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Biomedical subjects

Zheng Liu

Publications and source records attributed to Zheng Liu.

At least 19 recordsLinked to original sources
PubMed2026

Causal Relationship of Polyunsaturated Fatty Acids With Mental Disorders: A Systematic Review and Meta-analysis.

CONTEXT: Mental disorders (MDs) pose a important global health challenge, with a complex pathogenesis complicating treatment development. Nutritional interventions, particularly polyunsaturated fatty acids (PUFAs), have gained attention as potential therapeutic options. OBJECTIVE: This Mendelian randomization (MR) meta-analysis aimed to evaluate the potential causal relationship between PUFAs and MDs. DATA SOURCES: Genome-wide association study data were utilized to analyze the association between PUFAs (including omega-3, omega-3 percentage [omega-3%], omega-6, omega-6 percentage [omega-6%], and omega-6 to omega-3 ratio) and 12 major MDs. DATA EXTRACTION: Two-sample MR technology was used to assess the role of PUFAs in MDs. DATA ANALYSIS: The MR analysis revealed that genetically predicted omega-3 was causally linked to MDs, such as obsessive-compulsive disorder, bipolar disorder, schizophrenia, and major depressive disorder. Omega-3% exhibited protective effects against emotional personality disorder. Conversely, omega-6 was inversely correlated with attention-deficit/hyperactivity disorder risk, while a high omega-6 to omega-3 ratio was associated with an increased risk of depression and other mood disorders. CONCLUSION: High omega-3 levels and omega-3% may reduce the risk of MDs, whereas a high omega-6:omega-3 ratio may elevate the risk. These findings highlight the potential of PUFAs, particularly omega-3, in MD prevention and treatment, while underscoring the need for further research into the complex interactions between omega-3 and omega-6. The study provides a scientific foundation for future clinical trials and dietary intervention strategies. SYSTEMATIC REVIEW REGISTRATION: PROSPERO no. CRD42024598472.

Humans↗
PubMed2026

Deep learning techniques in predicting BRAF mutation status in cutaneous melanoma from histopathologic images.

AIMS: To develop and validate a deep learning framework for discriminating BRAF mutation status in cutaneous melanoma from routine H&E whole-slide images (WSIs) as a proof-of-concept complementary approach alongside molecular testing. METHODS: We built a two-stage pipeline comprising U-Net-based tumour segmentation followed by an Inception v3 classifier. In total, 272 institutional melanoma cases with confirmed BRAF status were used for model development (training and internal validation). Generalisability was assessed in an external test set of 76 cutaneous melanoma cases from the Cancer Genome Atlas (TCGA). Dermatopathologist-defined tumour-rich regions of interest were used to train and evaluate segmentation. WSIs were processed at 20×magnification using 512×512 tiles; slide-level mutation probabilities were obtained by averaging the predicted probabilities across all tumour-enriched tiles. RESULTS: Inception v3 achieved area under the receiver operating characteristic curve values of 0.973 (training), 0.954 (validation) and 0.915 (TCGA testing) and outperformed a ResNet50 baseline, showing stable external generalisation. Performance remained robust in advanced pathological T-category primary tumours (pT3-T4). Tumour probability heatmaps supported spatial interpretability by localising regions contributing most strongly to predicted mutation status. CONCLUSIONS: Deep learning applied to routine H&E WSIs can infer BRAF mutation status in cutaneous melanoma with consistent performance across institutional and external cohorts. Given the observed external sensitivity and negative predictive value, the model is not suitable for rule-out use or for deferring/omitting molecular testing. Any workflow integration is future work and would require prospective validation and calibration of probability outputs in real-world clinical series.

Artificial Intelligence↗
PubMed2026

Multi-omics analysis reveals coordinated epigenetic dysregulation in atrazine-induced dopaminergic neurotoxicity.

