Development of a novel recombinant strain Zygosacharomyces rouxii JL2011 for 1,3-propanediol production from glucose

1,3-propanediol (1,3-PDO) is one of the most important industrial chemicals due to its highly desired properties and its wide applications as a key component of the emerging polymer industry. Biotechnology route has been one of the most interesting methods for 1,3-PDO production, whereas, the dha genes were essential to 1,3-PDO biosynthesis. In this study, we cloned and placed the dha cassettes under the control of a glyceraldehyde 3-phosphate dehydrogenase gene promoter pGAP and homologous ZrFPS1 gene promoter pZrfps1; these two promoters were further integrated into the chromosome of Z. rouxii JL2011 to generate recombinant strain JL2011-GZ and JL2011-ZZ, respectively. The results showed that the two strains could produce 1,3-PDO from glucose with a final yield of 6.9 and 10.3 g/l, respectively. The engineered strain JL2011-ZZ showed a 2.3- and 1.5-fold increase in the specific activities and final concentration of 1,3-PDO, respectively, with respect to JL2011-GZ. Batch fermentation with aerobic/micro-aerobic combined strategy of JL2011-ZZ resulted a titer of 17.1 g/l and a yield from glucose of 8.6 %. These results demonstrated that JL2011-ZZ would be a potential strain for 1,3-PDO production from glucose.     

Coaxial Microincision Cataract Surgery versus Standard Coaxial Small-Incision Cataract Surgery: A Meta-Analysis of Randomized Controlled Trials

Background

We conducted this meta-analysis to compare the outcomes of coaxial microincision cataract surgery (C-MICS) and standard coaxial small incision cataract surgery (C-SICS).

Methods

The outcomes of randomized controlled trials (RCTs) reporting C-MICS and C-SICS were collected from PubMed, Web of Science, and The Cochrane Library in May 2015. The final meta-analysis was conducted on the following intraoperative and postoperative outcomes: ultrasound time (UST), effective phacoemulsification time (EPT), balanced salt solution use (BSS use), cumulative dissipated energy (CDE), mean surgery time, endothelial cell loss percentage (ECL%), best corrected visual acuity (BCVA), increased central corneal thickness (CCT), laser flare photometry values and surgically induced astigmatism (SIA).

Results

A total of 15 RCTs, involving 1136 eyes, were included in the final meta-analysis. No significant between-group differences were detected in EPT, BSS use, CDE, BCVA, laser flare photometry values or increased CCT. However, the C-MICS group showed less SIA (at postoperative day 7: p<0.01; at postoperative day 30 or more: p<0.01) and greater ECL% (at postoperative day 60 or more: p<0.01), whereas the C-SICS group required a shorter UST (p<0.01).

Conclusions

The present meta-analysis suggested that the C-MICS technique was more advantageous than C-SICS in terms of SIA, but C-MICS required a longer UST and induced a higher ECL%. Further studies should be done to confirm our results.     

Formation,regeneration, and transformation of protoplasts of Streptomyces diastatochromogenes 1628

Toyocamycin exhibits effective biological activities for use against plant pathogenic fungi thanks to its structural similarity to nucleoside. It has been recognized as a promising agricultural antibiotic utilized in controlling the occurrence of plant diseases. In our previous study, a strain that was isolated was identified and designated as Streptomyces diastatochromogenes whose major secondary metabolite was toyocamycin, but the production was largely limited. Protoplast transformation is a useful technique in the improvement of streptomycete. In this study, we optimized some key factors necessary for protoplast formation, regeneration, and transformation of S. diastatochromogenes. When mycelium was cultivated in CP medium with 1 % glycine, harvested at 48 h old, and then treated with 3 mg lysozyme/mL in P buffer for 1 h, the greatest regeneration frequency (42.5 %) of protoplasts was obtained. By using 1?×?10⁹/mL protoplasts with polyethylene glycol 1000 at a concentration of 30 % (w/v), the best performance of protoplast transformation efficiency was 4.8?×?10³/μg DNA transformants.     

Auto-adaptive Alpha Allocation: A Strategy to Mitigate Risk on Study Assumptions

In some clinical development programs, there are potential biomarkers with promising but uncertain predictive effect, while the probability of success in the overall population cannot be readily dismissed. It is risky to focus only on the overall population, or just the biomarker subpopulation. In 2009, Chen and Beckman proposed a Bayesian decision framework to optimize the type I error rate (alpha) allocation in a Phase III clinical study with possible predictive subset effect. The utilization of internal data in this framework is of particular interest because it provides an opportunity to mitigate the potential risk of misspecified study assumptions using an auto-adaptive strategy. In this paper, we examine this auto-adaptive strategy in detail through extensive numerical case studies and provide guidance on the appropriate use of partial current trial (internal) data in this data-driven optimization framework. We show that internal data can be used to inform the alpha allocation to hypothesis testing in the overall population and the subgroup. The resulting adaptive testing strategy is robust with respect to the uncertainty in the predictive subgroup effect and biomarker prevalence.     

