Biomedical subjects
Publications and source records attributed to Hui Lu.
A CRISPR/Cas9 toolkit was established for the rice leaffolder (Cnaphalocrocis medinalis) using entirely endogenous regulatory elements. An all-in-one plasmid was constructed containing an IE1-EGFP marker, a CmU6 promoter driven sgRNA targeting Cmebony, and a Cmactin5C promoter driven Cas9. This platform provides a system for functional genomics in this pest.
UNLABELLED: Species-level quantitative PCR (qPCR) provides in-depth knowledge of oral probiotics in the human gastrointestinal tract (GIT). However, it lacks the capability to differentiate exogenous strains from native microbiota, nor can it distinguish between live and dead bacteria. In this study, we employed improved propidium monoazide (PMAxx)-qPCR to evaluate the survival and colonization of Bifidobacterium longum subsp. longum ZS-8 (designated ZS-8) on the strain level in the GIT and its impact on human gut microbiota. By spiking in live and dead ZS-8, we demonstrated that strain-level PMAxx-qPCR could identify and quantify the viable ZS-8 in fecal samples accurately. Using this method, we found that, in healthy humans, oral administration of ZS-8 can transiently survive in the GIT, and multi-layer seamless capsules (MLSC) significantly improve the gastrointestinal tolerance and survivability of ZS-8 compared to its powder form. Furthermore, through selective cultivation and PMAxx-microbiome sequencing, we investigated the response of gut viable microbiome to ZS-8. Results showed that, while the microbiota diversity and total viable counts of Bifidobacterium and Lactobacillus remained stable, certain indigenous species of Bifidobacterium and Lactobacillus increased in abundance, confirming ZS-8's probiotic potential in healthy individuals. Overall, our study demonstrates the effectiveness of combining strain-specific comparative genomics with PMAxx-qPCR for evaluating probiotic survival and colonization in the human gut and highlights the safety of ZS-8 oral administration in healthy individuals. IMPORTANCE: The survival and colonization of probiotics in the gut are critical for their functional efficacy, yet conventional species-level quantitative PCR (qPCR) fails to distinguish exogenous strains from native microbiota or differentiate live from dead bacteria. By integrating strain-specific comparative genomics with propidium monoazide (PMAxx)-qPCR, we precisely quantified the viability of Bifidobacterium longum ZS-8 at the strain level in the human gut after its oral administration. Our study demonstrated that 1.53-6.90% of cells surviving transit and multi-layer seamless capsules (MLSC) significantly enhanced the gastrointestinal tolerance of ZS-8. While ZS-8 administration did not alter gut microbiota diversity or total viable counts of Bifidobacterium and Lactobacillus, it selectively increased the abundance of specific indigenous beneficial species. This method overcomes the dual limitations of traditional techniques (strain-level specificity and viability discrimination), providing a robust tool for probiotic research. Furthermore, our findings confirm the safety of ZS-8 in healthy individuals and its potential to modulate gut ecology, offering a scientific foundation for personalized probiotic development and clinical translation.
The introduction of disulfide bonds into proteins creates additional mechanical barriers and limits the unfolded contour length (i.e., the maximal extension) measured by single-molecule force spectroscopy. Here, we engineer single disulfide bonds into four different locations of the human cardiac titin module (I27) to control the contour length while keeping the distance to the transition state unchanged. This enables the study of several biologically important parameters. First, we are able to precisely determine the end-to-end length of the transition state before unfolding (53 Angstrom), which is longer than the end-to-end length of the protein obtained from NMR spectroscopy (43 Angstrom). Second, the measured contour length per amino acid from five different methods (4.0 +/- 0.2 Angstrom) is longer than the end-to-end length obtained from the crystal structure (3.6 Angstrom). Our measurement of the contour length takes into account all the internal degrees of freedom of the polypeptide chain, whereas crystallography measures the end-to-end length within the "frozen" protein structure. Furthermore, the control of contour length and therefore the number of amino acids unraveled before reaching the disulfide bond (n) facilitates the test of the chain length dependence on the folding time (tau(F)). We find that both a power law scaling tau(F) lambda n(lambda) with lambda = 4.4, and an exponential scaling with n(0.6) fit the data range, in support of different protein-folding scenarios.
