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Hui Yu

Publications and source records attributed to Hui Yu.

At least 19 recordsLinked to original sources
PubMed2026

Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.

Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.

Bacillus↗
PubMed2026

Metabolic Dysfunction-Associated Steatotic Liver Disease Is Associated With Adverse Social Factors: An Analysis Using All of Us.

BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is progressive, with estimated global prevalence exceeding 30%. Social determinants of health (SDOH) may impact MASLD risk and progression. However, this has not been fully characterized. We harnessed the power of the All of Us Research Program (AoU) dataset to conduct a comprehensive analysis examining the association between various SDOH and MASLD. METHODS: We conducted a retrospective cross-sectional analysis of the AoU database. We identified participants with MASLD using ICD-9 and -10 codes and excluded individuals with other chronic liver diseases or self-reported heavy alcohol use. Healthy control participants were devoid of chronic liver diseases, heavy alcohol use, and comorbidities associated with MASLD if obese. We examined SDOH by combining relevant questions from various AoU surveys and conducted univariate and multivariate logistic regression to examine the association between various SDOH and MASLD. RESULTS: After matching cases to controls by age and race/ethnicity, the sample of 57,895 participants had a 1:3 case to control ratio; 16,666 had complete SDOH survey data (MASLD to controls, 1:3.4). Compared to controls, individuals with MASLD were more likely to have less than a high school education (10.7% vs 9.7%; P < .001) and annual income &#x2264;$35,000 (42.4% vs 34.3%; P < .001). Compared to controls, participants with MASLD had significantly higher levels of social isolation, neighborhood disorder, perceived stress, food insecurity, and transportation insecurity (P < .001 for all). CONCLUSION: The study identified significant associations between MASLD and multiple SDOH. Future studies should investigate how SDOH interact to drive MASLD risk and progression.

All of Us↗
PubMed2026

In vivo immune cell engineering from bench to clinical reality.

Adoptive immune cell therapies, exemplified by chimeric antigen receptor T cells, have transformed the treatment of hematological malignancies. However, their broader clinical application is limited by complex ex vivo manufacturing, high cost, and safety concerns. In vivo immune cell engineering has emerged as an alternative strategy that delivers genetic instructions directly to immune cells, thereby generating or modulating therapeutic immune cells within the body and reducing the reliance on individualized in vitro operations. These advances underscore the need for a systematic evaluation of this emerging field. Therefore, this review systematically summarizes the mechanistic principles and delivery strategies underlying in vivo immune cell engineering, with an emphasis on in vivo CAR-T cell generation and the engineering of other immune cells. We then discuss major viral and non-viral delivery platforms and clarify how these platforms influence cargo delivery, cell specificity, and functional immune-cell programming. We further discuss recent preclinical and emerging clinical advances across cancer, autoimmune diseases, and degenerative diseases, while examining key translational challenges, including delivery specificity, off-target effects, controllability, persistence, and manufacturing standardization. Overall, although the field of in vivo immune cell engineering is advancing rapidly, its clinical success will depend on coordinated improvements in delivery precision, therapeutic efficacy, safety, and controllable immune-cell programming.

Cancer immunotherapy↗
PubMed2006

Biocalalyst effects of immobilized anthraquinone on the anaerobic reduction of azo dyes by the salt-tolerant bacteria.

The accelerating effect of dissolved redox mediators has been studied in details in the bio-decolorization processes, but there are little literatures about the non-dissolved redox mediators. Here we describe the accelerating effect of anthraquinone as a redox mediator in the bio-decolorization. Decolorization of azo dyes was carried out experimentally using the salt-tolerant bacteria under immobilized anthraquinone and high salt conditions. Anthraquinone as a redox mediator was able to increase the decolorization rate of azo dyes, and was immobilized by entrapment in calcium alginate (CA), Polyvinyl alcohol (PVA)-H(3)BO(3) and agar, respectively. The effects of various operating conditions such as anthraquinone bead number, dissolved oxygen, temperature and pH on microbial decolorization were investigated experimentally. The reusability of the anthraquinone immobilization beads was evaluated with repeated-batch decolorization experiments. After four repeated experiments, the decolorization rate of CA immobilized anthraquinone retained over 90% of their original value. The experiments explored a great improvement of the redox mediator application and the new bio-treatment concept.

