Biology subjects

Pramoj Na Ayutthaya, P.

Publications and source records attributed to Pramoj Na Ayutthaya, P..

2 recordsLinked to original sources

bioRxiv2021

Single-cell transcriptome reveals a testis-specific expression profile of TCEA in human spermatogenesis

Transcription elongation factor A (TCEA) is a eukaryotic transcriptional molecule, required for a formation of initiation and elongation of gene transcription-mediated RNA polymerase II (RNAPII) complex, to promote transcription-coupled nucleotide excision repair (TC-NER) after RNAPII backtracking recovery. TCEA shares three isoforms in which TCEA1 is ubiquitously expressed among all eukaryotic cells. We found a spermatogenesis TCEA1 and TCEA2 expression profile has a unique transcriptional programme, compared with embryogenesis. Moreover, the testis-specific TCEA2 profile correlates with gene transcription, whereas TCEA1 specifically correlates with genes transcribed for Nuclear excision repair (NER) during human spermatogenesis. We also found that the expression activation of RNF20, a TCEA1 inhibitor, leads to expressional TCEA1 reduction, but having no direct impact on TCEA2 expression, implying the potential RNF20-dependent transcriptional switching of TCEA2 in transcriptional regulation during spermatogenesis. Our analysis defined a transcriptional bursting event where transcription-coupled repair (both Base excision repair and Nuclear excision repair) is a major pathway highly expressed in early spermatogenesis, supporting the transcriptional scanning hypothesis of which mutation of transcribed genes is effectively repaired as proposed by Xia B., et al. (2020).

bioinformatics↗

bioRxiv2020

Measuring both microbial load and diversity with a single amplicon sequencing library

The ratio of microbial population size relative to the amount of host tissue, or "microbial load", is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because conventional methods to determine load, such as serial dilution plating or quantitative PCR, add substantial experimental burden, they are only rarely paired with amplicon sequencing. Alternatively, whole metagenome sequencing of DNA contributed by host and microbes both reveals microbial community composition and enables determination of microbial load, but host DNA typically greatly outweighs microbial DNA, severely limiting the cost-effectiveness and scalability of this approach. We introduce host-associated microbe PCR (hamPCR), a robust amplicon sequencing strategy to quantify microbial load and describe interkingdom microbial community composition in a single, cost-effective library. We demonstrate its accuracy and flexibility across multiple host and microbe systems, including nematodes and major crops. We further present a technique that can be used, prior to sequencing, to optimize the host representation in a batch of libraries without loss of information. Because of its simplicity, and the fact that it provides an experimental solution to the well-known statistical challenges provided by compositional data, hamPCR will become a transformative approach throughout culture-independent microbiology.

bioengineering↗