MicroRNA-221-3p inhibits the inflammatory response of keratinocytes by regulating the DYRK1A/STAT3 signaling pathway to promote wound healing in diabetes.

Diabetic foot ulcer (DFU), a serious complication of diabetes, remains a clinical challenge. MicroRNAs affect inflammation and may have therapeutic value in DFU. Here, we find that an miR-221-3p mimic reduces the inflammatory response and increases skin wound healing rates in a mouse model of diabetes, whereas miR-221-3p knockout produced the opposite result. In human keratinocytes cells, miR-221-3p suppresses the inflammatory response induced by high glucose. The gene encoding DYRK1A is a target of miR-221-3p. High glucose increases the expression of DYRK1A, but silencing DYRK1A expression decreases high glucose-induced inflammatory cytokine release via dephosphorylation of STAT3, a substrate of DYRK1A. Application of miR-221-3p mimic to human keratinocytes cells not only decreases DYRK1A expression but also inhibits high glucose-induced production of inflammatory cytokines to promote wound healing. This molecular mechanism whereby miR-221-3p regulates inflammation through the DYRK1A/STAT3 signaling pathway suggests targets and therapeutic approaches for treating DFU.

Alkylated Sulfonium Modification of Low Molecular Weight Polyethylenimine to Form Lipopolymers as Gene Vectors.

Hydrophobic modification of low molecular weight polyethylenimine (PEI) is an efficient method to form ideal gene-transfer carriers. Sulfonium-a combination of three different functional groups, was conjugated onto PEI 1.8k at a conjugation ratio of 1:0.1 to form a series of sulfonium PEI (SPs). These SPs were hydrophobically modified and characterized by Fourier transform infrared and HNMR. DNA-condensing abilities of SPs were tested with gel retardation experiment, and their cytotoxicity was evaluated via the MTT assay. The particle size and zeta potential of SP/DNA nanoparticles were measured and evaluated for cellular uptake and transfection ability on HepG2 cell line. The results showed that the sulfonium moiety was attached to PEI 1.8k with a high yield at a conjugation ratio of 1:0.1. SPs containing longer alkyl chains condensed DNA completely at an SP/DNA weight ratio of 2:1. The formed nanoparticle size was in the range of 168-265 nm, and the zeta potential was +16-45 mV. The IC50 values of SPs were 6.5-43.2 µg/mL. The cytotoxicity of SPs increased as the hydrophobic chain got longer. SP/DNA showed much stronger cellular uptakes than PEI 25k; however, pure SPs presented almost no gene transfection on cells. Heparin release experiment showed that SP's strong binding of DNA resulted in low release of DNA and thus hindered the gene transfection process. By mixing SP with PEI 1.8k, the mixture presented adjustable DNA binding and releasing. The mixture formed by 67% SP and 33% PEI 1.8k showed strong gene transfection. In conclusion, sulfonium is an effective linkage to carry hydrophobic groups to adjust cell compatibilities and gene transfection capabilities of PEI.

Single-cell sequencing analysis reveals the relationship between tumor microenvironment cells and oxidative stress in breast cancer bone metastases.

Bone metastasis (BM) is one of the main manifestations of advanced breast cancer (BC), causing complications such as pathological fractures, which seriously affects the quality of life of patients and even leads to death. In our study, a global single-cell landscape of the tumor microenvironment was constructed using single cell RNA sequencing data from BM. BC cells were found to be reduced in the BM, while mesenchymal stem cells (MSCs), Fibroblasts and other cells were significantly more abundant in the BM. The subpopulations of these cells were further identified, and the pathways, developmental trajectories and transcriptional regulation of different subpopulations were discussed. The results suggest that with the development of BM, BC cells were vulnerable to oxidative damage, showing a high level of oxidative stress, which played a key role in cell apoptosis. Fibroblasts were obviously involved in the biological processes (BPs) related to ossification and bone remodeling, and play an important role in tumor cell inoculation to bone marrow and growth. MSC subpopulations were significantly enriched in a number of BPs associated with bone growth and development and oxidative stress and may serve as key components of BC cells homing and adhesion to the ecological niche of BM. In conclusion, our research results describe the appearance of tumor microenvironment cell subpopulations in breast cancer patients, reveal the important role of some cells in the balance of BM bone remodeling and the imbalance of BM development, and provide potential therapeutic targets for BM.

