Competition between H4PteGlu and H2PtePAS Confers para-Aminosalicylic Acid Resistance in Mycobacterium tuberculosis

Tuberculosis remains a serious challenge to human health worldwide. para-Aminosalicylic acid (PAS) is an important anti-tuberculosis drug, which requires sequential activation by Mycobacterium tuberculosis (M. tuberculosis) dihydropteroate synthase and dihydrofolate synthase (DHFS, FolC). Previous studies showed that loss of function mutations of a thymidylate synthase coding gene thyA caused PAS resistance in M. tuberculosis, but the mechanism is unclear. Here we showed that deleting thyA in M. tuberculosis resulted in increased content of tetrahydrofolate (H4PteGlu) in bacterial cells as they rely on the other thymidylate synthase ThyX to synthesize thymidylate, which produces H4PteGlu during the process. Subsequently, data of in vitro enzymatic activity experiments showed that H4PteGlu hinders PAS activation by competing with hydroxy dihydropteroate (H2PtePAS) for FolC catalysis. Meanwhile, over-expressing folC in ΔthyA strain and a PAS resistant clinical isolate with known thyA mutation partially restored PAS sensitivity, which relieved the competition between H4PteGlu and H2PtePAS. Thus, loss of function mutations in thyA led to increased H4PteGlu content in bacterial cells, which competed with H2PtePAS for catalysis by FolC and hence hindered the activation of PAS, leading to decreased production of hydroxyl dihydrofolate (H2PtePAS-Glu) and finally caused PAS resistance. On the other hand, functional deficiency of thyA in M. tuberculosis pushes the bacterium switch to an unidentified dihydrofolate reductase for H4PteGlu biosynthesis, which might also contribute to the PAS resistance phenotype. Our study revealed how thyA mutations confer PAS resistance in M. tuberculosis and provided new insights into studies on the folate metabolism of the bacterium.

[Prognostic value of a predictive model comprising preoperative inflammatory response and nutritional indexes in patients with gastric cancer]

Objective: To investigate the prognostic value of preoperative inflammatory and nutritional condition detection in the postoperative survival, and establish a prognostic model for predicting the survival of patients with gastric cancer. Methods: The clinicopathological data of 1123 patients with gastric cancer who had undergone radical gastrectomy in Tianjin Medical University Cancer Institute & Hospital from January 2005 to December 2014 were retrospectively analyzed. Patients with history of other malignancy, with history of gastrectomy, who had received preoperative treatment, who died during the initial hospital stay or first postoperative month, and missing clinical and pathological information were excluded. Cox univariate and multivariate analyses were used to identify independent clinicopathological factors associated with the survival of these gastric cancer patients. Cox univariate analysis was used to identify preoperative inflammatory and nutritional indexes related to the survival of patients with gastric cancer after radical gastrectomy. Moreover, the Cox proportional regression model for multivariate survival analysis (forward stepwise regression method based on maximum likelihood estimation) was used. The independent clinicopathological factors that affect survival were incorporated into the following three new prognostic models: (1) an inflammatory model: significant preoperative inflammatory indexes identified through clinical and univariate analysis; (2) a nutritional model: significant preoperative nutritional indexes identified through clinical and univariate analysis; and (3) combined inflammatory/nutritional model: significant preoperative inflammatory and nutritional indexes identified through clinical and univariate analysis. A model that comprised only pT and pN stages in tumor TNM staging was used as a control model. The integrated area under the receiver operating characteristic curve (iAUC) and C-index were used to evaluate the discrimination of the model. Model fitting was evaluated by Akaike information criterion analysis. Calibration curves were used to assess agreement between the predicted probabilities and actual probabilities at 3-year or 5-year overall survival (OS). Results: The study cohort comprised 1 123 patients with gastric cancer. The mean age was 58.9±11.6 years, and 783 were males. According to univariate analysis, age, surgical procedure, extent of lymph node dissection, tumor location, maximum tumor size, number of examined lymph nodes, pT stage, pN stage, and nerve invasion were associated with 5-year OS after radical gastrectomy for gastric cancer (all P<0.050). Multivariate analysis further identified age (HR: 1.18, 95%CI: 1.03-1.36, P=0.019), maximum tumor size (HR: 1.19, 95%CI: 1.03-1.38, P=0.022), number of examined lymph nodes (HR: 0.79, 95%CI: 0.68-0.92, P=0.003), pT stage (HR: 1.40, 95%CI: 1.26-1.55, P<0.001) and pN stage (HR: 1.28, 95%CI: 1.21-1.35, P<0.001) as independent prognostic factors for OS of gastric cancer patients. Additionally, according to univariate survival analysis, the preoperative inflammatory markers of neutrophil count, percentage of neutrophils, neutrophil/lymphocyte ratio, platelet/neutrophil ratio and preoperative nutritional indicators of serum albumin and body mass index were potential prognostic factors for gastric cancer (all P<0.05). On the basis of the above results, three models for prediction of prognosis were constructed. Variables included in the three models are as follows. (1) Inflammatory model: age, maximum tumor size, number of examined lymph nodes, pT stage, pN stage, percentage of neutrophils, and neutrophil-lymphocyte ratio; (2) nutritional model: age, maximum tumor size, number of examined lymph nodes, pT stage, pN stage, and serum albumin; and (3) combined inflammatory/nutritional model: age, maximum tumor size, number of examined lymph nodes, pT stage, pN stage, percentage of neutrophils, neutrophil-lymphocyte ratio, and serum albumin. We found that the predictive accuracy of the combined inflammatory/nutritional model, which incorporates both inflammatory indicators and nutrition indicators (iAUC: 0.676, 95% CI: 0.650-0.719, C-index: 0.698),was superior to that of the inflammation model (iAUC: 0.662, 95% CI: 0.673-0.706;C-index: 0.675), nutritional model (iAUC: 0.666, 95% CI: 0.642-0.698, C-index: 0.672), and TNM staging control model (iAUC: 0.676, 95% CI: 0.650-0.719, C-index: 0.658). Furthermore, the combined inflammatory/nutritional model had better fitting performance (AIC: 10 762) than the inflammatory model (AIC: 10 834), nutritional model (AIC: 10 810), and TNM staging control model (AIC: 10 974). Conclusions: Preoperative percentage of neutrophils, NLR, and BMI have predictive value for the prognosis of gastric cancer patients. The inflammatory / nutritional model can be used to predict the survival and prognosis of gastric cancer patients on an individualized basis.

[Clinical controversy and research thoughts on lymphadenectomy of gastric cancer]

Lymphadenectomy, as one of the controversial foci in clinic, is an extremely important part of radical surgery for gastric cancer. So far, the preliminary consensus has been reached on the scope and number of lymph node dissection, based on the etiological mechanism, disease progression, diagnosis and treatment prognosis of gastric cancer. At present, some clinical issues of lymphadenectomy in curative gastrectomy are still need to be addressed. Firstly, standardized procedure in lymph node dissection for gastric cancer is a prerequisite to decrease the incidence of postoperative complications and to improve the prognosis of gastric cancer patients. Furthermore, the plausible treatment strategy in perioperative phase is also deemed as the other key method to offer a benefit of survival rate for advanced stage patients after lymphadenectomy. Last but not least, the technologies for enhancement the prediction accuracy of lymph node metastasis preoperatively or intraoperatively should be worthy in-depth study.

