Biomedical subjects

Mi Zhou

Publications and source records attributed to Mi Zhou.

At least 19 recordsLinked to original sources

PubMed2026

Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.

BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons. RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes. CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.

Auxiliary metabolic genes↗

PubMed2026

LncRNA DNAJC3-AS1 promotes gastric cancer malignancy through miR-576-5p-mediated upregulation of LYPLA1.

Long non-coding RNAs (lncRNAs) are involved in tumor progression, but the role of lnc-DNAJC3-AS1 in gastric cancer (GC) remains unclear. This study aimed to investigate the biological function and regulatory mechanism of lnc-DNAJC3-AS1 in GC. Reverse transcription quantitative PCR (RT-qPCR) was used to detect the expression levels of lnc-DNAJC3-AS1, miR-576-5p, and LYPLA1, and Western blot was used to analyze protein expression. The Cancer Genome Atlas (TCGA) database and clinical samples were used to evaluate their clinical relevance. Cell viability, cell cycle distribution, apoptosis, migration, and invasion were assessed using Cell Counting Kit-8 (CCK-8), flow cytometry, wound-healing, Transwell, and immunofluorescence assays. Dual-luciferase reporter assay, RNA immunoprecipitation (RIP), fluorescence in situ hybridization (FISH), and rescue assays were performed to explore the potential regulatory relationship among lnc-DNAJC3-AS1, miR-576-5p, and LYPLA1. A xenograft tumor model was also established to evaluate the role of lnc-DNAJC3-AS1 in vivo. The results showed that lnc-DNAJC3-AS1 and LYPLA1 were upregulated, whereas miR-576-5p was downregulated in GC tissues and cells. Knockdown of lnc-DNAJC3-AS1 inhibited GC cell viability, migration, and invasion, induced G0/G1 phase arrest and apoptosis, and suppressed tumor growth in vivo. Mechanistically, lnc-DNAJC3-AS1 was mainly localized in the cytoplasm and was associated with miR-576-5p-related RNA-induced silencing complex (RISC) complexes. MiR-576-5p targeted LYPLA1, and restoration of miR-576-5p or knockdown of LYPLA1 partially attenuated the effects of lnc-DNAJC3-AS1 overexpression on GC cell phenotypes and LYPLA1 enzymatic activity. These findings suggest that lnc-DNAJC3-AS1 promotes GC progression, at least in part, through the miR-576-5p/LYPLA1 pathway, providing a potential target for GC treatment.

Gastric cancer↗

PubMed2026

Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.

BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics. RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.

Metagenome↗

PubMed2006

PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.

Polymorphism in microRNA Target Site (PolymiRTS) database is a collection of naturally occurring DNA variations in putative microRNA target sites. PolymiRTSs may affect gene expression and cause variations in complex phenotypes. The database integrates sequence polymorphism, phenotype and expression microarray data, and characterizes PolymiRTSs as potential candidates responsible for the quantitative trait locus (QTL) effects. It is a resource for studying PolymiRTSs and their implications in phenotypic variations. PolymiRTS database can be accessed at http://compbio.utmem.edu/miRSNP/.

Animals↗

PubMed2006

Clinical report of cervical arthroplasty in management of spondylotic myelopathy in Chinese.

OBJECTIVES: To investigate clinical effects and manual operational point of Bryan cervical disc prosthesis in Chinese, to observe the stability and range of movement (ROM) post-operatively. METHODS AND MATERIALS: From 2003,12 to 2005,12, Bryan disc prosthesis replacement applied in 83 cases (102 levels) of cervical spondylotic myelopathy (CSM) after anterior decompression in our hospital. Clinical (JOA grade and Odom's scale) and radiological (X-ray of flexion, extension; left and right bending position) follow-up was performed. Systemic radiographic study about stability and ROM of replaced level post operationally were measured. CT or MRI scans were applied in all cases to evaluate the signs of the prosthesis deflexion and hetero-ossification in the replaced levels. RESULTS: At least 12 months follow-up were done in 65/83 of these patients. All of 83 patients were improved according to Odsm's scale. JOA score increased from average 8.7 to 15.5. There was no prosthesis subsidence. Replaced segment achieved stability and restored partial of normal ROM 4.73 degrees (3.7 degrees -5.9 degrees ) early postoperation and 8.12 degrees (5.8 degrees -13.6 degrees ) more than 12 months postoperation in flex and extension position. No obvious loss of lordosis was found. CT or MRI follow-up shows position deflexion of the prosthesis metal endplates (<1.5 mm) in 14/77 levels and (1.5-3 mm) in 4/77. heter-ossification was found in the replaced levels only in 2 cases. CONCLUSION: Byran cervical disc prosthesis restored motion to the level of the intact segment in flexion-extension and lateral bending in post-operative images. At the same time, it can achieve good anterior decompression treatment effect and immediate stability in replaced 1 or 2 levels, and which is a new choice for the treatment of CSM.

