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Biomedical subjects

Ji Yang

Publications and source records attributed to Ji Yang.

At least 19 recordsLinked to original sources
PubMed2026

Intratumoral Mycobacterium abscessus promotes cytidine deaminase mutagenesis in non-small cell lung cancer.

The intratumoral microbiota is increasingly recognized as an active component of the tumor microenvironment, yet whether it directly drives tumor mutagenesis remains unclear. Here, integrated multi-omics analysis of human non-small cell lung cancer (NSCLC) identifies Mycobacterium abscessus as a microbial determinant of APOBEC3A-associated mutagenesis. Mechanistically, the bacterial effector nucleoside diphosphate kinase (NDK) directly targets the host transcription factor IRF3 and installs a non-canonical 1-phosphohistidine modification at H263, thereby amplifying type I interferon signaling and sustaining APOBEC3A expression. This inter-kingdom phosphotransfer event links intratumoral microbial colonization to an endogenous mutational process that promotes genomic diversification. Genetic inactivation of NDK, or pharmacologic elimination using an engineered NDK-PROTAC, suppresses APOBEC3A activation and attenuates microbe driven mutagenesis. Together, these findings establish a direct microbial effector mechanism that promotes APOBEC3A-associated mutagenesis and provide a therapeutic framework to intercept microbiome driven mutagenesis in NSCLC.

Humans↗
PubMed2026

Genetic basis of escape-related locomotor performance in a wild-introgressed sheep population.

Rapid running and jumping are core components of escape responses in prey animals and provide measurable traits for studying locomotor performance in large mammals. The genetic basis of these escape-related locomotor traits remains poorly understood in large mammals, partly because repeated, standardized phenotyping under field conditions is challenging. Here, we leveraged a sheep population carrying argali-introgressed genetic components to map genetic variations associated with running speed and jumping height. Through controlled field experiments, automated high-resolution phenotyping, whole-genome analysis, and gene-edited mouse models, we identified two loci associated with escape-related locomotor traits: one in ABCC4 (Chr10:71,849,347; p = 5.03 × 10-7) linked to maximum running speed and another in GRID2 (Chr6:32,120,477; p = 1.30 × 10-9) associated with jumping height. Functional assays in knockout mice reveal that disruption of Grid2 reduces jumping ability, whereas Abcc4 knockout and knockdown increase running speed through enhanced heart contractility under stress. These results elucidated the genetic bases of wild-derived variations in affecting locomotor performance.

Animals↗
PubMed2025

Genetic history and adaptation of Eurasian wild boars inform livestock breeding.

Historical expansions of wild boars (Sus scrofa) across Eurasia have shaped phenotypic variation, genetic diversity, and local adaptation of their populations. The study by Wang et al.1 investigates the demographic history and genetic adaptation of Eurasian wild boars based on 96 whole-genome sequences, informing a critical role of Central Asian populations in their expansions and identifying key genes and variants associated with their local adaptation. Also, the adaptive variants are potentially useful for domestic pig breeding in future.

Animals↗
PubMed2006

Transcriptional regulation of the yghJ-pppA-yghG-gspCDEFGHIJKLM cluster, encoding the type II secretion pathway in enterotoxigenic Escherichia coli.

The gene cluster gspCDEFGHIJKLM codes for various structural components of the type II secretion pathway which is responsible for the secretion of heat-labile enterotoxin by enterotoxigenic Escherichia coli (ETEC). In this work, we used a variety of molecular approaches to elucidate the transcriptional organization of the ETEC type II secretion system and to unravel the mechanisms by which the expression of these genes is controlled. We showed that the gspCDEFGHIJKLM cluster and three other upstream genes, yghJ, pppA, and yghG, are cotranscribed and that a promoter located in the upstream region of yghJ plays a major role in the expression of this 14-gene transcriptional unit. Transcription of the yghJ promoter was repressed 168-fold upon a temperature downshift from 37 degrees C to 22 degrees C. This temperature-induced repression was mediated by the global regulatory proteins H-NS and StpA. Deletion mutagenesis showed that the promoter region encompassing positions -321 to +301 relative to the start site of transcription of yghJ was required for full repression. The yghJ promoter region is predicted to be highly curved and bound H-NS or StpA directly. The binding of H-NS or StpA blocked transcription initiation by inhibiting promoter open complex formation. Unraveling the mechanisms of regulation of type II secretion by ETEC enhances our understanding of the pathogenesis of ETEC and other pathogenic varieties of E. coli.

Bacterial Proteins↗
PubMed2006

Study on a novel circulating cooling solid-phase microextraction method.