[In vitro and in vivo anti-periodontitis effects of combination treatment of photodynamic and antibiotic therapies]

Objective: To investigate the effects of combination treatment of photodynamic therapy (PDT) based on photosensitizer chlorin e6 (Ce6) and antibiotic agent tinidazole (TNZ) against periodontitis both in vitro and in vivo. Methods: The Sprague-Dewley (SD) rat periodontitis model was constructed using the method of orthodontic wire ligation. After successful modeling, SD rats were randomly divided into the following 6 groups (3 rats in each group): positive control (Ctrl+), Ce6, TNZ, a mixture of Ce6 and TNZ (Ce6/TNZ), Ce6 with laser irradiation (Ce6+L), a mixture of Ce6 and TNZ with laser irradiation (Ce6/TNZ+L). Methyl thiazolyl tetrazolium (MTT) assay was used to assess the cytotoxic activities of Ce6 (concentration range: 0-20 mg/L), TNZ (concentration range: 0-16.6 mg/L) and their mixture (Ce6/TNZ) in mouse fibroblast L929 cells. Fluorescence probe method was applied to measure the production of reactive oxygen species in the dental plaque biofilms after various treatments with and without 5-minute laser irradiation at 635 nm at a power density of 0.5 W/cm² (Ce6+L and Ce6/TNZ+L groups), thus to evaluate the PDT performances. Cell counting kit-8 (CCK-8) and live/dead staining were used to assess the antibacterial activity in each of the groups and the combination index (CI) of PDT combined with TNZ was calculated subsequently. Flow cytometry was utilized to detect the apoptosis-inducing effects of these treatments in macrophage RAW264.7 cells after processing with the apoptosis detection kit. The inhibitory effects of various treatments on the absorption of alveolar bone of SD rats were further evaluated in the periodontitis rats by using the micro-CT. Results: The survival rates of L929 cells in the preset concentration range were all above 90% in Ce6, TNZ and Ce6/TNZ groups. Upon laser irradiation, the plaque biofilms in Ce6 and Ce6/TNZ groups showed significant green fluorescence, indicating that large amounts of reactive oxygen species were triggered and generated significantly in the dental plaque biofilms. However, the survival rates of dental plaque microorganisms in 5 Ce6/TNZ concentrations were (85.4±5.5)%, (76.0±8.9)%, (61.7±0.6)%, (56.3±2.6)% and (43.5±0.6)% respectively, which were significantly lower than that in Ce6 only and TNZ only groups (P<0.01). The CI levle of each drug concentration group was less than 1.0, which showed a significant synergistic antibacterial efficiency. Stronger apoptotic activities were observed in Ce6+L and Ce6/TNZ+L groups compared with those in Ce6 only and Ce6/TNZ only groups (P<0.01). In periodontitis rats, Ce6/TNZ combined laser irradiation could effectively inhibit the absorption of alveolar bone. The alveolar bone volume and the ratio of bone volume and tissue volume were (1.49±0.07) mm³ and (47.08±0.71)%, respectively. The distances between cementoenamel junction to alveolar bone crest on buccal and palatal sites decreased to (2.13±0.07) mm and (1.94±0.10) mm respectively, showing a high inhibition efficiency. Conclusions: Ce6-mediated PDT combined with TNZ possessed notable synergistic effects against periodontitis, reflecting in the efficient antibacterial effect, the apoptosis-inducing action on macrophages, and the inhibitory efficacy on the alveolar bone absorption in vivo.

MgrB Inactivation Confers Trimethoprim Resistance in Escherichia coli

After several decades of use, trimethoprim (TMP) remains one of the key access antimicrobial drugs listed by the World Health Organization. To circumvent the problem of trimethoprim resistance worldwide, a better understanding of drug-resistance mechanisms is required. In this study, we screened the single-gene knockout library of Escherichia coli, and identified mgrB and other several genes involved in trimethoprim resistance. Subsequent comparative transcriptional analysis between ΔmgrB and the wild-type strain showed that expression levels of phoP, phoQ, and folA were significantly upregulated in ΔmgrB. Further deleting phoP or phoQ could partially restore trimethoprim sensitivity to ΔmgrB, and co-overexpression of phoP/Q caused TMP resistance, suggesting the involvement of PhoP/Q in trimethoprim resistance. Correspondingly, MgrB and PhoP were shown to be able to modulated folA expression in vivo. After that, efforts were made to test if PhoP could directly modulate the expression of folA. Though phosphorylated PhoP could bind to the promotor region of folA in vitro, the former only provided a weak protection on the latter as shown by the DNA footprinting assay. In addition, deleting the deduced PhoP box in ΔmgrB could only slightly reverse the TMP resistance phenotype, suggesting that it is less likely for PhoP to directly modulate the transcription of folA. Taken together, our data suggested that, in E. coli, MgrB affects susceptibility to trimethoprim by modulating the expression of folA with the involvement of PhoP/Q. This work broadens our understanding of the regulation of folate metabolism and the mechanisms of TMP resistance in bacteria.

[Regulatory effect of microRNA-126 on macrophage proliferation caused by high glucose stimulation]

Objective: To explore the effects of microRNA-126 (miR-126) on the proliferation of human myeloid leukemia mononuclear cells (THP-1)-derived macrophages in high glucose environment and the regulatory role of miR-126 in periodontitis with diabetes. Methods: THP-1 cells were cultured in vitro and 5 μg/L phorbol-12-myristate-13-acetate was applied to induce THP-1 cells differentiating into macrophages for 48 h in low glucose culture medium (5.5 mmol/L). THP-1-derived macrophages were then cultured with low glucose, medium glucose (15 mmol/L) or high glucose (25 mmol/L) media respectively. The proliferation of THP-1-derived macrophages was detected by cell counting kit-8 (CCK-8) method and the expressions of miR-126 and proliferation-associated factors were detected by quantitative real time PCR (qRT-PCR). The miR-126 mimic or inhibitor was transfected into THP-1-derived macrophages for 72 h. The proliferation of cells was detected by CCK-8 method and the expressions of miR-126 or proliferation-associated factors were detected by qRT-PCR. Results: Increasing glucose concentration decreased the proliferation of THP-1-derived macrophages (day 7, A values in low, medium and high glucose groups were 0.369±0.014, 0.214±0.009 and 0.200±0.010, respectively, P<0.01) as well as the survival rate (P<0.05), promoted the expression of miR-126, B-cell lymphoma-2 (Bcl-2)-associated X protein (BAX) and caspase-3 (P<0.05), and suppressed Bcl-2, phosphoinositol-3 kinase regulatory subunit 2 (PIK3R2) expression (P<0.05). After the miR-126 mimic was transfected in cells in low glucose medium for 72 h, compared with negative control (1.005±0.118), the expression of miR-126 significantly increased (2 980.227±170.431, P<0.05), and the proliferation of THP-1 derived macrophages decreased (negative control: 1.816±0.013, mimic group: 1.310±0.048, P<0.01), the level of BAX and caspase-3 significantly increased (P<0.01, P<0.05), PIK3R2 and Bcl-2 significantly decreased (P<0.05, P<0.01). After the miR-126 inhibitor was transfected in cells cultured in high glucose medium for 72 h, compared with negative control (0.723±0.133), the proliferation of inhibitor group increased (0.984±0.049, P<0.05), the level of BAX and caspase-3 significantly decreased (P<0.01, P<0.05), PIK3R2 and Bcl-2 significantly increased (P<0.01, P<0.05). Conclusions: High glucose condition can inhibit the proliferation of THP-1-derived macrophages and increase the expression of miR-126. MiR-126 can inhibit the proliferation of THP-1-derived macrophages in high glucose environment through up-regulating the expression of BAX and caspase-3 and down-regulating the expression of PIK3R2 and Bcl-2.