Atrazine (ATR), a widely used triazine herbicide, has been linked to neurotoxicity, yet the epigenetic mechanisms underlying its dopaminergic effects remain unclear. This study investigated whether coordinated miRNA dysregulation and DNA methylation alterations contribute to ATR-induced Parkinson's disease (PD)-like neurotoxicity. Male Sprague-Dawley rats were administered ATR (50&#x202f;mg/kg/day) for 90 days, resulting in motor and cognitive deficits with dopaminergic dysfunction, including increased &#x3b1;-synuclein and reduced tyrosine hydroxylase expression. Small RNA sequencing identified 72 differentially expressed miRNAs in the substantia nigra, enriched in PI3K-Akt, MAPK, and Ras signaling pathways. In a cohort of six PD patients and six matched controls, genome-wide DNA methylation profiling revealed 4694 differentially methylated positions, predominantly hypomethylated, with overlapping enrichment in neuronal signaling pathways. Weighted gene co-expression network analysis identified a PD-associated module strongly correlated with disease status (r&#x202f;=&#x202f;-0.95, P&#x202f;<&#x202f;0.001). Multi-omics integration identified CASP3 as a central hub gene. External validation supported CASP3 relevance in PD (AUC&#x202f;=&#x202f;0.833), and molecular docking suggested potential ATR-CASP3 interaction. Further analysis predicted upregulated miR-3552 as a potential upstream regulator of CASP3. These findings indicate that ATR-induced neurotoxicity may be mediated through the miR-3552/CASP3 signaling axis, ultimately regulating apoptosis and contributing to neurodegeneration.

Animals↗
PubMed2024

DNA polymerase delta governs parental histone transfer to DNA replication lagging strand.

Chromatin replication is intricately intertwined with the recycling of parental histones to the newly duplicated DNA strands for faithful genetic and epigenetic inheritance. The transfer of parental histones occurs through two distinct pathways: leading strand deposition, mediated by the DNA polymerase &#x3b5; subunits Dpb3/Dpb4, and lagging strand deposition, facilitated by the MCM helicase subunit Mcm2. However, the mechanism of the facilitation of Mcm2 transferring parental histones to the lagging strand while moving along the leading strand remains unclear. Here, we show that the deletion of Pol32, a nonessential subunit of major lagging-strand DNA polymerase &#x3b4;, results in a predominant transfer of parental histone H3-H4 to the leading strand during replication. Biochemical analyses further demonstrate that Pol32 can bind histone H3-H4 both in vivo and in vitro. The interaction of Pol32 with parental histone H3-H4 is disrupted through the mutation of the histone H3-H4 binding domain within Mcm2. Our findings identify the DNA polymerase &#x3b4; subunit Pol32 as a critical histone chaperone downstream of Mcm2, mediating the transfer of parental histones to the lagging strand during DNA replication.

DNA Polymerase III↗
PubMed2007

MRG-1, an autosome-associated protein, silences X-linked genes and protects germline immortality in Caenorhabditis elegans.

MRG15, a mammalian protein related to the mortality factor MORF4, is required for cell proliferation and embryo survival. Our genetic analysis has revealed that the Caenorhabditis elegans ortholog MRG-1 serves similar roles. Maternal MRG-1 promotes embryo survival and is required for proliferation and immortality of the primordial germ cells (PGCs). As expected of a chromodomain protein, MRG-1 associates with chromatin. Unexpectedly, it is concentrated on the autosomes and not detectable on the X chromosomes. This association is not dependent on the autosome-enriched protein MES-4. Focusing on possible roles of MRG-1 in regulating gene expression, we determined that MRG-1 is required to maintain repression in the maternal germ line of transgenes on extrachromosomal arrays, and of several X-linked genes previously shown to depend on MES-4 for repression. MRG-1 is not required for PGCs to acquire transcriptional competence or for the turn-on of expression of several PGC-expressed genes (pgl-1, glh-1, glh-4 and nos-1). By contrast to this result in PGCs, MRG-1 is required for ectopic expression of those germline genes in somatic cells lacking the NuRD complex component MEP-1. We discuss how an autosome-enriched protein might repress genes on the X chromosome, promote PGC proliferation and survival, and influence the germ versus soma distinction.

