Fast optimal genome tiling with applications to microarray design and homology search.

In this paper, we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size-bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a number of computational biology applications such as selecting genomic DNA fragments for PCR-based amplicon microarrays and performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we first discuss the solution to a basic online interval maximum problem via a sliding-window approach and show how to use this solution in a nontrivial manner for many of the tiling problems introduced. We also discuss NP-hardness results and approximation algorithms for generalizing our basic tiling problem to higher dimensions. Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported.     

Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM,pharmacophore and docking model

Abstract

Cyclin-dependent kinase 2 (CDK2) is the family of Ser/Thr protein kinases that has emerged as a highly selective with low toxic cancer therapy target. A multistage virtual screening method combined by SVM, protein-ligand interaction fingerprints (PLIF) pharmacophore and docking was utilised for screening the CDK2 inhibitors. The evaluation of the validation set indicated that this method can be used to screen large chemical databases because it has a high hit-rate and enrichment factor (80.1% and 332.83 respectively). Six compounds were screened out from NCI, Enamine and Pubchem database. After molecular dynamics and binding free energy calculation, two compounds had great potential as novel CDK2 inhibitors and they also showed selective inhibition against CDK2 in the kinase activity assay.     

菌根真菌对白及种子萌发和幼苗生根的作用

自然条件下,兰科植物需要依赖菌根真菌获得营养才能萌发。本研究对白及根和原球茎中分离的4株菌根真菌（WQ17-33、WQ17-43、JST-3和SL15-7）进行分子鉴定,并评价光照和黑暗条件下不同菌株促白及种子萌发和幼苗生根的效果。结果表明,4个菌株分别隶属于鬼伞属Coprinus、胶膜菌属Tulasnella、腊壳菌属Sebacina和Serendipita。在种子萌发前期（未形成叶子）进行暗培养较光照对菌株JST-13和SL15-7处理组原球茎阶段萌发具有显著的促进作用。不同菌株共生萌发效果不同,菌株SL15-7较其他处理原球茎和幼苗发育阶段的萌发率高。菌株JST-13和SL15-7处理组形成的幼苗较其他处理组强壮,定殖的菌丝团也较多,其幼苗生根效果也较对照组好。该研究表明白及可与多种不同类群的菌根真菌菌株形成共生关系,这些真菌在促进白及种子萌发和生根能力方面存在差异。     

Hepatocyte growth factor stimulates the growth and activates mitogen-activated protein kinase in human hepatoma cells

Hepatocyte growth factor (HGF) is a potent mitogen for hepatocytes and various epithelial cells. Unexpectedly, it has been reported to inhibit the growth of hepatoma cells in vitro. To clarify this phenomenon, we examined the effects of recombinant baculovirus-expressed HGF on the growth of 6 human hepatoma cell lines. The growth of Hep3B and HepG2 cells was markedly stimulated to 1.8- and 1.7-fold, respectively, PLC/PRF/5 to 1.4-fold, and SK-Hep-1 to 1.2-fold in a dose-dependent manner under HGF concentrations below 20 ng/ml. Neither HuH-7 nor HCC36 were affected. None of these cells were inhibited. All these cells expressed c-Met, the membrane receptor for HGF, and their c-Met would be activated to be phosphorylated upon addition of HGF. They also contained the ERK2 subgroup of mitogen-activated protein kinases (MAPKs). When HGF was added, their ERK2 would also be phosphorylated. The extent of ERK2 phosphorylation was partially correlated to their growth response to HGF. In conclusion, HGF could stimulate the growth of certain human hepatoma cells, probably through activation of c-Met and MAPKs.     

Polyomavirus BK-encoded microRNA suppresses autoregulation of viral replication

Polyomavirus BK (BKV) infection is an important cause of renal allograft failure. Viral microRNAs are known to play a crucial role in viral replication. This study investigated the expression of BKV-encoded microRNAs (miR-B1) in patients with polyomavirus-associated nephropathy (PVAN) and their role in viral replication. Following BKV infection in renal proximal tubular cells, the 3p and 5p miR-B1 levels were significantly increased. Cells transfected with the vector containing the miR-B1 precursor (the miR-B1 vector) showed a significant increase in expression of 3p and 5p miR-B1 and decrease in luciferase activity of a reporter containing the 3p and 5p miR-B1 binding sites, compared to cells transfected with the miR-B1-mutated vector. Transfection of the miR-B1 expression vector or the 3p and 5p miR-B1 oligonucleotides inhibited expression of TAg. TAg-enhanced promoter activity and BKV replication were inhibited by miR-B1. In contrast, inhibition of miR-B1 expression by addition of miR-B1 antagomirs or silencing of Dicer upregulated the expression of TAg and VP1 proteins in BKV-infected cells. Importantly, patients with PVAN had significantly higher levels of 3p and 5p miR-B1 compared to renal transplant patients without PVAN. In conclusion, we demonstrated that (1) miR-B1 expression was upregulated during BKV infection and (2) miR-B1 suppressed TAg-mediated autoregulation of BKV replication. Use of miR-B1 can be evaluated as a potential treatment strategy against BKV infection.     