[Verification of clinical applicability of the non-special perioperative administration for enhanced recovery after surgery of gastric cancer patients: a Chinese single-center observational report]

Objective: To verify clinical applicability of the non-special perioperative administration for enhanced recovery after surgery (ERAS) proposed by Japanese scholars in Chinese gastric cancer patients. Methods: The main measures of the non-special perioperative administration for ERAS are as follows: (1) discussion of multiple disciplinary team before surgery; (2) rehabilitation education for patients; (3) no routine bowel preparation before surgery; (4) placement of nasogastric tube for decompression routinely before operation and removal as early as 24 hours after surgery; (5) appropriate rehydration; (6) antibiotic prophylaxis before surgery; (7) place abdominal drainage tubes when necessary; (8) epidural patient-controlled analgesia and oral medication for postoperative pain management; (9) start low-molecular-weight heparin injection 48h after surgery and ambulation every day to prevent deep vein thrombosis; (10) postoperative dietary management and supplement with parenteral nutrition intermittently; (11) remove Foley catheter about 24 hours after surgery. A retrospective cohort study was performed, including 203 patients undergoing radical gastrectomy at Department of Gastroenterology, Tianjin Medical University Cancer Institute and Hospital from January 2017 to December 2018. Inclusion criteria were patients who were ≤75 years old without distant metastasis by preoperative examination, were diagnosed as gastric adenocarcinoma by postoperative histopathology and had complete clinicopathological and follow-up data. Patients with history of other malignancies and gastrectomy, extensive implantation of the abdominal cavity or malignant ascites by intraoperative exploration, death within 1 month after surgery, and residual gastric cancer were excluded. The perioperative management methods were chosen by patients. There were 123 patients who followed non-special perioperative administration for ERAS (non-special preparation group) and 80 patients who underwent traditional perioperative management (traditional method group). The primary outcomes (postoperative hospital stay, time to the first flatus, time to the first fluid diet, time to the first ambulatory activity, morbidity of postoperative complication, mortality, and readmission rate) and secondary outcomes (operative time, intraoperative blood loss and postoperative pain score) were compared between the two groups. Results: Compared to the traditional method group, the non-special preparation group had shorter time to the first flatus [(3.6±1.1) days vs. (4.8±1.4) days, t=3.134, P=0.003], shorter time to the first liquid diet [(2.6±0.9) days vs. (5.5±1.6) days, t=15.105, P<0.001], shorter time to the first ambulatory activity [(1.9±0.5) days vs. (4.1±1.1) days, t=8.543, P<0.001] and shorter postoperative hospital stay [(9.6±2.3) days vs. (12.9±2.3) days, t=5.020, P<0.001]. Besides, incidences of pancreatic leakage [6.5% (8/123) vs. 16.3% (13/80), χ(2)=4.964, P=0.026], lymphatic leakage [1.6% (2/123) vs. 13.8% (11/80), χ(2)=11.887, P=0.001], peritoneal effusion [2.4% (3/123) vs. 10.0% (8/80), χ(2)=4.032, P=0.045], and gastroparesis [0.8% (1/123) vs. 7.5% (6/80), χ(2)=4.657, P=0.031] in the non-special preparation group were significantly lower. The overall morbidity of postoperative complications and incidences of pulmonary infection and intestinal adhesion were not significantly different between the two groups (all P>0.05). As for the secondary outcomes, compared to the traditional method group, the non-special preparation group had less intraoperative blood loss [(80.4±24.4) ml vs. (100.5±19.4) ml, t=3.134, P=0.003] and lower postoperative pain score [postoperative day 1: (4.4±0.3) vs. (5.3±0.8), t=2.504, P=0.037],while the difference in operative time was not significant (P>0.05). Conclusion: The non-special perioperative administration for ERAS proposed by Japanese scholars is effective and safe, which has certain clinical applicability and value for Chinese patients with gastric cancer.

[Brief discussion on prevention of the secondary damage in the procedures of D2 lymphadenectomy for gastric cancer]

So far, D2 lymphadenectomy has been recognized as the key one of the procedures in curative resection for gastric cancer. In summary, the standardized implementation of D2 lymphadenectomy can contribute to both surgical quality and patients' prognosis. Lymph node dissection, as an important basis for local surgical treatment of gastric cancer, involves certain technical risks due to complex adjacent relationship and anatomical variation of organs or blood vessels, and so on. There is a certain incidence of side injuries in D2 lymphadenectomy for a surgeon, regardless of the experience of learning curve. Complying with specification of surgical procedures and summarizing the vital points of lymph node dissection in each curative gastrectomy for gastric cancer is the principal method to reduce or avoid the occurrence of relevant complications after surgery.

Global Profiling of PknG Interactions Using a Human Proteome Microarray Reveals Novel Connections with CypA

Mycobacterium tuberculosis (Mtb) serine/threonine kinase PknG plays an important role in the Mtb-host interaction by facilitating the survival of Mtb in macrophages. However, the human proteins with which the PknG interacts, and the underlying molecular mechanisms are still largely unknown. In this study, a HuProt array is been applied to globally identify the host proteins to which PknG binds. In this way, 125 interactors are discovered, including a cyclophilin protein, CypA. This interaction between PknG and CypA is validated both in vitro and in vivo, and functional studies show that PknG significantly reduces the protein levels of CypA through phosphorylation, which consequently inhibit the inflammatory response through downregulation of NF-κB and ERK1/2 pathways. Phenotypically, overexpression of PknG reduces cytokine levels and promotes the survival of Mycobacterium smegmatis (Msm) in macrophages. Overall, it is expected that the PknG interactors identified in this study will serve as a useful resource for further systematic studies of the roles that PknG plays in the Mtb-host interactions.

Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis

Owing to the spread of multidrug resistance (MDR) and extensive drug resistance (XDR), there is a pressing need to identify potential targets for the development of more-effective anti-M. tuberculosis (Mtb) drugs. PafA, as the sole Prokaryotic Ubiquitin-like Protein ligase in the Pup-proteasome System (PPS) of Mtb, is an attractive drug target. Here, we show that the activity of purified Mtb PafA is significantly inhibited upon the association of AEBSF (4-(2-aminoethyl) benzenesulfonyl fluoride) to PafA residue Serine 119 (S119). Mutation of S119 to amino acids that resemble AEBSF has similar inhibitory effects on the activity of purified Mtb PafA. Structural analysis reveals that although S119 is distant from the PafA catalytic site, it is located at a critical position in the groove where PafA binds the C-terminal region of Pup. Phenotypic studies demonstrate that S119 plays critical roles in the function of Mtb PafA when tested in M. smegmatis. Our study suggests that targeting S119 is a promising direction for developing an inhibitor of M. tuberculosis PafA.

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The pupylation activity of purified M. tuberculosis PafA is almost completely inhibited upon the association of AEBSF.

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The AEBSF binding site, Ser 119 plays critical roles in both the pupylation and depupylation activity of purified M. tuberculosis PafA.

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Disruption of purified M. tuberculosis PafA Ser 119 causes a dramatic reduction in Pup binding.

Drug-resistant tuberculosis is a major challenge worldwide, there is an urgent need to identify potential drug targets for developing more effective anti-tubercular drugs. M. tuberculosis ubiquitin-like protein ligase PafA is an attractive drug target, however, effective PafA inhibitors have not yet been identified. Here, we show that interruption of a single amino acid, S119, causes dramatic loss of PafA activity. S119 could thus serve as a promising precise target for developing M. tuberculosis PafA inhibitors.

Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity

Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.

Deletion of sigB Causes Increased Sensitivity to para-Aminosalicylic Acid and Sulfamethoxazole in Mycobacterium tuberculosis

Although the de novo folate biosynthesis pathway has been well studied in bacteria, little is known about its regulation. In the present study, the sigB gene in Mycobacterium tuberculosis was deleted. Subsequent drug susceptibility tests revealed that the M. tuberculosis ΔsigB strain was more sensitive to para-aminosalicylic acid (PAS) and sulfamethoxazole. Comparative transcriptional analysis was performed, and downregulation of pabB was observed in the ΔsigB strain, which was further verified by a quantitative reverse transcription-PCR and Western blot assay. Then, the production levels of para-aminobenzoic acid (pABA) were compared between the sigB deletion mutant and wild-type strain, and the results showed that sigB deletion resulted in decreased production of pABA. In addition, SigB was able to recognize the promoter of pabB in vitro Furthermore, we found that deleting pabC also caused increased susceptibility to PAS. Taken together, our data revealed that, in M. tuberculosis, sigB affects susceptibility to antifolates through multiple ways, primarily by regulating the expression of pabB To our knowledge, this is the first report showing that SigB modulates pABA biosynthesis and thus affecting susceptibility to antifolates, which broadens our understanding of the regulation of bacterial folate metabolism and mechanisms of susceptibility to antifolates.

The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb.

Anti-folates potentiate bactericidal effects of other antimicrobial agents

Synergies between sulfonamides and other antimicrobial agents have long been reported, but the reason still remains unclear. Previously, Vilchèze et al. found that, sulfamethoxazole (SMX) could potentiate the bacterialcidal activity of isoniazid (INH) and rifampin (RIF) in Mycobacterium tuberculosis. To test if this was also the case in other bacteria, the ability to potentiate bactericidal effect of RIF by SMX was evaluated in Escherichia coli, Staphylococcus aureus, Salmonella typhimurium and Mycobacterium smegmatis. And the ability to potentiate bactericidal effect of streptomycin (SM) by SMX was also evaluated in E. coli and M. Smegmatis. Susceptibility tests and drug exposure experiments were performed for RIF and SM in the presence of sub-ICs of SMX. In drug exposure experiments, 10 mg l^-1 of 7,8-dihydropteroic acid (DHP) was used to reverse the effect of SMX. In the presence of sub-ICs of SMX, MIC of RIF for E. coli and M. smegmatis decreased 2 and 16 fold, respectively. In the drug exposure experiments, addition of sub-ICs of SMX suppressed the growth of RIF and SM resistant population in a pool of susceptible bacteria, and the effects of SMX could be reversed by DHP. Besides, we also found that, sub-ICs of para-aminosalicylic acid (PAS) could bactericidal effects of INH, RIF and SM in M. tuberculosis. Taken together, our data suggest that, sub-ICs of anti-folates can potentiate bactericidal effects of other antimicrobial agents in various bacteria.

Columnar structured FePt films epitaxially grown on large lattice mismatched intermediate layer

The microstructure and magnetic properties of the FePt films grown on large mismatched ZrN (15.7%) intermediate layer were investigated. With using ZrN intermediate layer, FePt 10 nm films exhibited (001) texture except for some weaker FePt (110) texture. Good epitaxial relationships of FePt (001) <100>//ZrN (001) <100>//TiN (001) <100> among FePt and ZrN/TiN were revealed from the transmission electron microscopy (TEM) results. As compared with TiN intermediate layer, although FePt-SiO₂-C films grown on ZrN/TiN intermediate layer showed isotropic magnetic properties, the large interfacial energy and lattice mismatch between FePt and ZrN would lead to form columnar structural FePt films with smaller grain size and improved isolation. By doping ZrN into the TiN layer, solid solution of ZrTiN was formed and the lattice constant is increased comparing with TiN and decreased comparing with ZrN. Moreover, FePt-SiO₂-C films grown on TiN 2 nm-20 vol.% ZrN/TiN 3 nm intermediate layer showed an improved perpendicular magnetic anisotropy. Simultaneously, columnar structure with smaller grain size retained.

Mutagenesis of mNeptune Red-Shifts Emission Spectrum to 681-685 nm

GFP-like fluorescent proteins with diverse emission wavelengths have been developed through mutagenesis, offering many possible choices in cellular and tissue imaging, such as multi-targets imaging, deep tissue imaging that require longer emission wavelength. Here, we utilized a combined approach of random mutation and structure-based rational design to develop new NIR fluorescent proteins on the basis of a far-red fluorescent protein, mNeptune (Ex/Em: 600/650 nm). We created a number of new monomeric NIR fluorescent proteins with the emission range of 681-685 nm, which exhibit the largest Stocks shifts (77-80 nm) compared to other fluorescent proteins. Among them, mNeptune681 and mNeptune684 exhibit more than 30 nm redshift in emission relative to mNeptune, owing to the major role of the extensive hydrogen-bond network around the chromophore and contributions of individual mutations to the observed redshift. Furthermore, the two variants still maintain monomeric state in solution, which is a trait crucial for their use as protein tags. In conclusion, our results suggest that there is untapped potential for developing fluorescent proteins with desired properties.

YcgC represents a new protein deacetylase family in prokaryotes

Reversible lysine acetylation is one of the most important protein posttranslational modifications that plays essential roles in both prokaryotes and eukaryotes. However, only a few lysine deacetylases (KDACs) have been identified in prokaryotes, perhaps in part due to their limited sequence homology. Herein, we developed a ‘clip-chip’ strategy to enable unbiased, activity-based discovery of novel KDACs in the Escherichia coli proteome. In-depth biochemical characterization confirmed that YcgC is a serine hydrolase involving Ser200 as the catalytic nucleophile for lysine deacetylation and does not use NAD⁺ or Zn²⁺ like other established KDACs. Further, in vivo characterization demonstrated that YcgC regulates transcription by catalyzing deacetylation of Lys52 and Lys62 of a transcriptional repressor RutR. Importantly, YcgC targets a distinct set of substrates from the only known E. coli KDAC CobB. Analysis of YcgC’s bacterial homologs confirmed that they also exhibit KDAC activity. YcgC thus represents a novel family of prokaryotic KDACs.

