Biomedical subjects

Xin Jiang

Publications and source records attributed to Xin Jiang.

At least 19 recordsLinked to original sources

PubMed2025

Genetic pleiotropy underlying obesity and autoimmune disorders: a large-scale cross-trait gwas analysis in European ancestry populations.

BACKGROUND: Obesity and autoimmune disorders represent a significant comorbidity burden, yet their shared genetic architecture is not fully understood. Elucidating the pleiotropic genetic basis underlying both conditions is crucial for unraveling the mechanisms driving their co-occurrence and advancing therapeutic strategies. METHODS: We conducted a large-scale cross-trait analysis integrating genome-wide association study (GWAS) summary data for obesity and 17 autoimmune diseases. Genetic correlations were assessed using LD score regression and high-definition likelihood. Cross-trait pleiotropic analysis was performed using Stratified Pleiotropic Locus Mapping (PLACO) to identify shared loci, followed by Bayesian colocalization to confirm shared causal variants. Gene-level and tissue-specific heritability analyses were conducted, and drug targets were prioritized via summary-based Mendelian randomization (SMR). Finally, immune co-localization and bidirectional Mendelian randomization were employed to elucidate immunological mechanisms and causal relationships. RESULTS: Our analysis identified eight autoimmune diseases with significant genetic correlations to obesity. We discovered 10,324 pleiotropic SNPs, which mapped to 52 independent risk loci, with nine loci confirmed as shared causal variants by colocalization. Gene-level analysis revealed 133 unique pleiotropic genes, including CLN3, SH2B1, and MMEL1, enriched in pathways of hematopoietic cell differentiation and immune homeostasis. Tissue-specific heritability was most prominent in the spleen, whole blood, and EBV-transformed lymphocytes. Immuno-co-localization implicated six IgD+ CD38- %B cell-related traits as key pathological conduits. Bidirectional Mendelian randomization established a causal role of obesity in hypothyroidism, psoriasis, and multiple sclerosis, while revealing an inverse causal association of type 1 diabetes with obesity risk. CONCLUSIONS: This study demonstrates a robust shared genetic foundation between obesity and multiple autoimmune diseases, pinpointing specific pleiotropic loci, genes, and immune cell subsets. Our findings provide a mechanistic framework for their comorbidity and highlight potential targets for therapeutic intervention.

Humans↗

PubMed2024

Transfer of antibiotic resistance genes from soil to rice in paddy field.

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

Oryza↗

PubMed2024

Biochemical insights into the biodegradation mechanism of typical sulfonylureas herbicides and association with active enzymes and physiological response of fungal microbes: A multi-omics approach.

The extensive use of sulfonylurea herbicides has raised major concerns regarding their long-term soil residues and agroecological risks despite their role in agricultural protection. Microbial degradation is an important approach to remove sulfonylureas, whereas understanding the associated biodegradation mechanisms, enzymes, and physiological responses remains incomplete. Based on the rapid biodegradation of nicosulfuron by typical fungal isolate Talaromyces flavus LZM1, the dependency on cellular accumulation and environmental conditions, e.g. pH and nutrient supplies, was shown in the study. The biodegradation of nicosulfuron occurred intracellularly and followed the cascade of reactions including hydrolysis, Smile contraction rearrangement, hydroxylation, and opening of the pyrimidine ring. Besides 2-amino-4,6-dimethoxypyrimidine (ADMP) and 2-aminosulfonyl-N,N-dimethylnicotinamide (ASDM), numerous products and intermediates were newly identified and the structural forms of methoxypyrimidine and sulfonylurea bridge contraction rearrangement are predicted to be more toxic than nicosulfuron. The biodegradation should be enzymatically regulated by glycosylphosphatidylinositol transaminase (GPI-T) and P450s, which were manifested with the significant upregulation in proteomics. It is the first time that the hydrolysis of nicosulfuron into ADMP and ASDM have been associated with GPI-T. The integrated pathways of biodegradation were further elucidated through the involvement of various active enzymes. Except for the enzymatic catalysis, the physiological responses verified by metabolo-proteomics were critical not only to regulate material synthesis, uptake, utilization, and energy transfer but also to maintain antioxidant homeostasis, biodegradability, and tolerance of nicosulfuron by the differentially expressed metabolites, such as acetolactate synthase and 3-isopropylmalate dehydratase. The obtained results would help understand the biodegradation mechanism of sulfonylurea from chemicobiology and enzymology and promote the use of fungal biodegradation in pollution rehabilitation.