AIM: To investigate the dynamic change and role of neuronal nitric oxide synthase (nNOS) and inducible nitric oxide synthase (iNOS) in neonatal rat with intestinal injury and to define whether necrotizing enterocolitis (NEC) is associated with the levels of nitric oxide synthase (NOS) in the mucosa of the affected intestine tissue. METHODS: Wistar rats less than 24 h in age received an intraperitoneal injection with 5 mg/kg lipopolysaccharide (LPS). Ileum tissues were collected at 1, 3, 6, 12 and 24 h following LPS challenge for histological evaluation of NEC and for measurements of nNOS and iNOS. The correlation between the degree of intestinal injury and levels of NOS was determined. RESULTS: The LPS-injected pups showed a significant increase in injury scores versus the control. The expression of nNOS protein and mRNA was diminished after LPS injection. There was a negative significant correlation between the nNOS protein and the grade of median intestinal injury within 24 h. The expression of iNOS protein and mRNA was significantly increased in the peak of intestinal injury. CONCLUSION: nNOS and iNOS play different roles in LPS-induced intestinal injury. Caution should be exerted concerning potential therapeutic uses of NOS inhibitors in NEC.
Membrane-binding peripheral proteins play important roles in many biological processes, including cell signaling and membrane trafficking. Unlike integral membrane proteins, these proteins bind the membrane mostly in a reversible manner. Since peripheral proteins do not have canonical transmembrane segments, it is difficult to identify them from their amino acid sequences. As a first step toward genome-scale identification of membrane-binding peripheral proteins, we built a kernel-based machine learning protocol. Key features of known membrane-binding proteins, including electrostatic properties and amino acid composition, were calculated from their amino acid sequences and tertiary structures, which were then incorporated into the support vector machine to perform the classification. A data set of 40 membrane-binding proteins and 230 non-membrane-binding proteins was used to construct and validate the protocol. Cross-validation and holdout evaluation of the protocol showed that the accuracy of the prediction reached up to 93.7% and 91.6%, respectively. The protocol was applied to the prediction of membrane-binding properties of four C2 domains from novel protein kinases C. Although these C2 domains have 50% sequence identity, only one of them was predicted to bind the membrane, which was verified experimentally with surface plasmon resonance analysis. These results suggest that our protocol can be used for predicting membrane-binding properties of a wide variety of modular domains and may be further extended to genome-scale identification of membrane-binding peripheral proteins.
OBJECTIVE: To detect the in vitro effect of the traditional Chinese medicine on the tachyzoites of Toxoplasma gondii. METHODS: Supernatant (1.5 ml) of different doses of the traditional Chinese medicine (Changqing capsule) was collected by normal saline immersion and 2.5 x 10(4) Toxoplasma gondii tachyzoites were added in each paste well for 8 hours. Spiramycin, pyrimethamine and azithromycin in different doses were used as controls. Normal saline was used as negative control. Mice were inoculated with drug-treated tachyzoites intraperitoneally or intragastrically. The normal mice were subcultured after 8 days for 3 generations. RESULTS: The incident number of the infected mice was significantly different among groups with different drugs and doses: 2/60, 16/60, 10/60 and 10/60 in the groups of Changqing capsule, spiramycin, pyrimethamine and azithromycin respectively (P < 0.05). No mice were found incident in groups of high and medium dose Changqing capsule while 2 out of 20 found sick in the low dose group (P < 0.05). The subculture observation showed that 2 and 1 mice in the first generation of the low dose Changqing capsule group inoculated intraperitonelly and intragastrically were found infected respectively. 2 mice of the second generation in low dose spiramycin group and 1 mouse of the third generation in low dose pyrimethamine group were also found infected. CONCLUSION: The in vitro killing effect of the Changqing capsule on the tachyzoites of Toxoplasma gondii is better than the current clinical drugs and shows a positive correlation with the dosages.