DOI:http://dx.doi.org/10.7554/eLife.05322.001

After proteins have been made, they can be modified in several ways. For example, chemical tags called acetyl groups may be added to (and later removed from) the protein to regulate cell activities such as aging and metabolism. Enzymes are proteins that help catalyze the reactions that add or remove the acetyl tags on certain “substrate” proteins. In the bacteria species Escherichia coli, many enzymes that help to add acetyl groups to proteins have been discovered. However, only a single E. coli “deacetylase” enzyme that removes the acetyl group has been identified.

Now, Tu, Guo, Chen et al. have devised a technique to identify new deacetylases, called the “clip-chip” approach. In this method, thousands of proteins that are potential deacetylases are arrayed on a glass slide, and substrate proteins are immobilized on another slide. The two slides are then clipped together face-to-face, allowing the potential enzymes to transfer to the substrate slide and interact with the substrates.

Using this approach, Tu, Guo, Chen et al. identified a protein called YcgC as a deacetylase in bacteria. Further characterization experiments revealed that YcgC works in a different way to other known deacetylases, and that it targets different substrates to the previously known E. coli deacetylase.

Tu, Guo, Chen et al. found that the equivalents of YcgC in other bacteria species are also deacetylases; these enzymes therefore represent a new deacetylase family. In the future, the clip-chip approach could be used to discover new members of other enzyme families.

DOI:http://dx.doi.org/10.7554/eLife.05322.002

Self-Assembly of Ferritin Nanoparticles into an Enzyme Nanocomposite with Tunable Size for Ultrasensitive Immunoassay

The self-assembly of nanoparticles into larger superstructures is a powerful strategy to develop novel functional nanomaterials, as these superstructures display collective properties that are different to those displayed by individual nanoparticles or bulk samples. However, there are increasing bottlenecks in terms of size control and multifunctionalization of nanoparticle assemblies. In this study, we developed a self-assembly strategy for construction of multifunctional nanoparticle assemblies of tunable size, through rational regulation of the number of self-assembling interaction sites on each nanoparticle. As proof-of-principle, a size-controlled enzyme nanocomposite (ENC) was constructed by self-assembly of streptavidin-labeled horseradish peroxidase (SA-HRP) and autobiotinylated ferritin nanoparticles (bFNP). Our ENC integrates a large number of enzyme molecules, together with a streptavidin-coated surface, allowing for a drastic increase in enzymatic signal when the SA is bound to a biotinylated target molecule. As result, a 10 000-fold increase in sensitivity over conventional enzyme-linked immunosorbent assays (ELISA) methods was achieved in a cardiac troponin immunoassay. Our method presented here should provide a feasible approach for constructing elaborate multifunctional superstructures of tunable size useful for a broad range of biomedical applications.

Double anterior (anterolateral and anteromedial) thigh flap for oral perforated defect reconstruction

OBJECTIVE

The purpose of this study was to assess the therapeutic efficacy of oral perforated defect reconstruction with a double anterior (anterolateral and anteromedial) thigh flap through the modified lateral lip-submandibular approach.

MATERIALS AND METHODS

From July 2010 to August 2013, eight patients with oral perforated defects secondary to oral cancer ablation involving the superior partial mandible or the posterior partial maxilla, with immediate reconstruction by double anterior (anterolateral and anteromedial) thigh flaps, were retrospectively enrolled into this study.

RESULTS

All double anterior flaps were musculocutaneous flaps. Seven double flaps resulted in good functional and aesthetic outcomes with complete flap survival. One patient required operative exploration in the postoperative period due to thrombosis in the external jugular vein. After the salvage, one of the double flaps in the intraoral region resulted in partial failure of the superficial skin of the flap. No functional impairment at the donor sites occurred in any of the cases.

CONCLUSION

The double anterior (anterolateral and anteromedial) thigh flap is a feasible and acceptable technique for reconstruction of an oral perforated defect involving the mandible or the maxilla through the modified lateral lip-submandibular approach. It presents a very acceptable aesthetic and functional result with the additional advantage of low morbidity at the donor site.

The S28H mutation on mNeptune generates a brighter near-infrared monomeric fluorescent protein with improved quantum yield and pH-stability

For living deep-tissue imaging, the optical window favorable for light penetration is in near-infrared wavelengths, which requires fluorescent proteins with emission spectra in the near-infrared region. Here, we report that a single mutant Ser28His of mNeptune with a near-infrared (≥650 nm) emission maxima of 652 nm is found to improve the brightness, photostability, and pH stability when compared with its parental protein mNeptune, while it remains as a monomer, demonstrating that there is still plenty of room to improve the performance of the existing near infrared fluorescence proteins by directed evolution.

Acetylation reduces the ability of CheY to undergo autophosphorylation

CheY, the response regulator of the chemotaxis system in Escherichia coli, can be regulated by two covalent modifications - phosphorylation and acetylation. Both covalent modifications are involved in chemotaxis, but the mechanism and role of the acetylation are still obscure. While acetylation was shown to repress the binding of CheY to its target proteins, the effect of acetylation on the ability of CheY to undergo autophosphorylate with AcP is not fully investigated. To obtain more information on the function of this acetylation, we successfully expressed and purified CheY protein with a 6 × His-tag on the C-terminus. Subsequently, acetylated CheY (AcCheY) was obtained with AcCoA as the acetyl donor, and the acetylation level of AcCheY was confirmed by Western blotting and then mass spectrometry. Using tryptophan fluorescence intensity measurements as a monitor of phosphorylation, we showed that acetylation reduces the ability of CheY to undergo autophosphorylation.

Quantum dot-induced viral capsid assembling in dissociation buffer

Viruses encapsulating inorganic nanoparticles are a novel type of nanostructure with applications in biomedicine and biosensors. However, the encapsulation and assembly mechanisms of these hybridized virus-based nanoparticles (VNPs) are still unknown. In this article, it was found that quantum dots (QDs) can induce simian virus 40 (SV40) capsid assembly in dissociation buffer, where viral capsids should be disassembled. The analysis of the transmission electron microscope, dynamic light scattering, sucrose density gradient centrifugation, and cryo-electron microscopy single particle reconstruction experimental results showed that the SV40 major capsid protein 1 (VP1) can be assembled into ≈25 nm capsids in the dissociation buffer when QDs are present and that the QDs are encapsulated in the SV40 capsids. Moreover, it was determined that there is a strong affinity between QDs and the SV40 VP1 proteins (K_D = 2.19E-10 M), which should play an important role in QD encapsulation in the SV40 viral capsids. This study provides a new understanding of the assembly mechanism of SV40 virus-based nanoparticles with QDs, which may help in the design and construction of other similar virus-based nanoparticles.