Moxifloxacin-containing triple therapy versus bismuth-containing quadruple therapy for second-line treatment of Helicobacter pylori infection: a meta-analysis

Background: Moxifloxacin‐containing triple therapy has been suggested as an alternative second‐line therapy for Helicobacter pylori infection. Aims: To systematically review the efficacy and tolerance of moxifloxacin‐containing triple therapy in second‐line H. pylori eradication, and to conduct a meta‐analysis of studies comparing this regimen with bismuth‐containing quadruple therapy. Materials and Methods: Electronic databases including Medline, Embase, Cochrane controlled trials register, Web of Science, PubMed, Chinese Biomedical Literature Database (updated to December 2010), and manual searches were conducted. A meta‐analysis of all randomized controlled trials (RCTs) comparing moxifloxacin‐containing triple therapy to bismuth‐containing quadruple therapy in the second‐line treatment of H. pylori infection was performed. Results: Seven RCTs including 787 patients were assessed. The meta‐analysis showed that the eradication rate in the moxifloxacin group was significantly higher than that in the quadruple therapy group (74.9 vs 61.4%, OR 1.89, 95% CI: 1.38–2.58, p < .0001); besides, the rates of side effects and discontinuing therapy because of side effects in the moxifloxacin group were significantly lower than those in the quadruple therapy group (side effects: 10.1 vs 27.8%, OR 0.27, 95% CI: 0.18–0.41, p < .00001; discontinuing therapy because of side effects: 1.4 vs 8.2%, OR 0.18, 95% CI: 0.08–0.40, p < .0001). These results were constant in the sensitivity analyses. Conclusion: Moxifloxacin‐containing triple regimen is more effective and better tolerated than the bismuth‐containing quadruple therapy in the second‐line treatment of H. pylori infection.     

Elastolytic Mechanism of a Novel M23 Metalloprotease Pseudoalterin from Deep-sea Pseudoalteromonas sp. CF6-2: CLEAVING NOT ONLY GLYCYL BONDS IN THE HYDROPHOBIC REGIONS BUT ALSO PEPTIDE BONDS IN THE HYDROPHILIC REGIONS INVOLVED IN CROSS-LINKING*

Elastin is a common insoluble protein that is abundant in marine vertebrates, and for this reason its degradation is important for the recycling of marine nitrogen. It is still unclear how marine elastin is degraded because of the limited study of marine elastases. Here, a novel protease belonging to the M23A subfamily, secreted by Pseudoalteromonas sp. CF6-2 from deep-sea sediment, was purified and characterized, and its elastolytic mechanism was studied. This protease, named pseudoalterin, has low identities (<40%) to the known M23 proteases. Pseudoalterin has a narrow specificity but high activity toward elastin. Analysis of the cleavage sites of pseudoalterin on elastin showed that pseudoalterin cleaves the glycyl bonds in hydrophobic regions and the peptide bonds Ala–Ala, Ala–Lys, and Lys–Ala involved in cross-linking. Two peptic derivatives of desmosine, desmosine-Ala-Ala and desmosine-Ala-Ala-Ala, were detected in the elastin hydrolysate, indicating that pseudoalterin can dissociate cross-linked elastin. These results reveal a new elastolytic mechanism of the M23 protease pseudoalterin, which is different from the reported mechanism where the M23 proteases only cleave glycyl bonds in elastin. Genome analysis suggests that M23 proteases may be popular in deep-sea sediments, implying their important role in elastin degradation. An elastin degradation model of pseudoalterin was proposed, based on these results and scanning electron microscopic analysis of the degradation by pseudoalterin of bovine elastin and cross-linked recombinant tropoelastin. Our results shed light on the mechanism of elastin degradation in deep-sea sediment.     

