Biology subjects

Nguyen, S. V.

Publications and source records attributed to Nguyen, S. V..

4 recordsLinked to original sources

bioRxiv2023

Craniofacial diversity across Danionins and the effects of TH status on craniofacial morphology of two Danio species

The model zebrafish (Danio rerio) belongs to the Danioninae subfamily with a range of informative phenotypes. However, the craniofacial diversity across the subfamily is not fully described. To better understand craniofacial phenotypes across Danioninae we used microCT and 3D geometric morphometrics to capture skull shapes from nine species. The Danio species examined showed largely similar skull shapes, although D. aesculapii, the sister species to D. rerio showed a unique morphology. Two non-Danio species examined, Chela dadiburjori and Devario aequipinnatus showed distinct skull morphologies unique from those of other species examined. Thyroid hormone regulates skeletal development and remodeling, and we asked if changes in developmental thyroid hormone metabolism could underlie some of the craniofacial diversity across Danioninae. We reared two Danio species under altered thyroid profiles, finding that hypothyroid individuals from both species showed corresponding morphological shifts in skull shape. Hypothyroid Danios showed skull morphologies closer to that of Chela and unlike any of the examined wild-type Danio species. We provide an examination of the evolved craniofacial diversity across Danioninae, and demonstrate that alterations to thyroid hormone have the capacity to create unique skull phenotypes.

evolutionary biology↗

bioRxiv2021

Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms

Assessments of genomic prediction accuracies using artificial intelligence (AI) algorithms (i.e., machine and deep learning methods) are currently not available or very limited in aquaculture species. The principal aim of this study was to examine the predictive performance of these new methods for disease resistance to Edwardsiella ictaluri in a population of striped catfish Pangasianodon hypophthalmus and to make comparisons with four common methods, i.e., pedigree-based best linear unbiased prediction (PBLUP), genomic-based best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP) and a non-linear Bayesian approach (notably BayesR). Our analyses using machine learning (i.e., ML-KAML) and deep learning (i.e., DL-MLP and DL-CNN) together with the four common methods (PBLUP, GBLUP, ssGBLUP and BayesR) were conducted for two main disease resistance traits (i.e., survival status coded as 0 and 1 and survival time, i.e., days that the animals were still alive after the challenge test) in a pedigree consisting of 560 individual animals (490 offspring and 70 parents) genotyped for 14,154 Single Nucleotide Polymorphism (SNPs). The results using 6470 SNPs after quality control showed that AI methods outperformed PBLUP, GBLUP and ssGBLUP, with the increases in the prediction accuracies for both traits by 9.1 - 15.4%. However, the prediction accuracies obtained from AI methods were comparable to those estimated using BayesR. Imputation of missing genotypes using AlphaFamImpute increased the prediction accuracies by 5.3 - 19.2% in all the methods and data used. On the other hand, there were insignificant decreases (0.3 - 5.6%) in the prediction accuracies for both survival status and survival time when multivariate models were used in comparison to univariate analyses. Interestingly, the genomic prediction accuracies based on only highly significant SNPs (P < 0.00001, 318 - 400 SNPs for survival status and 1362 - 1589 SNPs for survival time) were somewhat lower (0.3 to 15.6%) than those obtained from the whole set of 6,470 SNPs. In most of our analyses, the accuracies of genomic prediction were somewhat higher for survival time than survival status (0/1 data). It is concluded that there are prospects for the application of genomic selection to increase disease resistance to Edwardsiella ictaluri in striped catfish breeding programs.

genetics↗

bioRxiv2019

Yersinia canariae sp. nov., isolated from a human yersiniosis case

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technology (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within Yersinia, despite biochemical similarities to Yersinia enterocolitica. The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is CFS3336T (=NCTC 14382T/ =LMG Accession under process).

microbiology↗

bioRxiv2019

Biological Impact of a Large Scale Genomic Inversion that Grossly Disrupts the Relative Positions of the Origin and Terminus Loci of the Streptococcus pyogenes Chromosome

A large-scale genomic inversion encompassing 0.79 Mb of the 1.816 Mb-long Streptococcus pyogenes serotype M49 strain NZ131 chromosome spontaneously occurs in a minor subpopulation of cells, and in this report genetic selection was used to obtain a stable lineage with this chromosomal rearrangement. This inversion, which drastically displaces the ori site, changes the relative length of the replication arms so that one replichore is approximately 0.41 Mb while the other is about 1.40 Mb in length. Genomic reversion to the original chromosome constellation is not observed in PCR-monitored analyses after 180 generations of growth in rich medium. As compared to the parental strain, the inversion surprisingly demonstrates a nearly identical growth pattern in exponential phase. Similarly, when cultured separately in rich medium during prolong stationary phase or in an experimental acute infection animal model (Galleria mellonella), the survival rate of both the parental strain and the invertant is equivalent. However, when co-incubated together, both in vitro and in vivo, the survival of the invertant declines relative to the parental strain. The accompanying aspect of the study suggests that inversions taking place nearby oriC, always happen to secure the linkage of oriC to DNA sequences responsible for chromosome partition. The biological relevance of large scale inversions is also discussed. IMPORTANCEBased on our previous work, we created to our knowledge the largest asymmetric inversion covering 43.5% of the S. pyogenes genome. In spite of a drastic replacement of origin of replication and the unbalanced size of replichores (1.4 Mb vs 0.41 Mb), the invertant, when not challenged with its progenitor, showed impressive vitality for growth in vitro and pathogenesis assays. The mutant supports the existing idea that slightly deleterious mutations can provide the setting for secondary adaptive changes. Furthermore, comparative analysis of the mutant with previously published data strongly indicate that even large genomic rearrangements survive provided that the integrity of the oriC and the chromosome partition cluster is preserved.

microbiology↗