PubMed Health⌕ Search

Biomedical subjects

Yong Shi

Publications and source records attributed to Yong Shi.

At least 19 recordsLinked to original sources
PubMed2026

Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae.

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences (accD, ycf1, clpP, ndhF, and rpl22) and intergenic spacers (rpl33-rps18, the trnG-UCC intron, trnH-GUG-psbA, accD-psaI, and petA-psbJ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Hamamelidaceae↗
PubMed2026

Small nucleolar RNA HIDDEN TREASURE 2 reduces drought tolerance via multiple pathways in Arabidopsis.

Small nucleolar RNAs (snoRNAs) contribute to ribosome biogenesis and modulate various aspects of plant growth and development. Given that osmotic stress downregulates numerous genes associated with ribosome biogenesis in roots, we hypothesize that snoRNAs might function in modulating plant responses to osmotic and drought stresses. To prove this hypothesis, we assessed the role of a C/D-box snoRNA, namely the HIDDEN TREASURE 2 (HID2), in Arabidopsis thaliana responses to drought using both loss-of-function and overexpression approaches. Under drought conditions, the Arabidopsis hid2 mutant displayed a significantly higher survival rate than both wild-type (WT) and HID2-complemented plants, while HID2-overexpressing plants showed a lower survival rate than WT. A series of physiological assays indicated that the hid2 mutant maintained a slower rate of water loss and more intact cell membranes than WT plants under drought, which supported their drought-tolerant phenotype. Comparative leaf transcriptome and proteome analyses revealed that processes related to wax biosynthesis, senescence, and anthocyanin accumulation were differentially regulated between hid2 and WT plants under water-deficit conditions. Consistently, the hid2 mutant accumulated higher amounts of wax and anthocyanins and exhibited delayed leaf senescence relative to WT plants under drought. Additionally, the hid2 mutant showed improved ability to increase sensitivity to abscisic acid (ABA), scavenge reactive oxygen species (ROS), and extended root hairs. Overall, these findings demonstrate HID2's role as a negative modulator in Arabidopsis drought tolerance by negatively affecting cell membrane stability, wax and anthocyanin biosynthesis, senescence, ROS-scavenging capacity, ABA responsiveness, and root hair formation.

Arabidopsis↗
PubMed2025

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

Quercus↗
PubMed2006

Conversion to the amyotrophic lateral sclerosis phenotype is associated with intermolecular linked insoluble aggregates of SOD1 in mitochondria.

Twenty percent of the familial form of amyotrophic lateral sclerosis (ALS) is caused by mutations in the Cu, Zn-superoxide dismutase gene (SOD1) through the gain of a toxic function. The nature of this toxic function of mutant SOD1 has remained largely unknown. Here we show that WT SOD1 not only hastens onset of the ALS phenotype but can also convert an unaffected phenotype to an ALS phenotype in mutant SOD1 transgenic mouse models. Further analyses of the single- and double-transgenic mice revealed that conversion of mutant SOD1 from a soluble form to an aggregated and detergent-insoluble form was associated with development of the ALS phenotype in transgenic mice. Conversion of WT SOD1 from a soluble form to an aggregated and insoluble form also correlates with exacerbation of the disease or conversion to a disease phenotype in double-transgenic mice. This conversion, observed in the mitochondrial fraction of the spinal cord, involved formation of insoluble SOD1 dimers and multimers that are crosslinked through intermolecular disulfide bonds via oxidation of cysteine residues in SOD1. Our data thus show a molecular mechanism by which SOD1, an important protein in cellular defense against free radicals, is converted to aggregated and apparently ALS-associated toxic dimers and multimers by redox processes. These findings provide evidence of direct links among oxidation, protein aggregation, mitochondrial damage, and SOD1-mediated ALS, with possible applications to the aging process and other late-onset neurodegenerative disorders. Importantly, rational therapy based on these observations can now be developed and tested.

Amyotrophic Lateral Sclerosis↗
PubMed2006

Lattice Boltzmann method for incompressible flows with large pressure gradients.

