Biology subjects

Press, C. M.

Publications and source records attributed to Press, C. M..

4 recordsLinked to original sources

bioRxiv2023

Krisp: A python package for designing CRISPR and amplification-based diagnostic assays from whole genome data

Recent pandemics such as COVID-19 have highlighted the importance of rapidly developing diagnostics to detect and monitor evolving pathogens. CRISPR-Cas technology, combined with isothermal DNA amplification methods, has recently been used to develop diagnostic assays for sequence-specific recognition of DNA or RNA. These assays have similar sensitivity to the gold standard qPCR but can be deployed as easy to use and inexpensive test strips. However, the discovery of diagnostic regions of a genome flanked by conserved regions where primers can be designed requires extensive bioinformatic analyses of genome sequences. We developed the python package krisp to find primers and diagnostic sequences that differentiate groups of samples from each other at any taxonomic scale, using either unaligned genome sequences or a variant call format (VCF) file as input. Krisp has been optimized to handle large datasets by using efficient algorithms that run in near linear time, use minimal RAM, and leverage parallel processing when available. The validity of krisp results has been demonstrated in the laboratory with the successful design of SHERLOCK assays to distinguish the sudden oak death pathogen Phytophthora ramorum from closely related Phytophthora species. Krisp is released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays. Author summaryPathogens continue to emerge at accelerated rates affecting animals, plants, and ecosystems. Rapid development of novel diagnostic tools is needed to monitor novel pathogen variants or groups. We developed the computational tool krisp to identify genetic regions suitable for development of CRISPR diagnostics and traditional amplification-based diagnostics such as PCR. Krisp scans whole genome sequence data for target and non-target groups to identify diagnostic regions based on DNA or RNA sequences. This computational tool has been validated using genome data for the sudden oak death pathogen Phytophthora ramorum. Krisp is released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays and other amplification-based assays.

bioinformatics↗

bioRxiv2021

High quality, phased genomes of Phytophthora ramorum clonal lineages NA1 and EU1

Phytophthora ramorum is the causal agent of sudden oak death in West Coast forests and currently two clonal lineages, NA1 and EU1, cause epidemics in Oregon forests. Here, we report on two high-quality genomes of individuals belonging to the NA1 and EU1 clonal lineages respectively, using PacBio long-read sequencing. The NA1 strain Pr102, originally isolated from coast live oak in California, is the current reference genome and was previously sequenced independently using either Sanger (P. ramorum v1) or PacBio (P. ramorum v2) technology. The EU1 strain PR-15-019 was obtained from tanoak in Oregon. These new genomes have a total size of 57.5 Mb, with a contig N50 length of ~3.5-3.6 Mb and encode ~15,300 predicted protein-coding genes. Genomes were assembled into 27 and 28 scaffolds with 95% BUSCO scores and are considerably improved relative to the current JGI reference genome with 2,575 or the PacBio genomes with 1,512 scaffolds. These high-quality genomes provide a valuable resource for studying the genetics, evolution, and adaptation of these two clonal lineages.

plant biology↗

bioRxiv2021

Small intestine lactobacilli growth promotion and immunomodulation in weaner pigs fed Cyberlindnera jadinii yeast high inclusion diet and exposed to enterotoxigenic Escherichia coli F4+: O149

1Enterotoxigenic Escherichia coli (ETEC) F4+: O149 is a causative agent for the development of post-weaning diarrhoea (PWD) in pigs that contributes to production losses. Yeast cell wall components used as a feed additive can modulate gut immunity and help protect animals from enteric infections. This work investigated how a novel yeast diet with high inclusion of yeast proteins (40% of crude protein) affected the course of ETEC mediated diarrhoea in weaner piglets from a farm with or without a history of post-weaning diarrhoea. We found that immune response to F4ab ETEC infection and appetite of the animals were altered by high inclusion C. jadinii yeast. The results indicate that the novel diet can support the diseased animals either directly through the effect of yeast beta-glucans and mannans or indirectly through the promotion of small intestine lactobacilli or both.

microbiology↗

bioRxiv2019

Candida utilis yeast as a functional protein source for Atlantic salmon (Salmo salar L.): Local intestinal tissue and plasma proteome responses

Microbial ingredients such as Candida utilis yeast are known to be functional protein sources with immunemodulating effects whereas soybean meal causes soybean meal-induced enteritis in the distal intestine of Atlantic salmon (Salmo salar L.). Inflammatory or immunomodulatory stimuli at the local level in the intestine may alter the plasma proteome profile of Atlantic salmon. These deviations can be helpful indicators for fish health and therefore potential tools in diagnosis of fish diseases. The present work aimed to identify local intestinal tissue responses and changes in plasma protein profiles of Atlantic salmon fed inactive dry Candida utilis yeast biomass, soybean meal, or combination of soybean meal based diet with various inclusion levels of Candida utilis. A fishmeal based diet was used as control diet. Inclusion of Candida utilis yeast to a fishmeal based diet did not alter the morphology, immune cell population or gene expression of the distal intestine, but gave a plasma proteome profile different from the fishmeal based control. Lower levels of Candida utilis combined with soybean meal modulated immune cell populations in the distal intestine and reduced the severity of soybean meal-induced enteritis, while higher inclusion levels of Candida utilis were less effective. The results suggest that Candida utilis could induce systemic responses without altering intestinal morphology, and thus could be a high-quality alternative protein source with potential functional properties in diets for Atlantic salmon.

immunology↗