Journal Article↗

PubMed2006

Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships.

Gene expression QTL (eQTL) mapping can suggest candidate regulatory relationships between genes. Recent advances in mammalian phenotype annotation such as mammalian phenotype ontology (MPO) enable systematic analysis of the phenotypic spectrum subserved by many genes. In this study we combined eQTL mapping and phenotypic spectrum analysis to predict gene regulatory relationships. Five pairs of genes with similar phenotypic effects and potential regulatory relationships suggested by eQTL mapping were identified. Lines of evidence supporting some of the predicted regulatory relationships were obtained from biological literature. A particularly notable example is that promoter sequence analysis and real-time PCR assays support the predicted regulation of protein kinase C epsilon (Prkce) by cAMP responsive element binding protein 1 (Creb1). Our results show that the combination of gene eQTL mapping and phenotypic spectrum analysis may provide a valuable approach to uncovering gene regulatory relations underlying mammalian phenotypes.

Animals↗

PubMed2005

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Genetic loci that regulate inherited traits are routinely identified using quantitative trait locus (QTL) mapping methods. However, the genotype-phenotype associations do not provide information on the gene expression program through which the genetic loci regulate the traits. Transcription modules are 'self-consistent regulatory units' and are closely related to the modular components of gene regulatory network [Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176]. We used genome-wide genotype and gene expression data of a genetic reference population that consists of mice of 32 recombinant inbred strains to identify the transcription modules and the genetic loci regulating them. Twenty-nine transcription modules defined by genetic variations were identified. Statistically significant associations between the transcription modules and 18 classical physiological and behavioral traits were found. Genome-wide interval mapping showed that major QTLs regulating the transcription modules are often co-localized with the QTLs regulating the associated classical traits. The association and the possible co-regulation of the classical trait and transcription module indicate that the transcription module may be involved in the gene pathways connecting the QTL and the classical trait. Our results show that a transcription module may associate with multiple seemingly unrelated classical traits and a classical trait may associate with different modules. Literature mining results provided strong independent evidences for the relations among genes of the transcription modules, genes in the regions of the QTLs regulating the transcription modules and the keywords representing the classical traits.

Animals↗

PubMed2005

Catalytic reduction of chlorinated and recalcitrant compounds in contaminated water.

Catalysis dechlorination of chlorinated organic matter by palladium/iron bimetallic particles represents one of the latest innovative technologies for contaminated soil and groundwater remediation. The reaction of dechlorination is believed to take place on the surface site of the catalyst in a pseudo-first-order mode. The dechlorination rate increases with an increase of the bulk loading of palladium due to the increase of both the surface loading of palladium and the total surface area exposed. The results show that no other intermediates were generated besides Cl-, benzene and chlorobenzene during dechlorination of o-dichlorobenzene.

Catalysis↗

PubMed2005

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

Nonsynonymous single nucleotide polymorphisms (nsSNPs) are prevalent in genomes and are closely associated with inherited diseases. To facilitate identifying disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the nsSNP's phenotypic effect (disease-associated versus neutral). nsSNPAnalyzer, a web-based software developed for this purpose, extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP's phenotypic effect. nsSNPAnalyzer server is available at http://snpanalyzer.utmem.edu/.

Algorithms↗

PubMed2005

Catalytic amination and dechlorination of para-nitrochlorobenzene (p-NCB) in water over palladium-iron bimetallic catalyst.

Chemical treatment of para-nitrochlorobenzene (p-NCB) by palladium/iron (Pd/Fe) bimetallic particles represents one of the latest innovative technologies for the remediation of contaminated soil and groundwater. The amination and dechlorination reaction is believed to take place predominantly on the surface site of the Pd/Fe catalysts. The p-NCB was first transformed to p-chloroaniline (p-CAN) then quickly reduced to aniline. 100% of p-NCB was removed in 30 min when bimetallic Pd/Fe particles with 0.03% Pd at the Pd/Fe mass concentration of 3g 75 ml(-1) were used. The p-NCB removal efficiency and the subsequent dechlorination rate increased with the increase of bulk loading of palladium and Pd/Fe. As expected, p-NCB removal efficiency increased with temperature as well. In particular, the removal efficiency of p-NCB was measured to be 67%, 79%, 80%, 90% and 100% for reaction temperature 20, 25, 30, 35 and 40 degrees C, respectively. Our results show that no other intermediates were generated besides Cl(-), p-CAN and aniline during the catalytic amination and dechlorination of p-NCB.

