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Biomedical subjects

Xin Yu

Publications and source records attributed to Xin Yu.

At least 19 recordsLinked to original sources

Complete genome sequence of multidrug-resistant Salmonella enterica subsp. enterica serovar Enteritidis SD191 isolated from chicken liver, harboring a novel imipenem resistance mechanism.

We present the complete genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis SD191 isolated from Gallus gallus liver in China, harboring plasmid pSE191. The genome reveals multiple antibiotic resistance mechanisms and phenotypic imipenem resistance without canonical genes.

antibiotic resistance↗

Spatially resolved single-cell atlas reveals the macroevolutionary trajectory of animal hearts.

Animal hearts display diverse anatomical structures during adaptive evolution. Here, we present a multiomics atlas of adult hearts from 27 species across chordates, arthropods, and mollusks. Joint analysis indicates that Bilateria hearts share a core gene repertoire, taking a stepwise "add-on" approach as a universal evolutionary strategy. The "proto-heart" is populated by key cell types, including cardiomyocytes, fibroblasts, endothelial cells, and neural cells, which maintained core signatures while evolving with shifts in living environments and corresponding adaptations in the cardiovascular system. Additionally, we reveal an evolutionarily conserved cardiomyocyte state dynamic potentially linked to cardiac development and stress responses. Finally, we identify a common molecular program underpinning chamber evolution from a ventricular foundation. This work establishes a resource for understanding the intrinsic mechanisms of heart evolution.

Animals↗

Distinct contributions of schizophrenia and neurotransmitter pathway genetic liability to neurocognition and antipsychotic efficacy in drug-naïve first-episode schizophrenia.

The genetic mechanisms underlying heterogeneity in symptom presentation and antipsychotic response in schizophrenia remain unclear, limiting the development of personalized treatment. We integrated genome-wide schizophrenia polygenic risk scores (SZ-PRS) and pathway-specific PRSs (pPRSs) for four major neurotransmitter systems to examine their associations with clinical phenotypes across the course of illness. Primary analyses were conducted in 394 drug-naïve, first-episode patients from the Chinese First-Episode Schizophrenia Trial (CNFEST) to investigate associations with baseline symptom severity, neurocognitive impairment, and longitudinal treatment response. The CNFEST cohort included 52-week longitudinal assessments of symptoms and neurocognition using the Positive and Negative Syndrome Scale and a modified version of the MATRICS Consensus Cognitive Battery. An independent case-control cohort evaluated associations with schizophrenia diagnosis, while a cohort of 514 healthy adults assessed whether PRS-cognition associations are specific to schizophrenia. Higher SZ-PRS predicted schizophrenia diagnosis (OR = 2.28, Pfdr = 0.003) and poorer baseline executive function (β = -0.44, Pfdr = 0.006) and working memory (β = -0.49, Pfdr = 0.018), but these associations were absent in healthy adults. In contrast, pPRSs showed weaker associations with diagnosis and baseline cognition but were more informative for treatment outcomes: higher serotonin-pPRS predicted greater improvement in depressive symptoms (Pfdr = 0.023-0.032), and higher GABA-pPRS predicted greater improvement in overall symptoms (Pfdr = 0.038-0.043) during weeks 4-24. Exploratory drug-specific analyses further suggested that treatment response varied across antipsychotics and was differentially associated with pPRSs. These findings demonstrate that genome-wide and pathway-specific PRSs contribute distinctly to schizophrenia phenotypes, supporting their integration for personalized stratification and treatment.

Humans↗

Eta1 and eta2 complexes of lambda3-1,2,4,6-thiatriazinyls with CpCr(CO)x.

The title heterocyclic radicals coordinate to either 17e CpCr(CO)3 or 15e CpCr(CO)2 moieties as one-electron or as three-electron donors, respectively; in the former the bonding is via the perpendicular p orbital of the sulfur atom, while in the latter bonding is via p(pi) orbitals on both sulfur and nitrogen.

Journal Article↗

Carbon nanotube amplification strategies for highly sensitive immunodetection of cancer biomarkers.