Reversibly acetylated lysine residues play important roles in the enzymatic activity of Escherichia coli N-hydroxyarylamine O-acetyltransferase

CobB is a bacterial NAD(+)-dependent protein deacetylase. Although progress has been made in functional studies of this protein in recent years, its substrates and biological functions are still largely unclear. Using proteome microarray technology, potential substrates of Escherichia coli CobB were screened and nine proteins were identified, including N-hydroxyarylamine O-acetyltransferase (NhoA). In vitro acetylation/deacetylation of NhoA was verified by western blotting and mass spectrometry, and two acetylated lysine residues were identified. Site-specific mutagenesis experiments showed that mutation of each acetylated lysine decreased the acetylation level of NhoA in vitro. Further analysis showed that variant NhoA proteins carrying substitutions at the two acetylated lysine residues are involved in both the O-acetyltransferase and N-acetyltransferase activity of NhoA. Structural analyses were also performed to explore the effects of the acetylated lysine residues on the activity of NhoA. These results suggest that reversible acetylation may play a role in the activity of Escherichia coli NhoA.

Computer-assisted virtual technology in intracapsular condylar fracture with two resorbable long-screws

Our aim was to fix intracapsular condylar fractures (ICF) with two resorbable long screws using preoperative computer-assisted virtual technology. From February 2008 to July 2011, 19 patients with ICF were treated with two resorbable long screws. Preoperatively we took panoramic radiographs and spiral computed tomography (CT). Depending on their digital imaging and communications in medicine (DICOM) data, the dislocated condylar segments were restored using the SimPlant Pro™ software, version 11.04. The mean (SD) widths of the condylar head and neck from lateral to medial were 19.01 (1.28)mm and 13.84 (1.13)mm, respectively. In all patients, the mandibles and the ICF seen intraoperatively corresponded with the preoperative three-dimensional and virtual reposition. All patients were followed up for 6-46 months (mean 21). Occlusion and mouth opening had been restored completely in all but one patient, and absolute anatomical reduction was also achieved in most cases. Computer-assisted virtual technology plays an important part in the diagnosis of ICF, as well as in its preoperative design. Fixation with only two resorbable long screws is an effective and reliable method for fixing ICF.

Preoperative three-dimensional reconstruction in vascularized fibular flap transfer

OBJECTIVE

The objective of this study was to investigate the added value of preoperative computerized tomographic angiography (CTA) and three-dimensional reconstruction of the lower limb in vascularized fibular flap transfer.

METHODS

Eighteen patients who underwent mandibular or maxillary reconstruction with a vascularized fibular flap were studied retrospectively by image analysis. The original DICOM data of preoperative CTA were analysed and applied to the reconstruction of the lower limb using SimPlant Pro software (version 11.04).

RESULTS

The course of the peroneal artery in 17 patients was the same except for one patient. The peroneal artery originates from the posterior tibial artery. The original external diameters of the peroneal artery were 2.99 ± 0.64 mm. The perpendicular lengths from fibular head to the origin of the peroneal artery and to the fibular perforator vessel were 42.88 ± 8.84 mm and 174.55 ± 25.62 mm, respectively.

CONCLUSION

The course of peroneal artery was relatively invariable, its original external diameter was thick. Preoperative CTA and three-dimensional reconstruction of the lower limb, which are noninvasive, accurate and direct-viewing methods, play an important, preoperative role in vascularized fibular flap transfer for lower limb vascular assessment.

Comparative analysis of mycobacterial NADH pyrophosphatase isoforms reveals a novel mechanism for isoniazid and ethionamide inactivation

NADH pyrophosphatase (NudC) catalyses the hydrolysis of NAD(H) to AMP and NMN(H) [nicotinamide mononucleotide (reduced form)]. NudC multiple sequence alignment reveals that homologues from most Mycobacterium tuberculosis isolates, but not other mycobacterial species, have a polymorphism at the highly conserved residue 237. To elucidate the functional significance of this polymorphism, comparative analyses were performed using representative NudC isoforms from M. tuberculosis H37Rv (NudC_Rv) and M. bovis BCG (NudC_BCG). Biochemical analysis showed that the P237Q polymorphism prevents dimer formation, and results in a loss of enzymatic activity. Importantly, NudC_BCG was found to degrade the active forms of isoniazid (INH), INH-NAD and ethionamide (ETH), ETH-NAD. Consequently, overexpression of NudC_BCG in Mycobacterium smegmatis mc²155 and M. bovis BCG resulted in a high level of resistance to both INH and ETH. Further genetic studies showed that deletion of the nudC gene in M. smegmatis mc²155 and M. bovis BCG resulted in increased susceptibility to INH and ETH. Moreover, inactivation of NudC in both strains caused a defect in drug tolerance phenotype for both drugs in exposure assays. Taken together, these data suggest that mycobacterial NudC plays an important role in the inactivation of INH and ETH.

Quantum dot-aptamer nanoprobes for recognizing and labeling influenza A virus particles

The fluorescence labeling of viruses is a useful technology for virus detection and imaging. By combining the excellent fluorescence properties of quantum dots (QDs) with the high affinity and specificity of aptamers, we constructed a QD-aptamer probe. The aptamer A22, against the hemagglutinin of influenza A virus, was linked to QDs, producing the QD-A22 probe. Fluorescence imaging and transmission electron microscopy showed that the QD-A22 probe could specifically recognize and label influenza A virus particles. This QD labeling technique provides a new strategy for labeling virus particles for virus detection and imaging.

Characterization of a monomeric heat-labile classical alkaline phosphatase from Anabaena sp. PCC7120

Alkaline phosphatases (APs), known inducible enzymes of the Pho regulon and poorly characterized in cyanobacteria, hydrolyze phosphomonoesters to produce inorganic phosphate (P(i)) during P(i) starvation. In this study, two predicted alkaline phosphatase genes in the genome of Anabaena sp. PCC 7120, all2843 and alr5291, were apparently induced during P(i) starvation. Sequence analysis showed that alr5291 encodes a protein that is an atypical alkaline phosphatase like other cyanobacteria PhoAs, but the protein encoded by all2843 is very similar to the classical PhoAs, such as Escherichia coli alkaline phosphatase (EAP). To date, there have been no reports about classical phoA in cyanobacterial genomes. The alkaline phosphatase AP(A), coded by all2843, is characterized as a metalloenzyme containing Mg2+ and Zn2+ with molar ratio of 1 : 2. Site-directed mutagenesis analysis indicated that, though the active center of AP(A) is highly conserved in comparison with EAP, differences do exist between AP(A) and EAP in metal ion coordination. Besides, biochemical analysis revealed that AP(A) is a monomeric protein and inactivated rapidly at 50 degrees C. These results suggest that AP(A) is the first monomeric heat-labile classical PhoA found in cyanobacteria.

