Methods genome fungal. Medical search. Frequent questions

and 6 (3%) concerned genomes of other animal species (Figure). (cdc.gov)
Compared to other species of the species complex, the species best adapted to oilseed rape, L. maculans "brassicae", causing important losses in the crop, has a genome that was submitted to a recent and massive burst of transposition by a few families of transposable elements (TEs). (pasteur.fr)
Whether the genome invasion contributed to speciation is still unclear to-date but there is a coincidence between this burst of TEs and divergence between two species. (pasteur.fr)
Species concepts criteria for fungal delimitation. (frontiersin.org)
Furthermore the amino acid biosynthesis pathways of the fungal species Trichoderma reesei discovered from atom-level data are shown to closely correspond to those of Saccharomyces cerevisiae. (helsinki.fi)
Experimenting with 16 fungal species, we show that the method is able to generate results that are easily interpretable and that provide hypotheses about the evolution of metabolism. (helsinki.fi)
We needed to sequence the avocado genome to make the species accessible to modern genomic-assisted breeding efforts," says Luis Herrera-Estrella, President's Distinguished Professor of Plant Genomics at Texas Tech University, who conceived of the study and completed much of the work at LANGEBIO, where he is emeritus professor, prior to joining Texas Tech University. (buffalo.edu)
Unfortunately, the size and complexity of the genomes of many agronomically important species currently hinders the undertaking of such projects. (biomedcentral.com)
An adapted figure of fungal species on the threat list for organizations like CDC and WHO. (asm.org)
In addition to changing environmental factors that drive evolution in fungal species (e.g., global warming and climate change have resulted in identification of new fungal pathogens, including new clades of C. auris ), multiple anthropological factors contribute to the development of antifungal resistance. (asm.org)
The polymorphism observed in the organization of the subtelomeric region in the genome of two Penicillium species within the high homogeneous Penicillium subgenus is for the first time reported and perhaps can be employed in future phylogenetic studies. (scielo.br)
To validate its involvement in fungal detrimental activity, a gene from this family was introduced into the genome of a fungal species that naturally does not harbor it. (scitechdaily.com)
Comparison with genetically characterized clusters from six fungal species showed that SMURF accurately recovered all clusters and detected additional potential clusters. (jcvi.org)
With the availability of more high-quality reference genome sequences from different species, the use of fungal genome resequencing becomes common. (cd-genomics.com)
With the increasing number of full genomes available for fungal species, the study of filamentous fungi has brought about a wider range of genetic manipulation opportunities. (sipav.org)
The number and size of these chromosomes can vary greatly among different fungal species. (mycologyst.art)
By performing PCR and sequencing the entire ribosomal operon (~10kb) instead of sequencing each region individually through Sanger Sequencing, scientists can gain high quality data in a high throughput manner, providing clarity and resolution of fungal species relatedness. (msu.edu)
To address a knowledge gap about the grape berry mycobiome from Washington State vineyards, next-generation sequencing of the internal transcribed spacer region (ITS1) was used to identify native yeast and fungal species on berries of cultivar 'Cabernet Sauvignon' from two vineyards at veraison and harvest in 2015 and 2016. (bvsalud.org)
Certain yeast and non-yeast fungal species known to suppress diseases or modify wine sensory properties were present in Washington vineyards, and likely have consequences to vineyard health and wine quality. (bvsalud.org)