Conventional lattice Boltzmann Bhatnagar-Gross-Krook (LBGK) models can simulate incompressible flows correctly only if the Mach number M and the density variation deltarho are negligibly small. However, the equation of state p=RTrho resulting from the conventional models limits their application to incompressible flows with a rather small pressure gradient. In this paper, based on the Enskog equation, we propose a finite difference lattice BGK model for isothermal incompressible flows with the resulting equation of state and transport properties suitable for nonideal fluids. We validated this model by simulating the plane Poiseuille flow, the two dimensional Womersley flow, and the backward-facing step flow and found that the numerical results obtained by the proposed model are more accurate than those by the conventional LBGK models when the pressure gradient imposed on the flows increases.

Journal Article↗
PubMed2006

Combined treatment of landfill leachate with fecal supernatant in sequencing batch reactor.

A laboratory-scale sequencing batch reactor (SBR) is used to treat landfill leachate containing high concentration of ammonium nitrogen with municipal fecal supernatant. The SBR system is operated in the following sequential phases: fill period, anoxic period, aeration period, settling period, decant and idle period. The results indicated that the average removal efficiencies of COD, BOD(5), TN,NH(4)(+)-N were 93.76%, 98.28%, 84.74% and 99.21%, respectively. The average sludge removal loading rates of COD, BOD(5), TN and NH(4)(+)-N were 0.24 kg/(kg SS.d), 0.08 kg/(kg SS.d), 0.04 kg/(kg SS.d) and 0.036 kg/(kg SS.d), respectively. Highly effective simultaneous nitrification and denitrification was achieved in the SBR system. The ratio of nitrification and denitrification was 99% and 84%, respectively. There was partial NO(2)(-) denitrification in the system.

Alkalies↗
PubMed2005

Temperature dependence of the velocity boundary condition for nanoscale fluid flows.

Velocity slips may occur as a fluid flows over a solid surface in the nanometer scale. The slip length L(s) , characterizing the degree of slip, is usually used to describe the velocity boundary condition at the fluid/solid interface. In this work, we show that for a given wall-fluid system, the slip length L(s) generally varies with the system temperature T . In particular, we show that it is possible to create a pair of solid wall and fluid systems, in which the velocity slip becomes rather small and independent of temperature.

Journal Article↗
PubMed2005

A lattice Boltzmann algorithm for electro-osmotic flows in microfluidic devices.

In this paper, a finite-difference-based lattice Boltzmann (LB) algorithm is proposed to simulate electro-osmotic flows (EOF) with the effect of Joule heating. This new algorithm enables a nonuniform mesh to be adapted, which is desirable for handling the extremely thin electrical double layer in EOF. The LB algorithm has been validated by simulating a problem with an available analytical solution and it is found that the numerical results predicted by the algorithm are in good agreement with the analytical solution. The LB algorithm is also applied to modeling a mixed electro-osmotic/pressure driven flow in a channel. The numerical results show that Joule heating plays an important role in EOF.

Journal Article↗
PubMed2005

Simple kinetic model for fluid flows in the nanometer scale.

Fluid flows in the nanometer scale can be studied by molecular dynamics or Monte Carlo methods, but the time and length scales are usually limited to rather short ranges due to the computational expense. Kinetic theory is an alternative tool for studying nanoscale flows, but the existing models are rather complicated and difficult to implement. In this paper, we propose a simple Enskog-like kinetic model for nanoscale flows. The results predicted by this model compare well with molecular dynamics or Monte Carlo simulation results in the literature.