A novel solid-phase microextraction (SPME) setup, circulating cooling solid-phase microextraction (CC-SPME), is developed for determining organochlorine pesticides (OCPs) in water. The linearity area of this method is 0.5-120 microg/l, its RSD value is less than 10% and detection limit is in the low ng/l when it is used to detect gamma-hexachlorocyclohexane, which is better than traditional headspace SPME (HS-SPME) and direct immersion SPME (DI-SPME) methods. The influence of factors such as pH, ionic intensity, adsorption time, and adsorption temperature were also investigated, respectively.

Adsorption↗
PubMed2006

The effects of jet cavitation on the growth of Microcystis aeruginosa.

Different operating factors of jet cavitation method affecting one of cyanobacterial's (Microcystis aeruginosa) growths were investigated. The inhibition on M. aeruginosa growth by the jet cavitation method depended strongly on the hydraulic characteristics of cavitation tube, inlet pressure, cavitation number, light and different algae concentrations. The inhibitive efficiency of 64.58% in field water sample was obtained by this method. Moreover, the ultrastructural changes of M. aeruginosa before and after treatment were observed by the transmission electron microscope (TEM). The changes of UV-Visible spectra further demonstrated the inhibitive behaviors of jet cavitation on the growth of M. aeruginosa. The experimental results showed that jet cavitation method was a potential physical technology that could effectively inhibit the growth of M. aeruginosa.

Biomass↗
PubMed2006

Molecular evidence for multiple polyploidization and lineage recombination in the Chrysanthemum indicum polyploid complex (Asteraceae).

The Chrysanthemum indicum polyploid complex comprises morphologically differentiated diploids, tetraploids and hybrids between C. indicum and C. lavandulifolium. The relationships between species and cytotypes within this complex remain poorly understood. Random amplified polymorphic DNAs (RAPDs), intersimple sequence repeats (ISSRs) and chloroplast SSR markers were used to elucidate the genetic diversity and relationships of the C. indicum polyploid complex. Molecular analysis of three diploid and nine tetraploid populations provided strong evidence for recurrent origins and lineage recombination in the C. indicum polyploid complex. The high similarity in molecular marker profiles and cpDNA haplotypes between the diploids and tetraploids distributed in the Shen-Nong-Jia Mountain area of China suggested an autopolyploid origin of the tetraploids, while the tetraploids from other populations may have originated via allopolyploidization. Lineage recombination was revealed by the extensive sharing of chloroplast haplotypes and genetic markers among the tetraploid populations with different origins. Multiple differentiation and hybridization/polyploidization cycles have led to an evolutionary reticulation in the C. indicum polyploid complex, and resulted in the difficulties in systematic classification.

China↗
PubMed2005

A circumstellar disk associated with a massive protostellar object.

The formation process for stars with masses several times that of the Sun is still unclear. The two main theories are mergers of several low-mass young stellar objects, which requires a high stellar density, or mass accretion from circumstellar disks in the same way as low-mass stars are formed, accompanied by outflows during the process of gravitational infall. Although a number of disks have been discovered around low- and intermediate-mass young stellar objects, the presence of disks around massive young stellar objects is still uncertain and the mass of the disk system detected around one such object, M17, is disputed. Here we report near-infrared imaging polarimetry that reveals an outflow/disk system around the Becklin-Neugebauer protostellar object, which has a mass of at least seven solar masses (M(o)). This strongly supports the theory that stars with masses of at least 7M(o) form in the same way as lower mass stars.

Journal Article↗
PubMed2005

Restriction of DNA encoding selectable markers decreases the transformation efficiency of Helicobacter pylori.

Helicobacter pylori populations recovered from the human stomach display extensive recombination and quasispecies development, and this suggests frequent exchange of DNA between different strains in vivo. In vitro, however, most H. pylori strains display restriction to the uptake of non-self DNA, as measured using selectable markers, regardless of their competency for transformation with self DNA. We have examined the effect of different selectable markers on double-crossover recombination efficiencies in three reference strains (1061, 26695 & SS1) and one clinical isolate (CHP1) of H. pylori. All strains were efficiently transformable to kanamycin or chloramphenicol resistance by using self-genomic DNA from isogenic mutants bearing the aphA3 or cat cassettes, respectively. However, strains 26695 and CHP1 showed a 3-5-log reduction in transformation efficiency by non-self recombinant DNA containing aphA3, when compared to cat. Strain 1061 readily accepted either cassette, and strain SS1 was poorly tolerant of any non-self DNA. Genome-wide random mutagenesis of these strains was only achievable with a selectable marker that allowed high transformation efficiency. Digestion of 32P-labelled cassettes by H. pylori lysates mirrored the transformation results and indicated that in some strains these cassettes are the targets of enzymatic restriction.