Advance the use of genomics and metagenomics for detecting fungal pathogens and antifungal drug resistance. (cdc.gov)
WGST for outbreak investigation caused by eukaryotic pathogens without reference genomes or existing genotyping methods enables accurate source identification to guide implementation of appropriate control and prevention measures. (cdc.gov)
Genomes are found at all three corners of the epidemiologic triangle: human or animal hosts are engaged in genomic contests with pathogens of all kinds, played out in an environment teeming with the genomes of other people, animals, plants, and microbes. (cdc.gov)
Sub-objective 3.1: Determine the genomic diversity and population affinities of NX-2 strains in relation to other FHB pathogens in North America, and utilize comparative genomics to identify regions of the genome influenced by adaptive evolution. (usda.gov)
Dr Kathie Grant is an internationally recognised expert in the field of foodborne pathogens with 30 years experience in clinical and public health microbiology and a research interest in exploiting whole genome sequencing (WGS) of bacterial pathogens to improve the understanding and control of foodborne bacterial illness. (nottingham.ac.uk)
Sarah then worked on the use of fungal pathogens as biocontrol agents based in Nova Scotia and Saskatchewan, Canada from 1995-2001, latterly as part of the Canadian Government Visiting Fellowship Scheme. (forestresearch.gov.uk)

Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
More basic research concerned microbial ecology of BCAs including molecular interactions with their host fungal pathogen. (slu.se)
Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. (bmj.com)
The traceability and authentication of microbial genome assemblies to physical biological materials is typically poorly documented and not a requirement for many public genome databases. (atcc.org)
The ATCC Genome Portal was created to reestablish the trustworthiness, reliability, and accuracy of genome assemblies associated with ATCC microbial strains . (atcc.org)
As we continue to carry out whole-genome sequencing of ATCC's microbial collection, the number of reference genomes in the ATCC Genome Portal will continue to grow every month for the foreseeable future, and we encourage the research community to contact us with suggestions on taxa to prioritize in our pipeline. (atcc.org)
However, the intricacies of fungal genetics offer a unique perspective on inheritance, variation, and evolution in the microbial world. (mycologyst.art)
Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. (biomedcentral.com)
Comparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. (biomedcentral.com)
The rise of whole genome microbial sequencing: A new era for human microbiome analysis (webinar) Noon, Oct 4, 2017. (cdc.gov)
Ultimately, I hope to offer the community of soil microbial ecologists a game-changing new tool to study chemistry and ecosystem functions of microbial metabolites (including 'fungal warfare' compounds) in more realistic settings. (lu.se)

Generate new information about fungal diseases and disease-causing fungi. (cdc.gov)
Use whole genome sequencing to study how and why certain fungi spread and make people sick. (cdc.gov)
Given this data, we would hypothesize that: (i) the evolution of the fungal PPIases is driven, at least in part, by the size of the proteome, (ii) evolutionary pressures differ both between the different PPIase families and the different fungi, and (iii) whilst the cyclophilins and parvulins have evolved to perform conserved functions, the FKBPs have evolved to perform more variable roles. (biomedcentral.com)
Despite modern advances in technology to control fungal contamination in clinical settings, fungi are continuously implicated in clusters or outbreaks of infections, particularly among immunosuppressed patients ( 1 ). (cdc.gov)
The sources of fungal nosocomial outbreaks often are difficult to assess because of the widespread prevalence of fungi in the environment. (cdc.gov)
However, the robustness and accuracy of such genotyping tools depend largely on the discriminatory power of the genotyping method and availability of reference data, which often are inconsistent or incomplete for many fungi. (cdc.gov)
The advent of whole-genome sequence typing (WGST) has made fungal genotyping feasible for outbreak investigations ( 3 - 7 ), especially for fungi for which conventional genotyping methods do not exist. (cdc.gov)
In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi. (springer.com)
These data are substantiated by other examples in the literature showing that fungi tend to have a "two-speed" genome, in which a plastic compartment enriched in TE host genes is involved in pathogenicity and adaptation to host. (pasteur.fr)
Supercharging SIP in the Fungal Hyphosphere Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi. (doe.gov)
In this we have gathered complementing methodological competences so we now have a platform for exploiting technologies with filamentous fungi such as: Fungal transformation & gene constructions, DNA reporter technology (GFP, DsRed etc.), advanced fluorescent microscopy, gene knock outs and complementation, arrays and quantitative PCR, fungal characterization and diagnostic molecular tools as well as methods in evolutionary genetics. (slu.se)
To better characterize these root-colonizing fungi in their broad diversity, researchers have isolated a variety of fungal strains from the roots of healthy plants across Europe and selected 41 that are representative of the root mycobiome of A.thaliana (Figure 1). (scitechdaily.com)
In collaboration with INRAE Nancy (France) and the JGI (USA), the genomes of these fungi were sequenced and compared to other fungi that were previously described as saprotrophic, pathogenic, endophytic, or mycorrhizal. (scitechdaily.com)
Surprisingly, the scientists found that most root mycobiota members - isolated from the roots of healthy plants - derived from ancestors that were likely pathogenic, and have retained a battery of genes that were previously shown to be lost in genomes of beneficial mycorrhizal fungi. (scitechdaily.com)
However, the utilization of traditional methods to study fungi is time consuming and laborious. (sipav.org)
Recent rapid progress and wide application of a versatile genome editing technology, i.e., the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-related nuclease 9) system, has revolutionized biological research and has many innovative applications in a wide range of fields showing great promise in research and application of filamentous fungi. (sipav.org)
In this review, we introduce the CRISPR/Cas9 genome editing technology focusing on its application in research of filamentous fungi and we discuss the general considerations of genome editing using CRISPR/Cas9 system illustrating vector construction, multiple editing strategies, technical consideration of different sizes of homology arms on genome editing efficiency, off-target effects, and different transformation methodologies. (sipav.org)
The genetic basis of mating in fungi is controlled by specific loci in their genome. (mycologyst.art)
Since the beginning of my research career, I have worked with Boolean gene regulatory network models, the HP model of protein folding, stem cell regulation, circadian clocks in plants, plant-pathogen interactions, evolutionary algorithms, degradation of soil organic matter by fungi and methods for processing spectroscopic imaging data. (lu.se)