Journal Article↗
PubMed2005

Specific cleavage of Mcl-1 by caspase-3 in tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in Jurkat leukemia T cells.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces programmed cell death through the caspase activation cascade and translocation of cleaved Bid (tBid) by the apical caspase-8 to mitochondria to induce oligomerization of multidomain Bax and Bak. However, the roles of prosurvival Bcl-2 family proteins in TRAIL apoptosis remain elusive. Here we showed that, besides the specific cleavage and activation of Bid by caspase-8 and caspase-3, TRAIL-induced apoptosis in Jurkat T cells required the specific cleavage of Mcl-1 at Asp-127 and Asp-157 by caspase-3, while other prototypic antiapoptotic factors such as Bcl-2 or Bcl-X(L) seemed not to be affected. Mutation at Asp-127 and Asp-157 of Mcl-1 led to cellular resistance to TRAIL-induced apoptosis. In sharp contrast to cycloheximide-induced Mcl-1 dilapidation, TRAIL did not activate proteasomal degradation of Mcl-1 in Jurkat cells. We further established for the first time that the C-terminal domain of Mcl-1 became proapoptotic as a result of caspase-3 cleavage, and its physical interaction and cooperation with tBid, Bak, and voltage-dependent anion-selective channel 1 promoted mitochondrial apoptosis. These results suggested that removal of N-terminal domains of Bid by caspase-8 and Mcl-1 by caspase-3 enabled the maximal mitochondrial perturbation that potentiated TRAIL-induced apoptosis.

Amino Acid Sequence↗
PubMed2004

Thermal lattice Bhatnagar-Gross-Krook model for flows with viscous heat dissipation in the incompressible limit.

In this paper, by introducing a different distribution function and starting from the Boltzmann equation as well as the Maxwell-Boltzmann distribution, we obtain a Boltzmann Bhatnagar-Gross-Krook (BGK) equation for thermal flows with viscous heat dissipation in the incompressible limit. The continuous thermal BGK model is then discretized over both time and phase space to form a lattice BGK model, which is shown to be consistent with some existing double distribution function lattice BGK models based on macroscopic governing equations. We have also demonstrated that the lattice BGK model derived theoretically in this work can be used to simulate laminar incompressible convention heat transfer with/without viscous heat dissipation.

Journal Article↗
PubMed2004

Preconditioned lattice-Boltzmann method for steady flows.

In this paper we propose a preconditioned lattice Boltzmann (LB) method for steady incompressible flows. For steady flows, the macroscopic equations derived from this LB model are equivalent to those from the standard LB model, but with an improved eigenvalue system. The proposed model can be viewed as an explicit solver for preconditioned compressible Navier-Stokes equations. Linear stability analysis is performed and the results show that the stability of the model is the same as that of the standard LB model for low Mach numbers. The proposed model retains the structure of the standard LB model and, hence, possesses all the advantages. Numerical tests show that the convergence rate can be enhanced as much as an order of magnitude compared to the standard lattice Boltzmann method. The accuracy of the solutions is improved as well.

Journal Article↗
PubMed2004

Channel switching effect in photodissociating N2O+ ion at 312.5 nm.

A experimental observation is presented on the N2O+ photodissociation process, which exhibits a complete channel switching effect in a narrow energy range. The N2O+ ions, prepared at the X2Pi (000) state by (3+1) multiphoton ionization of neutral N2O molecules at 360.6 nm, were excited to different vibrational levels in the A2Sigma+ state in a wavelength range of 275-328 nm. Based on the estimates of total released kinetic energies from the time-of-flight mass spectrum, it was found that the dissociation pathway of N2O+ (A2Sigma+), NO+ (X1Sigma+) + N(4S) with lower dissociation limit, changes abruptly and completely to NO+ (X1Sigma+) + N(2D) with higher dissociation limit, in a excitation energy range of merely 250 cm(-1) at lambda approximately 312.5 nm. This phenomenon was explained by competition between the two dissociation pathways across the special excitation energy region.

Journal Article↗
PubMed2004

Essential role of the voltage-dependent anion channel (VDAC) in mitochondrial permeability transition pore opening and cytochrome c release induced by arsenic trioxide.

