Biomedical subjects

Zhihong Liu

Publications and source records attributed to Zhihong Liu.

At least 19 recordsLinked to original sources

PubMed2025

Chromosome-level genome assembly of starry flounder (Platichthys stellatus).

Starry flounder (Platichthys stellatus) is widely distributed along the coastlines of the North Pacific. As an euryhaline flatfish, it can adapt to a wide range of environmental salinity ranging from freshwater to seawater, and is a promising aquaculture flatfish species in Korea and North China. However, no high-quality starry flounder reference genome has been reported to date, which greatly limits the studies of genetics and functional genomics. Here, we obtained a high-quality chromosome-level starry flounder genome assembly with a length of 643.56 Mb (scaffold N50: 26.19 Mb, contig N50: 10.00 Mb) combining short-reads sequencing, PacBio HiFi sequencing, and Hi-C sequencing. Approximately 94.02% of assembled sequences were anchored into 24 pseudochromosomes, and a total of 18 telomeres were detected. Totally 22,835 protein-coding genes and 227.87 Mb repetitive sequences were identified. In summary, the high-quality chromosome-level genome assembly not only provides valuable resources for genetic research in starry flounder, but also advances the development of molecular breeding technology of starry flounder.

Animals↗

PubMed2025

Ras-MAPK pathway in patients with lupus nephritis.

BACKGROUND: Pathogenic mutations in genes encoding components of the Ras/mitogen-activated protein kinase (Ras-MAPK) pathway cause RASopathy. Here, we describe five unrelated patients with SLE carrying mutations associated with RASopathy and investigate the activity of the Ras-MAPK pathway. METHODS: Pathogenic variants were identified by whole-exome/whole-genome sequencing. The activity of the Ras-MAPK pathway in peripheral blood mononuclear cells (PBMC) and kidneys was evaluated using RNA sequencing and datasets from the nephroseq database, respectively. RESULTS: Five (likely) pathogenic variants in four Ras-MAPK genes were identified, including NRAS: c.G38A: p.G13D; ARAF: c.C1435T: p.R479C; KRAS: c.T341C: p.V114A; PTPN11: c.G455A: p.R152H and NRAS: c.G34A: p.G12S. Kidney injury is the main feature, presenting with nephrotic syndrome (2/5), proteinuria and haematuria (2/5). Acute kidney injury and rapidly progressive nephritic syndrome were noted in one patient each. Other clinical features included mucocutaneous lesions (5/5), cardiac involvement (4/5) and arthralgia (3/5). Laboratory abnormalities included hypocomplementaemia (5/5), presence of antiphospholipid antibodies (4/5), decreased regulatory T cells (3/3), pancytopenia (3/5) and persistent monocytosis (2/5). Kidney biopsy revealed lupus nephritis. Most patients responded well to standard therapy, with the exception of the patient with the NRAS p.G13D mutation who died. The Ras-MAPK pathway was activated in both PBMC and kidney of patients with LN as indicated by increased expression of NRAS, KRAS, RIT1, MRAS, PPP1CB, SHOC2, SOS2 and MAP2K1, as well as decreased expression of negative regulators of the Ras-MAPK pathway, CBL, LZTR1 and NF1. CONCLUSION: Kidney involvement may be the main feature of the clinical spectrum of RASopathy. Genetic screening should be considered for patients with early onset lupus.

Humans↗

PubMed2005

Fluorometric assay of tiopronin based on inhibition of multienzyme redox system.

In this paper, a simple and sensitive fluorimetric method for the determination of tiopronin (N-(2-mercaptopropionyl)-glycine) is proposed. The method is based on the strong inhibitory effect of tiopronin on the multienzyme redox system of hemoglobin, nicotinamide adenine dinucleotide (NADH) and H(2)O(2), in which the intrinsic fluorescence of NADH was employed as the detection signal. The calibration graph is linear in the range 6.13 x 10(-7) to 6.13 x 10(-6) M with a detection limit of 1.65 x 10(-7) M and the relative standard deviation of 2.02%. Kinetics in the pseudo-first-order conditions was investigated by stopped-flow spectrofluorometry and the inhibition mechanism of tiopronin was verified of the competitive type.

Multienzyme Complexes↗

PubMed2005

Label-free electrochemical detection for aptamer-based array electrodes.