This approach has been called " genomic epidemiology "-using pathogen genome sequences to detect emerging diseases, assess their potential virulence and resistance to antibiotics, and monitor their spread in populations. (cdc.gov)
First, we reported the draft genome sequences of the cucumber-sampled C. cassiicola isolate HGCC with high virulence. (biomedcentral.com)
The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
Through the ATCC Genome Portal, you can easily search, access, and analyze thousands of reference-quality genome sequences. (atcc.org)
Burt proposed that such methods could be applied to engineer HEGs that recognise and cleave sequences within coding sequences of genes in insect genomes, with the subsequent invasion of these HEGs into a population leading to the inactivation of target genes and the subsequent decline in fitness of the targeted population [2] . (plos.org)
A large number of reads generated from sequencers are subjected to quality control, and the clean data are subsequently aligned to reference genome sequences. (cd-genomics.com)
The fungal genome can range from simple, streamlined sequences to more complex arrangements with a plethora of genes, introns, exons, and regulatory elements. (mycologyst.art)
Within the vast expanse of the fungal genome lie genes, which are sequences of DNA that code for proteins or functional RNA molecules. (mycologyst.art)
These sequences are very close together, and are often found clustered in tandem repeats in fungal genomes known as a ribosomal operon (Fig. 1). (msu.edu)
Broad Genomics Platform sequences a whole human genome every four minutes. (broadinstitute.org)
The blue bars show the number of matched mNGS sequences corresponding to various positions in the genome of the fungus. (cdc.gov)

In this paper, we evaluate the link between genome plasticity and adaptive potential using genomics and comparative genomics approaches. (pasteur.fr)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
We are also building up expertise in genomics and transcriptomics for studying community structures and their function, and gene expression in fungal host interactions. (slu.se)
Aspergillus flavus genomics such as expressed sequenced tags (EST), gene chip technologies, and whole genome sequencing strategies promises effective control strategy being developed through biotechnology. (usda.gov)
Ewan's main areas of research include functional genomics, DNA algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences in humans and Medaka fish) and use of images for chromatin structure. (nottingham.ac.uk)
Fungal genomic analysis begins with the extraction of DNA, followed by sequencing, annotation, and comparative genomics. (mycologyst.art)
Comparative genomics, on the other hand, involves comparing the genome of one fungus with another, revealing evolutionary relationships, functional adaptations, and unique genetic traits. (mycologyst.art)
The Fungal Genomics group at the Broad Institute has sequenced and analyzed a wide range of fungal organisms that are important to medicine, agriculture, and industry. (broadinstitute.org)
In partnership with the wider fungal research community, organisms have been targeted for sequencing as part of a cohesive strategy that considers both the value of sequencing data to research, health, agriculture, and industry, as well as its value in comparative genomics. (broadinstitute.org)

Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.com)
In addition, the location of effector genes within genome regions enriched in TEs has direct consequences on adaptation to plant resistance and favours a multiplicity of mutation events allowing "breakdown" of resistance. (pasteur.fr)
If you can identify the genes that control resistance, and if you know where they are in the genome, you can try to change their regulation. (buffalo.edu)
To facilitate annotation of these clusters in sequenced fungal genomes, we developed the web-based software Secondary Metabolite Unique Regions Finder (SMURF) to systematically predict clustered SM genes based on their genomic context and domain content. (jcvi.org)
These genes govern various fungal processes, from metabolism to reproduction. (mycologyst.art)
The expression of these genes, which can be influenced by both internal and external factors, leads to the synthesis of proteins that carry out specific functions within the fungal cell. (mycologyst.art)

The focus is on pathogen genomes, applying advances in molecular and bioinformatics methods first developed for human genome research. (cdc.gov)
In 2015, he joined the National Human Genome Research Institute as a founding member of the Genome Informatics Section. (nottingham.ac.uk)
Ewan led the analysis of the Human Genome gene set, mouse and chicken genomes and the ENCODE project, focusing on non-coding elements of the human genome. (nottingham.ac.uk)

As humans and animals end up consuming antifungals as medicines , they might also inhale/ingest fungal spores from the environment, thus disrupting the microbiome by tampering with the equilibrium and potentially prompting the evolution of resistance. (asm.org)

We used whole-genome sequence typing (WGST) to investigate an outbreak of Sarocladium kiliense bloodstream infections (BSI) associated with receipt of contaminated antinausea medication among oncology patients in Colombia and Chile during 2013-2014. (cdc.gov)
Small-scale DNA-based typing methods, such as variable-number tandem-repeat typing and multilocus sequence typing (MLST), use genomic similarity to assist in determining epidemiologic relatedness of fungal isolates in an outbreak investigation ( 2 ). (cdc.gov)
Genome sequence and spore germination-associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola . (biomedcentral.com)
Although conspecific, HGCC exhibited distinct genome sequence differences from a rubber tree-sampled isolate (CCP) and a human-sampled isolate (UM591). (biomedcentral.com)
When a HEG is integrated into its recognition sequence in the genome, its protein product acts to cleave its cognate site on the homologous chromosome and gene conversion or homologous recombination can result in a new copy of the HEG being inserted. (plos.org)
Fungal whole genome resequencing is an effective and accurate, method to quickly sequence and analyze fungal genomes. (cd-genomics.com)
In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. (researchsquare.com)
Four hundred fifty-six different yeast amplicon sequence variants (ASV), representing 184 distinct taxa, and 2467 non-yeast fungal ASV (791 distinct taxa) were identified in this study. (bvsalud.org)
The red line represents the average sequence depth distribution at different positions in the bacterial genome. (cdc.gov)

He was also the coordinator of an international consortium of institutions that has deciphered the genome of mycorrhizal fungus, a fungus whose symbiotic properties allow trees to generate large amounts of biomass. (wikipedia.org)
The Genome of an Important Symbiotic Fungus Has Been Sequenced. (wikipedia.org)
Fungal whole genome resequencing refers to the high-throughput sequencing of each fungus or fungal populations with a reference genome. (cd-genomics.com)
Our focus is the HIV/AIDS-related fungus, Cryptococcus neoformans, the world's most common cause of fungal meningitis, resulting in an estimated 200,000 deaths each year. (westmeadinstitute.org.au)