Herbicides↗

PubMed2007

Synthesis of psymberin analogues: probing a functional correlation with the pederin/mycalamide family of natural products.

In this letter we describe an efficient synthesis of "psympederin", a hybrid between the novel antitumor natural product psymberin and the blister beetle toxin pederin. Evaluation of antiproliferative activity reveals that the dihydroisocoumarin fragment is important for psymberin toxicity and the cyclic pederate fragment is important for pederin/mycalamide toxicity. On the basis of preliminary results described herein, we speculate that, despite their structural resemblance, psymberin and pederin/mycalamide induce toxicity through different mechanisms. [reaction: see text].

Cell Line, Tumor↗

PubMed2007

Isolation and characterization of 1,2,4-trichlorobenzene mineralizing Bordetella sp. and its bioremediation potential in soil.

A soil which has been polluted with chlorinated benzenes for more than 25 years was used for isolation of adapted microorganisms able to mineralize 1,2,4-trichlorobenzene (1,2,4-TCB). A microbial community was enriched from this soil and acclimated in liquid culture under aerobic conditions using 1,2,4-TCB as a sole available carbon source. From this community, two strains were isolated and identified by comparative sequence analysis of their 16S-rRNA coding genes as members of the genus Bordetella with Bordetella sp. QJ2-5 as the highest homological strain and with Bordetella petrii as the closest related described species. The 16S-rDNA of the two isolated strains showed a similarity of 100%. These strains were able to mineralize 1,2,4-TCB within two weeks to approximately 50% in liquid culture experiments. One of these strains was reinoculated to an agricultural soil with low native 1,2,4-TCB degradation capacity to investigate its bioremediation potential. The reinoculated strain kept its biodegradation capability: (14)C-labeled 1,2,4-TCB applied to this inoculated soil was mineralized to about 40% within one month of incubation. This indicates a possible application of the isolated Bordetella sp. for bioremediation of 1,2,4-TCB contaminated sites.

Biodegradation, Environmental↗

PubMed2006

QSARs for the toxicity of polychlorinated dibenzofurans through DFT-calculated descriptors of polarizabilities, hyperpolarizabilities and hyper-order electric moments.

DFT-B3LYP method with 6-31G(**) basis set was employed to fully optimize the electronic structures of 135 polychlorinated dibenzofurans and parent compound, namely dibenzofuran. It was demonstrated that polarizability anisotropy and mean polarizability could change sensitively and systematically with chlorine number and substitution pattern. And new quantitative structure-activity relationships (QSARs) focused on the binding affinities of aryl hydrocarbon receptor (AhR), aryl hydrocarbon hydroxylase (AHH) and 7-ethoxyresorufin O-deethylase (EROD) induction potencies of PCDFs were developed. It was concluded that polarizability anisotropy in conjunction with hyperpolarizabilties and hyper-order electric moments, e.g. octupole moments could well interpret the variation of toxicity of different congeners and dispersion interaction should be the leading form among various interactions. Although the terms of hyperpolarizabilities and hyper-order electric moments were not the same significant ones as polarizability anisotropy, the long-range interactions characterized by them should not be ignored in explaining the toxicity.

Algorithms↗

PubMed2006

Identification of unique genetic markers in Rv0927c among Mycobacterium tuberculosis W-Beijing strains.