Amination↗

PubMed2005

Inferring gene transcriptional modulatory relations: a genetical genomics approach.

Bayesian network modeling is a promising approach to define and evaluate gene expression circuits in diverse tissues and cell types under different experimental conditions. The power and practicality of this approach can be improved by restricting the number of potential interactions among genes and by defining causal relations before evaluating posterior probabilities for billions of networks. A newly developed genetical genomics method that combines transcriptome profiling with complex trait analysis now provides strong constraints on network architecture. This method detects those chromosomal intervals responsible for differences in mRNA expression using quantitative trait locus (QTL) mapping. We have developed an efficient Bayesian approach that exploits the genetical genomics method to focus computational effort on the most plausible gene modulatory networks. We exploit a dense marker map for a genetic reference population (GRP) that consists of 32 BXD strains of mice made by intercrossing two progenitor strains--C57BL/6J and DBA/2J. These progenitors differ at approximately 1.3 million known single nucleotide polymorphisms (SNPs), all of which can be exploited to estimate the probability that a gene contains functional polymorphisms that segregate within the GRP. We constructed 66 candidate networks that include all the candidate modulator genes located in the 209 statistically significant trans-acting QTL regions. SNPs that distinguish between the two progenitor strains were used to further winnow the list of candidate modulators. Bayesian network was then used to identify the genetic modulatory relations that best explain the microarray data.

Algorithms↗

PubMed2005

[The clinical application and biomechanical study of reconstruction of anterior and posterior cruciate ligament with hamstring tendons knot implant fixation].

OBJECTIVE: To investigate the feasibility of reconstruction of anterior cruciate ligament (ACL) and posterior cruciate ligament (PCL) with hamstring tendons knot implant fixation. METHODS: Fifty-two cases of ACL and PCL old injury were reconstructed under the arthroscopy with double bundles hamstring tendons knot implant fixated in the bottle-necked femoral tunnel. The tibia side were fixated by tendon weave suture cross tied a knot at the bone bridge of tibia. In this group reconstruction of ACL was in 25, PCL and ACL at the same time reconstruction in 15, PCL in 12. The failure test and displacement evaluation were used to study the biomechanics of reconstruction of ACL by hamstring tendon knot implant fixation (n = 13) in porcine knees. The control group were reconstructed with bone-patellar tendon-bone B-PT-B and interference screw (n = 11). The tibia side tendon weave suture immobility by cross tied a knot at the tibia bone bridge (n = 7) and interference screw in the tibia tunnel (n = 8). RESULTS: Forty-nine cases were followed up, average 14.6 months. The results of Lanchman test was negative in 46 cases, positive in 3 cases. Preoperative Lysholm score was 56.7, and postoperative was 92.8. According to the knee joint effective evaluate standard, 46 were excellent and 3 good. The maximal pull-out force of hamstring tendons knot implanted fixation had been greater than B-PT-B fixation by interference screw. There were similar displacement in 100 N and 400 N load between hamstring tendons knot implant fixation and B-PT-B (P > 0.05). Peak force test maximal displacement evaluation and failure energy absorption measurement showed that hamstring tendons knot implant fixation was significantly greater than B-PT-B (P < 0.01). The failure test and displacement evaluation of tendon fixation by weave suture knot at the tibia bone bridge cross tie were greater than B-PT-B fixation by interference screw. CONCLUSION: The methods of reconstruct of ACL and PCL by hamstring tendons knot implant fixation are feasible. The advantages include: it is biological fixation, not machine fixation; it may benefit for tendons with bone tunnel healing and decrease medical cost. Decreasing or eliminating displacement is helpful to prevent relaxation after reconstruction of ACL and PCL.

Animals↗

PubMed2005

Enhanced catalytic degradation process of o-nitrochlorobenzene by palladium-catalyzed fe0 particles.

Over Pd/Fe bimetallic catalyst, o-nitrochlorobenzene (o-NCB), at a concentration of 20 mg/L in aqueous solutions, is rapidly converted to o-chloroaniline (o-CAN) first, and then quickly dechlorinated to aniline(AN) and Cl-, without other intermediate reaction products. The aminated and dechlorinated reactions are believed to take place on the surface site of the Pd/Fe. The o-NCB removal efficiency and the next dechlorination rate increase with an increase of bulk loading of palladium and catalysts addition due to the increase of both the surface loading of palladium and the total surface area. These results indicate that reduction, amination and dechlorination of o-NCB by palladium-catalyzed Fe0 particles, can be designed for remediation of contaminated groundwater.