During this time, he pioneered the use of single-molecule sequencing for the reconstruction of complete genomes. (nottingham.ac.uk)
Multiple best practices are available to construct accurate and complete genomes from metagenomes, but high-quality MAGs are still relatively rare. (biomedcentral.com)

Each bacterial and fungal genome is sequenced on both Illumina and Oxford Nanopore platforms, resulting in a "hybrid-assembly" incorporating both sequencing technologies. (atcc.org)
We studied the successional changes in bacterial and fungal communities during the natural fermentation (0 h-96 h) of toddy. (bvsalud.org)

Using this novel high-throughput whole-genome assay, we could identity and quantify the activity of DNA regulatory elements (e.g. enhancers) that play critical roles in cell type specification and disease pathogenesis. (mpg.de)

2002). Handbook of molecular and cellular methods in biology and medicine. (wikipedia.org)
Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
It will give me the opportunity to assemble a research team that will work together both towards the novel spectroscopy method development, but also addressing specific research questions and pushing the frontier in soil fungal biology. (lu.se)

We work with partners to understand who gets fungal infections and why they get them by using epidemiology and microbiology research. (cdc.gov)
Specifically, differentiating between fungal infections originating from a single contaminated point source and those independently acquired from the environment frequently is difficult. (cdc.gov)
Molecular typing methods for discriminating strains have been an essential tool to identify potential source(s) of fungal infections in outbreaks. (cdc.gov)
It is estimated that over 2 million people die annually due to fungal infections. (asm.org)
Whole-Genome Sequencing and Variant Analysis of Human Papillomavirus 16 Infections. (cdc.gov)

Point source outbreaks are typically clonal, and the resulting isolate genomes display few to no SNP differences. (cdc.gov)
All the following culture methods include an incubation step to help grow and isolate C. auris from this community. (cdc.gov)
The resulting mutant strain was able to colonize roots more aggressively than the original isolate and this increase in fungal load in roots was associated with a penalty on plant performance. (scitechdaily.com)

Track the emergence and spread of fungal diseases by conducting molecular surveillance and genomic epidemiology. (cdc.gov)
Since joining the laboratory in 2001 she has championed the use of molecular methods leading to improvements in the detection and investigation of bacterial foodborne disease within the UK. (nottingham.ac.uk)
Our laboratory has established reliable methods for manipulating the cryptococcal genome and for studying fungal cells at the molecular level. (westmeadinstitute.org.au)
The experiment shows that the setup, based on JUNGFRAU detector and Jungfraujoch data-acquisition system, can provide a molecular moving picture of up to 500 microseconds in resolution of protein dynamics - providing ten times finer details than the previously available method. (lu.se)

With WGST, genetic relationships among isolates are determined by the phylogenetic analysis of single-nucleotide polymorphism (SNP) differences among analyzed genomes a population: typically, the fewer the number of SNPs observed between the strains, the more closely the strains are related, and the more likely they are to have a point source, provided supporting epidemiologic evidence exists. (cdc.gov)

orientalis reference genome (GenBank accession no. (cdc.gov)
reference genome. (cdc.gov)
orientalis reference genome. (cdc.gov)

The method generates highly-specific genetic information directly from diseased wheat samples to determine the identity of the pathogen strain that's associated with an epidemic. (sciencedaily.com)
Application of this method to wheat blast should unmask the pathogen in Bangladesh and contribute to a response plan. (sciencedaily.com)