We describe herein the combination of electrochemical immunosensors using single-wall carbon nanotube (SWNT) forest platforms with multi-label secondary antibody-nanotube bioconjugates for highly sensitive detection of a cancer biomarker in serum and tissue lysates. Greatly amplified sensitivity was attained by using bioconjugates featuring horseradish peroxidase (HRP) labels and secondary antibodies (Ab(2)) linked to carbon nanotubes (CNT) at high HRP/Ab(2) ratio. This approach provided a detection limit of 4 pg mL(-)(1) (100 amol mL(-)(1)), for prostate specific antigen (PSA) in 10 microL of undiluted calf serum, a mass detection limit of 40 fg. Accurate detection of PSA in human serum samples was demonstrated by comparison to standard ELISA assays. PSA was quantitatively measured in prostate tissue samples for which PSA could not be differentiated by the gold standard immunohistochemical staining method. These easily fabricated SWNT immunosensors show excellent promise for clinical screening of cancer biomarkers and point-of-care diagnostics.

Biomarkers, Tumor↗

Depression and suicidality in HIV/AIDS in China.

BACKGROUND: This pilot study examined rates of major depression and suicidality and their associations with daily functioning in HIV infected (HIV+) and uninfected (HIV-) persons in China. METHOD: HIV+ participants (N=28) and demographically matched HIV- controls (N=23) completed the Chinese Composite International Diagnostic Interview to determine lifetime rates of major depressive disorder (MDD) and suicidality. Current mood and suicidal ideation were assessed with the Beck Depression Inventory-I. The impact of depression and HIV infection on daily functioning was measured by an Activity of Daily Living questionnaire. RESULTS: Mean duration of known HIV+ status was 2 years. Almost 79% (n=22) of HIV+ but just 4% (n=1) of HIV- groups reported lifetime major depression. Of the 22 HIV+ individuals with lifetime MDD, only one had onset before learning of HIV status. The remainder developed MDD within 6 months after testing HIV positive. In those HIV+ subjects who met MDD criteria after HIV diagnosis, only two (9%) had received depression treatment, yet four (18%) had persisting active suicidal thoughts. Depression and HIV+ status independently predicted worse daily functioning. LIMITATIONS: Representativeness is limited in this small sample of convenience. CONCLUSION: This preliminary study presents evidence of high rates of major depression and suicidality in HIV-infected persons in China. Despite this, few had sought mental health assistance, suggesting a need to increase awareness of psychiatric comorbidity and access to mental health services.

Acquired Immunodeficiency Syndrome↗

MR tagging demonstrates quantitative differences in regional ventricular wall motion in mice, rats, and men.

Rats and genetically manipulated mouse models have played an important role in the exploration of molecular causes of cardiovascular diseases. However, it has not been fully investigated whether mice or rats and humans manifest similar patterns of ventricular wall motion. Although similarities in anatomy and myofiber architecture suggest that fundamental patterns of ventricular wall motion may be similar, the considerable differences in heart size, heart rate, and sarcomeric protein isoforms may yield quantitative differences in ventricular wall mechanics. To further our understanding of the basic mechanisms of myofiber contractile performance, we quantified regional and global indexes of ventricular wall motion in mice, rats, and men using magnetic resonance (MR) imaging. Both regular cine and tagged MR images at apical, midventricular, and basal levels were acquired from six male volunteers, six Fischer 344 rats, and seven C57BL/6 mice. Morphological parameters and ejection fraction were computed directly from cine images. Myocardial twist (rotation angle), torsion (net twist per unit length), circumferential strain, and normalized radial shortening were calculated by homogeneous strain analysis from tagged images. Our data show that ventricular twist was conserved among the three species, leading to a significantly smaller torsion, measured as net twist per unit length, in men. However, both circumferential strain and normalized radial shortening were the largest in male subjects. Although other parameters, such as circumferential-longitudinal shear strain, need to be evaluated, and the causes of these differences in contractile mechanics remain to be elucidated, the preservation of twist appears fundamental to cardiac function and should be considered in studies that extrapolate data from animals to humans.

Adolescent↗

Nontranscriptional regulation of SYK by the coactivator OCA-B is required at multiple stages of B cell development.

OCA-B was originally identified as a nuclear transcriptional coactivator that is essential for antigen-driven immune responses. The later identification of a membrane bound, myristoylated form of OCA-B suggested additional, unique functions in B cell signaling pathways. This study has shown that OCA-B also functions in the pre-B1-to-pre-B2 cell transition and, most surprisingly, that it directly interacts with SYK, a tyrosine kinase critical for pre-BCR and BCR signaling. This unprecedented type of interaction-a transcriptional coactivator with a signaling kinase-occurs in the cytoplasm and directly regulates SYK stability. This study indicates that OCA-B is required for pre-BCR and BCR signaling at multiple stages of B cell development through its nontranscriptional regulation of SYK. Combined with the deregulation of OCA-B target genes, this may help explain the multitude of defects observed in B cell development and immune responses of Oca-b-/- mice.

