comprehensive collection of information on the gut microbiome and its metabolome in order to assess the influence of the gut microbiota on host physiology on a whole-systems level...
November 6, 2015: Diseases (Basel)
https://www.readbyqxmd.com/read/28904137/seasonal-variation-in-nutrient-utilization-shapes-gut-microbiome-structure-and-function-in-wild-giant-pandas
#9
Qi Wu, Xiao Wang, Yun Ding, Yibo Hu, Yonggang Nie, Wei Wei, Shuai Ma, Li Yan, Lifeng Zhu, Fuwen Wei
Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different...
September 13, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28817927/identification-of-biosynthetic-gene-clusters-from-metagenomic-libraries-using-pptase-complementation-in-a-streptomyces-host
#10
J Kipchirchir Bitok, Christophe Lemetre, Melinda A Ternei, Sean F Brady
The majority of environmental bacteria are not readily cultured in the lab, leaving the natural products they make inaccessible using culture-dependent discovery methods. Cloning and heterologous expression of DNA extracted from environmental samples (environmental DNA, eDNA) provides a means of circumventing this discovery bottleneck. To facilitate the identification of clones containing biosynthetic gene clusters, we developed a model heterologous expression reporter strain Streptomyces albus::bpsA ΔPPTase...
September 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28725217/metagenomics-the-next-culture-independent-game-changer
#11
REVIEW
Jessica D Forbes, Natalie C Knox, Jennifer Ronholm, Franco Pagotto, Aleisha Reimer
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28667801/a-study-of-selected-factors-affecting-efficacy-of-compost-tea-against-several-fungal-pathogens-of-potato
#12
W K Mengesha, W M Gill, S M Powell, K J Evans, K M Barry
AIM: To investigate selected factors of two nonaerated compost teas (NCT) and mechanisms that influence the restriction of several fungal potato pathogens. METHODS AND RESULTS: Two NCTs, made from either commercial compost, (CCT) or vineyard compost (VCT), were tested for their ability to suppress potato pathogens. The VCT was more suppressive than CCT to mycelial growth of Alternaria solani and Rhizoctonia solani isolate 299, but not for R. solani isolate 422. Metagenomic studies of microbial diversity revealed that the CCT had higher fungal and bacterial diversity and richness than the VCT...
September 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28646670/a-metagenomic-assessment-of-viral-contamination-on-fresh-parsley-plants-irrigated-with-fecally-tainted-river-water
#13
X Fernandez-Cassi, N Timoneda, E Gonzales-Gustavson, J F Abril, S Bofill-Mas, R Girones
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food...
September 18, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28618206/grazing-of-leaf-associated-cercomonads-protists-rhizaria-cercozoa-structures-bacterial-community-composition-and-function
#14
Sebastian Flues, David Bass, Michael Bonkowski
Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria...
August 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28454776/functional-association-prediction-by-community-profiling
#15
Dazhi Jiao, Wontack Han, Yuzhen Ye
Recent years have witnessed unprecedented accumulation of DNA sequences and therefore protein sequences (predicted from DNA sequences), due to the advances of sequencing technology. One of the major sources of the hypothetical proteins is the metagenomics research. Current annotation of metagenomes (collections of short metagenomic sequences or assemblies) relies on similarity searches against known gene/protein families, based on which functional profiles of microbial communities can be built. This practice, however, leaves out the hypothetical proteins, which may outnumber the known proteins for many microbial communities...
October 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28341909/metagenomic-analyses-of-bacterial-endophytes-associated-with-the-phyllosphere-of-a-bt-maize-cultivar-and-its-isogenic-parental-line-from-south-africa
#16
Ramadimetja A Mashiane, Obinna T Ezeokoli, Rasheed A Adeleke, Cornelius C Bezuidenhout
Genetic modification of maize with Bacillus thuringiensis (Bt) cry proteins may predispose shifts in the bacterial endophytes' community associated with maize shoots. In this study, the diversity of bacterial endophytes associated with a Bt maize genotype (Mon810) and its isogenic non-transgenic parental line were investigated at pre-flowering (50 days) and post-flowering (90 days) developmental stages. PCR-DGGE and high throughput sequencing on the Illumina MiSeq sequencer were used to characterize bacterial 16S rRNA gene diversity in leaves, stems, seeds and tassels...
April 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28005056/new-crispr-cas-systems-from-uncultivated-microbes
#17
David Burstein, Lucas B Harrington, Steven C Strutt, Alexander J Probst, Karthik Anantharaman, Brian C Thomas, Jennifer A Doudna, Jillian F Banfield
CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped...
February 9, 2017: Nature
https://www.readbyqxmd.com/read/28003936/towards-quantitative-viromics-for-both-double-stranded-and-single-stranded-dna-viruses
#18
Simon Roux, Natalie E Solonenko, Vinh T Dang, Bonnie T Poulos, Sarah M Schwenck, Dawn B Goldsmith, Maureen L Coleman, Mya Breitbart, Matthew B Sullivan
BACKGROUND: Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation)...
2016: PeerJ
https://www.readbyqxmd.com/read/27965238/vertical-stratification-of-the-foliar-fungal-community-in-the-world-s-tallest-trees
#19
Joshua G Harrison, Matthew L Forister, Thomas L Parchman, George W Koch
PREMISE OF THE STUDY: The aboveground tissues of plants host numerous, ecologically important fungi, yet patterns in the spatial distribution of these fungi remain little known. Forest canopies in particular are vast reservoirs of fungal diversity, but intracrown variation in fungal communities has rarely been explored. Knowledge of how fungi are distributed throughout tree crowns will contribute to our understanding of interactions between fungi and their host trees and is a first step toward investigating drivers of community assembly for plant-associated fungi...
December 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27769778/a-bioinformatics-approach-reveals-seven-nearly-complete-rna-virus-genomes-in-bivalve-rna-seq-data
#20
Umberto Rosani, Marco Gerdol
Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events...
July 15, 2017: Virus Research
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