An electrochemical impedance spectroscopy method of detection for aptamer-based array electrodes is reported in which the binding of aptamers immobilized on gold electrodes leads to impedance changes associated with target protein binding events. Human IgE was used as a model target protein and incubated with the aptamer-based array consisting of single-stranded DNA containing a hairpin loop. To increase the binding efficiency for proteins, a hybrid modified layer containing aptamers and cysteamine was fabricated on the photolithographic gold surface through molecular self-assembly. Atomic force microscopy analysis demonstrated that human IgE could be specifically captured by the aptamer and stand well above the self-assembled monolayer (SAM) surface. Compared to immunosensing methods using anti-human IgE antibody as the recognition element, impedance spectroscopy detection could provide higher sensitivity and better selectivity for aptamer-modified electrodes. The results of this method show good correlation for human IgE in the range of 2.5-100 nM. A detection limit of 0.1 nM (5 fmol in a 50-microL sample) was obtained, and an average of the relative standard deviation was <10%. The method herein describes the first label-free detection for arrayed electrodes utilizing electrochemical impedance spectroscopy.

Aptamers, Nucleotide↗

PubMed2005

Detectable circulating antiendothelial cell antibodies in renal allograft recipients with C4d-positive acute rejection: a report of three cases.

It is suggested that non-HLA endothelial antigens may also cause C4d-positive acute rejection, but this is very rare. We report on three renal allograft recipients who developed C4d-positive acute rejection with detectable circulating antiendothelial cell antibodies (AECAs). All patients had severe dialysis-dependent graft dysfunction. Histologic manifestations include neutrophils infiltration on peritubular capillaries and glomeruli. Endoarteritis can be seen in all the patients. Two patients lost grafts after the rescue therapy including immunoadsorption, mycophenolate mofetil with or without tacrolimus. The titer variation of AECAs might be associated with the graft outcome. In patients those who lost grafts, AECAs titer increased from 1:10 to 1:80 in one patient, and was kept positive during the treatment in the other patient. In the recovered patient, however, the titer became negative from 1:40. From our report, it appears that persisting circulating AECAs during the rescue treatment of C4d-positive acute rejection may be associated with a poor outcome.

Acute Disease↗

PubMed2005

Solution structure of human survivin and its binding interface with Smac/Diablo.

NMR studies of the antiapoptotic protein survivin have been used to determine the homodimer interface of the protein in solution and to identify residues of the protein that interact with Smac/Diablo. In solution, survivin(1-120) forms a bow-tie-shaped dimer whose interface is composed of its N-terminal residues as well as residues connecting its BIR domain to the C-terminal alpha helix. The solution structure resolves the controversy regarding the two possible dimer interfaces for survivin observed in X-ray crystal structures. The structural basis for the interaction between survivin and Smac/Diablo was also investigated. When Smac/Diablo or N-terminal Smac/Diablo peptide analogues are added to a solution of survivin, specific residues near alpha4 and beta3 are perturbed. NMR experiments indicate that the peptides bind across the third beta-strand of survivin in a manner similar to the way Smac/Diablo peptides bind to the BIR3 domain of X-linked IAP (XIAP).

Amino Acid Sequence↗

PubMed2005

Effects of mycophenolic acid on endothelial cells.

Mycophenolate mofetil (MMF) is a potent immunosuppressant that inhibits the activity of inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme in de novo synthesis of guanosine nucleotides. MMF has been used widely in solid-organ transplantation. Increased evidence indicated that MMF exhibited beneficial effects on various types of vasculitis, for reasons that were not fully understood. Endothelial cells play a pivotal role in the pathogenesis of vasculitis. Endothelium may not only be the main target for injury, but also be able to amplify the inflammatory response by adhesion molecule expression, leukocyte adhesion, cytokine production and angiogenesis. In the present study, the effect of mycophenolic acid (MPA), the active metabolite of MMF, on human umbilical vein endothelial cells (HUVECs) was investigated. MPA markedly inhibited tumor necrosis factor-alpha (TNFalpha)-induced intercellular adhesion molecule-1 (ICAM-1) mRNA and surface expression, suppressed TNFalpha-induced neutrophils adhesion to endothelial cells, and reduced TNFalpha-induced interleukin-6 (IL-6) secretion. The inhibitory effects of MPA on ICAM-1 surface expression and IL-6 secretion were not attenuated by addition of guanosine, implying that inhibition of these processes were not due to intracellular guanosine nucleotides depletion. MPA also decreased angiogenesis of endothelial cells in three-dimensional collagen gel culture system, reduced the migration in a wounded monolayer of endothelial cells, and inhibited the proliferation of endothelial cells. In conclusion, MPA exhibited multifarious effects on endothelial cells including inhibition of ICAM-1 expression, neutrophil attachment, IL-6 secretion, and the process of angiogenesis, which might contribute to the efficacy of MMF in the treatment of vasculitis.