Animals↗
PubMed2006

cAMP/protein kinase A signalling pathway protects against neuronal apoptosis and is associated with modulation of Kv2.1 in cerebellar granule cells.

Previously, we have reported that apoptosis of cerebellar granular neurons induced by incubation in 5 mm K(+) and serum-free medium (LK-S) was associated with an increase in the delayed rectifier K(+) current (I(K)). Here, we show that I(K) associated with apoptotic neurons is mainly encoded by a Kv2.1 subunit. Silencing Kv2.1 expression by small interfering RNA reduces I(K) and increases neuron viability. Forskolin is able to decrease the I(K) amplitude recording from neurons of both the LK-S and control group, and prevents apoptosis of granule cells that are induced by LK-S. Dibutyryl cAMP mimicks the effect of forskolin on the modulation of I(K) and, accordingly, the inhibitor of protein kinase A, H-89, aborts the neuron-protective effect induced by forskolin. Whereas the expression of Kv2.1 was silenced by Kv2.1 small interfering RNA, the inhibition of forskolin on the current amplitude was significantly reduced. Quantitative RT-PCR and whole-cell recording revealed that the expression of Kv2.1 was elevated in the apoptotic neurons, and forskolin significantly depressed the expression of Kv2.1. We conclude that the protection against apoptosis via the protein kinase A pathway is associated with a double modulation on I(K) channel properties and its expression of alpha-subunit that is mainly encoded by the Kv2.1 gene.

Animals↗
PubMed2006

Complex zeolite structure solved by combining powder diffraction and electron microscopy.

Many industrially important materials, ranging from ceramics to catalysts to pharmaceuticals, are polycrystalline and cannot be grown as single crystals. This means that non-conventional methods of structure analysis must be applied to obtain the structural information that is fundamental to the understanding of the properties of these materials. Electron microscopy might appear to be a natural approach, but only relatively simple structures have been solved by this route. Powder diffraction is another obvious option, but the overlap of reflections with similar diffraction angles causes an ambiguity in the relative intensities of those reflections. Various ways of overcoming or circumventing this problem have been developed, and several of these involve incorporating chemical information into the structure determination process. For complex zeolite structures, the FOCUS algorithm has proved to be effective. Because it operates in both real and reciprocal space, phase information obtained from high-resolution transmission electron microscopy images can be incorporated directly into this algorithm in a simple way. Here we show that by doing so, the complexity limit can be extended much further. The power of this approach has been demonstrated with the solution of the structure of the zeolite TNU-9 (|H9.3|[Al9.3Si182.7O384]; ref. 10) with 24 topologically distinct (Si,Al) atoms and 52 such O atoms. For comparison, ITQ-22 (ref. 11), the most complex zeolite known to date, has 16 topologically distinct (Si,Ge) atoms.

Journal Article↗
PubMed2006

Encapsulation of single enzyme in nanogel with enhanced biocatalytic activity and stability.

Single protein encapsulated into nanogels with uniformed size and controllable shell thickness were prepared by surface acryloylation of a protein molecule followed by aqueous in situ polymerization. Compared to its free counterpart, the encapsulated protein exhibits similar biocatalytic behavior and significantly improved stability at high temperature and in the presence of organic solvent.

Catalysis↗
PubMed2006

4-aminopyridine, a Kv channel antagonist, prevents apoptosis of rat cerebellar granule neurons.