CDC's lead group for preventing illness and death from fungal diseases in the United States and throughout the world. (cdc.gov)
The goal of CDC's Mycotic Diseases Branch (MDB) is to prevent illness and death from fungal diseases . (cdc.gov)
We are one of few public health groups in the world devoted to the prevention and control of fungal diseases. (cdc.gov)
We also investigate outbreaks and develop interventions to prevent fungal diseases. (cdc.gov)
Provide training and education about fungal diseases. (cdc.gov)
Calculate the number of people who get sick from fungal diseases. (cdc.gov)
Track trends and patterns in how fungal diseases affect people. (cdc.gov)
Promote education and awareness about fungal diseases. (cdc.gov)
Develop and evaluate ways to prevent fungal diseases. (cdc.gov)
Help prepare healthcare facilities and laboratories in other countries to better detect and treat fungal diseases. (cdc.gov)
Many people at risk for and suffering from fungal diseases live in limited-resource settings. (cdc.gov)
These areas of the world often lack the laboratory infrastructure needed to diagnose fungal diseases, and limited availability of antifungal medications means that some patients may not have access to lifesaving treatments. (cdc.gov)
Sign up for the Fungal Diseases Newsletter for updates from CDC's Mycotic Diseases Branch. (cdc.gov)
Fungal drugs are categorized into 4 main classes , which may be used alone or in combination to treat various fungal diseases. (asm.org)
Responsible for management of the Forest Research Northern Research Station's (NRS) pathology laboratory, and for developing and carrying out research projects to address important tree health problems in UK forests, focusing on oomycete, fungal and bacterial diseases. (forestresearch.gov.uk)
Fungal diseases are a growing global health problem and a leading cause of blindness, meningitis and death, but this area is under-researched worldwide. (westmeadinstitute.org.au)

2022). Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. (caltech.edu)
2022). Harmonizing model organism data in the Alliance of Genome Resources. (caltech.edu)

SNP detection for massively parallel whole-genome resequencing. (cd-genomics.com)
Development of massively parallel genome-wide DNA regulatory region screen for mammalian genomes (STARR-seq). (mpg.de)

Each genome entry is provided with sequencing and assembly quality metrics, annotation metrics, and additional metadata for each strain such as antibiotic susceptibility, geographical origins, and phenotypic data. (atcc.org)
He led experimental projects relating to improving genome annotation methods and created automated systems of gene dataset refinement to guide more accurate gene prediction of fungal mitochondrial DNA. (marshallip.com)
FunGAP: Fungal Genome Annotation Pipeline Using Evidence-based Gene Model Evaluation. (cdc.gov)

The first mycorrhizal fungal genome project was a success. (wikipedia.org)

Our comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control. (researchsquare.com)
Via collaborations with academic and industry partners, we explore the evolutionary basis of drug and insecticide resistance, develop new methods of generating and applying genomic data in parasite and vector systems, and identify the genetic determinants of vaccine efficacy. (broadinstitute.org)

Photograph of 41 fungal isolates representative of the A. thaliana root mycobiome. (scitechdaily.com)
To test this hypothesis, A. thaliana plants were grown in a closed system in the absence of any microorganism, or re-colonized with each of the selected 41 fungal isolates. (scitechdaily.com)

CDC is working with partners to improve access to fungal diagnostics and antifungal medications around the globe. (cdc.gov)
Novel antifungal therapies selective for fungal cellular components are urgently needed to reduce the high global morbidity, mortality and cost associated with treating invasive fungal disease. (westmeadinstitute.org.au)

F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level. (researchsquare.com)
However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics. (biomedcentral.com)

Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. (frontiersin.org)
Advances in whole-genome sequencing technologies have enabled numerous key discoveries. (researchsquare.com)
Advances in the application of genetic manipulation methods to Apicomplexan parasites. (cdc.gov)

But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)
The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low-dose irradiation compared to the evolution of microbes here on Earth. (biomedcentral.com)
The researchers concluded that fungal evolution proceeded more gradually and with more diversity than previously suspected. (phys.org)

I also want to clarify how interspecific fungal interactions under varying nutrient conditions affect the composition and function of their secreted chemical compounds, and how that, in turn, affects fungal decomposition of organic matter. (lu.se)

We provide fungal whole genome resequencing using a whole-genome shotgun strategy by next generation sequencing (Illumina HiSeq PE150/251, 100X) or long-read sequencing platforms (PacBio RSII or Nanopore MinION instrument). (cd-genomics.com)