Acute kidney injury biomarkers for patients in a coronary care unit: a prospective cohort study

Background

Renal dysfunction is an established predictor of all-cause mortality in intensive care units. This study analyzed the outcomes of coronary care unit (CCU) patients and evaluated several biomarkers of acute kidney injury (AKI), including neutrophil gelatinase-associated lipocalin (NGAL), interleukin-18 (IL-18) and cystatin C (CysC) on the first day of CCU admission.

Methodology/Principal Findings

Serum and urinary samples collected from 150 patients in the coronary care unit of a tertiary care university hospital between September 2009 and August 2010 were tested for NGAL, IL-18 and CysC. Prospective demographic, clinical and laboratory data were evaluated as predictors of survival in this patient group. The most common cause of CCU admission was acute myocardial infarction (80%). According to Acute Kidney Injury Network criteria, 28.7% (43/150) of CCU patients had AKI of varying severity. Cumulative survival rates at 6-month follow-up following hospital discharge differed significantly (p<0.05) between patients with AKI versus those without AKI. For predicting AKI, serum CysC displayed an excellent areas under the receiver operating characteristic curve (AUROC) (0.895±0.031, p<0.001). The overall 180-day survival rate was 88.7% (133/150). Multiple Cox logistic regression hazard analysis revealed that urinary NGAL, serum IL-18, Acute Physiology, Age and Chronic Health Evaluation II (APACHE II) and sodium on CCU admission day one were independent risk factors for 6-month mortality. In terms of 6-month mortality, urinary NGAL had the best discriminatory power, the best Youden index, and the highest overall correctness of prediction.

Conclusions

Our data showed that serum CysC has the best discriminative power for predicting AKI in CCU patients. However, urinary NGAL and serum IL-18 are associated with short-term mortality in these critically ill patients.     

Risk Models and Scoring Systems for Predicting the Prognosis in Critically Ill Cirrhotic Patients with Acute Kidney Injury: A Prospective Validation Study

Background

Cirrhotic patients with acute kidney injury (AKI) admitted to intensive care units (ICUs) show extremely high mortality rates. We have proposed the MBRS scoring system, which can be used for assessing patients on the day of admission to the ICU; this new system involves determination of mean arterial pressure (MAP) and bilirubin level and assessment of respiratory failure and sepsis. We had used this scoring system to analyze the prognosis of ICU cirrhotic patients with AKI in 2008, and the current study was an external validation of this scoring system.

Methods

A total of 190 cirrhotic patients with AKI were admitted to the ICU between March 2008 and February 2011. We prospectively analyzed and recorded the data for 31 demographic parameters and some clinical characteristic variables on day 1 of admission to the ICU; these variables were considered as predictors of mortality.

Results

The overall in-hospital mortality rate was 73.2% (139/190), and the 6-month mortality rate was 83.2% (158/190). Hepatitis B viral infection (43%) was observed to be the cause of liver disease in most of the patients. Multiple logistic regression analysis indicated that the MBRS and Acute Physiology and Chronic Health Evaluation III (ACPACHE III) scores determined on the first day of admission to the ICU were independent predictors of in-hospital mortality in patients. In the analysis of the area under the receiver operating characteristic (AUROC) curves, the MBRS scores showed good discrimination (AUROC: 0.863±0.032, p<0.001) in predicting in-hospital mortality.

Conclusion

On the basis of the results of this external validation, we conclude that the MBRS scoring system is a reproducible, simple, easy-to-apply evaluation tool that can increase the prediction accuracy of short-term prognosis in critically ill cirrhotic patients with AKI.     

A combinatorial toolbox for protein sequence design and landscape analysis in the grand canonical model.

In modern biology, one of the most important research problems is to understand how protein sequences fold into their native 3D structures. To investigate this problem at a high level, one wishes to analyze the protein landscapes, i.e., the structures of the space of all protein sequences and their native 3D structures. Perhaps the most basic computational problem at this level is to take a target 3D structure as input and design a fittest protein sequence with respect to one or more fitness functions of the target 3D structure. We develop a toolbox of combinatorial techniques for protein landscape analysis in the Grand Canonical model of Sun, Brem, Chan, and Dill. The toolbox is based on linear programming, network flow, and a linear-size representation of all minimum cuts of a network. It not only substantially expands the network flow technique for protein sequence design in Kleinberg's seminal work but also is applicable to a considerably broader collection of computational problems than those considered by Kleinberg. We have used this toolbox to obtain a number of efficient algorithms and hardness results. We have further used the algorithms to analyze 3D structures drawn from the Protein Data Bank and have discovered some novel relationships between such native 3D structures and the Grand Canonical model.