Biology subjects

Yang, Y.-F.

Publications and source records attributed to Yang, Y.-F..

4 recordsLinked to original sources

bioRxiv2024

Previously uncharacterized aliphatic amino acid positions modulate the apparent catalytic activity of the EAL domain of ZMO_1055 and other cyclic di-GMP specific EAL phosphodiesterases

The ubiquitous second messenger cyclic di-GMP signaling system decides bacterial life style transition between sessility and motility. GGDEF diguanylate cyclase and EAL phosphodiesterase domains conventionally direct the turnover of this signaling molecule being subject to micro- and macroevolution. While the highly conserved signature amino acids involved in divalent ion binding and catalysis have readily been identified, recognition of amino acid substitutions that modulate the catalytic activity is rare. Associated with development towards cellulose-mediated self-flocculation in Zymomonas mobilis ZM401, the A526V substitution, previously not been recognized to affect the functionality of the EAL domain, downregulates the apparent catalytic activity of the PAS-GGDEF-EAL ZMO1055 phosphodiesterase compared to parental Z. mobilis ZM4 and equally in homologous protein domains independently of the genetic background. Substitution of A526, which is conserved among homologs, with amino acids with longer aliphatic side chains than valine have an even more pronounced effect. Thus single amino acid substitutions that lead to alterations in the catalytic activity of cyclic di-GMP turnover domains amplify the signaling output and thus significantly contribute to the flexibility and adaptability of the cyclic di-GMP signaling network. In this context, ZMO1055 seems to be a current evolutionary target.

microbiology↗

bioRxiv2024

Profiling IOP-responsive genes in anterior and posterior ocular tissues in the rat CEI glaucoma model

PurposeThe rat Controlled Elevation of Intraocular pressure (CEI) model allows study of in vivo responses to defined intraocular pressures (IOP). In this study, we use Nanostring technology to investigate in vivo IOP-related gene responses in the trabecular meshwork (TM) and optic nerve head (ONH) simultaneously from the same animals. MethodsMale and female rats (N=35) were subject to CEI for 8-hours at pressures simulating mean, daytime normotensive rat IOP (CEI-20), or 2.5x IOP (CEI-50). Naive animals, receiving no anesthesia or surgical interventions, served as controls. Immediately after CEI, TM and ONH tissues were dissected, RNA isolated, and samples were analyzed with a Nanostring panel containing 770 genes. Post-processing, raw count data were uploaded to Rosalind(R) for differential gene expression analyses. ResultsFor the TM, 45 IOP-related genes were significant in the "CEI-50 vs. CEI-20" and "CEI-50 vs. naive" comparisons, with 15 genes common to both comparisons. Bioinformatics analysis identified Notch and TGF{beta} pathways to be the most up- and down-regulated KEGG pathways, respectively. For ONH, 22 significantly regulated genes were identified in the "CEI-50 vs. naive" comparison. Pathway analysis identified defense response and immune response as two significantly upregulated biological process pathways. ConclusionsThis study demonstrates the ability to assay IOP-responsive genes in both TM and ONH tissues simultaneously. In the TM, downregulation of TGF{beta} pathway genes suggest that TM responses may prevent TGF{beta}-induced extracellular matrix synthesis. For ONH, the initial response to elevated IOP may be protective, with astrocytes playing a key role in these gene responses.

molecular biology↗

bioRxiv2024

BayVarC: an ultra-sensitive ctDNA variant caller using Bayesian approach

In liquid biopsy, it is critical to detect variants of allele frequencies as low as 0.1% or even lower, especially when used to monitor secondary resistant mutations and minimal residual disease. Despite the efforts on improving experimental design, it remains challenging to distinguish low-frequency variants from technical noises in the downstream bioinformatic analysis. Here, we introduce BayVarC, a novel variant caller specifically designed for variant calling in liquid biopsy. It applies Bayesian inference to accurately quantify noise level in a locus-specific manner, enabling the discrimination between technical noise and low-frequency cancer variants. Detailed in-silico simulation and in-vitro experiments demonstrated BayVarC superior performance over existing state-of-the-art tools. BayVarC can effectively detect low frequency variants while maintaining low false positive rate (0.05 FP/KB). Meanwhile, it achieves Limit of Detection (LoD) as low as 0.1%. Furthermore, empowered by its architecture, BayVarC shows promising applicability in Minimal Residual Disease (MRD) detection. BayVarC is freely available at https://github.com/GenetronBioinfomatics/BayVarC.

