Biology subjects

Karoonuthaisiri, N.

Publications and source records attributed to Karoonuthaisiri, N..

3 recordsLinked to original sources

bioRxiv2021

Molecular effects of mannanase-hydrolyzed coprameal to intestinal immunity in the Pacific white shrimp (Litopenaeus vannamei )

To mitigate disease outbreak, an alternative approach through enhancing shrimp immunity was explored. Mannan oligosaccharides (MOS) have been previously reported to enhance shrimp immune system. Here, coprameal samples were digested with mannanase to yield MOS, namely, mannanase-hydrolyzed coprameal (MCM) and feasibility of MCM as shrimp immunostimulant in grow-out ponds was determined. Pacific white shrimp (Litopenaeus vannamei) were fed with the commercial diet containing 1% MCM as the MCM-supplemented group and compared to the non-MCM control diet. There was no significant difference in survival rates between the MCM-supplemented and the control groups throughout the 4-month-period of the trial (p > 0.05). Gene expression analysis in shrimp intestines revealed that the transcript levels of antimicrobial peptides (anti-lipopolysaccharide factor isoform 1 (alf1), penaeidin (pen3a) and crustin (crus)) and lysozymes (lyz) were not significantly different in the MCM-supplemented group. Meanwhile, C-type lectin and toll-like receptor transcript levels, whose gene products play roles as pattern recognition proteins, were significantly higher in a group fed with MCM for 2- and 4-month periods than those of the control group (p < 0.05). The increased transcript levels of C-type lectin and toll-like receptor provide evidence for potential implementation of MCM as feed supplement to modulate shrimp immune system.

molecular biology↗

bioRxiv2020

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

genomics↗

bioRxiv2018

A genomic island of Streptomyces coelicolor harbors the self-contained regulon of an ECF sigma factor

Streptomycetes constitute the largest genus of actinobacteria, living predominantly in soil and decaying vegetation. The bacteria are widely known for their filamentous morphologies and their capacity to synthesize antibiotics and other biologically active molecules. More than a decade ago, we and others identified 22 genomic islands that Streptomyces coelicolor M145 possesses and other Streptomyces strains lack. One of these genomic islands, Genomic Island (GI) 6, encodes an extracytoplasmic function (ECF) sigma factor that we were characterizing in separate work. Here we report that artificial induction of the ECF sigma factor, which is encoded by SCO3450, causes the transcription of approximately one-fourth of GI 6, or ~26 mostly contiguous genes, to increase. More than half of the regulon encodes putative enzymes involved in small molecule metabolism. A putative haloacid dehalogenase is present. Genes encoding two putative anti-sigma factors flank SCO3450, the three genes residing within the regulon. Our data suggest that the ECF sigma factor and its regulon are a self-contained transcriptional unit that can be transferred by horizontal gene transfer. To our knowledge, only one other example has been identified of an ECF sigma factor and its contiguous regulon appearing to be transferrable by horizontal gene transfer [18,19]. Because the regulon appears not to be induced by the 44 growth conditions recently examined by Byung-Kwan Cho and colleagues [20], if it confers fitness to S. coelicolor, the regulon likely does so in as-yet unknown situations. Those situations might range from scavenging to detoxification to even communication within microbial communities.\n\nIMPORTANCEStreptomyces bacteria grow as hyphae that colonize soil and differentiate into spores when nutrients become scarce. In their terrestrial habitats, the bacteria encounter diverse conditions. Presumably so that the bacteria can cope with those conditions, the chromosomes of streptomycetes are highly dynamic, varying greatly in structure not only between species but also between closely related strains of a single species. The bacteria also have large numbers of extracytoplasmic function (ECF) sigma factors, which undoubtedly help the microorganisms respond to the plethora of challenges coming from the environment. This work illustrates these two threads of Streptomyces biology dovetailing: Genetic adaptability through horizontal gene transfer seems to have enabled Streptomyces coelicolor to acquire a self-contained transcriptional unit that consists of an ECF sigma factor and its regulon. The suggested facile movement of the regulon between microbial hosts indicates the value of the metabolism of small molecules possibly mediated by the regulon.

microbiology↗