The precise molecular mechanism underlying arsenic trioxide (As(2)O(3))-induced apoptosis is a subject of extensive study. Here, we show that clinically relevant doses of As(2)O(3) can induce typical apoptosis in IM-9, a multiple myeloma cell line, in a Bcl-2 inhibitable manner. We confirmed that As(2)O(3) directly induced cytochrome c (cyto c) release from isolated mouse liver mitochondria via the mitochondrial permeability transition pore, and we further identified the voltage-dependent anion channel (VDAC) as a biological target of As(2)O(3) responsible for eliciting cyto c release in apoptosis. First, pretreatment of the isolated mitochondria with an anti-VDAC antibody specifically prevented As(2)O(3)-induced cyto c release. Second, in proteoliposome experiments, VDAC by itself was sufficient to mediate As(2)O(3)-induced cyto c release, which could be specifically inhibited by Bcl-X(L). Third, As(2)O(3) induced mitochondria membrane potential (DeltaPsim) reduction and cyto c release only in the VDAC-expressing, but not in the VDAC-deficient yeast strain. Finally, we found that As(2)O(3) induced the increased expression and homodimerization of VDAC in IM-9 cells, but not in Bcl-2 overexpressing cells, suggesting that VDAC homodimerization could potentially determine its gating capacity to cyto c, and Bcl-2 blockage of VDAC homodimerization represents a novel mechanism for its inhibition of apoptosis.

Animals↗
PubMed2003

Identification of the protein-protein contact site and interaction mode of human VDAC1 with Bcl-2 family proteins.

Bcl-2 family of proteins plays differential roles in regulation of mitochondria-mediated apoptosis, by either promoting or inhibiting the release of apoptogenic molecules from mitochondria to cytosol. Bcl-2 family proteins modulate the mitochondrial permeability through interaction with adenine nucleotide translocator (ANT), voltage-dependent anion channel (VDAC), ADP/ATP exchange, or oxidative phosphorylation during apoptosis. Although the mitochondrial homeostasis is affected by the relative ratio of pro- and anti-apoptotic Bcl-2 family members, the molecular mechanism underlying the release of mitochondrial intermembrane proteins remains elusive. Here we reported the biochemical evidence that both pro-apoptotic Bax and anti-apoptotic Bcl-X(L) might simultaneously contact the putative loop regions of human VDAC1, and the existence of VDAC1-Bax-Bcl-X(L) tertiary complex in vitro suggested that VDAC1 channel conformation and mitochondrial permeability could be determined by the delicate balance between Bax and Bcl-X(L).

Binding Sites↗
PubMed2003

One-step on-column affinity refolding purification and functional analysis of recombinant human VDAC1.

The outer mitochondrial membrane porin, voltage-dependent anion-selective channel (VDAC), is believed to play an important role in mediating mitochondria-dependent apoptosis. However, detailed structure-function studies of VDAC have been hindered by the difficulties to obtain a soluble, correctly folded, and fully active form of the recombinant VDAC and its mutant variants due to its transmembrane nature. Here we report a high-throughput one-step chromatographic procedure in purification of recombinant human VDAC1 (rhVDAC1) protein overexpressed in bacteria. The improved methodology could generate a large quantity of rhVDAC1 with correct folding in terms of the secondary structure, with full biological activities in mediating cytochrome c release and in interaction with Bcl-X(L). The method will significantly benefit genetic, biochemical, and structural studies of this critical channel protein.

Chromatography, Affinity↗
PubMed2002

Analysis with gas chromatography and mass spectrography of volatile components of Ligusticum wallichii Franch extracted by CO2 supercritical fluid extraction in combination with molecular distillation.

OBJECTIVE: To evaluate the possibility of using the technique of CO2 supercritical fluid extraction (SFE) combined with molecular distillation (MD) to extract, separate and purify the volatile components of Ligusticum wallichii Franch, a Chinese herbal medicine. METHODS: SFE was employed to extract the volatile components of Ligusticum wallichii Franch, followed by MD of the product. Analysis of the chemical constituents of the extract both before and after MD was performed with gas chromatography (GC) in conjunction with mass spectrography (MS). RESULTS: There were 45 kinds of chemical constituents in the extract of Ligusticum wallichii Franch yielded from SFE, among which 39 were left after distillation by MD. Changes also took place in the content of the constituents in the extract after distillation. CONCLUSIONS: SFE combined with MD, a technique better than simple SFE, can be used to extract, separate and purify the volatile components of Chinese herbs.

Carbon Dioxide↗