Fifty-six clinical isolates of Mycobacterium tuberculosis were analyzed by spoligotyping to determine the prevalence of W-Beijing strains. Forty-nine of the 56 isolates belonged to W-Beijing strains and 7 isolates were non-Beijing strains. Comparative two-dimensional gel electrophoresis analysis of protein patterns between the W-Beijing and non-Beijing strains identified a unique protein Rv0927c that is absent in the former but present in the latter and the reference strain M. tuberculosis H37Rv. Compared with 7 non-Beijing clinical isolates and H37Rv, all 49 W-Beijing strains had two characteristic mutations, a deletion of AGC at nucleotide position 421 of Rv0927c gene encoding a putative short dehydrogenase/reductase, causing deletion of serine codon at amino acid position 141 and a -127 G-->A mutation in Rv0927c-pstS3 intergenic region, resulting in failure to express Rv0927c. Western blot analysis indicated that polyclonal antibody raised against H37Rv Rv0927c overexpressed in Escherichia coli reacted with non-Beijing strains and H37Rv but not W-Beijing strains. Characteristic mutations of Rv0927c that are present in W-Beijing strains can be used as a novel genetic marker for rapid molecular typing of M. tuberculosis W-Beijing strains.

Antibodies, Bacterial↗

PubMed2006

Temperature dependence of current-induced magnetization switching in spin valves with a ferrimagnetic CoGd free layer.

The temperature dependence of current-induced magnetization switching of ferrimagnetic CoGd free layers in spin valves is explored. At temperatures well above and well below the magnetization compensation temperature (T(MC)) of CoGd, a current flowing from the free layer to the CoFe fixed layer aligns the moments of the two layers parallel, and a current flowing in the opposite direction aligns them antiparallel. However, for intermediate temperatures just above T(MC), the current-induced alignment of the moments is reversed. We attribute this effect to the different compensation temperatures of the net magnetization and angular momentum of CoGd.

Journal Article↗

PubMed2006

Dependence of current and field driven depinning of domain walls on their structure and chirality in permalloy nanowires.

A magnetic domain wall (DW) injected and pinned at a notch in a permalloy nanowire is shown to exhibit four well-defined magnetic states, vortex and transverse, each with two chiralities. These states, imaged using magnetic force microscopy, are readily detected from their different resistance values arising from the anisotropic magnetoresistance effect. Whereas distinct depinning fields and critical depinning currents in the presence of magnetic fields are found, the critical depinning currents are surprisingly similar for all four DW states in low magnetic fields. We observe current-induced transformations between these DW states below the critical depinning current which may account for the similar depinning currents.

Journal Article↗

PubMed2006

Effects of aspirin on atherosclerosis and the cyclooxygenase-2 expression in atherosclerotic rabbits.

BACKGROUND: Atherosclerosis is a complex vascular inflammatory disease. Aspirin is a mainstay in the prevention of vascular complications of atherosclerosis. In this study, the effectiveness of aspirin in suppressing atherosclerosis and the inflammation process was evaluated in rabbits fed with a high fat diet. METHODS: Eighteen male New Zealand rabbits were randomly divided into 3 groups: control group, untreated cholesterol-fed group, aspirin treated cholesterol-fed group, which were fed for 12 weeks. After 12 weeks, the aorta was harvested for pathologic morphology observation. Immunohistochemical analysis of cyclooxygenase-2 (COX-2), macrophage and vascular smooth muscle cell (VSMC) was performed. The statistical analysis was performed by the statistical program SPSS10.0. RESULTS: The aorta plaque/intima size (P/I) by pathologic morphology observation was 0%, (59.6 +/- 13.7)% and (36.3 +/- 16.5)% in the control, untreated cholesterol-fed group and aspirin treated group, respectively. The maximum plaque thickness, the degree of artery stenosis and the proportion of the intimal circumference occupied by atheroma of the 3 groups were significantly different from each other (P < 0.01). The expression of COX-2 and macrophage in plaque of the aspirin treated group were decreased compared with that in untreated cholesterol-fed group. However, no difference was found in the expression of VSMC between the aspirin treated and the untreated cholesterol-fed group. CONCLUSION: The mechanism of atherosclerosis suppression by aspirin in cholesterol-fed rabbits is related to the inhibition of COX-2 expression together with the reduced inflammation followed by, but not related to the hypolipidemic effects.

Animals↗

PubMed2006

Oscillatory dependence of current-driven magnetic domain wall motion on current pulse length.