Pulmonary nodule detection on lung parenchyma images using hyber-deep algorithm.

The incidence of lung cancer has seen a significant increase in recent times, leading to a rise in fatalities. The detection of pulmonary nodules from CT images has emerged as an effective method to aid in the diagnosis of lung cancer. Ensuring information security holds utmost significance in the detection of nodules, with particular attention given to safeguarding patient privacy within the context of the Internet of Things (IoT). In this regard, migration learning emerges as a potent technique for preserving the confidentiality of patient data. Firstly, we applied several data-preprocessing steps such as lung segmentation based on K-Means, denoising methods, and lung parenchyma extraction through a dedicated medical IoT network. We used the Microsoft Common Object in Context (MS-COCO) dataset to pre-train the detection framework and fine-tuned it with the Lung Nodule Analysis 16 (LUNA16) dataset to adapt to nodule detection tasks. To evaluate the effectiveness of our proposed pipeline, we conducted extensive experiments that included subjective evaluation of detection results and quantitative data analysis. The results of these experiments demonstrated the efficacy of our approach in accurately detecting pulmonary nodules. Our study provides a promising framework for trustworthy pulmonary nodule detection on lung parenchyma images using a secured hyper-deep algorithm, which has the potential to improve lung cancer diagnosis and reduce fatalities associated with it.

3D printed biocompatible graphene oxide, attapulgite, and collagen composite scaffolds for bone regeneration.

Tissue-engineered bone material is one of the effective methods to repair bone defects, but the application is restricted in clinical because of the lack of excellent scaffolds that can induce bone regeneration as well as the difficulty in making scaffolds with personalized structures. 3D printing is an emerging technology that can fabricate bespoke 3D scaffolds with precise structure. However, it is challenging to develop the scaffold materials with excellent printability, osteogenesis ability, and mechanical strength. In this study, graphene oxide (GO), attapulgite (ATP), type I collagen (Col I) and polyvinyl alcohol were used as raw materials to prepare composite scaffolds via 3D bioprinting. The composite materials showed excellent printability. The microcosmic architecture and properties was characterized by scanning electron microscopy, Fourier transform infrared and thermal gravimetric analyzer, respectively. To verify the biocompatibility of the scaffolds, the viability, proliferation and osteogenic differentiation of Bone Marrow Stromal Cells (BMSCs) on the scaffolds were assessed by CCK-8, Live/Dead staining and Real-time PCR in vitro. The composited scaffolds were then implanted into the skull defects on rat for bone regeneration. Hematoxylin-eosin staining, Masson staining and immunohistochemistry staining were carried out in vivo to evaluate the regeneration of bone tissue.The results showed that GO/ATP/COL scaffolds have been demonstrated to possess controlled porosity, water absorption, biodegradability and good apatite-mineralization ability. The scaffold consisting of 0.5% GO/ATP/COL have excellent biocompatibility and was able to promote the growth, proliferation and osteogenic differentiation of mouse BMSCs in vitro. Furthermore, the 0.5% GO/ATP/COL scaffolds were also able to promote bone regeneration of in rat skull defects. Our results illustrated that the 3D printed GO/ATP/COL composite scaffolds have good mechanical properties, excellent cytocompatibility for enhanced mouse BMSCs adhesion, proliferation, and osteogenic differentiation. All these advantages made it potential as a promising biomaterial for osteogenic reconstruction.

Anti-neuroinflammatory Effect of Short-Chain Fatty Acid Acetate against Alzheimer's Disease via Upregulating GPR41 and Inhibiting ERK/JNK/NF-κB.