Tracing the Evolution of Shiitake Mushrooms Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. (doe.gov)
When available, the information provided by whole-genome sequencing projects provides an entry into an understanding of genome structure and evolution and gene discovery, and function. (biomedcentral.com)

To date, viral genomes have been produced using only Illumina sequencing. (atcc.org)
Novel Stable Ebola Virus Minigenome Replicon Reveals Remarkable Stability of the Viral Genome. (cdc.gov)

Prior to his legal career at Marshall Gerstein, Spencer was an Associate Researcher at the Joint Genome Institute and the Lawrence Berkeley National Lab. (marshallip.com)

We found that a lot of the primary assumptions that haploid gives rise to diploid lifestyle-increasing complexity through the fungal kingdom-were not true. (phys.org)

Esa Pitkänen will defend his thesis 'Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks' on 12 Nov 2010 at 12 noon in the Main building, auditorium XII. (helsinki.fi)
In this thesis, we propose efficient computational methods for metabolic modeling. (helsinki.fi)
In the second part, we propose computational methods for metabolic reconstruction in the gapless modeling framework. (helsinki.fi)
In silico simulation of a genome-scale metabolic model ( i ZX637) further verified that pyruvate carboxylase ( pyc ) via the reductive tricarboxylic acid cycle strengthened carbon flux for PMA synthesis. (biomedcentral.com)
We showed that integrated metabolome- and genome-scale model analyses were an effective approach for engineering the metabolic node for PMA synthesis, and also developed an economical and green process for PMA and MA production from renewable biomass feedstocks. (biomedcentral.com)
Using these methods, we have identified a fungal metabolic pathway that may potentially be blocked by drugs. (westmeadinstitute.org.au)

Silencing of transposable elements (TEs) is essential for maintaining genome stability. (edu.au)

The research projects aim to advance methods in microbiological ecology and map the development of sex chromosomes. (lu.se)

This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures. (springer.com)
Professor Kamoun, with colleagues at The Genome Analysis Centre and John Innes Centre in Norwich, and with Professor Tofazzal Islam's Team of Bangabndhu Sheikh Mujubur Rahman Agricultural University (BSMRAU) in Bangladesh, is hoping that the www.wheatblast.net website, together with an accompanying Facebook page, will provide a hub for information, collaboration and comment. (sciencedaily.com)
The group of scientists includes Dr Diane Saunders at The Genome Analysis Centre and John Innes Centre who developed a technique last year, known as Field Pathogenomics. (sciencedaily.com)
Professor Neil Hall, Director of The Genome Analysis Centre said: "It is critical in emerging crises like this that scientific data is rapidly generated and made available as soon as possible. (sciencedaily.com)
Subsequent comparative analysis revealed the striking biosynthetic capacity and variability of the fungal SM pathways and the correlation between unicellularity and the absence of SMs. (jcvi.org)
His research focuses on the efficient analysis of large-scale genomic datasets and new methods for metagenomic analysis and assembly of high-noise single-molecule sequencing data. (nottingham.ac.uk)
Currently, he is also a volunteer at the Rare Genome Institute performing computational variant analysis. (marshallip.com)
Re-Assembly and Analysis of an Ancient Variola Virus Genome. (cdc.gov)
CDC used whole genome sequencing (WGS) analysis to link one case to contaminated opened powdered formula from the patient's home and the other to contaminated breast pump equipment. (medscape.com)
These chips reveal fungal cells for microscopic analysis. (lu.se)

Among the 106 recurring non-yeast fungal taxa, Alternaria, Cladosporium and Ulocladium were especially abundant in the vineyard. (bvsalud.org)

Aflatoxins are natural secondary metabolites produced by the fungal mold Aspergillus flavus and A. parasiticus. (usda.gov)
eg, ingestion of food contaminated with fungal aflatoxins is believed to contribute to the high incidence of HCC in subtropical regions. (msdmanuals.com)

This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. (springer.com)