DNA-binding proteins (DNA-BPs) play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Attempts have been made to identify DNA-BPs based on their sequence and structural information with moderate accuracy. Here we develop a machine learning protocol for the prediction of DNA-BPs where the classifier is Support Vector Machines (SVMs). Information used for classification is derived from characteristics that include surface and overall composition, overall charge and positive potential patches on the protein surface. In total 121 DNA-BPs and 238 non-binding proteins are used to build and evaluate the protocol. In self-consistency, accuracy value of 100% has been achieved. For cross-validation (CV) optimization over entire dataset, we report an accuracy of 90%. Using leave 1-pair holdout evaluation, the accuracy of 86.3% has been achieved. When we restrict the dataset to less than 20% sequence identity amongst the proteins, the holdout accuracy is achieved at 85.8%. Furthermore, seven DNA-BPs with unbounded structures are all correctly predicted. The current performances are better than results published previously. The higher accuracy value achieved here originates from two factors: the ability of the SVM to handle features that demonstrate a wide range of discriminatory power and, a different definition of the positive patch. Since our protocol does not lean on sequence or structural homology, it can be used to identify or predict proteins with DNA-binding function(s) regardless of their homology to the known ones.
Tim10 and all the small Tim proteins of the mitochondrial intermembrane space contain a consensus twin CX3C Zn2+-finger motif. While disulphide bond formation between the Cys residues of this motif is essential for complex formation by the small Tim proteins, the specific role of Zn2+-binding during the import and assembly of these proteins is not clear. In this study, we investigated the effects of the biologically relevant thiol-disulphide redox molecule, glutathione, and Zn2+-binding on the oxidative folding of yeast mitochondrial Tim10 using both biochemical and biophysical methods in vitro. We show that, whilst oxidized Tim10 cannot be reduced by reduced glutathione, reduced Tim10 is effectively oxidized at levels of glutathione comparable to those found in the cytosol. The oxidized Tim10 generated in the presence of glutathione is competent for complex formation with its partner protein Tim9, confirming it has a native fold. The standard redox potential of Tim10 at pH 7.4 was determined to be -0.32 V, confirming that Tim10 is a much stronger reductant than glutathione (-0.26 V, at pH 7.4) and could therefore be oxidized rapidly by oxidized glutathione in the cytosol. However, we found that Zn2+-binding can stabilize the reduced Tim10, decreasing the rate of the oxidative folding more than tenfold. In addition, we show that protein disulphide isomerase can catalyse the oxidative folding of Tim10 provided that Zn2+ was removed. We propose that Zn2+-binding is essential to maintain the protein in a reduced and import-competent state in the cytosol, and that zinc has to be removed after the protein is imported into mitochondria to initiate protein oxidative folding and assembly.
OBJECTIVES: The goal of this work was to investigate the feasibility of formulating novel dental restorative materials that utilize a step-growth thiol-ene photopolymerization. Particularly, we are aiming to significantly reduce the polymerization shrinkage and shrinkage stress while retaining adequate physical properties as compared to current dimethacrylatre-based systems. METHODS: The thiol-ene system is composed of a 4:3 molar mixture of triallyl-1,3,5-triazine-2,4,6-trione (TATATO) and pentaerythritol tetramercaptopropionate (PETMP). The simultaneous measurement of shrinkage stress and functional group conversion was performed. Solvent extraction of unreacted monomers and dynamic mechanical analysis on the polymer networks that were formed were also studied. Flexural strength was measured for both filled and unfilled PETMP/TATATO and Bis-GMA/TEGDMA systems. RESULTS: Photopolymerization of PETMP/TATATO occurs at a much higher rate, with the maximum polymerization rate six times faster, than Bis-GMA/TEGDMA cured under the identical conditions. The results from the simultaneous measurement of shrinkage stress and conversion showed that the onset of shrinkage stress coincides with the delayed gel point conversion, which is predicted to be 41% for the 3:4 stoichiometric PETMP/TATATO resin composition. The maximum shrinkage stress developed for PETMP/TATATO was about 0.4 MPa, which was only approximately 14% of the maximum shrinkage stress of the Bis-GMA/TEGDMA system. Adequate flexural strength and flexural modulus values were obtained for both filled and unfilled PETMP/TATATO systems. SIGNIFICANCE: The dramatically reduced shrinkage stress, increased polymerization rate, significance increased functional group conversion, and decreased leachable species are all benefits for the use-of thiol-ene systems as potential dental restorative materials.