Alzheimer's disease (AD) is a high-incidence neurodegenerative disease in the elderly. Acetate (Ace) is a short-chain fatty acid (SCFA) with neuroprotective activity. The purpose of this study was to investigate the effects and its possible mechanisms of SCFA Ace on AD. A male APP/PS1 transgenic mouse was given intragastric administration Ace for 4 weeks. Cognitive function and microglia activation in mice were assessed. Furthermore, Ace pretreated amyloid-ß (Aß)-induced BV2 microglia, and the levels of CD11b, COX-2, and G-protein-coupled receptor 41 (GPR41) and phosphorylation of ERK, JNK, and NF-κB p65 were determined. Our results revealed that Ace significantly attenuated the cognitive impairment and decreased the CD11b level in the APP/PS1 mice. Moreover, Ace inhibited the phosphorylation of NF-κB p65, ERK, and JNK and decreased the levels of COX-2 and interleukin 1ß in the Aß-stimulated BV2 microglia. Finally, Ace increased the GPR41 level in the Aß-stimulated BV2 cells. The finding indicated that Ace exerted antineuroinflammatory effects via the upregulation of GPR41 and suppression of the ERK/JNK/NF-κB pathway, which might provide an alternative therapy strategy of AD.

Transcriptional alterations of genes related to fertility decline in male rats induced by chronic sleep restriction.

The adverse effects of sleep disorders on male fertility are of increased concern. In this study, a rat model of chronic sleep restriction (CSR) was established using the modified multiplatform method. The effects of CSR on the fertility of male rats were evaluated first based on sexual behavior. Serum hormones, including testosterone (T), prolactin (PRL), luteinizing hormone (LH) and follicle-stimulating hormone (FSH), and sperm parameters (concentration, viability, motility, deformation rate) were measured, and testicular histology was analysed by hematoxylin and eosin staining. The transcriptional differences between CSR rats and control rats were detected by RNA sequencing (RNA-Seq), and DNA methylation was then detected by bisulfite sequencing. After the differentialy expressed genes of CSR rats were sequenced and screened, representative up- and down-regulated genes were randomly sampled to verify the sequencing results by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, functional annotations were completed, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomic (KEGG) pathway analyses. The results showed that the sexual behavior of CSR rats did not change when compared with control group rats. The sperm concentration, viability and motility of the CSR rats decreased significantly, while the sperm malformation rate increased significantly. In the KEGG pathway analysis database, some specific differentially expressed genes were screened, which are involved in metabolic pathways, inflammation-related pathways, the renin-angiotensin system, as well as others. However, the aforesaid differentially expressed genes in the testes were not related to their DNA methylation status. CSR could significantly reduce the fertility of male rats, and one of its mechanisms occurs by altering gene expression in the testes, which is not related to their  state of  DNA methylation. The results of this study suggest that CSR could cause male infertility by significantly altering the testicular transcriptome.Abbreviations: CSR: chronic sleep restriction; SD: sleep deprivation; RNA-Seq: RNA sequencing; NGS: next generation sequencing; qRT-PCR: real-time quantitative reverse transcription polymerase chain reaction; KEGG: Kyoto encyclopedia of genes and genomic; NO: nitric oxide; INOS: Inducible nitric oxide synthase; Il6: interleukin-6; Tnf: tumour necrosis factor alpha; Hsd11b1: hydroxysteroid 11-beta dehydrogenase 1; Dnmt3a: DNA methyltransferase 3Ax; PSD: paradoxic sleep deprivation; DNMTs: DNA methyltransferases family; REM: rapid eye movement sleep; PGD: preimplantation genetic diagnosis; PGS: preimplantation genetic screening; ECS: expanded carrier screening; T: testosterone; FSH: follicle stimulating hormone; LH: luteinizing hormone; PRL: prolactin; BC group: Blank Control group; MC group: Model Control group; Hist1h2ba: histone cluster 1 H2ba; Lgr4: leucine-rich repeat-containing G protein-coupled receptor 4; Atrn: attractin ; Ogg1: 8-oxoguanine DNA glycosylase; SNVs: single nucleotide variants ; HPG axis: hypothalamic-pituitary-adrenal axis; Star protein: steroid acute regulatory protein; Dmac2l: distal membrane arm assembly complex 2 like; Esr1: estrogen receptor 1; MAPK pathways: mitogen-activated protein kinase pathways; Sos2: SOS Ras/Rho guanine nucleotide exchange factor 2; Jak2: Janus kinase 2; Pik3cb: phosphatidylinositol-4,5-bisphosphate 3-kinase, and catalytic subunit beta; Kras: KRAS proto-oncogene and GTPase; RRBS: reduced representation bisulfite sequencing; DEGs: differently expressed genes; SPF: Specific Pathogen Free; HE: hematoxylin & eosin; DMR: differentially methylated region; GO Analysis: Gene Ontology analysis; SINE: short interspersed nuclear elements; LINE: long interspersed nuclear elements; LTR: long terminal repeats.