Magnetic domain walls, in which the magnetization direction varies continuously from one direction to another, have long been objects of considerable interest. New concepts for devices based on such domain walls are made possible by the direct manipulation of the walls using spin-polarized electrical current through the phenomenon of spin momentum transfer. Most experiments to date have considered the current-driven motion of domain walls under quasi-static conditions, whereas for technological applications, the walls must be moved on much shorter timescales. Here we show that the motion of domain walls under nanosecond-long current pulses is surprisingly sensitive to the pulse length. In particular, we find that the probability of dislodging a domain wall, confined to a pinning site in a permalloy nanowire, oscillates with the length of the current pulse, with a period of just a few nanoseconds. Using an analytical model and micromagnetic simulations, we show that this behaviour is connected to a current-induced oscillatory motion of the domain wall. The period is determined by the wall's mass and the slope of the confining potential. When the current is turned off during phases of the domain wall motion when it has enough momentum, the domain wall is driven out of the confining potential in the opposite direction to the flow of spin angular momentum. This dynamic amplification effect could be exploited in magnetic nanodevices based on domain wall motion.

Journal Article↗

PubMed2006

Behavior and fate of chlorpyrifos introduced into soil-crop systems by irrigation.

The effect of chlorpyrifos added in irrigation water to a red soil from Central South China on the growth of wheat and oilseed rape seedlings, together with its uptake, was studied in a pot experiment. Addition of chlorpyrifos (1-10 microg g-1) in a single irrigation with distilled water resulted in absorption of chlorpyrifos by wheat (0.257-4.50 microg g-1) and also oilseed rape seedlings (0.249-2.02 microg g-1) during 20 d of plant growth. An initial concentration of chlorpyrifos in soil that is equivalent to or below 10 microg g-1 did not significantly influence the growth of wheat seedlings. Similarly, an initial concentration equivalent to or below 5 microg g-1 did not significantly influence the growth of oilseed rape seedlings. The degradation rate of chlorpyrifos was 1.4-4.2 times larger in oilseed rape rhizosphere soil than in unvegetated soil. The numbers of bacteria and fungi in oilseed rape rhizosphere soil were 3.18 times and 1.84 times larger, respectively, than those in unvegetated soil. This helps to explain the difference in degradation rates obtained.

Biodegradation, Environmental↗

PubMed2006

Src homology 2 domain-based high throughput assays for profiling downstream molecules in receptor tyrosine kinase pathways.

Src homology 2 (SH2) domains are evolutionary conserved small protein modules that bind specifically to tyrosine-phosphorylated peptides. More than 100 SH2 domains have been identified in proteins encoded by the human genome. The binding specificity of these domains plays a critical role in signaling within the cell, mediating the relocalization and interaction of proteins in response to changes in tyrosine phosphorylation states. Here we developed an SH2 domain profiling method based on a multiplexed fluorescent microsphere assay in which various SH2 domains are used to probe the global state of tyrosine phosphorylation within a cell and to screen synthetic peptides that specifically bind to each SH2 domain. The multiplexed, fluorescent microsphere-based assay is a recently developed technology that can potentially detect a wide variety of interactions between biological molecules. We constructed 25-plex SH2 domain-GST fusion protein-conjugated fluorescent microsphere sets to investigate phosphorylation-mediated cell signaling through the specific binding of SH2 domains to activated target proteins. The response of HeLa, COS-1, A431, and 293 cells and four breast cancer cell lines to epidermal growth factor and insulin were quantitatively profiled using this novel microsphere-based, multiplexed, high throughput assay system.

Amino Acid Sequence↗

PubMed2006

Regulation of sodium and calcium channels by signaling complexes.

Membrane depolarization and intracellular calcium transients generated by activation of voltage-gated sodium and calcium channels are local signals, which initiate physiological processes such as action potential conduction, synaptic transmission, and excitation-contraction coupling. Targeting of effector proteins and regulatory proteins to ion channels is an important mechanism to ensure speed, specificity, and precise regulation of signaling events in response to local stimuli. In this article, we review recent experimental results showing that sodium and calcium channels form local signaling complexes, in which effector proteins, anchoring proteins, and regulatory proteins interact directly with ion channels. The intracellular domains of these channels serve as signaling platforms, mediating their participation in intracellular signaling processes. These protein-protein interactions are important for efficient synaptic transmission and for regulation of ion channels by neurotransmitters and intracellular second messengers. These localized signaling complexes are essential for normal function and regulation of electrical excitability, synaptic transmission, and excitation-contraction coupling.