Catalysis↗

PubMed2004

Integrated analysis of microarray data and gene function information.

Microarray data should be interpreted in the context of existing biological knowledge. Here we present integrated analysis of microarray data and gene function classification data using homogeneity analysis. Homogeneity analysis is a graphical multivariate statistical method for analyzing categorical data. It converts categorical data into graphical display. By simultaneously quantifying the microarray-derived gene groups and gene function categories, it captures the complex relations between biological information derived from microarray data and the existing knowledge about the gene function. Thus, homogeneity analysis provides a mathematical framework for integrating the analysis of microarray data and the existing biological knowledge.

Algorithms↗

PubMed2004

GeneInfoViz: constructing and visualizing gene relation networks.

Large amounts of knowledge about genes have been stored in public databases. One of the most challenging problems in Bioinformatics is, given all the information about the genes in the databases, determining the relationships between the genes. For example, how can we determine if genes are related and how closely they are related based on existing knowledge about their biological roles. We developed GeneInfoViz, a web tool for batch retrieval of gene information and construction and visualization of gene relation networks. We created a database containing compiled Gene Ontology information for the genes of several model organisms. Users can batch search for a group of genes and get the Gene Ontology terms that are associated with the genes. Directed acyclic graphs are generated to show the hierarchical structure of the Gene Ontology tree. GeneInfoViz calculates an adjacency matrix to determine whether the genes are related and, if so, how closely they are related based on biological processes, molecular functions, or cellular components they are associated with and then displays a dynamic graph layout of the network among the selected genes.

Databases, Genetic↗

PubMed2003

Coupling development and elution, a new thin-layer chromatography technique.

Three methods of coupling development and elution were studied in this paper. (1) A new mode of solvent supplementation and eluate collection was developed for descending development. By using a new distributor and collector in descending development, components can be separated and eluted continuously. (2) The same effect can be realized with a slope distributor [Su et al., J. Planar Chromatogr. 14 (2001) 203] and a collector by horizontal development. (3) In-situ elution can be used to treat a developed silica plate, which can elute the separated components to the receptor without scraping them off. These three methods can be used individually, and the in-situ elution can be used with other modes of development.

Chromatography, Thin Layer↗

PubMed2003

[Effect of T3 on the expression of transferrin receptor and ferritin in K562 cells and its possible mechanism].

OBJECTIVE: To explore the effect of T(3) on the expression of transferrin receptor (TfR) and ferritin (Fn) in K562 cells and its possible mechanism. METHODS: Flow cytometry was used for the detection of TfR expression, radioimmunoassay for Fn expression, RNA/protein band shift assay for the binding activity of iron regulatory protein (IRP) and iron responsive elements (IRE), and RT-PCR for TfR and Fn mRNA levels. RESULTS: Different concentration of T(3) significantly increased Fn expression of K562 cells, especially at 100 nmol/L and 200 nmol/L (p < 0.05). However, T(3) had no effect on TfR expression. T(3) decreased the binding activity between IRP and IRE, particularly at concentration of 50 nmol/L. Different concentration of T(3) increased Fn-H mRNA level at different time point while it had no effect on TfR mRNA level. CONCLUSION: T(3) increased Fn expression of K562 cells through the possible mechanisms of either the post-transcriptional regulation or transcriptional modulation.

Ferritins↗

PubMed2003

[The effect of erythropoitin and thyroid hormone on K562 iron metabolism].

OBJECTIVE: To explore the effect of recombinant human erythropoitin (rhEPO) and T3 on the iron metabolism of K562 cells and its possible mechanism. METHODS: With the use of the bone marrow iron stain method, the positive stained cells rate was calculated. Flow cytometry was performed to detect the transferrin receptor (TfR) expression of K562 cells. RESULTS: rhEPO increased the positive cell rate of iron stain, which was especially noticeable in the rhEPO 5 U/ml group (P < 0.01), and the effect was time-dependant, i.e., the longer the incubating time, the higher the positive rate. T3 also elevated the positive cell rate of iron stain significantly at different concentrations, and the highest rate was seen when incubating K562 cells for 48 hours. The expression of TfR was increased significantly when incubating with rhEPO for 72 hours (P < 0.05), but there was no marked change when incubating with T3. CONCLUSION: The possible mechanism by which rhEPO increased the positive cell rate of iron stain might be due to the enhancement of TfR expression and hence the increase in iron intake of K562 cells.

Bone Marrow Cells↗