[Effect of icariin/attapulgite/collagen type â /polycaprolactone composite scaffold in repair of rabbit tibia defect].

OBJECTIVE: To investigate the effect of icarin/attapulgite/collagen type Ⅰ/polycaprolactone (ICA/ATP/Col Ⅰ/PCL) composite scaffold in repair of rabbit tibia defect. METHODS: The ICA/20%ATP/Col Ⅰ/PCL (scaffold 1), ICA/30%ATP/Col Ⅰ/PCL (scaffold 2), 20%ATP/Col Ⅰ/PCL (scaffold 3), and 30%ATP/Col Ⅰ/PCL (scaffold 4) composite scaffolds were constructed by solution casting-particle filtration method. The structure characteristics of the scaffold 2 before and after cross-linking were observed by scanning electron microscopy, and the surface contact angles of the scaffold 2 and the scaffold 4 were used to evaluate the water absorption performance of the material. The in vitro degradation test was used to evaluate the sustained-release effect of the scaffold 2. Thirty male Japanese white rabbits, weighing (2.0±0.1) kg, were randomly divided into groups A, B, C, D, and E, 6 in each group. After making a 1 cm- diameter bilateral tibial defects model, group A was the defect control group without any material implanted. Groups B, C, D, and E were implanted with scaffolds 3, 4, 1, and 2 at the defect sites, respectively. At 4, 8, and 12 weeks after operation, the repairing effects of 4 scaffolds were observed by gross observation, histological observation of HE and Masson staining, and immunohistochemical staining of osteogenic specific transcription factor (runt-related transcription factor 2, RUNX2), osteogenic related transcription factor [Osterix (OSX), Col Ⅰ, osteopontin (OPN)]. RESULTS: Scanning electron microscopy observation showed that the scaffolds were all porous. The structure of the material was loose before and after cross-linking. The surface contact angle showed that the scaffold was hydrophobic, and the scaffold 2 was more hydrophobic than scaffold 4. The sustained-release effect in vitro showed that the drug could be released in a micro and long-term manner. In the animal implantation experiment, the gross observation showed that the defects were significantly smaller in groups D and E than in groups A, B, and C at 4 and 12 weeks after operation. HE and Masson staining showed that the defect of group A was full of connective tissue at 4 weeks after operation, a large number of fibers were seen in groups B and C, and the new bone formation was observed in groups D and E. The increase of new bone was observed in each group at 8 weeks after operation. The defect of group A was still dominated by connective tissue at 12 weeks after operation, and a small amount of new bone tissue was observed in groups B and C, and a large number of new bone tissue was observed in groups D and E, especially in group E, and most of the materials degraded. Immunohistochemical staining showed that the expressions of RUNX2 and OSX in the new tissues of groups D and E were significantly higher than those of the other groups at 4 weeks after operation. The expression of RUNX2 decreased at 8 and 12 weeks after operation. After 8 weeks and 12 weeks, the expressions of Col Ⅰand OPN increased than in 4 weeks. And the expressions of Col Ⅰ and OPN in the new tissues of groups D and E were significantly more than those of the other groups. CONCLUSION: ICA/ATP/Col I/PCL composite scaffolds have good porosity and biocompatibility, can promote bone formation, and have good bone regeneration and repair effect.

Circulating microRNA-23b as a new biomarker for rheumatoid arthritis.