Alginates↗
PubMed2006

p53 independent induction of PUMA mediates intestinal apoptosis in response to ischaemia-reperfusion.

BACKGROUND: The small intestine is highly sensitive to ischaemia-reperfusion (I/R) induced injury which is associated with high morbidity and mortality. Apoptosis, or programmed cell death, is a major mode of cell death occurring during I/R induced injury. However, the mechanisms by which I/R cause apoptosis in the small intestine are poorly understood. p53 upregulated modulator of apoptosis (PUMA) is a p53 downstream target and a member of the BH3-only group of Bcl-2 family proteins. It has been shown that PUMA plays an essential role in apoptosis induced by a variety of stimuli in different tissues through a mitochondrial pathway. AIMS: The role of PUMA in I/R induced injury and apoptosis in the small intestine was investigated. The mechanisms by which PUMA is regulated in I/R induced intestinal apoptosis were also studied. METHODS: Ischaemia was induced by superior mesenteric artery occlusion in the mouse small intestine. Induction of PUMA in response to ischaemia alone, or ischaemia followed by reperfusion (I/R), was examined. I/R induced intestinal apoptosis and injury were compared between PUMA knockout and wild-type mice. The mechanisms of I/R induced and PUMA mediated apoptosis were investigated through analysis of caspase activation, cytosolic release of mitochondrial cytochrome c and alterations of the proapoptotic Bcl-2 family proteins Bax and Bak. To determine whether PUMA is induced by reactive oxygen species and/or reactive nitrogen species generated by I/R, superoxide dismutase (SOD) and N-nitro-l-arginine methyl ester (L-NAME) were used to treat animals before I/R. To determine whether p53 is involved in regulating PUMA during I/R induced apoptosis, PUMA induction and apoptosis in response to I/R were examined in p53 knockout mice. RESULTS: PUMA was markedly induced following I/R in the mucosa of the mouse small intestine. I/R induced intestinal apoptosis was significantly attenuated in PUMA knockout mice compared with that in wild-type mice. I/R induced caspase 3 activation, cytochrome c release, Bax mitochondrial translocation and Bak multimerisation were also inhibited in PUMA knockout mice. SOD or L-NAME significantly blunted I/R induced PUMA expression and apoptosis. Furthermore, I/R induced PUMA expression and apoptosis in the small intestine were not affected in the p53 knockout mice. CONCLUSIONS: Our data demonstrated that PUMA is activated by oxidative stress in response to I/R to promote p53 independent apoptosis in the small intestine through the mitochondrial pathway. Inhibition of PUMA is potentially useful for protecting against I/R induced intestinal injury and apoptosis.

Animals↗
PubMed2006

Differentiated cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer.

Since the creation of Dolly via somatic cell nuclear transfer (SCNT), more than a dozen species of mammals have been cloned using this technology. One hypothesis for the limited success of cloning via SCNT (1%-5%) is that the clones are likely to be derived from adult stem cells. Support for this hypothesis comes from the findings that the reproductive cloning efficiency for embryonic stem cells is five to ten times higher than that for somatic cells as donors and that cloned pups cannot be produced directly from cloned embryos derived from differentiated B and T cells or neuronal cells. The question remains as to whether SCNT-derived animal clones can be derived from truly differentiated somatic cells. We tested this hypothesis with mouse hematopoietic cells at different differentiation stages: hematopoietic stem cells, progenitor cells and granulocytes. We found that cloning efficiency increases over the differentiation hierarchy, and terminally differentiated postmitotic granulocytes yield cloned pups with the greatest cloning efficiency.

Adult Stem Cells↗
PubMed2006

Analytical model for the grazing reflection of a narrow beam.

We propose an analytical model for the grazing reflection of a narrow beam. For the special incidence condition, the output field is the superposition of the incidence and reflected fields, so the incidence cutoff frequency is defined in the angular spectrum. With the definition, we deduce the effective plane-wave-reflection coefficient, together with angular spectrum of the output field. The model is verified by numerical simulation. Calculation in ordinary linear, nonabsorbing media with this model reveals some remarkable characteristics of the output fields, such as negative lateral shift and a beam-width compression effect.

Journal Article↗
PubMed2006

Cadmium accumulation in different rice cultivars and screening for pollution-safe cultivars of rice.

