Biology subjects

Yong, D.

Publications and source records attributed to Yong, D..

3 recordsLinked to original sources

bioRxiv2021

Reduced production of the major allergen Bla g 1 and Bla g 2 in Blattella germanica after antibiotic treatment

PurposeAllergens present in the feces or frass of cockroaches can cause allergic sensitization in humans. The use of fecal and frass extracts for immunotherapy has been previously investigated but has not yet been fully standardized. Here, we treated cockroaches with ampicillin to produce extracts with reduced amounts of total bacteria. MethodsWe performed targeted high-throughput sequencing of 16S rDNA to compare the microbiomes of ampicillin-treated and untreated (control) cockroaches. RNA-seq was performed to identify differentially expressed genes (DEGs) in ampicillin-treated cockroaches. ResultsAnalysis of the microbiome revealed that alpha diversity was lower in the ampicillin-treated group than in the control group. Beta diversity analysis indicated that ampicillin treatment altered bacterial composition in the microbiome of cockroaches. Quantitative polymerase chain reaction revealed that almost all bacteria were removed from ampicillin-treated cockroaches. RNA-seq analysis revealed 1,236 DEGs in ampicillin-treated cockroaches (compared to untreated cockroaches). Unlike bacterial composition, the DEGs varied between the two groups. Among major allergens, the expression of Bla g 2 decreased significantly in ampicillin-treated cockroaches (compared to untreated group). ConclusionsIn this study, the reduced level of allergens observed in cockroaches may be related to lower amounts of total bacteria caused by treatment with antibiotics. It is possible to make a protein extract with few bacteria for use in immunotherapy.

bioinformatics↗

bioRxiv2021

Internet of Things Architecture for High Throughput Biology

The Internet of Things (IoT) provides a simple framework to easily control online devices. IoT is now a commonplace tool used by technology companies, but it is rarely used in biology experiments. IoT can benefit research through alarm notifications, automation, and the real-time monitoring of experiments. We developed and implemented an IoT architecture to control biological devices used in experiments. We developed our own electrophysiology, microscopy, and microfluidic devices so that may be controlled through a unified IoT architecture. The system allows each device to be monitored and controlled through an online web tool. We present our IoT architecture so other labs may replicate it for their own experiments.

bioengineering↗

bioRxiv2020

Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes

Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Here, we present a substantially expanded microbiome catalog, the Human Reference Gut Microbiome (HRGM). Incorporating newly assembled 29,082 genomes from 845 fecal samples collected from three under-represented Asian countries--Korea, India, and Japan--the HRGM contains 232,098 non-redundant genomes of 5,414 representative prokaryotic species, >103 million unique proteins, and >274 million single-nucleotide variants. This is an over 10% increase from the largest reference database. The newly assembled genomes were enriched for members of the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diet. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. Ultra-deep sequencing facilitated the assembly of genomes of low-abundance taxa, and deep sequencing (>20 million read pairs) was needed for the profiling of low-abundance taxa. Importantly, the HRGM greatly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, mapping homologous sequences for human auto-antigens onto the HRGM genomes revealed the association of commensal bacteria with high cross-reactivity potential with autoimmunity. The HRGM (www.mbiomenet.org/HRGM/) will facilitate the identification and functional analysis of disease-associated gut microbiota.

microbiology↗