MicroRNA-23b (miR-23b) is associated with inflammation and autoimmune diseases. This study evaluated miR-23b expression and assessed its potential as a biomarker of disease activity for rheumatoid arthritis (RA). Differential expression of microRNAs was determined by miRNA microarray analysis in fibroblast-like synoviocytes (FLSs) from four trauma patients as healthy controls (HCs) and eight RA patients. The microarray results showed elevated expression of miR-23b in FLSs from RA patients and this finding was corroborated by real-time quantitative polymerase chain reaction (RT-qPCR) and in situ hybridization using synovial tissues (STs). Furthermore, we found miR-23b levels in plasma of RA patients were significantly higher than in HCs, and plasma miR-23b levels positively correlated with the erythrocyte sedimentation rate (ESR), hypersensitive C-reactive protein (hs-CRP), C-reactive protein (CRP), DAS28, and platelet (PLT) count (P < 0.05). MiR-23b levels in plasma inversely correlated with the levels of hemoglobin (Hb), total bilirubin (TBIL), direct bilirubin (DBIL), indirect bilirubin (IBIL), total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) (P < 0.05), but not with rheumatoid factor (RF) or anti-cyclic citrullinated peptide antibodies (ACPA) (P > 0.05). Moreover, patients with anorexia showed higher levels of miR-23b in plasma than those without anorexia. Similar results were observed with fatigue. Appropriate treatment for RA not only ameliorated the disease condition but also reversed the elevated plasma miR-23b level remarkably. These results suggest that circulating miR-23b may be a promising biomarker for RA disease activity.

Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition.

IS607-family transposons are unusual because they do not have terminal inverted repeats or generate target site duplications. They encode two protein-coding genes, but only tnpA is required for transposition. Our X-ray structures confirm that TnpA is a member of the serine recombinase (SR) family, but the chemically-inactive quaternary structure of the dimer, along with the N-terminal location of the DNA binding domain, are different from other SRs. TnpA dimers from IS1535 cooperatively associate with multiple subterminal repeats, which together with additional nonspecific binding, form a nucleoprotein filament on one transposon end that efficiently captures a second unbound end to generate the paired-end complex (PEC). Formation of the PEC does not require a change in the dimeric structure of the catalytic domain, but remodeling of the C-terminal α-helical region is involved. We posit that the PEC recruits a chemically-active conformer of TnpA to the transposon end to initiate DNA chemistry.

Follistatin-like protein 1 induction of matrix metalloproteinase 1, 3 and 13 gene expression in rheumatoid arthritis synoviocytes requires MAPK, JAK/STAT3 and NF-κB pathways.

Elevated levels of follistatin-like protein 1 (FSTL1) have been found both in mouse models for human rheumatoid arthritis (RA) and collagen-induced arthritis (CIA). In this study, we elucidated the potential mechanisms by which FSTL1 contributes to the pathogenesis of RA. Fibroblast-like synoviocytes (FLSs) were established from synovial tissues of RA patients and stimulated with human recombinant FSTL1. Protein and mRNA expression levels of select matrix metalloproteinases (i.e., MMP1, MMP3, MMP13) in FLS were measured by, respectively, real-time RT-qPCR and ELISA. Activation of MAPK and other pathways that affect MMPs were evaluated by Western blotting. We also compared concentrations of MMPs in plasma in RA patients versus healthy controls (HC). Expression levels of MMP1, MMP3, and MMP13 were clearly stimulated by FSTL1 in vitro. FSTL1 activated the inflammation-related NF-κB signaling pathway, as well as all three mitogen-activated protein kinase (MAPK) pathways and the JAK/STAT3 pathway. Moreover, select chemical inhibitors that target p38 (SB203580), Erk1/2 (SP600125), JNK (SCH772984), STAT3 (AG490), and NF-κB (BAY 11-7082) significantly attenuated MMP expression. Inhibition of Toll-like receptor 4 by compound TAK-242 significantly abolished those effects of FSTL1. Importantly, elevated plasma concentrations of MMP3 were found to correlate with plasma FSTL1 levels in RA patients. These findings suggest that FSTL1 accelerates RA progression by activating MAPK, JAK/STAT3, and NF-κB pathways to enhance secretion of different MMPs and this enhancement is via TLR4. Targeting FSTL1 may provide a promising pharmacological drug therapy to ameliorate RA symptoms and perhaps reverse disease progression.

Topical treatment of corneal alkali burns with Gly-thymosin ß4 solutions and in situ hydrogels via inhibiting corneal neovascularization and improving corneal epidermal recovery in experimental rabbits.