Large areas of contaminated land are being used for agricultural production in some countries due to the high demand for food. To minimize the influx of pollutants to the human food chain through consumption of agricultural products, we propose the concept of pollution-safe cultivars (PSCs), i.e. cultivars whose edible parts accumulate a specific pollutant at a level low enough for safe consumption, even when grown in contaminated soil. We tested the feasibility of the PSC concept by growing 43 cultivars of paddy rice (Oryza sativa L., including 20 normal and 23 hybrid cultivars) under a high (75.69-77.55 mg kg(-1)) and a low (1.75-1.85 mg kg(-1)) cadmium (Cd) exposure. These pot experiments took place in the spring and summer of 2004. At the low level of Cd exposure, 30 out of the 43 tested cultivars were found to be Cd-PSCs. Grain Cd concentrations were highly correlated (p<0.01) between the two experiments, suggesting that Cd accumulation in rice grain is genotype-dependent and that the selection of PSCs is possible, at least at a certain level of soil contamination. No Cd-PSCs were found under the high level of Cd exposure. Yield was enhanced in some cultivars and depressed in others in response to elevated soil Cd, indicating that farmers cannot rely on yield depression as an indicator of toxicity of the grains. It is therefore important and feasible to screen for PSCs and to establish PSC breeding programs to effectively and efficiently reduce the risk of human exposure to soil pollutants, such as Cd, through crop consumption.

Cadmium↗
PubMed2006

Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance.

Several "head-to-head" (or "bidirectional") gene pairs have been studied in individual experiments, but genome-wide analysis of this gene organization, especially in terms of transcriptional correlation and functional association, is still insufficient. We conducted a systematic investigation of head-to-head gene organization focusing on structural features, evolutionary conservation, expression correlation and functional association. Of the present 1,262, 1,071, and 491 head-to-head pairs identified in human, mouse, and rat genomes, respectively, pairs with 1- to 400-base pair distance between transcription start sites form the majority (62.36%, 64.15%, and 55.19% for human, mouse, and rat,respectively) of each dataset, and the largest group is always the one with a transcription start site distance of 101 to 200 base pairs. The phylogenetic analysis among Fugu, chicken, and human indicates a negative selection on the separation of head-to-head genes across vertebrate evolution, and thus the ancestral existence of this gene organization. The expression analysis shows that most of the human head-to-head genes are significantly correlated,and the correlation could be positive, negative, or alternative depending on the experimental conditions. Finally, head to-head genes statistically tend to perform similar functions, and gene pairs associated with the significant cofunctions seem to have stronger expression correlations. The findings indicate that the head-to-head gene organization is ancient and conserved, which subjects functionally related genes to correlated transcriptional regulation and thus provides an exquisite mechanism of transcriptional regulation based on gene organization. These results have significantly expanded the knowledge about head-to-head gene organization. Supplementary materials for this study are available at http://www.scbit.org/h2h.

Animals↗
PubMed2006

Relationship between IFN-gamma gene polymorphism and susceptibility to intrauterine HBV infection.

AIM: To explore the susceptibility of children to intrauterine HBV infection by studying the relationship between IFN-gamma gene polymorphism, including IFN-gamma+874A/T single nucleotide polymorphism (SNP) and CA repeat microsatellite polymorphism and intrauterine HBV infection. METHODS: A TaqMan fluorescence polymerase chain reaction in the IFN-gamma+874A/T single nucleotide polymorphism was tested in the intrauterine HBV infection group (group I) and the normal immune children group (group II). Capillary electrophoresis was performed in the above two groups to assay the IFN-gamma CA repeat microsatellite polymorphism. RESULTS: Frequencies of AA, AT and TT genotypes were 67.4%, 19.6% and 13.0% in the intrauterine HBV infection group, and 45.2%, 30.1% and 24.7% in the normal immune children group, respectively. A significant difference was found in the frequency distribution of IFN-gamma+874 genotype between the two groups (chi2 = 5.102, P = 0.02389). In the intrauterine HBV infection group the AA genotype was more common than in the normal immune group. Frequency of IFN-gamma+874A allele was 77.17% in the intrauterine HBV infection group, and 60.27% in the normal immune children group. In the intrauterine HBV infection group the IFN-gamma+874A allele was more common than in normal immune group. A significant difference was found in the frequency distribution between the two groups (chi2 = 7.238, P = 0.02389, OR = 2.228, 95% CI = 1.244-3.992). (CA12)+/(CA12)+ of IFN-gamma CA microsatellite polymorphism was 11.90% in the intrauterine HBV infection group and 26.47% in the normal immune children group. A significant difference was found in the frequency distribution between the two groups (chi2 = 5.64, P = 0.0176). Frequency of IFN-gamma CA repeat was 25% in the intrauterine HBV infection group and 43.38% in the normal immune children group. The frequency of IFN-gamma CA repeat was less in the intrauterine HBV infection group than in normal immune group. A significant difference was found in the frequency distribution between the two groups (chi2 = 7.548, P = 0.0060). CONCLUSION: There is a relationship between IFN-gamma+874A/T SNP and intrauterine HBV infection as well as between IFN-gamma CA microsatellite polymorphism and intrauterine HBV infection. IFN-gamma gene polymorphism might be important in determining individual's susceptibility to intrauterine HBV infection.