Antibiotics, Antineoplastic↗

PubMed2005

Determination of myoglobin based on its enzymatic activity by stopped-flow spectrophotometry.

A new method has been developed for the determination of myoglobin (Mb) based on its enzymatic activity for the oxidation of o-phenylenediamine (OPDA) with hydrogen peroxide. Stopped-flow spectrophotometry was used to study the kinetic behavior of the oxidation reaction. The catalytic activity of Mb was compared to other three kinds of catalyst. The time dependent absorbance of the reaction product, 2,3-diamimophenazine (DAPN), at a wavelength of 426 nm was recorded. The initial reaction rate obtained at 40 degrees C was found to be proportional to the concentration of Mb in the range of 1.0 x 10(-6) to 4.0 x 10(-9)mol L(-1). The detection limit of Mb was found to be 9.93 x 10(-10)mol L(-1). The relative standard deviations were within 5% for the determination of different concentrations of Mb. Excess of bovine serum albumin (BSA), Ca(II), Mg(II), Cu(II), glucose, caffeine, lactose and uric acid did not interfere.

Animals↗

PubMed2005

Mast cell infiltration associated with tubulointerstitial fibrosis in chronic Aristolochic Acid Nephropathy.

Aristolochic Acid Nephropathy (AAN) is regarded as a kind of toxic nephropathy caused by the formation of DNA- aristolochic acid adducts in renal parenchymal cells. However, the underlying mechanisms driving the progression of renal interstitial fibrosis in AAN still remains unclear. This study aims to elucidate the role of some immunological factors, especially mast cells (MCs), in the pathogenesis of AAN. Sixteen patients with AAN were enrolled in this study, including five acute and 11 chronic AAN. Monoclonal antibodies against human tryptase, alpha smooth muscle actin (alpha-SMA), and CD68 were applied on serial sections, which were further counterstained with Periodic Acid-Schiff. It was found that massive tryptase-positive MCs were observed in the fibrotic areas in chronic AAN, especially around thickened tubular basement membranes where myofibroblasts accumulated too. In contrast, MCs infiltrated to a less extent in acute AAN, and were barely found in normal control kidneys. In chronic AAN, the number of MCs in the tubulointerstitium was positively correlated with the degree of renal fibrosis (r=0.64, P <0.05), but not with serum creatinine levels. Meanwhile, the recruitment of MCs into the renal interstitium is accompanied with local proliferation of myofibroblasts. Macrophages were not abundant, neither in acute nor in chronic AAN. Our findings show for the first time that mast cell infiltration seems to be associated with the progression of fibrosis in the renal tubulointerstitium in chronic AAN.

Acute Disease↗

PubMed2004

The monocyte dysfunction induced by acute tetramine poisoning and corrected by continuous blood purification.

The monocyte function of patients with severe tetramine poisoning and the effects of sequential hemoperfusion (HP) and continuous veno-venous hemofiltration (CVVH) on the immune status of the patients were investigated. Eleven patients with severe acute tetramine poisoning were treated with sequential HP and CVVH. The APACHE II score and Glasgow score were used to evaluate the disease status during the therapy. Blood samples were collected at 0, 2, 6, 12, 24, 48, and 72 h. Peripheral monocytes were isolated and stimulated with lipopolysaccharide (LPS) to detect the ability of monocytes to secrete tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-6, and IL-10. The number of monocytes was counted at the same time. As expected, three patients died and the clinical manifestations were improved in the other patients. The production of cytokines (TNF-alpha, IL-6, and IL-10) by monocytes of patients with tetramine poisoning was much lower than normal controls (P<0.001), and was significantly increased after HP and CVVH in the survivors (TNF-alpha, IL-6, IL-10, P<0.05, P<0.01, P<0.05, respectively). The blood concentration of tetramine was 0.124+/-0.082 mg/l at prehemoperfusion and 0.080+/-0.055 mg/l at posthemoperfusion (P<0.05). It was concluded that there was severe damage to monocyte function in patients with tetramine poisoning, and that sequential HP and CVVH can effectively ameliorated monocyte function and eliminate tetramine from blood.