AIM: Corneal alkali burns are a severe disease and commonly encountered in the emergent clinic. A rapid medical treatment for the burn is very important. Gly-thymosin ß4 (Gly-Tß4) is a biomimic derivative of natural thymosin ß4. The aim of this study is to evaluate the corneal recovery effects of Gly-Tß4 topical therapy on alkali burns in rabbit corneas. METHODS: Rabbit alkali burns were induced with NaOH-contained filter paper. Phosphate-buffered solutions at pH 7.0, Gly-Tß4 solutions, blank in situ hydrogels, and Gly-Tß4in situ hydrogels were dropped on the burned corneas. The treatments were continued for 14 days. Conjunctiva hyperemia, corneal edema, intraeye extravasation, hemorrhaging, corneal neovascularization (CNV), and corneal opacity were observed. Corneal immunohistochemistry and histopathology were performed. RESULTS: Gly-Tß4 solutions led to a lower corneal burn index than the other regimens. Hydrogels may stimulate the burned corneas due to the direct contact of them, and prevent the rapid release of Gly-Tß4. Gly-Tß4 significantly inhibited CNV according to the images of the corneas, CNV areas, and CD31 expression. Furthermore, Gly-Tß4 improved corneal epidermal recovery according to the histopathological result. CONCLUSION: Gly-Tß4 solutions are a promising formulation for topical treatment of corneal alkali burns.

Effect of Sophora flavescens alkaloid on aerobic vaginitis in gel form for local treatment.

OBJECTIVE: To investigate the effect of Sophora flavescens alkaloid (SFA) in gel form on aerobic vaginitis (AV) and the possible mechanism underlying the effects. METHODS: AV rat models were prepared by intravaginal inoculation of Escherichia coli and Staphylococcus aureus. SFA gel and placebo gel were intravaginally administered. In vivo antibacterial effects, vaginal microenvironment, vaginal smears, pathological tissues of vaginas, and retention of gel in the vaginal cavity were investigated. RESULTS: SFA gel had much higher antibacterial effect than placebo gel. SFA gel protected the vaginal mucosa from erosion of bacteria. At the same time, they inhibited the inflammatory responses, exhibiting little leukocytes and parabasal cells. Furthermore, the number of vaginal Lactobacilli remarkably increased following administration of SFA gel. However, the vaginal pH did not recover to the healthy acidic levels after treatment due to the buffering effect of gel. The gel of a fluorescent agent, Cyanine 7, showed very long retention time in the vaginal cavity, up to more than 24 h, much longer than the solutions. CONCLUSION: The SFA gel is a promising medicine for local treatment of AV with the advantages of anti-bacteria, protection of vaginal mucosa, increase of Lactobacilli, and long retention time in the vaginal cavity.

pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis.

BACKGROUND: The ethanol-producing bacterium Zymomonas mobilis has attracted considerable scientific and commercial interest due to its exceptional physiological properties. Shuttle vectors derived from native plasmids have previously been successfully used for heterologous gene expression in this bacterium for a variety of purposes, most notably for metabolic engineering applications. RESULTS: A quantitative PCR (qPCR) approach was used to determine the copy numbers of two endogenous double stranded DNA plasmids: pZMO1A (1,647 bp) and pZMO7 (pZA1003; 4,551 bp) within the NCIMB 11163 strain of Z. mobilis. Data indicated pZMO1A and pZMO7 were present at ca. 3-5 and ca. 1-2 copies per cell, respectively. A ca. 1,900 bp fragment from plasmid pZMO7 was used to construct two Escherichia coli - Z. mobilis shuttle vectors (pZ7C and pZ7-184). The intracellular stabilities and copy numbers of pZ7C and pZ7-184 were characterized within the NCIMB 11163, ATCC 29191 and (ATCC 10988-derived) CU1 Rif2 strains of Z. mobilis. Both shuttle vectors could be stably maintained within the ATCC 29191 strain (ca. 20-40 copies per cell), and the CU1 Rif2 strain (ca. 2-3 copies per cell), for more than 50 generations in the absence of an antibiotic selectable marker. A selectable marker was required for shuttle vector maintenance in the parental NCIMB 11163 strain; most probably due to competition for replication with the endogenous pZMO7 plasmid molecules. N-terminal glutathione S-transferase (GST)-fusions of four endogenous proteins, namely the acyl-carrier protein (AcpP); 2-dehydro-3-deoxyphosphooctonate aldolase (KdsA); DNA polymerase III chi subunit (HolC); and the RNA chaperone protein Hfq; were successfully expressed from pZ7C-derived shuttle vectors, and their protein-protein binding interactions were analyzed in Z. mobilis ATCC 29191. Using this approach, proteins that co-purified with AcpP and KdsA were identified. CONCLUSIONS: We show that a shuttle vector-based protein affinity 'pull-down' approach can be used to probe protein interaction networks in Z. mobilis cells. Our results demonstrate that protein expression plasmids derived from pZMO7 have significant potential for use in future biological or biotechnological applications within Z. mobilis.