Animals↗

Hydration dependence of the mass fractal dimension and anomalous diffusion of vibrational energy in proteins.

Vibrational dynamics of proteins and energy flow depend on protein geometry as well as interactions of a protein molecule with the surrounding solvent. We compute the mass fractal dimension D of proteins ranging from 100 to over 10,000 amino acids comparing values for the bare protein with those computed when buried and hydration waters are included in the calculation. Including water in the calculation increases D by about 0.3 to 2.87 on average above D computed for the dehydrated protein. The mass fractal dimension of proteins that are partially unfolded by molecular dynamics (MD) simulation is also computed and found to vary little when the radius of gyration changes within about 10% of that for the Protein Data Bank structure. MD simulations of vibrational energy diffusion in proteins reveal that the exponent characterizing anomalous diffusion of vibrational energy does not change much with hydration, which is seen to be due to an increase in the spectral dimension with hydration by a factor similar to the increase in D.

Computer Simulation↗

The regulation of exosome secretion: a novel function of the p53 protein.

The p53 protein responds to stress signals by regulating the transcription of a variety of genes. Some of these genes encode secreted proteins that may be involved in the communication between adjacent cells. In this study, a proteomics approach was employed to identify proteins secreted by cells in a p53-dependent manner after DNA damage. In addition to the known transcriptional targets of p53, a set of proteins encoded by genes that are not transcriptional targets of p53 were found to increase in the culture medium after p53 activation. These proteins exit the cell via small, secreted vesicles called exosomes and exosome production by cells was found to be regulated by the p53 response. A p53-regulated gene product, TSAP6, was shown to enhance exosome production in cells undergoing a p53 response to stress. Thus, the p53 pathway regulates the production of exosomes into the medium and these vesicles can communicate with adjacent cells and even cells of the immune system.

Alleles↗

A loss-of-function RNA interference screen for molecular targets in cancer.

The pursuit of novel therapeutic agents in cancer relies on the identification and validation of molecular targets. Hallmarks of cancer include self-sufficiency in growth signals and evasion from apoptosis; genes that regulate these processes may be optimal for therapeutic attack. Here we describe a loss-of-function screen for genes required for the proliferation and survival of cancer cells using an RNA interference library. We used a doxycycline-inducible retroviral vector for the expression of small hairpin RNAs (shRNAs) to construct a library targeting 2,500 human genes. We used retroviral pools from this library to infect cell lines representing two distinct molecular subgroups of diffuse large B-cell lymphoma (DLBCL), termed activated B-cell-like DLBCL and germinal centre B-cell-like DLBCL. Each vector was engineered to contain a unique 60-base-pair 'bar code', allowing the abundance of an individual shRNA vector within a population of transduced cells to be measured using microarrays of the bar-code sequences. We observed that a subset of shRNA vectors was depleted from the transduced cells after three weeks in culture only if shRNA expression was induced. In activated B-cell-like DLBCL cells, but not germinal centre B-cell-like DLBCL cells, shRNAs targeting the NF-kappaB pathway were depleted, in keeping with the essential role of this pathway in the survival of activated B-cell-like DLBCL. This screen uncovered CARD11 as a key upstream signalling component responsible for the constitutive IkappaB kinase activity in activated B-cell-like DLBCL. The methodology that we describe can be used to establish a functional taxonomy of cancer and help reveal new classes of therapeutic targets distinct from known oncogenes.

Adaptor Proteins, Signal Transducing↗

Interaction of the B cell-specific transcriptional coactivator OCA-B and galectin-1 and a possible role in regulating BCR-mediated B cell proliferation.

OCA-B is a B cell-specific transcriptional coactivator for OCT factors during the activation of immunoglobulin genes. In addition, OCA-B is crucial for B cell activation and germinal center formation. However, the molecular mechanisms for OCA-B function in these processes are not clear. Our previous studies documented two OCA-B isoforms and suggested a novel mechanism for the function of the myristoylated, membrane-bound form of OCA-B/p35 as a signaling molecule. Here, we report the identification of galectin-1, and related galectins, as a novel OCA-B-interacting protein. The interaction of OCA-B and galectin-1 can be detected both in vivo and in vitro. The galectin-1 binding domain in OCA-B has been localized to the N terminus of OCA-B. In B cells lacking OCA-B expression, increased galectin-1 expression, secretion, and cell surface association are observed. Consistent with these observations, and a reported inhibitory interaction of galectin-1 with CD45, the phosphatase activity of CD45 is reduced modestly, but significantly, in OCA-B-deficient B cells. Finally, galectin-1 is shown to negatively regulate B cell proliferation and tyrosine phosphorylation upon BCR stimulation. Together, these results raise the possibility that OCA-B may regulate BCR signaling through an association with galectin-1.