APACHE↗

PubMed2004

Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein.

The severe acute respiratory syndrome (SARS) virus belongs to the Coronaviridea family of viruses. Its virion encodes several proteins including a replicase and four structural proteins. Here we describe the three-dimensional structure of the N-terminal domain of the SARS coronavirus (CoV) nucleocapsid protein. The protein consists of a five-stranded beta sheet with a folding topology distinct from other RNA-binding proteins. Single-stranded RNAs bind to the protein surface at the junction between a flexible, positively charged beta hairpin and the core structure. NMR-based screening was used to identify low molecular weight compounds that bind to this site.

Animals↗

PubMed2004

Retardation of ice growth in glass capillaries: measurement of the critical capillary radius.

An experiment was designed to compare the freezing of an aqueous solution in glass microcapillaries and in thin films. The velocity dependence of the ice front propagation in glass capillaries with radii of 87.5 microm-1.5 microm was observed. A critical capillary radius r(0), corresponding to certain thermal conditions, was obtained, below which the ice growth inside the capillaries was retarded. This critical capillary radius is further related to lambda(0), the smallest wavelength used in the Mullins-Sekerka criterion for the instability analysis of bulk solidifications [Mullins and Sekerka, J. Appl. Phys. 35, 444 (1964)]. It was found that for the present hypothesis, r(0)=lambda(0)/4 gives good predictions. The relation between the propagation velocity (or cooling rate) and the critical radius (or pore size) is summarized in a chart for applications in capillary-porous media, such as in the freezing of biological tissues.

Journal Article↗

PubMed2004

Effects of pulse strength, width, and sample spinning speed on the spectral spin diffusion of multiquantum coherences of spin-3/2 quadrupolar nuclei.

The effects of radio-frequency pulse strength, width, and sample spinning speed on the spin-diffusion spectrum of half-integer quadrupolar spins in solids have been studied by theoretical, numerical, and experimental investigations. It is revealed that the line shape of the cross peaks changes nonmonotonically with respect to the change of pulse strength, pulse width, or sample spinning speed. It is also found that the sample spinning speed has much more pronounced influence on the spin diffusion spectral line shape. In many cases of practical importance, the effect of sample spinning must be included in spectral analysis, in contrast to the practice of previous studies. Moreover, this effect can be exploited to further improve the precision in the determination of relative orientation of the electric-field gradient tensors of the exchange partners.

Journal Article↗

PubMed2004

Over-expression of the human MDM2 p53 binding domain by fusion to a p53 transactivation peptide.

MDM2 binds to the tumor suppressor protein p53 and regulates the level of p53 in cells. Although it is possible to prepare a small amount of the region of MDM2 that binds to p53, the expression level of this fragment of MDM2 is relatively low, limiting the studies involving this protein. Here, we describe a construct for the optimized bacterial expression and purification of the MDM2 p53 binding domain. We found that the expression level of the soluble MDM2 p53 binding domain in bacteria was increased dramatically by fusing it to its interaction partner, the p53 transactivation peptide. Attachment of the p53 transactivation peptide (residues 17-29) to the N-terminus of MDM2 resulted in a more than 200-fold increase of soluble protein expression of the p53 binding domain in bacteria. To obtain the final MDM2 p53 binding domain (residues 5-109) we inserted a tobacco etch virus protease recognition site between the P53 peptide and the MDM2 p53 binding domain. To weaken the protein/peptide interaction and facilitate the separation of the protein from the complex, we introduced a point mutation of one of the key interaction residues (F19A or W23A) in the p53 peptide. The advantages of our new construct are high yield and easy purification of the MDM2 protein.

Cloning, Molecular↗

PubMed2004

Studies on the photodegradation of Rhodamine dyes on nanometer-sized zinc oxide.

