Search results for "genomic"
showing 10 items of 1737 documents
Global variation in the genetic and biochemical basis of diamondback moth resistance to Bacillus thuringiensis
1997
Insecticidal proteins from the soil bacterium Bacillus thuringiensis (Bt) are becoming a cornerstone of ecologically sound pest management. However, if pests quickly adapt, the benefits of environmentally benign Bt toxins in sprays and genetically engineered crops will be short-lived. The diamondback moth ( Plutella xylostella ) is the first insect to evolve resistance to Bt in open-field populations. Here we report that populations from Hawaii and Pennsylvania share a genetic locus at which a recessive mutation associated with reduced toxin binding confers extremely high resistance to four Bt toxins. In contrast, resistance in a population from the Philippines shows multilocus control, a …
Bacterial Community Structure of an IFAS-MBRs Wastewater Treatment Plant
2017
TIn this work, the bacterial community putatively involved in BNR events of a UCT-MBMBR pilot plant was elucidated by both culture-dependent and metagenomics DNA analyses. The presence of bacterial isolates belonging to Bacillus (in the anoxic compartment) and to Acinetobacter, Stenotrophomonas, Rhodococcus, Escherichia and Aeromonas (in the aerobic compartment) is in agreement with the nitrification/denitrification processes observed in the plant. Moreover, the study of bacterial community structure by NGS revealed a microbial diversity suggesting a biochemical complexity which can be further explored and exploited to improve UCT-MBMBR plant performance.
Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis
2011
Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, parti…
A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella
2013
Gene transfer agents (GTAs) randomly transfer short fragments of a bacterial genome. A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii. Although GTAs are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. Here, we present a comparative analysis of 16 Bartonella genomes ranging from 1.4 to 2.6 Mb in size, including six novel genomes from Bartonella isolated from a cow, two moose, two dogs, and a kangaroo. A phylogenetic tree inferred from 428 orthologous core genes indicates that the deadly human pathogen B. bacilliformis is related to the ruminant-adapted clade, rather than being the earliest diverging…
Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022
2022
Background The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Aim To comprehensively describe Omicron spread in Italy in the 2 subsequent months and its impact on the overall SARS-CoV-2 circulation at population level. Methods We analyse data from four genomic surveys conducted across the country between December 2021 and January 2022. Combining genomic sequencing results with epidemiological records collated by the National Integrated Surveillance System, the Omicron reproductive number and exponential growth rate are estimated, as well as SARS-CoV-2 transmissibility. Results Omicron became dominant in Italy less than 1 month after its first detection,…
Beckwith–Wiedemann syndrome: multiple molecular mechanisms
2006
Beckwith–Wiedemann syndrome (BWS) is a congenital overgrowth condition with an increased risk of developing embryonic tumours, such as Wilms' tumour. The cardinal features are abdominal wall defects, macroglossia and gigantism. BWS is generally sporadic; only 10–15% of cases are familial. A variety of molecular aberrations have been associated with BWS. The only mutations within a gene are loss-of-function mutations in the CDKN1C gene, which codes for an imprinted cell-cycle regulator. CDKN1C mutations appear to be particularly associated with umbilical abnormalities, but not with increased predisposition to Wilms' tumour. In the remaining BWS subgroups, a disturbance of the tight epigeneti…
Big Data in metagenomics: Apache Spark vs MPI.
2020
The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when…
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
2021
Abstract Background Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen as the future for genomic data storage and processing, with MapReduce-Hadoop as leaders. Somewhat surprisingly, none of the specialized FASTA/Q compressors is available within Hadoop. Indeed, their deployment there is not exactly immediate. Such a State of the Art is problematic. Results We provide major advances in two different directions. Methodologically, we propose two general methods, with the corresponding software, that make very easy to deploy …
Radiation therapy after radical prostatectomy: what has changed over time?
2021
The role and timing of radiotherapy (RT) in prostate cancer (PCa) patients treated with radical prostatectomy (RP) remains controversial. While recent trials support the oncological safety of early salvage RT (SRT) compared to adjuvant RT (ART) in selected patients, previous randomized studies demonstrated that ART might improve recurrence-free survival in patients at high risk for local recurrence based on adverse pathology. Although ART might improve survival, this approach is characterized by a risk of overtreatment in up to 40% of cases. SRT is defined as the administration of RT to the prostatic bed and to the surrounding tissues in the patient with PSA recurrence after surgery but no …
Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis
2021
International audience; Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand our understanding of soil viruses and their putative contributions to soil microbial processes, we analysed metagenomes of community-level virus-enriched suspensions by tangential flow filtration obtained from two French agricultural soils. We found viral sequences representing a total of 239 viral operational taxonomic units that corresponded to 29.5% of the mapping reads in the metagenomic datasets.…