Bacterial Proteins↗
PubMed2005

Dual electrodes oxidation of dye wastewater with gas diffusion cathode.

The high energy cost of an electrochemical method is the fatal drawback that hinders its large scale application in wastewater treatment. In traditional single-chamber electrolysis cell, only direct oxidation at an anode exists. Although a small amount of hydrogen peroxide is produced at the cathode by reduction, it is transferred to the anode and destroyed there without adding much benefit to organic decomposition. A two-chamber electrolytic cell, connected with an electrolyte bridge, was developed in this work. In this new reactor, direct oxidation at anode and indirect oxidation by hydrogen peroxide at cathode can occur simultaneously. Therefore "dual electrodes oxidation" in one electrochemical reactor was achieved successfully. Compared to a traditional one cell reactor, this reactor cuts the energy cost by 50%, and thus might lead to reconsideration of the electrochemical role in wastewater treatment. A Pt/C gas diffusion electrode (GDE) is fabricated and used as a cathode fed with oxygen-containing gases to produce hydrogen peroxide. When purified air diffuses through the active layer on the GDE, oxygen is reduced to hydrogen peroxide with a high yield to decompose organics. It has been found that the direct oxidation process at an anodic zone is slightly affected by factors such as pH variation, Fe(II) existence and aeration, while indirect oxidation at the cathodic zone is strongly affected. Dye used as a model pollutant was oxidized into small organic acids in both anode and cathode regions in this electrolytic reactor. GC-MS and IR spectrum were employed to analyze the intermediates formed during the degradation. Twenty intermediates have been detected, including 14 esters, 3 acids and 3 compounds with NO2 or N-OH groups. Thereafter, the degradation pathways of dye Acid Red B are proposed.

Coloring Agents↗
PubMed2005

Spark-induced consolidation of biological sludge.

Subjecting a suspension of biological sludge to underwater sparks (3kV, 50kA) leads to its consolidation, decreases the charge density on the solids, and increases its settling rate. The cake solids increase, but by only one percentage point. High-speed video images show that the spark generates a steam bubble. The dynamics of bubble growth could be estimated through the Rayleigh model. The bubble collapses into an acoustic field, which then agglomerates the particles. Sparking does not affect the settling rate of an aqueous slurry of softwood pulp because the fibrous particles are too large to be aggregated by an acoustic pulse.

Acoustics↗
PubMed2005

The H-NS protein represses transcription of the eltAB operon, which encodes heat-labile enterotoxin in enterotoxigenic Escherichia coli, by binding to regions downstream of the promoter.

Heat-labile enterotoxin, a major virulence determinant of enterotoxigenic Escherichia coli, is encoded by the eltAB operon. To elucidate the molecular mechanism by which the heat-stable nucleoid-structural (H-NS) protein controls transcription of eltAB, the authors constructed an eltAB-lacZ transcriptional fusion and performed beta-galactosidase analysis. The results showed that H-NS protein exerts fivefold repression on transcription from the eltAB promoter at 37 degrees C and 10-fold repression at 22 degrees C. Two silencer regions that were required for H-NS-mediated repression of eltAB expression were identified, both of which were located downstream of the start site of transcription. One silencer was located between +31 and +110, the other between +460 and +556, relative to the start site of transcription, and they worked cooperatively in repression. DNA sequences containing the silencers were predicted to be curved by in silico analysis and bound H-NS protein directly in vitro. Repression of eltAB transcription by H-NS was independent of promoter strength, and the presence of H-NS protein did not affect promoter opening in vitro, indicating that repression was achieved by inhibiting promoter clearance or blocking transcription elongation, probably via DNA looping between the two silencers.

Artificial Gene Fusion↗
PubMed2005

The TyrR regulon.

