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A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi

Jana Sperschneider, Donald M Gardiner, Jennifer M Taylor, James K Hane, Karam B Singh, John M Manners
2013 BMC Genomics  
Results: We take advantage of the availability of sequenced fungal genomes and present an unbiased method for finding putative pathogen proteins and secreted effectors in a query genome via comparative  ...  Three F. graminearum protein clusters are found with an enriched secretion signal.  ...  Our comparative analysis pipeline predicts proteins in a query pathogen genome which have HMM sequence similarity hits predominantly in fungal pathogens.  ... 
doi:10.1186/1471-2164-14-807 pmid:24252298 pmcid:PMC3914424 fatcat:d7nnzxbc2vhw7hkju53egcjdce

Genome and Bioinformatic Analysis of a HAdV-B14p1 Virus Isolated from a Baby with Pneumonia in Beijing, China

Liuying Tang, Junjing An, Zhengde Xie, Shoaleh Dehghan, Donald Seto, Wenbo Xu, Yixin Ji, Amit Kapoor
2013 PLoS ONE  
These genome data, its analysis, and this report provide a reference for any additional HAdV-B14 outbreak in China and provide the basis for the development of adenovirus vaccines and molecular pathogen  ...  reference adenovirus genome sequences archived in GenBank.  ...  Sequence analysis shows a small number of genome changes between the recent China and USA strains of HAdV-B14p1, with nearly identical differences in both that are divergent from the genome sequenced from  ... 
doi:10.1371/journal.pone.0060345 pmid:23555956 pmcid:PMC3612040 fatcat:xcu4ybaml5cf5lajq32ieieclm

Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray

S. Fukiya, H. Mizoguchi, T. Tobe, H. Mori
2004 Journal of Bacteriology  
Comparative genomic hybridization (CGH) microarray analysis was used to compare the gene content of E. coli K-12 with the gene contents of pathogenic strains.  ...  The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified becasue of insertions and deletions.  ...  This result suggested that duplicated genomic regions in pathogenic strains could be also detected as spots with higher signal ratios in the CGH microarray analysis.  ... 
doi:10.1128/jb.186.12.3911-3921.2004 pmid:15175305 pmcid:PMC419953 fatcat:tilzze5kdzh4nfwimz2vn4k35m

A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

Shamira J Shallom, Jenni N Weeks, Cristi L Galindo, Lauren McIver, Zhaohui Sun, John McCormick, L Adams, Harold R Garner
2011 BMC Microbiology  
Current approaches for pathogen detection rely on prior genomic sequence information.  ...  Each genome hybridized on this array has a unique pattern of signal intensities corresponding to each of these probes.  ...  We appreciate the assistance of Linda Gunn, Renee Nester, Traci Roberts and Laurie Spotswood for administrative assistance. We also appreciate Zyagen and BEI resources for providing genomic DNA.  ... 
doi:10.1186/1471-2180-11-132 pmid:21672191 pmcid:PMC3130645 fatcat:snez54arl5gz7mp4ez3a2bkiym

Structured Framework and Genome Analysis of Magnaporthe grisea Inciting Pearl Millet Blast Disease Reveals Versatile Metabolic Pathways, Protein Families, and Virulence Factors

Bhaskar Reddy, Sahil Mehta, Ganesan Prakash, Neelam Sheoran, Aundy Kumar
2022 Journal of Fungi  
Here, we aimed to determine the genomic basis of the pathogenicity and underlying biochemical pathways in Magnaporthe using the genome sequence of a pearl millet-infecting M. grisea PMg_Dl generated by  ...  In silico virulence analysis revealed the presence of 51VFs and 539 CAZymes in the genome.  ...  The authors acknowledge the assistance rendered by Asharani Patel, PhD scholar, IARI, New Delhi for microscopic imaging of M. grisea PMg_Dl.  ... 
doi:10.3390/jof8060614 pmid:35736098 pmcid:PMC9225118 fatcat:5im2pvjbx5gkhppjggdwysuv2q

Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array

C. Jaing, S. Gardner, K. McLoughlin, J. B. Thissen, T. Slezak
2011 PDA journal of pharmaceutical science and technology  
In addition, the oligonucleotide probes were selected to enable detection of novel, divergent species with homology to sequenced organisms.  ...  This array can detect any sequenced viruses or bacteria within 24 hours.  ...  Given that approximately 1000 species of human viral and bacterial pathogens have been sequenced at present, PCR assays are too limited for broad-spectrum microbial analysis.  ... 
doi:10.5731/pdajpst.2011.00838 pmid:22294595 fatcat:pqr5p4ol6rdqnbomutkrf5djci

Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

D. A. Baldwin, M. Feldman, J. C. Alwine, E. S. Robertson
2014 mBio  
of upstream sample preparation protocols and downstream data analysis.  ...  These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.  ...  The authors have no sources of financial support that pose a conflict of interest for conducting or interpreting the work presented in this paper.  ... 
doi:10.1128/mbio.01714-14 pmid:25227467 pmcid:PMC4172075 fatcat:x7igyl7fafadrovj3yja7iijqq

Detection of ESKAPE pathogens and Clostridioides difficile in Simulated Skin Transmission Events with Metagenomic and Metatranscriptomic Sequencing [article]

Krista L. Ternus, Nicolette C. Keplinger, Anthony D. Kappell, Gene D. Godbold, Veena Palsikar, Carlos A. Acevedo, Katharina L. Weber, Danielle S. LeSassier, Kathleen Q. Schulte, Nicole M. Westfall, F. Curtis Hewitt
2021 bioRxiv   pre-print
of metagenomic analysis in clinical settings or for epidemiological studies, but also highlight the limits associated with the detection and characterization of pathogens at low abundance in a microbial  ...  Next generation sequencing (NGS) has the capacity to detect a wide variety of pathogens, virulence elements, and antimicrobial resistance (AMR) signatures in healthcare settings without the need for culturing  ...  Alignment of 296 reads to the expected pathogen genomes showed a similar trend of stronger genomic signals in 297 the direct, high-spike-in scenarios (x axes).  ... 
doi:10.1101/2021.03.04.433847 fatcat:x3omopg4obh4lcf3ouua3um3mq

Microarray-based comparison of genetic differences between strains of Streptomyces turgidiscabies with focus on the pathogenicity island

2010 Molecular plant pathology  
Data from comparative genomic hybridization with probes designed for S. scabies genes and for the PAI of S. turgidiscabies were compared by multilocus cluster analysis, which revealed two strains of S.  ...  The areas of the pathogenicity island (PAI) designated as 'colonization region' (CR) and 'toxicogenic region' (TR) [Lerat et al. (2009) Mol.  ...  Financial support from the Finnish Ministry of Agriculture and Forestry (grant 4541/501/2006) is gratefully acknowledged.  ... 
doi:10.1111/j.1364-3703.2010.00641.x pmid:21029319 fatcat:3gdphfjedvf3dcbewowzlibvaq

Insights from Sequencing Fungal and Oomycete Genomes: What Can We Learn about Plant Disease and the Evolution of Pathogenicity?

D. M. Soanes, T. A. Richards, N. J. Talbot
2007 The Plant Cell  
THE RAPID PACE OF FUNGAL GENOME SEQUENCING There are currently genome sequences from 12 plant pathogenic fungi and two oomycetes that are publicly available, out of a total of .40 fungal genomes that have  ...  Analysis of the genome of the Dothideomycete wheat pathogen S. nodurum reveals only three Pth11-like proteins in contrast with other ascomycete pathogens.  ... 
doi:10.1105/tpc.107.056663 pmid:18024565 pmcid:PMC2174898 fatcat:ybwtguo77fdnbheycrleghvp6u