Overall, there is growing recognition that a single set of criteria do not sufficiently describe the diversity seen among fungal lineages. (frontiersin.org)
Here, we describe our laboratory and bioinformatics methods, the diversity of the current contents of the ATCC Genome Portal , it's current capabilities, and new features for use by the research community. (atcc.org)
This experiment identified a wide diversity of fungal effects on plant growth, ranging from highly detrimental to beneficial. (scitechdaily.com)

others described or applied epidemiologic methods (Table). (cdc.gov)

In recent years, the world has experienced an increase in mycotoxin contamination of grains due to climatic and agronomic changes that encourage fungal growth during cultivation. (usda.gov)

Dr. Jonathan Jacobs leads ATCC's Sequencing & Bioinformatics Center and the development of the ATCC Genome Portal. (atcc.org)

Climate induced physiological changes that occur in the host and influence mycotoxins and/or Fusarium infection will be useful as markers in plant breeding programs aimed at developing climate resilient fungal resistance strategies. (usda.gov)

We provide the fungal whole genome resequencing platform to help you determine single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs), and copy number variations (CNVs) in the fungal genomes. (cd-genomics.com)

PPIase numbers within these fungal repertoires appears associated with genome size and orthology between repertoires was found to be low. (biomedcentral.com)
Also, the repertoire of Cryptococcus neoformans may represent a better model fungal system within which to study the functions of the PPIases as its genome size and genetic tractability are equal to those of Saccharomyces cerevisiae , whilst its repertoires exhibits greater orthology to that of humans. (biomedcentral.com)
According to the last author of the study Stéphane Hacquard, "These results indicate that repertoires of plant cell-wall degrading enzymes in fungal genomes are key genetic determinants driving access to the root endosphere and explaining why robust root colonizers can potentially become harmful if they degrade roots too aggressively. (scitechdaily.com)

Respond quickly to fungal disease outbreaks and other emerging issues. (cdc.gov)
Detecting fungal outbreaks early is important so that the people affected can get the right treatment and so that health officials can prevent others from getting sick. (cdc.gov)

Research and develop new detection, diagnostic, and subtyping methods. (cdc.gov)
The ATCC Genome Portal and the data contained therein is freely available for research-use and is accessible online ( https://genomes.atcc.org ) or via an authenticated REST-API. (atcc.org)
Genome research , 2009, 19(6): 1124-1132. (cd-genomics.com)
Moreover, the traditional methods for functional gene discovery are insufficient to meet the modern-day research demands due to the high error rates and low efficiencies. (researchsquare.com)

Genome Insider: A Shrubbier Version of Rubber Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant. (doe.gov)
Alliance of Genome Resources Consortium. (caltech.edu)

They often have a high adaptive potential allowing them to rapidly counteract the control methods used by men in agrosystems. (pasteur.fr)

Anatomy15

Organisms33

Diseases3

Chemicals and Drugs38

Analytical, Diagnostic and Therapeutic Techniques and Equipment31

Phenomena and Processes142

Disciplines and Occupations5

Technology, Industry, Agriculture3

Information Science15

Health Care5

Species19

Pathogens6

Microbial11

Fungi19

Sequences11

Genomics9

Genes6

Human genome3

Microbiome1

Sequence10

Fungus4

Complete genomes2

Bacterial and fungal2

High-throughput1

Biology3

Infections5

Isolate3

Molecular4

Strains1

Reference genome3

Pathogen2

Diseases16

20222

Massively parallel2

Annotation3

Mycorrhizal1

Evolutionary2

Isolates2

Antifungal2

Phylogenetic2

Advances3

Researchers3

Decomposition1

Illumina HiSeq1

Evolution2

Viral2

Joint Genome In1

Complexity1

Metabolic6

Transposable elements1

Ecology1

Analysis10

Taxa1

Aflatoxins2

Interactions1

Diversity3

Epidemiologic1

Contamination1

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Fusarium1

SNPs1

Repertoires3

Outbreaks2

Research4

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Adaptive1