The nanometer-sized ZnO was prepared through the sol-gel method. Its average particle diameter, determined by TEM, was 20-30 nm. The specific surface area was determined to be 22 m2 g(-1) by BET. The photodegradation mechanism of Rhodamine dyes on nanometer-sized ZnO was studied by dynamic molecular spectra, and the results showed that the photodegradation of Rhodamine dyes obeyed the rules of a pseudo first-order kinetic reaction. The rate constant k of the degradation of Rhodamine B (RB) and butyl-Rhodamine (BR) were 0.0128 and 0.0154 min(-1), respectively, and the half period t(1/2) were 60 and 52 min, respectively. The photodegradation reaction conditions were optimized. After intermixing with silver, the photodegradation efficiency was greatly improved. A life-span test showed that nanometer-sized ZnO had a long life-span.

Adsorption↗

PubMed2004

The fate of glomerular mesangial IgA deposition in the donated kidney after allograft transplantation.

OBJECTIVE: To investigate the fate of the mesangial IgA deposits in the donor kidney after allograft transplantation. METHODOLOGY: Routine pre-transplant cadaveric donor kidney biopsy and repeated renal biopsies were performed at months 1, 3, and 6 after renal transplantation. The patients, 342 in number, were divided into IgA positive deposition kidney group (group A, n = 83) and non-IgA deposition kidney group (group B, n = 259). There were no significant differences between the two groups' sex, age, time of hemodialysis, warm ischemia time, cold ischemia time, complement-dependent cytotoxicity, level of panel-reactive assay, and the distribution of original disease. RESULTS: Recipients in group A received donor kidney with glomerular mesangial proliferation and marked diffuse granular IgA deposition. All of them showed edema, nephrotic range protienuria, microhematuria, hypoalbuminemia, hypertension, and delayed graft function. Borderline change was higher in group A than in group B, 37.3 and 16.2% (p < 0.001), respectively. Acute allograft rejection was higher in group A than in group B, 31.3 and 19.3% (p < 0.001), respectively. The glomerular mesangial IgA deposits gradually disappeared from the mesangial regions in grafts of acute rejection. Graft survival in both groups was not significant, being 93.8 and 95.6% in 1 yr, and 86.7 and 88.3% in 3 yr. CONCLUSION: Clinical features of the recipients which received from donor kidney with glomerular mesangial proliferation and marked diffuse granular IgA deposition: edema, proteinuria, microhematuria, hypoalbuminemia, hypertension, and delayed graft function. The presence of IgA deposits on donated kidney, by a possible increase of the immunogenicity of these kidneys, might be a cause of increased rejection. There were no significant differences between the two groups on long-term allograft survival.

Adult↗

PubMed2003

A finite element model for ice ball evolution in a multi-probe cryosurgery.

The ice formation in a water body is examined for the computation of temperature field, phase change and a moving ice-water interface whose location is not known á priori. This is classically referred to as the Stefan problem [Rubinstein, L.I. (1971) The Stefan Problem (American Mathematical Society, Providence, Rhode Island 02904]. Based on the Duvaut [Duvaut, G. (1973) "Résolution d'un probléme Stefan" C.R. Acad Sci. Paris 276, 1461-1463] transformation, the governing equations for heat conduction are formulated within a variational principle that is readily amenable to a standard finite element solution without remeshing. Numerical simulation results pertaining to the freezing of tumour tissue in a multi-cryoprobe cryosurgery are presented. These results lend both quantitative and graphical support to the current empirical standards of "effective therapy" in view of refining clinical applications.

Animals↗

PubMed2003

Structural analysis of UBL5, a novel ubiquitin-like modifier.

UBL5 is a widely expressed human protein that is strongly conserved across phylogeny. Orthologs of UBL5 occur in every eukaryotic genome characterized to date. The yeast ortholog of UBL5, HUB1, was reported to be a ubiquitin-like protein modifier important for modulation of protein function. However, unlike ubiquitin and all other ubiquitin-like modifiers, UBL5 and its yeast ortholog HUB1 both contain a C-terminal di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. Here we describe the three-dimensional structure of UBL5 determined by NMR. The overall structure of the protein was found to be very similar to ubiquitin despite the low approximately 25% residue similarity. The signature C-terminal di-tyrosine residues in UBL5 are involved in the final beta sheet of the protein. This is very different to the di-glycine motif found in ubiquitin, which extends beyond the final beta sheet. In addition, we have confirmed an earlier report of an interaction between UBL5 and the cyclin-like kinase, CLK4, which we have determined is specific and does not extend to other cyclin-like kinase family members.

Amino Acid Sequence↗