Compelling evidence indicates that excessive potassium (K+) efflux and intracellular K+ depletion are the key early steps in apoptosis. Previously, we reported that apoptosis of cerebellar granule neurons induced by incubation in low-K+ (5 mM) and serum-free medium was associated with an increase in A-type transient inactivation of K+ channel current (IA) amplitude and modulation of channels' gating properties. Here, we showed that a classic K+ channel blocker, 4-aminopyradine (4-AP), significantly inhibited IA amplitude in a concentration-dependent manner (reduction of current by 10 microM and 10 mM 4-AP was 11.4+/-1.3% and 72.2+/-3.3%, respectively). Moreover, 4-AP modified the steady-state activation and inactivation kinetics of IA channels, such that the activation and inactivation curves were shifted to the right about 20 mV and 17 mV, respectively. Fluorescence staining showed that 4-AP dramatically increased the viability of cells undergoing apoptosis in a dose-dependent manner. That is, while 5 mM 4-AP was present, cell viability was 84.9+/-5.2%. Consistent with the cell viability analysis, internucleosomal DNA fragmentation by gel electrophoresis analysis showed that 5 mM 4-AP also protected against neuronal apoptosis. Furthermore, 4-AP significantly inhibited cytochrome c release and caspase-3 activity induced by low-K+/serum-free incubation. Finally, current-clamp analysis indicated that 5 mM 4-AP did not significantly depolarize the membrane potential. These results suggest that 4-AP has robust neuroprotective effects on apoptotic granule cells. The neuroprotective effect of 4-AP is likely not due to membrane depolarization, but rather that 4-AP may modulate the gating properties of IA channels in an anti-apoptotic manner.

4-Aminopyridine↗
PubMed2006

A locus for autosomal dominant accessory auricular anomaly maps to 14q11.2-q12.

Accessory auricular anomaly is a small excrescence of skin that contains elastic cartilage on different regions of the helix and the face. Previous work has shown that the genetic trait of some patients with the isolated symptom of accessory auricular anomaly is autosomal dominant. To map the gene for autosomal dominant accessory auricular anomaly (ADAAA), we investigated a Chinese family with 11 affected individuals. We performed linkage analysis with microsatellite markers spanning the whole human-genome in the family. The inheritance pattern of the ADAAA family was autosomal dominant with complete penetrance. Two-point linkage analysis revealed significant maximum LOD scores of 4.20(D14S990 and D14S264, sita = 0) in the family. Haplotype construction and multipoint linkage analysis also confirmed the locus and defined the isolated ADAAA locus to a 9.84 cM interval between the markers D14S283 and D14S297. Our study assigned an isolated ADAAA locus to 14q11.2-q12. This is the first ADAAA locus reported to date.

Chromosome Mapping↗
PubMed2006

Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot.

Oligonucleotide fingerprinting of rRNA genes (OFRG) is an array-based method that generates microbial community profiles through analysis of rRNA gene clone libraries. The original OFRG method allowed 1536 clones to be analyzed per experiment. This report describes a procedure for analyzing 9600 clones per experiment, including a new probe set for bacterial analysis, and improved data processing and statistical analysis tools. The software tools are available at the OFRG website (). Use of the 9600-clone procedure was demonstrated by examining the bacterial rRNA gene compositions of soils subjected to various temperature treatments. These treatments produced a series of soils with a range of abilities to suppress avocado root rot, enabling the identification of bacterial rRNA genes that correlate in abundance with root rot suppressiveness. OFRG analysis of these soils produced 8876 bacterial rRNA gene fingerprints grouped into 5123 clusters, or operational taxonomic units (OTUs). Eleven OTUs exhibited a positive correlation between the number of clones and the percentage of healthy roots. An in silico analysis was performed to examine the relationship between the number of rRNA genes analyzed and the number of correlates (rRNA gene-avocado root rot symptoms) identified. As the number of clones decreased, fewer correlates were identified. To further increase the throughput of the OFRG method, use of a glass slide-fluorescent probe microarray format was also explored.

DNA Fingerprinting↗
PubMed2006

Transmission electron microscopy imaging of individual functional groups of fullerene derivatives.