Amino Acid Substitution↗

Cellular MRI contrast via coexpression of transferrin receptor and ferritin.

Recently there has been growing interest in the development and use of iron-based contrast agents for cellular imaging with MRI. In this study we investigated coexpression of the transferrin receptor and ferritin genes to induce cellular contrast in a biological system. Expression of transgenic human transferrin receptor and human ferritin H-subunit was induced in a stably transfected mouse neural stem cell line. When grown in iron-rich medium, the transgenic cells accumulated significantly more iron than control cells, with a trend toward an increase in reactive oxygen species, but no detrimental effects on cell viability. This cellular iron significantly increased the transverse relaxivities, R2 and R2*, at 1.5 T and 7 T. By comparing measurements in the same cell samples at 1.5 T and 7 T, we confirmed the expected increase in relaxivity with increasing field strength. Finally, supplemented transgenic cells transplanted into mouse brain demonstrated increased contrast with surrounding neural tissue on T2*-weighted MR brain images compared to controls. These results indicate that dual expression of proteins at different critical points in the iron metabolism pathway may improve cellular contrast without compromising cell viability.

Animals↗

High resolution computerized tomography of the chest and pulmonary function testing in evaluating the effect of tobramycin solution for inhalation in cystic fibrosis patients.

To evaluate the sensitivity of high-resolution computerized tomography (HRCT) of the chest compared to spirometry measures in evaluating the effects of tobramycin solution for inhalation (TSI) in cystic fibrosis (CF) patients.Thirty-two subjects >/=6 years old with mild to moderate CF lung disease were enrolled in a randomized, double-blind, placebo-controlled pilot study. Duration was 28 days; 31 subjects completed the study.HRCT scores decreased 4.06 +/- 3.20 (mean +/- SD) for TSI and decreased 0.17 +/- 1.78 for placebo subjects (P = 0.13). Mean forced expiratory flow during middle half of forced vital capacity (FEF(25%-75%)) predicted increased 6.08 +/- 4.86 for TSI and decreased 0.60 +/- 2.34 for placebo (P = 0.23). Percentage forced expiratory volume in 1 s (FEV(1)) predicted increased slightly for both TSI and placebo (1.29 +/- 3.33 for TSI and 1.17 +/- 1.4 for placebo) (P = 0.97). Two of eight HRCT component scores (atelectasis and inhomogeneity) were observed to be highly discordant with observed HRCT global total score and other HRCT component scores. A modified total score was calculated by dropping them from the global total score. The modified HRCT total scores decreased 6.68 +/- 3.09 for TSI subjects and increased 0.02 +/- 2.0 for the placebo subjects (P = 0.07). Sample sizes were calculated to show statistical significance by differences in modified total HRCT scores, global total HRCT scores, FEF(25%-75%) predicted or FEV(1) % predicted. A total of 60, 100, 200, and over 800 patients would be necessary respectively.HRCT can be a useful measure of change in CF pulmonary disease, requiring a smaller sample size than that required to show treatment effect by pulmonary function testing (PFT) alone.

Administration, Inhalation↗

Effect of non-specific HCN1 blocker CsCl on spatial learning and memory in mouse.

It has been suggested that HCN1 is primarily expressed in hippocampus, however little is known about its effects on spatial learning and memory. In the present study, we investigated the effects of non-specific HCN1 blocker CsCl on spatial learning and memory by using Morris water maze and in situ hybridization in mice. The results showed CsCl 160 mg/kg ip for 4 days, and the mean escape latency was 34 s longer than that of normal control (P<0.01). In hippocampal tissues, staining for the HCN1 mRNA was stronger in the DG and CA1 region of the hippocampus (P <0.05, P<0.05, when CsCl-administration group was compared with normal group). Our results suggested that CsCl could significantly affect the spatial learning and memory in mice, and HCN channel is involved in the process of learning and memory.

Animals↗

Upland rice and lowland rice exhibited different PIP expression under water deficit and ABA treatment.