OBJECTIVE: The aim of this work was to prereact thiol-ene monomers to create reactive thiol or vinyl (ene)-functionalized oligomers, and to investigate the use of these materials as novel dental restorative material. Investigation has focused on the application of oligomeric thiol-ene materials as dental restorative resins with lower polymerization shrinkage and polymerization stress as compared to monomeric thiol-ene systems and particularly with respect to current dimethacrylate-based systems. METHODS: Reactive thiol-functionalized oligomers were created via photopolymerization using triallyl-1,3,5-triazine-2,4,6-trione (TATATO), trimethylolpropane tris(3-mercaptopropionate) (trithiol) and pentaerythritol tetramercaptopropionate (tetrathiol). Kinetic and mechanical investigation of Bis-GMA/TEGDMA, and oligomeric and monomeric thiol-ene systems were conducted. More specifically, polymerization shrinkage and stress, polymerization kinetics, glass transition temperature, flexural strength and flexural modulus were evaluated. RESULTS: Upon evaluation, the polymerization stress of oligomeric thiol-ene systems was dramatically reduced by as much as 33% when compared with the stress exhibited by monomeric thiol-ene systems and as much as a 92% reduction in stress relative to the current dimethacrylate-based dental restorative materials. Furthermore, the flexural strength and modulus of the monomeric and oligomeric thiol-ene resins were not significantly different. SIGNIFICANCE: Oligomeric thiol-ene systems offer potential as alternative dental restorative resins due to the significant reduction in polymerization shrinkage and stress while retaining the mechanical properties of monomer-based thiol-ene resins.
AIM: To determine whether diminished levels of epidermal growth factor (EGF) were present in neo-natal rats with intestinal injury and related with the degree of intestinal injury, so we modeled a model in neo-natal rats of intestinal injury and to examine the dynamic levels of EGF on injury of intestine. METHODS: One-day-old Wistar rat pups received an intraperitoneally injection with 4 mg/kg lipopolysaccharide (LPS), followed by collection of ileum tissue at 1, 3, 6, 12, and 24 h following LPS administration. The ileum was for histological evaluation of NEC and for measurements of EGF using ABC-ELISA. The correlation between the degree of intestinal injury and levels of EGF was determined. RESULTS: The LPS-injected pups also showed a significant increase in injury scores at 1, 3, 6, 12, and 24 h (respectively, (1.08+/-0.61), (1.63+/-0.84), (1.95+/-0.72), (2.42+/-0.43) and (2.21+/-0.53)) vs the control (0.12+/-0.17) (P<0.01). EGF levels at 1, 3, 6, 12 h (respectively, (245.6+/-49.0), (221.4+/-39.0), (223.4+/-48.1), (246.0+/-46.6)) pg/mg were significantly loss than the control (275.6+/-50.4) pg/mg (P<0.05). There was a significant negative correlation between the EGF levels and the grade of intestinal injury within 24 h (P<0.05). CONCLUSION: Neo-natal rats with intestinal injury have significantly lower levels of ileum EGF. Reduced levels of this growth factor might be related to the pathogenesis of NEC.