Mobility and reactivity of the functionalized fullerenes with pyrrolidine (C60-C3NH7) incorporated in single-wall carbon nanotubes were examined by high-resolution transmission electron microscopy. An individual functional group attached to each fullerene cage is unambiguously visualized. This provides a direct evidence for the functionalized structure on a single-molecular basis. A rotational motion of the incorporated molecules tends to occur during the observation and, consequently, each fullerene molecule is likely to stand facing its functionalized group towards the nanotube wall. A fine structure analysis of electron energy-loss spectra for the nitrogen K(1s) edge shows a considerable change in the nitrogen chemical state and suggests a strong tube-fullerene interaction.

Journal Article↗
PubMed2006

A small interfering RNA screen for modulators of tumor cell motility identifies MAP4K4 as a promigratory kinase.

Cell motility is a complex biological process, involved in development, inflammation, homeostasis, and pathological processes such as the invasion and metastatic spread of cancer. Here, we describe a genomic screen designed to identify inhibitors of cell migration. A library of 10,996 small interfering RNAs (targeting 5,234 human genes) was screened for their ability to block the migration of a highly motile ovarian carcinoma cell line, SKOV-3, by using a 384-well wound-healing assay coupled with automated microscopy and wound quantification. Two or more small interfering RNAs against four genes, CDK7, DYRK1B, MAP4K4 (NIK/HGK) (MAP4K4, mitogen-activated protein 4 kinase 4), and SCCA-1 (SerpinB3), potently blocked the migration of SKOV-3 cells, concordant with reduced transcript levels. Further studies of the promigratory role of MAP4K4 showed that the knockdown of this transcript inhibited the migration of multiple carcinoma cell lines, indicating a broad role in cell motility and potently suppressed the invasion of SKOV-3 cells in vitro. The effect of MAP4K4 on cellular migration was found to be mediated through c-Jun N-terminal kinase, independent of AP1 activation and downstream transcription. Accordingly, small molecule inhibition of c-Jun N-terminal kinase suppressed SKOV-3 cell migration, underscoring the potential therapeutic utility of mitogen-activated protein kinase pathway inhibition in cancer progression.

Base Sequence↗
PubMed2006

Similarities and differences between selective and nonselective BAFF blockade in murine SLE.

B cells have multiple roles in immune activation and inflammation separate from their capacity to produce antibodies. B cell depletion is currently under intense investigation as a therapeutic strategy for autoimmune diseases. The TNF family members B cell-activating factor of the TNF family (BAFF) and its homolog A proliferation-inducing ligand (APRIL) are B cell survival and differentiation factors and are therefore rational therapeutic targets. We compared the effects of BAFF receptor-Ig, which blocks only BAFF, with those of transmembrane activator and calcium modulator ligand interactor-Ig, which blocks both BAFF and APRIL, in a murine SLE model. Both reagents prolonged the life of NZB/W F1 mice when given either before or after disease onset. Many immunologic effects of the 2 reagents were similar, including B cell and B cell subset depletion and prevention of the progressive T cell activation and dendritic cell accumulation that occurs with age in NZB/W mice without substantial effects on the emergence of the IgG anti-double-stranded DNA response. Furthermore, both reagents inhibited the T cell-independent marginal zone B cell response to particulate antigen delivered i.v., but not the B1 B cell response to the same antigen delivered i.p. In contrast, blockade of both BAFF and APRIL, but not blockade of BAFF alone, reduced the serum levels of IgM antibodies, decreased the frequency of plasma cells in the spleen, and inhibited the IgM response to a T cell-dependent antigen. The differences between selective and nonselective BAFF blockade are relevant to the choice of a BAFF blocking agent for the treatment of autoimmune and malignant diseases.

Animals↗
PubMed2006

Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation.