[Preparation, in vitro and in vivo evaluation of cataplasm of white mustard seed varnish to prevent asthma].

The aim of the manuscript was to optimize formulations and preparation technologies of cataplasm of white mustard seed varnish, and to evaluate its anti-asthma effect on rats. The single factor experiments included spreading thickness, types of crosslinking agents, dihydroxyaluminum aminoacetate amount, sodium polyacrylate amount, types of adhesive agents with human sense as the evaluation index. Blank cataplasm matrix was optimized by the orthogonal experiment with the amount of glycerine, citric acid, and sodium carboxymethylcellulose as the major influential factors. Initial adhesive force, peeling strength and human sense were as the evaluation index. The optimized formulation of blank cataplasm were as followings: glycerine-water-ethanol-PEG400-dihydroxyaluminum aminoacetate-citric acid-sodium carboxymethylcellulose-sodium carboxymethylcellulose 2 : 8 : 0.8 : 0.4 : 0.07: 0.15 : 0.1 : 0.5. The active ingredients of white mustard seed, corydalis, and gansui root were extracted by alcohol extraction method. Asiasarum volatile oil was extracted by oil extractor. The optimized drug loading amount was 11% with initial adhesive force, peeling strength and human sense as the evaluation index. Asthma rats model were established by sensitized with ovalbumin and nose-scratching time as the evaluation index. High dose (17%) group of drug-loaded cataplasm had the obvious inhibition effect on nose-scratching time of rats (P = 0.037 < 0.05). In comparison, middle dose (11%), low dose (4%) and positive-control groups had no obvious inhibitive effect on rats. White mustard seed cataplasm supplied a novel choice for anti-asthma therapy. And the overall pharmacodynamics assessment will be carried out on molecular level in near future.

The two PPX-GppA homologues from Mycobacterium tuberculosis have distinct biochemical activities.

Inorganic polyphosphate (poly-P), guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp) are ubiquitous in bacteria. These molecules play a variety of important physiological roles associated with stress resistance, persistence, and virulence. In the bacterial pathogen Mycobacterium tuberculosis, the identities of the proteins responsible for the metabolism of polyphosphate and (p)ppGpp remain to be fully established. M. tuberculosis encodes two PPX-GppA homologues, Rv0496 (MTB-PPX1) and Rv1026, which share significant sequence similarity with bacterial exopolyphosphatase (PPX) and guanosine pentaphosphate 5'-phosphohydrolase (GPP) proteins. Here we delineate the respective biochemical activities of the Rv0496 and Rv1026 proteins and benchmark these against the activities of the PPX and GPP proteins from Escherichia coli. We demonstrate that Rv0496 functions as an exopolyphosphatase, showing a distinct preference for relatively short-chain poly-P substrates. In contrast, Rv1026 has no detectable exopolyphosphatase activities. Analogous to the E. coli PPX and GPP enzymes, the exopolyphosphatase activities of Rv0496 are inhibited by pppGpp and, to a lesser extent, by ppGpp alarmones, which are produced during the bacterial stringent response. However, neither Rv0496 nor Rv1026 have the ability to hydrolyze pppGpp to ppGpp; a reaction catalyzed by E. coli PPX and GPP. Both the Rv0496 and Rv1026 proteins have modest ATPase and to a lesser extent ADPase activities. pppGpp alarmones inhibit the ATPase activities of Rv1026 and, to a lesser extent, the ATPase activities of Rv0496. We conclude that PPX-GppA family proteins may not possess all the catalytic activities implied by their name and may play distinct biochemical roles involved in polyphosphate and (p)ppGpp metabolic pathways.

Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis.