AIM: To provide hepatic protection through administration of doxorubicin before stop-flow chemotherapy (SFC) and to investigate the expression of heat shock protein 72 (HSP72) and role of nuclear factor kappa B (NF-kappaB) in this effect. METHODS: The hepatic preconditioning of doxorubicin was established in a porcine model by injection of doxorubicin (1 mg/kg) before SFC. The experimental animals were randomized into two groups: groups receiving doxorubicin (DOX) and normal saline (NS). Serial serum and tissue samples were taken from both groups to evaluate the protection of doxorubicin. Western blot and immuno-precipitation were applied to detect the expression of HSP72, NF-kappaB p65 protein, inhibitor kappaB-alpha (IkappaB-alpha) and phosphorylated IkappaB-alpha as well. The expression of tumor necrosis factor alpha (TNF-alpha) was estimated by semiquantitative RT-PCR. And the extent of the hepatic injury was estimated with the level of serum aminotransferases. RESULTS: An abundance production of HSP72 in porcine liver was observed after 24 h of intravenous administration of doxorubicin, but without any change in the expression of NF-kappaB p65 subunit in cytoplasm. NF-kappaB p65 subunit accumulated in nuclei at the end of SFC and reached its highest level at 30 min after the restoration of the abdominal circulation and decreased gradually during the 6 h after SFC in NS group, while there was little change in DOX group. There was also a slight decrease of IkappaB-alpha at 30 min after the restoration of the abdominal circulation in NS group accompanying with the appearance of phosphorylated IkappaB-alpha. The expression of TNF-alpha was significantly higher in NS group than that in DOX group (average 1.40+/-0.17 vs 0.62+/-0.22, P<0.01) at serial time points after SFC. Serum ALT and AST levels of NS group were higher after 24 h than those of DOX group (93.2+/-7.8 IU/L vs 53.3+/-13.9 IU/L, 217.0+/-29.4 IU/L vs 155.0+/-15.6 IU/L for ALT and AST respectively, P<0.05) and after 48 h than those of DOX group (66.6+/-18.1 IU/L vs 43.3+/-16.7 IU/L, 174.4+/-21.3 IU/L vs 125.7+/-10.5 IU/L for ALT and AST respectively, P<0.05). CONCLUSION: Doxorubicin renders the liver to be tolerant to the hepatic influence in SFC in a porcine model through the NF-kappaB/IkappaB-alpha pathway with the expression of HSP72.
MOTIVATION: Function annotation of an unclassified protein on the basis of its interaction partners is well documented in the literature. Reliable predictions of interactions from other data sources such as gene expression measurements would provide a useful route to function annotation. We investigate the global relationship of protein-protein interactions with gene expression. This relationship is studied in four evolutionarily diverse species, for which substantial information regarding their interactions and expression is available: human, mouse, yeast and Escherichia coli. RESULTS: In E.coli the expression of interacting pairs is highly correlated in comparison to random pairs, while in the other three species, the correlation of expression of interacting pairs is only slightly stronger than that of random pairs. To strengthen the correlation, we developed a protocol to integrate ortholog information into the interaction and expression datasets. In all four genomes, the likelihood of predicting protein interactions from highly correlated expression data is increased using our protocol. In yeast, for example, the likelihood of predicting a true interaction, when the correlation is > 0.9, increases from 1.4 to 9.4. The improvement demonstrates that protein interactions are reflected in gene expression and the correlation between the two is strengthened by evolution information. The results establish that co-expression of interacting protein pairs is more conserved than that of random ones.
Reactive diluents such as triethyleneglycol-dimethacrylate (TEGDMA) have been widely used with bisphenol-A-glycidyl-dimethacrylate (Bis-GMA) to achieve restorative resins with appropriate viscosity and higher conversion. However, additional water sorption and polymerization shrinkage were also introduced. The aim of this work is to investigate whether the cure and material properties can be improved in dental resins containing novel mono-(meth)acrylates as reactive diluents so that these Bis-GMA-based copolymers have reduced polymerization shrinkage but higher overall double bond conversion. Several ultra-high-reactivity mono-(meth)acrylates that contain secondary functionalities have been synthesized and investigated. The polymerization rate and double bond conversion were monitored using photo-FTIR. Polymerization shrinkage, dynamic mechanical analysis, and flexural strength were characterized. Compared with the Bis-GMA/TEGDMA control, the Bis-GMA/mono-methacrylate systems studied showed higher final conversions, faster curing rates, and decreased polymerization shrinkage. Our optimum system Bis-GMA/morpholine carbamate methacrylate achieved 86% final conversion (vs. 65%), a polymerization rate 3.5 times faster, and a 30% reduction in polymerization volumetric shrinkage. These results indicate that certain highly reactive, novel mono-(meth)acrylates possess very promising potential to replace TEGDMA as reactive diluents and can readily be applied to develop superior dental resins.