The TyrR protein of Escherichia coli can act both as a repressor and as an activator of transcription. It can interact with each of the three aromatic amino acids, with ATP and, under certain circumstances, with the C-terminal region of the alpha-subunit of RNA polymerase. TyrR protein is a dimer in solution but in the presence of tyrosine and ATP it self-associates to form a hexamer. Whereas TyrR dimers can, in the absence of any aromatic amino acids, bind to certain recognition sequences referred to as 'strong TyrR boxes', hexamers can bind to extended sequences including lower-affinity sites called 'weak TyrR boxes', some of which overlap the promoter. There is no single mechanism for repression, which in some cases involves exclusion of RNA polymerase from the promoter and in others, interference with the ability of bound RNA polymerase to form open complexes or to exit the promoter. When bound to a site upstream of certain promoters, TyrR protein in the presence of phenylalanine, tyrosine or tryptophan can interact with the alpha-subunit of RNA polymerase to activate transcription. In one unusual case, activation of a non-productive promoter is used to repress transcription from a promoter on the opposite strand. Regulation of individual transcription units within the regulon reflects their physiological function and is determined by the position and nature of the recognition sites (TyrR boxes) associated with each of the promoters. The intracellular levels of the various forms of the TyrR protein are also postulated to be of critical importance in determining regulatory outcomes. TyrR protein remains a paradigm for a regulator that is able to interact with multiple cofactors and exert a range of regulatory effects by forming different oligomers on DNA and making contact with other proteins. A recent analysis identifying putative TyrR boxes in the E. coli genome raises the possibility that the TyrR regulon may extend beyond the well-characterized transcription units described in this review.

Escherichia coli↗
PubMed2005

Asymmetric evolution of duplicate genes encoding the CCAAT-binding factor NF-Y in plant genomes.

NF-Y is a ubiquitous CCAAT-binding factor composed of NF-YA, NF-YB and NF-YC. Multiple genes encoding NF-Y subunits have been identified in plant genomes. It remains unclear whether the duplicate genes underwent different evolutionary patterns. Likelihood-ratio tests were used to examine whether the amino acid substitution rates are the same between duplicate genes. The influences of selection on evolution were evaluated by comparing the conservative and radical amino acid substitution rates, as well as maximum-likelihood analysis. Some NF-YB and NF-YC duplicates showed significant evidence of asymmetric evolution but not the NF-YA duplicates. Most amino acid replacements in the NF-YB and NF-YC duplicates result in changes in hydropathy, polar requirement and polarity. The physicochemical changes in the sequences of NF-YB seem to be coupled to asymmetric divergence in gene function. Plant NF-Y genes have evolved in different patterns. Relaxed selective constraints following gene duplication are most likely responsible for the unequal evolutionary rates and distinct divergence patterns of duplicate NF-Y genes. Positive selection may have promoted amino acid hydropathy changes in the NF-YC duplicates.

Amino Acid Substitution↗
PubMed2005

Evaluation on the therapeutic effects of digital acupoint pressure for obstetric spastic cerebral palsy.

To probe the evaluation methods for effects of TCM treatment of cerebral palsy through clinical observation on the digital acupoint pressure in treating obstetric spastic cerebral palsy. From 1998-2003, 40 cases of spastic cerebral palsy were treated with digital acupoint pressure therapy. Ten indexes including intelligence, language, salivation, hand-grasping, thumb-adduction, turnover, sitting, standing, walking, and scissors-gait were divided into the 4 grades of normal, mild abnormal, moderate abnormal, and severe abnormal (dysfunction), respectively marked as 6, 4, 2, and 0 point, with 2 points increased for improving each grade of each item after the treatment. Meanwhile, the ranges were recorded and evaluated before and after the treatment on shoulder-abduction, elbow-extension, wrist-extension, forearm-backward-rotation, hip-abduction, straight-leg-lifting, knee-extension, and ankle-dorsiflexion. Those with the improvement of 10 degrees, 15 degrees, 20 degrees, 25 degrees, and 30 degrees in the range of movement of their contractured joints would obtain respectively 1, 2, 3, 4, and 5 points. There were significant differences before and after the treatment in the 18 items under observation except for intelligence, with obvious improvement shown after the treatment (P<0.01), the effective rate being 92.5%. The therapeutic criteria set in this research are well established in reflecting the functional improvements of the patient.

Acupressure↗
PubMed2004

3-(4-phenoxyphenyl)pyrazoles: a novel class of sodium channel blockers.

A series of 3-(4-phenoxyphenyl)-1H-pyrazoles were synthesized and characterized as potent state-dependent sodium channel blockers. A limited SAR study was carried out to delineate the chemical requirements for potency. The results indicate that the distal phenyl group is critical for activity but will tolerate lipophilic (+pi) electronegative (+sigma) substituents at the ortho and/or para position. Substitution at the pyrazole nitrogen with a H-bond donor improves potency. Compound 18 showed robust activity in the rat Chung neuropathy paradigm.

Analgesics↗
PubMed2004

Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea).

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A-E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (omega = d(N)/ d(S)) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.

Acyltransferases↗