Alleles↗
PubMed2006

The 33 kDa protein can be removed without affecting the association of the 23 and 17 kDa proteins with the luminal side of PS II of spinach.

An earlier study shows that a 30 min incubation of spinach PS II submembrane fragments at pH 6.3 in the presence of 10 microM HgCl(2) induces a 40% depletion of the 33 kDa protein without the apparent release of the 17 and 23 kDa proteins [Bernier, M., and Carpentier, R. (1995) FEBS Lett. 360, 251-254]. Here we report that the photosystem II 33 kDa extrinsic protein is fully removed by HgCl(2) added at micromolar and higher concentrations (0.25, 20, and 50 microM), with the 17 and 23 kDa extrinsic proteins and other intrinsic proteins remaining bound to the reaction center. The data presented here put in doubt the "regulatory cap" model of PS II, which follows the OEC-33 kDa-23 kDa-17 kDa binding order, as these results directly demonstrate that the 33 kDa protein can be removed without affecting the binding of the 23 and 17 kDa proteins to the intrinsic subunits of PS II. This suggests that each extrinsic protein may possess its own binding site on PS II. A possible mechanism for HgCl(2) upon the release of the 33 kDa protein is discussed.

Binding Sites↗
PubMed2006

The leading role of association in framework modification of highly siliceous zeolites with adsorbed methylamine.

Affinity index (AT value), adsorption heat, X-ray diffraction (XRD), and 13C and 29Si magic-angle spinning (MAS) NMR, FTIR, and Raman spectroscopies were used to study the interaction of highly siliceous MFI-, FAU-, and FER-type zeolites with adsorbed methylamine (MA). Compared with the data for methanol, the much higher AT values and adsorption heats, and significant changes in XRD patterns, 29Si MAS NMR spectra, and FTIR spectra for the zeolites after adsorption of MA, revealed a strong hydrogen-bonding interaction between the perfect framework of the zeolites and the adsorbed MAs. This interaction results from the fact that the H atom of the amine group attacks the [Si-O] framework to form a Si-OHN bond, which leads to the appearance of Si-N bonds in the zeolites at 323 K. Therefore, the zeolite framework can be modified with MA under mild conditions. The highly siliceous MFI zeolite and the H-ZSM-5 zeolite with SiO2/Al2O3=31:1 were modified with MA and investigated by temperature-programmed desorption of CO2. The modified zeolites exhibited greatly enhanced basic properties in comparison with those of the raw materials. The influence of defects in the zeolite on the adsorption and the interaction with MA is discussed.

Journal Article↗
PubMed2006

Combining gene expression profiles and protein-protein interaction data to infer gene functions.

The ever-increasing flow of gene expression profiles and protein-protein interactions has catalyzed many computational approaches for inference of gene functions. Despite all the efforts, there is still room for improvement, for the information enriched in each biological data source has not been exploited to its fullness. A composite method is proposed for classifying unannotated genes based on expression data and protein-protein interaction (PPI) data, which extracts information from both data sources in novel ways. With the noise nature of expression data taken into consideration, importance is attached to the consensus expression patterns of gene classes instead of the actual expression profiles of individual genes, thus characterizing the composite method with enhanced robustness against microarray data variation. With regard to the PPI network, the traditional clear-cut binary attitude towards inter- and intra-functional interactions is abandoned, whereas a more objective perspective into the PPI network structure is formed through incorporating the varied function-function interaction probabilities into the algorithm. The composite method was implemented in two numerical experiments, where its improvement over single-data-source based methods was observed and the superiority of the novel data handling operations was discussed.