Aquaporins play a significant role in plant water relations. To further understand the aquaporin function in plants under water stress, the expression of a subgroup of aquaporins, plasma membrane intrinsic proteins (PIPs), was studied at both the protein and mRNA level in upland rice (Oryza sativa L. cv. Zhonghan 3) and lowland rice (Oryza sativa L. cv. Xiushui 63) when they were water stressed by treatment with 20% polyethylene glycol (PEG). Plants responded differently to 20% PEG treatment. Leaf water content of upland rice leaves was reduced rapidly. PIP protein level increased markedly in roots of both types, but only in leaves of upland rice after 10 h of PEG treatment. At the mRNA level, OsPIP1;2, OsPIP1;3, OsPIP2;1 and OsPIP2;5 in roots as well as OsPIP1;2 and OsPIP1;3 in leaves were significantly up-regulated in upland rice, whereas the corresponding genes remained unchanged or down-regulated in lowland rice. Meanwhile, we observed a significant increase in the endogenous abscisic acid (ABA) level in upland rice but not in lowland rice under water deficit. Treatment with 60 microM ABA enhanced the expression of OsPIP1;2, OsPIP2;5 and OsPIP2;6 in roots and OsPIP1;2, OsPIP2;4 and OsPIP2;6 in leaves of upland rice. The responsiveness of PIP genes to water stress and ABA were different, implying that the regulation of PIP genes involves both ABA-dependent and ABA-independent signaling pathways during water deficit.

Abscisic Acid↗

Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery.

A symptom of chilling injury is development of water deficit in shoots, resulting from an imbalance of water transport and transpiration. In this work, two rice varieties (Oryza sativa L. var. Wasetoitsu and Somewake) seedlings were chilled at 7 degrees C, followed by recovery at 28 degrees C. Based on the growth phenotype and electrolyte leakage tests, Somewake was shown to be a chilling-tolerant variety, and Wasetoitsu a chilling-sensitive one. The chilling stress reduced markedly the relative water content (RWC) of leaves, accumulative transpiration and osmotic root hydraulic conductivity (Lp) in both varieties. But when returned to 28 degrees C, the water relation balance of Somewake recovered better. The mRNA expression profile of all the 11 plasma membrane intrinsic proteins (PIPs), a subgroup of aquaporins, was subsequently determined by real-time reverse transcription (RT)-PCR with TaqMan-minor grove binder (MGB) probes derived from rice var. Nipponbare during chilling treatment and recovery. Most of the PIP genes was down-regulated at the low temperature, and recovered at the warm temperature. The relative expression of some PIPs in both Somewake and Wasetoitsu decreased in parallel during the chilling. However during the recovery, the relative expression of OsPIP1;1, OsPIP2;1, OsPIP2;7 in shoots and OsPIP1;1, OsPIP2;1 in roots were significantly higher in Somewake than Wasetoitsu. This supports the role of PIPs in re-establishing water balance after chilling conditions. We discuss the diversified roles played by members of the aquaporin PIP subfamily in plant chilling tolerance depending on aquaporin isoforms, plant tissue and the stage of chilling duration.

Aquaporins↗

Role of cellular compartmentation in the metabolic response to stress: mechanistic insights from computational models.

The mechanisms controlling ATP generation in the transition from normal resting conditions to either high work states or ischemia are poorly understood. ATP generation depends upon compartmentation between the mitochondria and cytosol of metabolic pathways and key energy transfer species that cannot be easily assessed experimentally. We developed a multicompartment mathematical model of cardiac metabolism to simulate the metabolic responses to ischemia and increased workload. The model is based on mass balances, transport, and metabolic processes in cardiac tissue, and has three distinct compartments (blood, cytosol, and mitochondria). In addition to distinguishing between cytosol and mitochondria, the model includes a cytosolic subcompartment for glycolytic metabolic channeling. The model simulations predict the rapid activation of glycogenolysis and lactate production at the onset of ischemia, and support the concept of localization of glycolysis to a cytosolic subcompartment. In addition, simulations show that mitochondrial NADH/NAD(+) is primarily determined by oxygen consumption during ischemia, while cytosolic NADH/NAD(+) and lactate production are largely a function of glycolytic flux during the initial phase, and is controlled by mitochondrial NADH/NAD(+) and the malate-aspartate shuttle during the steady state. Finally, the model predicts that metabolic activation with an abrupt increase in workload requires parallel activation of ATP hydrolysis, glycolysis, mitochondrial dehydrogenases, the electron transport chain, and ADP phosphorylation. Taken together, these studies demonstrate the importance of metabolic compartmentation in the regulation of cardiac energetics in response to acute stress, and they highlight the usefulness of computational models in this line of investigation.

Animals↗