Viral coat proteins as flexible nano-building-blocks for nanoparticle encapsulation

Viral capsid-nanoparticle hybrid structures offer new opportunities for nanobiotechnology. We previously generated virus-based nanoparticles (VNPs) of simian virus 40 (SV40) containing quantum dots (QDs) for cellular imaging. However, as an interesting issue of nano-bio interfaces, the mechanism of nanoparticle (NP) encapsulation by viral coat proteins remains unclear. Here, four kinds of QDs with the same core/shell but different surface coatings are tested for encapsulation. All the QDs can be encapsulated efficiently and there is no correlation between the encapsulation efficiency and the surface charge of the QDs. All the SV40 VNPs encapsulating differently modified QDs show similar structures, fluorescence properties, and activity in entering living cells. These results demonstrate the flexibility of SV40 major capsid protein VP1 in NP encapsulation and provide new clues to the mechanism of NP packaging by viral shells.

CobB regulates Escherichia coli chemotaxis by deacetylating the response regulator CheY

The silent information regulator (Sir2) family proteins are NAD+-dependent deacetylases. Although a few substrates have been identified, functions of the bacteria Sir2-like protein (CobB) still remain unclear. Here the role of CobB on Escherichia coli chemotaxis was investigated. We used Western blotting and mass spectrometry to show that the response regulator CheY is a substrate of CobB. Surface plasmon resonance (SPR) indicated that acetylation affects the interaction between CheY and the flagellar switch protein FliM. The presence of intact flagella in knockout strains DeltacobB, Deltaacs, Delta(cobB) Delta(acs), Delta(cheA) Delta(cheZ), Delta(cheA) Delta(cheZ) Delta(cobB) and Delta(cheA) Delta(cheZ) Delta(acs) was confirmed by electron microscopy. Genetic analysis of these knockout strains showed that: (i) the DeltacobB mutant exhibited reduced responses to chemotactic stimuli in chemotactic assays, whereas the Deltaacs mutant was indistinguishable from the parental strain, (ii) CheY from the DeltacobB mutant showed a higher level of acetylation, indicating that CobB can mediate the deacetylation of CheY in vivo, and (iii) deletion of cobB reversed the phenotype of Delta(cheA) Delta(cheZ). Our findings suggest that CobB regulates E. coli chemotaxis by deacetylating CheY. Thus a new function of bacterial cobB was identified and also new insights of regulation of bacterial chemotaxis were provided.

Escherichia coli mismatch repair protein MutL interacts with the clamp loader subunits of DNA polymerase III

It has been hypothesized that DNA mismatch repair (MMR) is coupled with DNA replication; however, the involvement of DNA polymerase III subunits in bacterial DNA MMR has not been clearly elucidated. In an effort to better understand the relationship between these 2 systems, the potential interactions between the Escherichia coli MMR protein and the clamp loader subunits of E. coli DNA polymerase III were analyzed by far western blotting and then confirmed and characterized by surface plasmon resonance (SPR) imaging. The results showed that the MMR key protein MutL could directly interact with both the individual subunits delta, delta', and gamma and the complex of these subunits (clamp loader). Kinetic parameters revealed that the interactions are strong and stable, suggesting that MutL might be involved in the recruitment of the clamp loader during the resynthesis step in MMR. The interactions between MutL, the delta and gamma subunits, and the clamp loader were observed to be modulated by ATP. Deletion analysis demonstrated that both the N-terminal residues (1-293) and C-terminal residues (556-613) of MutL are required for interacting with the subunits delta and delta'. Based on these findings and the available information, the network of interactions between the MMR components and the DNA polymerase III subunits was established; this network provides strong evidence to support the notion that DNA replication and MMR are highly associated with each other.

The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA)

As only the type II topoisomerase is capable of introducing negative supercoiling, DNA gyrase is involved in crucial cellular processes. Although the other domains of DNA gyrase are better understood, the mechanism of DNA binding by the C-terminal domain of the DNA gyrase A subunit (GyrA-CTD) is less clear. Here, we investigated the DNA-binding sites in the GyrA-CTD of Mycobacterium tuberculosis gyrase through site-directed mutagenesis. The results show that Y577, R691 and R745 are among the key DNA-binding residues in M.tuberculosis GyrA-CTD, and that the third blade of the GyrA-CTD is the main DNA-binding region in M.tuberculosis DNA gyrase. The substitutions of Y577A, D669A, R691A, R745A and G729W led to the loss of supercoiling and relaxation activities, although they had a little effect on the drug-dependent DNA cleavage and decatenation activities, and had no effect on the ATPase activity. Taken together, these results showed that the GyrA-CTD is essential to DNA gyrase of M.tuberculosis, and promote the idea that the M.tuberculosis GyrA-CTD is a new potential target for drug design. It is the first time that the DNA-binding sites in GyrA-CTD have been identified.

Construction and characterization of different MutS fusion proteins as recognition elements of DNA chip for detection of DNA mutations

Three MutS fusion systems were designed as the mutation recognition and signal elements of DNA chips for detection of DNA mutations. The expression vectors containing the encoding sequences of three recombinant proteins, Trx-His6-GFP-(Ser-Gly)6-MutS (THGLM), Trx-His6-(Ser-Gly)6-Strep tagII-(Ser-Gly)6-MutS (THLSLM) and Trx-His6-(Ser-Gly)6-MutS (THLM), were constructed by gene slicing in vitro. THGLM, THLSLM and THLM were then expressed in Escherichia coli AD494(DE3), respectively. SDS-PAGE analysis revealed that each of the expected proteins was approximately 30% of the total bacterial proteins. The recombinant proteins were purified to the purity over 90% by immobilized metal (Co2+) chelation affinity chromatography. Bioactivity assay indicated that three fusion proteins retained the mismatch-binding activity and the functions of other fusion partners. DNA chips arrayed both mismatched and unpaired DNA oligonucleotides as well as rpoB gene from Mycobacterium tuberculosis were prepared. THGLM, THLSLM and THLM that was labeled with Fluorolinktrade mark Cy3 reactive dye, were then used as both mutation recognition and labeling elements of DNA chips. The resulting DNA chips were used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides and single base mutation in rpoB gene of M. tuberculosis that is resistant to rifamycin.

Multiplex detection of mutations in clinical isolates of rifampin-resistant Mycobacterium tuberculosis by short oligonucleotide ligation assay on DNA chips

A new approach, short-oligonucleotide-ligation assay on DNA chip (SOLAC), is developed to detect mutations in rifampin-resistant Mycobacterium tuberculosis. The method needs only four common probes to detect 15 mutational variants of the rpoB gene within 12 h. Fifty-five rifampin-resistant M. tuberculosis isolates were analyzed, resulting in 87.3% accuracy and 83.6% concordance relative to DNA sequencing.

Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates.

A MutS-based protein chip for detection of DNA mutations

This paper describes a new protein chip method for detection of single-base mismatches and unpaired bases of DNA, using a genetic fusion molecular system Trx-His6-Linker peptide-Strep-tagII-Linker peptide-MutS (THLSLM). The THLSLM coding sequence was constructed by attaching Strep-tag II and mutS gene to pET32a (+) sequentially with insertion of a linker peptide coding sequence before and behind Strep-tagII gene, respectively. THLSLM was expressed in E. coli AD494 (DE3) and purified using Ni(2+)-chelation affinity resin. THLSLM retained both mismatch recognition activity and streptavidin binding affinity. THLSLM was then immobilized on the chip matrix coated with streptavidin through the Strep-tag II-streptavidin binding reaction. The resulting protein chip was used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides, as well as a single-base mutation in rpoB gene from Mycobacterium tuberculosis, with high specificity. The method could potentially serve as a platform to develop the high-throughput technology for screening and analysis of genetic mutations.