Animals↗

PubMed2006

Development of a fluorescent microsphere-based multiplexed high-throughput assay system for profiling of transcription factor activation.

Transcription factors (TFs), which play crucial roles in the regulation of gene expression in the human genome, are highly regulated by a variety of mechanisms. A single extracellular stimulus can trigger multiple signaling pathways, and these in turn can activate multiple TFs to mediate the inducible expression of target genes. Alterations in the activities of TFs are often associated with human diseases, such as altered activating factor 1, estrogen receptor, and p53 function in cancer, nuclear factor kappaB in inflammatory diseases, and peroxisome proliferator-activated receptor gamma in obesity. A systematic assay for profiling the activation of TFs will aid in elucidating the mechanisms of TF activation, reveal altered TFs associated with human diseases, and aid in developing assays for drug discovery. Here, we developed a 24-plex fluorescent microsphere-based TF activation assay system with a 96-well plate format. The assay system enabled high-throughput profiling of the DNA binding activity of TFs in multiple samples with high sensitivity.

DNA↗

PubMed2006

Profiling activities of transcription factors in breast cancer cell lines.

Transcription factors (TFs) are critical regulators of cell growth and differentiation, whose dysfunction is associated with many human diseases, including cancer. To facilitate the discovery of functionally altered TFs among the approximately 2,000 human TFs, we (Panomics, Inc., Fremont, CA) developed a Protein/DNA array technology that can be used to profile the activities of multiple TFs simultaneously. In this study, we applied this technology to examine the TF activities in three different breast cancer cell lines: MCF7 (estrogen receptor [ER] +, tamoxifen-sensitive), T47D (ER+, tamoxifen-resistant), and HCC1806 (ER-, tamoxifen-resistant). We compared the differences in TF activity in these cells lines following treatment with estradiol or tamoxifen. We found a number of TF activities unique to each of these cell lines. In addition to verifying previous findings, the novel findings of this study provide a more comprehensive view of the differences in the response of these cancer lines to estrogen and tamoxifen.

Animals↗

PubMed2006

Development of luciferase reporter-based cell assays.

Using luciferase reporter constructs driven by specific promoter response elements, we developed a series of stable reporter cell lines for monitoring the activity of specific transcription factors (TFs). These TFs, which play essential roles in regulating diverse biological functions, include nuclear factor kappaB (NFkappaB), cyclic AMP response element-binding protein, activator protein 1, signal transducer and activator of transcription 1 and 3, nuclear factor of activated T cells, serum response factor, and hypoxia-inducible factor. The response of the stable reporter cells was highly specific. For example, tumor necrosis factor-alpha (TNFalpha) strongly activated NFkappaB reporter cells, but not other cell lines. The NFkappaB reporter was active in multiple cell lines, including 293T, HeLa, A549, and NIH3T3 cells, in response to TNFalpha, indicating that this system is useful to monitor specific TFs in different model cell lines. To facilitate high throughput screening of these cell lines, they were adapted to a 96-well format. These stable reporter cells are also applicable for the analysis of steroid hormone receptors, which bind directly to the response element after ligand binding. With the HeLa/glucocorticoid response element-luciferase stable reporter cells, we were able to discriminate pharmacological activity of different compounds for the glucocorticoid receptor. Taken together, these results demonstrate that the stable reporter cells are useful tools for: (1) detection of signaling pathway-specific ligands; (2) identification of novel ligands for specific TFs, and (3) screening for agonists and antagonists of specific ligands/receptors.

Animals↗

PubMed2006

High throughput assays for analyzing transcription factors.

Transcription factors are a group of proteins that modulate the expression of genes involved in many biological processes, such as cell growth and differentiation. Alterations in transcription factor function are associated with many human diseases, and therefore these proteins are attractive potential drug targets. A key issue in the development of such therapeutics is the generation of effective tools that can be used for high throughput discovery of the critical transcription factors involved in human diseases, and the measurement of their activities in a variety of disease or compound-treated samples. Here, a number of innovative arrays and 96-well format assays for profiling and measuring the activities of transcription factors will be discussed.

Biological Assay↗