Proteins fold in a confined space not only in vivo, i.e., folding assisted by molecular chaperons and chaperonins in a crowded cellular medium, but also in vitro as in production of recombinant proteins. Despite extensive work on protein folding in bulk, little is known about how and to what extent the thermodynamics and kinetics of protein folding are altered by confinement. In this work, we use a Gō-like off-lattice model to investigate the folding and stability of an all beta-sheet protein in spherical cages of different sizes and surface hydrophobicity. We find whereas extreme confinement inhibits correct folding, a hydrophilic cage stabilizes the protein due to restriction of the unfolded configurations. In a hydrophobic cage, however, strong attraction from the cage surface destabilizes the confined protein because of competition between self-aggregation and adsorption of hydrophobic residues. We show that the kinetics of protein collapse and folding is strongly correlated with both the cage size and the surface hydrophobicity. It is demonstrated that a cage of moderate size and hydrophobicity optimizes both the folding yield and kinetics of structural transitions. To support the simulation results, we have also investigated the refolding of hen-egg lysozyme in the presence of cetyltrimethylammoniumbromide (CTAB) surfactants that provide an effective confinement of the proteins by micellization. The influence of the surfactant hydrophobicity on the structural and biological activity of the protein is determined with circular dichroism spectrum, fluorescence emission spectrum, and biological activity assay. It is shown that, as predicted by coarse-grained simulations, CTAB micelles facilitate the collapse of denatured lysozyme, whereas the addition of beta-cyclodextrin-grafted-PNIPAAm, a weakly hydrophobic stripper, dissociates CTAB micelles and promotes the conformational rearrangement and thereby gives an improved recovery of lysozyme activity.

Acrylic Resins↗
PubMed2006

Role of transforming growth factor-beta1-smad signal transduction pathway in patients with hepatocellular carcinoma.

AIM: To explore the role of transforming growth factor-beta1 (TGF-beta1)-smad signal transduction pathway in patients with hepatocellular carcinoma. METHODS: Thirty-six hepatocellular carcinoma specimens were obtained from Qidong Liver Cancer Institute and Department of Pathology of the Second Affiliated Hospital of Nanjing Medical University. All primary antibodies (polyclonal antibodies) to TGF-beta1, type II Transforming growth factor-beta receptor (TbetaR-II), nuclear factor-kappaB (NF-kappaB), CD34, smad4 and smad7,secondary antibodies and immunohistochemical kit were purchased from Zhongshan Biotechnology Limited Company (Beijing, China). The expressions of TGF-beta1, TbetaR-II, NF-kappaB, smad4 and smad7 proteins in 36 specimens of hepatocellular carcinoma (HCC) and its adjacent tissue were separately detected by immunohistochemistry to observe the relationship between TGF-beta1 and TbetaR-II, between NF-kappaB and TGF-beta1, between smad4 and smad7 and between TGF-beta1 or TbetaR-IIand microvessel density (MVD). MVD was determined by labelling the vessel endothelial cells with CD34. RESULTS: The expression of TGF-beta1, smad7 and MVD was higher in HCC tissue than in adjacent HCC tissue (P<0.01, P<0.05, P<0.01 respectively). The expression of TbetaR-IIand smad4 was lower in HCC tissue than in its adjacent tissue (P<0.01, P<0.05 respectively). The expression of TGF-beta1 protein and NF-kappaB protein was consistent in HCC tissue. The expression of TGF-beta1 and MVD was also consistent in HCC tissue. The expression of TbetaR-IIwas negatively correlated with that of MVD in HCC tissue. CONCLUSION: The expressions of TGF-beta1, TbetaR-II, NF-kappaB, smad4 and smad7 in HCC tissue, which are major up and down stream factors of TGF-beta1-smad signal transduction pathway , are abnormal. These factors are closely related with MVD and may play an important role in HCC angiogenesis. The inhibitory action of TGF-beta1 is weakened in hepatic carcinoma cells because of abnormality of TGF-beta1 receptors (such as TbetaR-II) and postreceptors (such as smad4 and smad7). NF-kappaB may cause activation and production of TGF-beta1.

Carcinoma, Hepatocellular↗