Bioinformatic Comparison of Bacterial Secretomes

Catharine Song, Aseem Kumar, Mazen Saleh
2009 Genomics, Proteomics & Bioinformatics  
Our analysis also suggests that even for a theoretical minimal genome of 300 open reading frames, a fraction of this gene pool (up to a maximum of 20%) may code for proteins with Sec-dependent signal sequences  ...  Specif ically, the secretome of Borrelia burgdoferi has an unusually large number of putative lipoproteins, and the signal peptides of mycoplasmas show closer sequence similarity to those of the Gramnegative  ...  WCFS1 (9 ) and the analysis of the genome sequence of Natronomonas pharaonis (10 ) .  ... 
doi:10.1016/s1672-0229(08)60031-5 pmid:19591790 pmcid:PMC5054224 fatcat:uipdzofbgzaetal7xtixrxkwxe

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

Derrick E. Fouts, Michael A. Matthias, Haritha Adhikarla, Ben Adler, Luciane Amorim-Santos, Douglas E. Berg, Dieter Bulach, Alejandro Buschiazzo, Yung-Fu Chang, Renee L. Galloway, David A. Haake, Daniel H. Haft (+18 others)
2016 PLoS Neglected Tropical Diseases  
While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species  ...  of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and PLOS Neglected Tropical Diseases |  ...  Craig Venter Institute sequencing, bioinformatics and IT departments for supporting the infrastructure required to determine the genome sequences, annotation and pan-genome and other analyses carried out  ... 
doi:10.1371/journal.pntd.0004403 pmid:26890609 pmcid:PMC4758666 fatcat:zb242j6gj5hslpbfuyj64gsnxe

Draft genome sequence of Karnal bunt pathogen (Tilletia indica) of wheat provides insights into the pathogenic mechanisms of quarantined fungus

Anil Kumar, Vishakha Pandey, Manoj Singh, Dinesh Pandey, M. S. Saharan, Soma S. Marla, Wujun Ma
2017 PLoS ONE  
Citation: Kumar A, Pandey V, Singh M, Pandey D, Saharan MS, Marla SS (2017) Draft genome sequence of Karnal bunt pathogen (Tilletia indica) of wheat provides insights into the pathogenic mechanisms of  ...  The T. indica genome was sequenced employing hybrid approach of PacBio Single Molecule Real Time (SMRT) and Illumina HiSEQ 2000 sequencing platforms.  ...  Thus, genome sequencing of the fungus T. indica is the only alternative to elucidate the pathogenic mechanisms of Karnal bunt of wheat.  ... 
doi:10.1371/journal.pone.0171323 pmid:28152050 pmcid:PMC5289553 fatcat:t7ymgugxcneprdrsonz7hascia

Secretome: clues into pathogen infection and clinical applications

Shoba Ranganathan, Gagan Garg
2009 Genome Medicine  
Recent studies on secretome analysis reveal that secretory proteins play an important role in pathogen infection and host-pathogen interactions.  ...  Excretory/secretory proteins of pathogens change the host cell environment by suppressing the immune system, to aid the proliferation of infection.  ...  We thank Dr SH Nagaraj for an initial version of Figure 1 .  ... 
doi:10.1186/gm113 pmid:19951402 pmcid:PMC2808748 fatcat:jyszul4ixfhopadhxjnb5ts3ge

Removing Contaminants from Metagenomic Databases [article]

Jennifer Lu, Steven Salzberg
2018 bioRxiv   pre-print
Using this pipeline, we have produced a database of "clean" eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools.  ...  However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison.  ...  Pathogen Discovery Bioinformatics Pipelines A critical step in using NGS for diagnosis is in the bioinformatics analysis of the millions (or billions) of genomic reads that result from a sequencing experiment  ... 
doi:10.1101/261859 fatcat:364k6kfj6fd2hjgcstx5kpcjse
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