The placement of dental composites is complicated by the contraction that accompanies polymerization of these materials. The resulting shrinkage stress that develops during cure of a bonded restoration can induce defects within the composite, the tooth or at the interface resulting in compromised clinical performance and/or esthetics. In light of the substantial efforts devoted to understanding and attempting to control shrinkage stress and strain in dental composite restoratives, this paper offers a perspective on the conversion dependent development of shrinkage and stress. The relationships between polymer property development and the physical evolution of the network structures associated with dental polymers as well as the interrelated kinetics of the photopolymerization reaction process are examined here. Some of the methods used to assess conversion in dental resins and composites are considered. In particular, newly introduced techniques that allow real time analysis of conversion by near-infrared spectroscopy to be coupled directly to simultaneous dynamic measurements of either shrinkage stress or strain are described. The results are compared with reports from the dental materials literature as well as complementary studies in other related fields of polymer science. The complex, nonlinear correlation between conversion, shrinkage and stress are highlighted. A brief review of some of the materials-based approaches designed to minimize polymerization shrinkage and stress is also provided.
OBJECTIVE: To observe the hepatic injury following stop- flow chemotherapy and investigate the potential mechanisms. METHODS: Twelve healthy hybrid female pigs were randomly divided into two groups as stop- flow group (SF) and stop- flow chemotherapy (SFC) group. The expression of IL- 8 and ICAM- 1 mRNA in hepatic biopsies was detected by RT- PCR, and the expression of NF- kappa B P65 subunit in nuclei was assessed by Western blot analysis. The levels of ALT and AST, and histopathologic alterations were examined to evaluate the hepatic function at different time before and after stop- flow procedure. RESULTS: The expression of NF- kappa B P65 subunit, IL- 8 and ICAM- 1mRNA increased at 30 min after stop- flow procedure, and gradually decreased at 3 h and 6 h after stop- flow procedure. The levels of ALT and AST decreased after reaching the peak at 24 h after stop- flow procedure, but removed one week after stop- flow procedure. Cytoplasmic microvascular steatosis developed with appreciable neutrophils infiltration after early stop- flow procedure without significant destroy occurred in the structure of hepatic lobule. No significant difference of various parameters above occurred between SF and SFC groups. CONCLUSION: The hepatic injury following stop- flow procedure was self-limited and reversible. There is no severe destroy of hepatic structure and disfunction during stop- flow chemotherapy.
This study probes the interrelationships between polymerization shrinkage stress development and the polymerization progress with a novel experimental technique. This technique is capable of real time, simultaneous measurement of double-bond conversion and shrinkage stress with the use of a noninvasive near-infrared fiber-optic system, along with a cantilever beam-based tensometer. The results from both filled and unfilled bis-GMA/TEGDMA (70:30 mass ratio) systems showed that the shrinkage stress buildup was concentrated in the latter stages of polymerization, with its dramatic increase linked to the asymptotic approach of conversion to its limiting value. The monotonic increase of shrinkage stress with conversion in the vitrified state is attributed to the dramatic increase of the sample's elastic modulus during the vitrification stage and a certain amount of cooling stress as the sample cools down from the temperature rise caused by the exothermic polymerization and light absorption. Excellent reproducibility of both the polymerization kinetics assessment and the shrinkage stress measurement has been achieved.
Proteins of many types experience tensile forces in their normal function, and vascular cell adhesion molecule-1 (VCAM-1) is typical in this. VCAM has seven Ig domains, and each has a disulfide bond (-S-S-) buried in its core that covalently stabilizes about half of each domain against unfolding. VCAM is extended here by single molecule atomic force microscopy in the presence or absence of reducing agents. In the absence of reducing agent, a sawtooth pattern of forced unfolding reveals an average period and total length consistent with disulfide locations in VCAM. With increasing reducing agent, accessible disulfides are specifically reduced (to SH); the average period for unfolding increases up to saturation together with additional metrics of unfolding. Steered molecular dynamics simulations of unfolding indeed show that the core disulfide bond is solvent-exposed in the very earliest stages of protein extension. Michaelis-Menten kinetics emerge with reduction catalyzed by force (tau(reduction) approximately 10(-4) s). The results establish single molecule reduction, one bond at a time, and show that mechanical forces can play a key role in modulating the redox state of cell adhesion proteins that are invariably stressed in cell adhesion.