Algorithms↗
PubMed2006

Hematopoietic stem cells are not the direct target of spontaneous leukemic transformation in p18(INK4C)-null reconstituted mice.

Cell cycle inhibitors are important regulators in normal tissue regeneration and disruption of the regulators are involved in cancer development. Our recent study showed that the absence of the CDK inhibitor p18(INK4C) (p18) enhances self-renewal of normal hematopoietic stem cell (HSC) in vivo, whereas previous studies by others showed an increased incidence of leukemogenesis in older p18-null mice. Here, we have examined potential leukemogenesis during experimentally induced regeneration of HSC in the absence of p18 in order to gauge the relation between these two processes. Reconstituted mice with p18-deficient HSCs under the condition of repetitive proliferative stress (serial transplantation) were followed for >3 years. T cell leukemia from the p18-/- origin was recapitulated 24 months after secondary transplantation. However, no myeloid leukemia was found in the recipients. The T cell leukemia-initiating cells (mainly in a CD3(lo) cell subset) did not share the same immunophenotype with normal HSCs and, in fact, the function of HSCs was significantly compromised with decreased abundance in the leukemic mice. Furthermore, we found that the p15 or p16 gene promoters were frequently methylated in the leukemic cells but not in HSCs. Our present study argues against the possibility of overgrowth of p18-null HSCs leading to a leukemic phenotype. The data also support the notion that p18 has an independent role in T cell maintenance such that CD3+ CD8+ cells, unlike HSCs, are more accessible to leukemogenic transformation after the loss of p18.

Animals↗
PubMed2006

Characterization of a bifunctional cytidine 5'-monophosphate N-acetylneuraminic acid synthetase cloned from Streptococcus agalactiae.

Recombinant CMP-sialic acid synthetase, cloned from Streptococcus agalactiae serotype V strain 2603 V/R, is bifunctional having both CMP-sialic acid synthetase and acetylhydrolase (acylesterase) activities. The enzyme is active over a wide pH range with an optimal CMP-sialic acid synthetase activity at pH 9.0 and an optimal acetylhydrolase activity at pH 8.0. A metal cofactor (either Mg(2+) or Mn(2+)) is required for the CMP-sialic acid synthetase activity but is not for acetylhydrolase activity. Both catalytic functions, however, are impaired by high concentrations of Mn(2+).

Catalysis↗
PubMed2006

Long-term engraftment of p18(INK4C)-deficient hematopoietic stem cells is enhanced in the sublethally-irradiated recipients.

Non-myeloablative regimens for host conditioning have been widely used in clinical hematopoietic stem cell transplantation due to their reduced toxicity on the recipients. But a milder conditioning regimen may require a higher engrafting ability of donor stem cells in competing with endogenous stem cells. Thus, new strategies for enhancing the competitiveness of donor stem cells in non-myeloablative recipients would have important implications for current clinical stem cell transplantation. It is known that the absence of p18(INK4C) (p18) gene can enhance the self-renewal potential of hematopoietic stem cells (HSCs). We applied the approach of competitive bone marrow transplantation to evaluate the impact of p18 gene deletion on long-term engraftment of HSCs in sublethally irradiated hosts. We found that p18(-/-) HSCs had a significant advantage over wild-type HSCs during long-term engraftment in the mouse recipients that received a sub-lethal irradiation (5-Gy). The engraftment efficiency of p18(-/-) HSCs in the sub-lethally irradiated recipients was similar to that in the lethally irradiated (10-Gy) recipients. Our current study demonstrates that enhanced engraftment of donor HSCs in the absence of p18 does not strictly depend on the dose of irradiation used for host conditioning. Therefore, p18 might serve as a potential drug target for increasing the efficacy of stem cell transplant in the patients that are preconditioned with either a myeloablative or non-myeloablative regimen.

Animals↗