A visual DNA chip for simultaneous detection of hepatitis B virus, hepatitis C virus and human immunodeficiency virus type-1

For the simultaneously visual detection of hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus type-1 (HIV-1), a qualitative DNA chip method, combining multiplex and nested polymerase chain reaction (PCR) with arrayed anchored primer PCR and a biotin-avidin alkaline phosphatase (Av-AP) indicator system, was developed. After pretreatment of infected blood samples and reverse transcription of the RNA virus genome, PCR was performed in a single tube by using the outer primer pairs. Second round nested multiplex PCR was performed on the DNA chip, on which the primers array had already been prepared. During the arrayed anchored multiplex PCR, 5[N-(N-biotinylaminocaproyl)-epsilon-3-aminoallyl]-2-deoxy-uridine-5-triphosphate (biotin-11-dUTP) was incorporated into the extended DNA chains in order to bind avidin alkaline phosphatase via avidin and biotin. To produce purple precipitates on the chips, the enzyme substrate 5-bromo-4-chloro-3-indolyl phosphate (BCIP) was used in conjunction with the enhancer, nitro blue tetrazolium (NBT). Blood samples containing the three viruses were tested using this DNA chip and about 1 pg of specific viral DNA fragments were detected on the chip wells after nested PCR.

Improvement of Homogeneity of Analytical Biodevices by Gene Manipulation

Homogeneity is proposed for evaluation of the quality of analytical biodevices, such as biosensors and biochips. As a demonstration, glucose oxidase (GOx) was modified at its C-terminal with a linker peptide with a cysteine residue at the end. The fusion structure (GOx-linker-cysteine) enables the enzyme to immobilize on gold surfaces with a Cys-S-Au bond or to immobilize on a silanized glass surface via disulfide chemistry. With this fusion structure, the enzyme can be anchored onto the substrate with well-controlled orientation, thus forming a homogeneous biological layer on biodevices. The linker peptide between GOx and the cysteine acts as a spacer to reduce the steric hindrance caused by the bulky body of the enzyme. Biochemistry experiments showed that this genetically modified glucose oxidase (shortened to GOxm) retained most of its catalytic characteristics, with K(m) and K(cat) similar to those of the wild-type GOx. Electrochemistry experiments showed that GOxm-modified electrode gave higher and more stable current responses than the electrode modified with GOx which has no free -SH on its surface. The coefficients of variation (used for evaluation of the interchangeability of the enzyme device from the same batch preparation) were 9.5% for the GOxm gold electrode and 20.0% for the GOx gold electrode and the GOxm oxygen electrode. The relative errors (used for evaluation of the precision of the individual enzyme device) were 2.9% for the GOxm gold electrode, 12.0% for the GOx gold electrode, and 11.2% for the GOxm oxygen electrode. Atomic force microscopy images revealed that GOxm formed a self-assembled monolayer in a hexagonal-like lattice packing arrangement on the gold surface, while GOx formed multilayer assembling or aggregated particles. The homogeneity of the protein chips, the GOxm array that was prepared through -S-S- formation, and the GOx array that was prepared through nonspecific adsorption was evaluated. The coefficients of variation, calculated with the signal level of all dots, were 5.4% for the GOxm array and 81.8% for the GOx array. All experimental results pointed to the fact that the homogeneity of the analytical biodevices could be considerably improved by using the proposed method.

[High expression and identification of DNA mismatch repair gene mutS in Escherichia coli]

DNA mismatch repair gene mutS (2.56 kb) was PCR modified and cloned into a secretive prokaryotic expression vector pET32a (+) which carries a N-terminal His.tag + and thioredoxin sequence. MutS protein was expressed with high level after IPTG induction using the strain E. coli AD494(DE3). SDS-PAGE revealed that the expected protein with a molecular weight of 108 kD which is about 35% of the total bacterial proteins is almost soluble. The expected protein was purified directly by immobilized metal (Ni2+) chelation affinity chromatography and the purity is over 90%. MutS protein activity verified using mismatch DNA showed that the expression product can recognize and bind to base-pair mismatch specifically.

[Care and analysis of cerebral hemorrhage]

The purpose of this study was to investigate the rule of incidence time of cerebral hemorrhage in order to provide nursing care efficiently. A circular distribution method was used to analyse the incidence time of cerebral hemorrhage patients. The result showed that tendency of month was March and time was 14:00. Further study will help the nursing implication in taking care of cerebral hemorrhage patients.

The effect of Isoptin SR on blood pressure, heart function and hypertrophy of left ventricle of hypertensive patients

Isoptin SR was used in 65 essential hypertensive patients. 240mg Isoptin SR (German Knoll Pharmaceutical company) per day was used in group A (35 cases) for 6 weeks, and in group B (30 cases) for 24 weeks, BP in group A and B decreased obviously in the first and second week after treatment. Marked effective rate and total effective rate were 65.7% and 74.3% respectively in group A, and 70.0% and 83.3% in group B. There were no significant changes of HR in group A before and after treatment while there was a decrease of HR in group B (P < 0.001). Left atrium (LA) decreased after 6 weeks in group A with an obvious increase of E/A ratio. There was significant decrease in LA, increase in E/A ratio, regression of IVS, LVPW and LVMI, but no changes in SV, CO, LVEF after 24 weeks of treatment of Isoptin SR in group B. E/A ratio was very sensitive and occurred earliest both in group A and group B. Side effects such as headache, dizziness, constipation, insomnia, peripheral oedema, sinus bradycardia occurred mainly in the first week of treatment. These symptoms disappeared gradually in the course of continued administration of Isoptin SR.

Restoration of gallbladder contractility after withdrawal of long-term octreotide therapy in acromegalic patients

We sought to examine how the discontinuation of octreotide in long-term octreotide-treated acromegalic patients affects the well-documented side-effect of cholelithiasis. In 14 acromegalic patients, serum growth hormone levels, insulin-like growth factor I levels and percentage of relative gallbladder contractility were measured prior to and after the discontinuation of octreotide. Compared to pretreatment values, the basal growth hormone and 5-h growth hormone profiles were 36% and 24%, and 60% and 56% at the end of 1 and 2 weeks, respectively. Octreotide was found to be eliminated completely from the serum within 3 days after its withdrawal. In all of six patients who did not develop gallstones, the percentage relative gallbladder contractility normalized within 1 week. In eight patients who developed gallstones, four of them had restoration of normal contractility within 2 weeks. Our results show that upon withdrawal of octreotide, gallbladder contractility returns to normal while growth hormone suppression persists for a longer period of time. Therefore, discontinuation of octreotide therapy may allow for the clearance of stagnated bile and hence decrease the incidence of cholelithiasis in acromegalic patients receiving long-term therapy.