Alkaline exonuclease and single-strand DNA (ssDNA) annealing proteins (SSAPs) are key components of DNA recombination and repair systems within many prokaryotes, bacteriophages and virus-like genetic elements. The recently sequenced ß-proteobacterium Laribacter hongkongensis (strain HLHK9) encodes putative homologs of alkaline exonuclease (LHK-Exo) and SSAP (LHK-Bet) proteins on its 3.17 Mb genome. Here, we report the biophysical, biochemical and structural characterization of recombinant LHK-Exo protein. LHK-Exo digests linear double-stranded DNA molecules from their 5'-termini in a highly processive manner. Exonuclease activities are optimum at pH 8.2 and essentially require Mg(2+) or Mn(2+) ions. 5'-phosphorylated DNA substrates are preferred over dephosphorylated ones. The crystal structure of LHK-Exo was resolved to 1.9 Å, revealing a 'doughnut-shaped' toroidal trimeric arrangement with a central tapered channel, analogous to that of λ-exonuclease (Exo) from bacteriophage-λ. Active sites containing two bound Mg(2+) ions on each of the three monomers were located in clefts exposed to this central channel. Crystal structures of LHK-Exo in complex with dAMP and ssDNA were determined to elucidate the structural basis for substrate recognition and binding. Through structure-guided mutational analysis, we discuss the roles played by various active site residues. A conserved two metal ion catalytic mechanism is proposed for this class of alkaline exonucleases.

Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis.

BACKGROUND: Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea and it can reside in human, fish, frogs and water. In this study, we performed an in-depth annotation of the genes in its genome related to adaptation to the various environmental niches. RESULTS: L. hongkongensis possessed genes for DNA repair and recombination, basal transcription, alternative σ-factors and 109 putative transcription factors, allowing DNA repair and global changes in gene expression in response to different environmental stresses. For acid stress, it possessed a urease gene cassette and two arc gene clusters. For alkaline stress, it possessed six CDSs for transporters of the monovalent cation/proton antiporter-2 and NhaC Na+:H+ antiporter families. For heavy metals acquisition and tolerance, it possessed CDSs for iron and nickel transport and efflux pumps for other metals. For temperature stress, it possessed genes related to chaperones and chaperonins, heat shock proteins and cold shock proteins. For osmotic stress, 25 CDSs were observed, mostly related to regulators for potassium ion, proline and glutamate transport. For oxidative and UV light stress, genes for oxidant-resistant dehydratase, superoxide scavenging, hydrogen peroxide scavenging, exclusion and export of redox-cycling antibiotics, redox balancing, DNA repair, reduction of disulfide bonds, limitation of iron availability and reduction of iron-sulfur clusters are present. For starvation, it possessed phosphorus and, despite being asaccharolytic, carbon starvation-related CDSs. CONCLUSIONS: The L. hongkongensis genome possessed a high variety of genes for adaptation to acid, alkaline, temperature, osmotic, oxidative, UV light and starvation stresses and acquisition of and tolerance to heavy metals.

Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae.

BACKGROUND: SXT is an integrating conjugative element (ICE) originally isolated from Vibrio cholerae, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA) genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo) and single strand annealing protein (S065, SXT-Bet) encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively. RESULTS: SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA) molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn2+ or Mg2+ ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb). When co-expressed in E. coli cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo. CONCLUSIONS: The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected V. cholerae cells, through facilitating homologous DNA recombination events. The results presented here significantly extend our general understanding of the properties and activities of alkaline exonuclease and single strand annealing proteins of viral/bacteriophage origin, and will assist the rational development of bacterial recombineering systems.

Biochemical characterization of two mutants of human pyruvate dehydrogenase, F205L and T231A of the E1alpha subunit.

Mutations in the E1alpha subunit of the pyruvate dehydrogenase multienzyme complex may result in congenital lactic acidosis, but little is known about the consequences of these mutations at the enzymatic level. Here we characterize two mutants (F205L and T231A) of human pyruvate dehydrogenase in vitro, using the enzyme expressed in Escherichia coli. Wild-type and mutant proteins were purified successfully and their kinetic parameters were measured. F205L shows impaired binding of the thiamin diphosphate cofactor, which may explain why patients carrying this mutation respond to high-dose vitamin B1 therapy. T231A has very low activity and a greatly elevated Km for pyruvate, and this combination of effects would be expected to result in severe lactic acidosis. The results lead to a better understanding of the consequences of these mutations on the functional and structural properties of the enzyme, which may lead to improved therapies for patients carrying these mutations.