bioinformatics↗

bioRxiv2023

Breaking the mold: The first report on germ-free adult marine medaka (Oryzias melastigma) models

Marine medaka (Oryzias melastigma) animal models play critical roles in environmental and human health by facilitating evaluation of pollutant toxicity and building of disease models. The fish gut microbiota contributes to host health and physiological metabolism, especially special bacterial strains and their functions in marine organisms. However, the distribution of the gut microbiota during medaka growth and development is still unclear, and successful generation of a germ-free (GF) marine medaka model has not been reported to date. In this study, we investigated the microbial composition with the major phyla and genera of marine fish at different life stages, as well as the isolated culturable intestinal bacteria, and then identified them by sequencing of the16S rRNA V3-V4 region. Importantly, the early stage model (larvae) of GF marine medaka without feeding and long-term (from juvenile to early adult stages) GF fish fed GF brine shrimp (Artemia sp.) were first generated. Moreover, the basic indexes and behavioral ability of GF fish showed weaker and delayed developmental changes compared to conventionally raised (CR) marine medaka at the same life stages. Notably, the significant differences in the histopathological characteristics of immune organs, intestinal tissues and the reproductive system were observed between GF and CR early-adult and adult fish. Furthermore, the transcriptomic profiles of the screened critical genes in signaling pathways in GF and CR marine medaka were also explored to illustrate the developmental impacts of the absence of the intestinal microbiota during the host growth. Comprehensively, our study provided novel insights into the intestinal microbiota distribution of CR fish during growth, and GF marine medaka from the larval to adult stages via GF fish food preparation. The histopathological and transcriptomic differences indicated the potential microbial regulation on growth, and application prospects of GF medaka fish models to clarify the relationships of intestinal bacterial functions to host health in the future. SignificanceThe generation and application of germ-free (GF) fish models are mostly limited to the early life stages with innate immunity and without feeding. Marine medaka (Oryzias melastigma) is a critical animal for evaluating environmental toxicity and human disease models. The gut microbiota contributes to host growth and development, but GF model of this organism has not been successfully generated. In this study, we revealed for the first time the distribution of the gut microbiota in marine medaka during growth and generated GF fish from the larval to adult stages with GF Artemia provided daily as food. According to the basic indexes, weaker behavioral ability, smaller immune organs, reproductive system, intestinal tissues, and transcriptome, the delayed development and differences indicated the negative influences of the absence of the microbiota in GF medaka, compared to conventionally raised (CR) fish at the same life stages. All these results provided novel insights into the application of GF medaka models to define intestinal bacterial functions in the host. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/536225v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@15625b5org.highwire.dtl.DTLVardef@c5cf62org.highwire.dtl.DTLVardef@b264c5org.highwire.dtl.DTLVardef@1f5e7d3_HPS_FORMAT_FIGEXP M_FIG C_FIG This work revealed the distribution of the gut microbiota in marine medaka during growth, and successfully generated GF marine medaka models from larvae to adults with GF Artemia as food, which indicated the delayed development in the absence of the microbiota in GF fish. Moreover, the histopathological analysis presented further evidence of developmental differences in immune organs, intestinal villi, goblet cells, gonad tissues and cell maturation between GF and CR fish at various life stages. Finally, the transcriptomic profile showed the significantly differentially regulated genes, which combined with the major bacteria can be potential "biomarkers" to explore the inner mechanisms or signaling pathways of GF fish models for studying host development and health.

microbiology↗