Context shapes: Efficient complementary shape matching for protein-protein docking

We describe an efficient method for partial complementary shape matching for use in rigid protein-protein docking. The local shape features of a protein are represented using boolean data structures called Context Shapes. The relative orientations of the receptor and ligand surfaces are searched using precalculated lookup tables. Energetic quantities are derived from shape complementarity and buried surface area computations, using efficient boolean operations. Preliminary results indicate that our context shapes approach outperforms state-of-the-art geometric shape-based rigid-docking algorithms.     

Degradation of the apical sodium-dependent bile acid transporter by the ubiquitin-proteasome pathway in cholangiocytes

To attenuate injury during cholestasis, adaptive changes in bile acid transporter expression in the liver provide alternative bile acid excretory pathways. Apical sodium-dependent bile acid transporter (ASBT) (SLC10A2), only expressed in the liver on the cholangiocyte apical membrane, is rapidly regulated in response to inflammation and bile acids. Here, we studied the mechanisms controlling ASBT protein levels in cholangiocytes to determine whether ASBT expression is regulated by ubiquitination and disposal through the proteasome. Protein turnover assays demonstrated that ASBT is an unstable and short-lived protein. Treatment with MG-132, a proteasome inhibitor, causes time-dependent increased ASBT levels and increased intracellular accumulation of ASBT. In cells cotransfected with green fluorescent protein-tagged ASBT and hemagglutinin-tagged ubiquitin, we demonstrated coimmunoprecipitation and colocalization of ASBT and ubiquitin. Interleukin-1beta (IL-1beta) induced down-regulation of ASBT is abrogated by a JNK inhibitor and is accompanied by an increase in ASBT polyubiquitin conjugates and a reduced ASBT half-life. In phosphorylation-deficient S335A and T339A mutants, the ASBT half-life is markedly prolonged, IL-1beta-induced ASBT ubiquitination is significantly reduced, and IL-1beta fails to increase ASBT turnover. These results indicate that ASBT undergoes ubiquitin-proteasome degradation under basal conditions and that ASBT proteasome disposal is increased by IL-1beta due to JNK-regulated serine/threonine phosphorylation of ASBT protein at both Ser-335 and Thr-339. These studies are the first report of regulation of a bile acid transporter expression by the ubiquitin-proteasome pathway.     

Role of aspartate 94 in the decay of the peroxide intermediate in the multicopper oxidase Fet3p

Fet3p is a multicopper oxidase that contains four Cu ions: one type 1, one type 2, and a coupled binuclear type 3 site. The type 2 and type 3 centers form a trinuclear cluster that is the active site for O(2) reduction to H(2)O. When the type 1 Cu is depleted (C484S mutation), the reaction of the reduced trinuclear cluster with O(2) generates a peroxide intermediate. Kinetic studies of the decay of the peroxide intermediate suggest that a carboxyl residue (D94 in Fet3p) assists the reductive cleavage of the O-O bond at low pH. Mutations at the D94 residue (D94A, D94N, and D94E) have been studied to evaluate its role in the decay of the peroxide intermediate. Spectroscopic studies show that the D94 mutations affect the geometric and electronic structure of the trinuclear cluster in a way that is consistent with the hydrogen bond connectivity of D94. While the D94E mutation does not affect the initial reaction of the cluster with O(2), the D94A mutation causes larger structural changes that render the trinuclear cluster unreactive toward O(2), demonstrating a structural role for the D94 residue. The decay of the peroxide intermediate is markedly affected by the D94E mutation, confirming the involvement of D94 in this reaction. The D94 residue appears to activate a proton of the type 2 Cu(+)-bound water for participation in the transition state. These studies provide new insight into the role of D94 and proton involvement in the reductive cleavage of the O-O bond.     

Integrated analyses of copy number variations and gene expression in lung adenocarcinoma

Numerous efforts have been made to elucidate the etiology and improve the treatment of lung cancer, but the overall five-year survival rate is still only 15%. Identification of prognostic biomarkers for lung cancer using gene expression microarrays poses a major challenge in that very few overlapping genes have been reported among different studies. To address this issue, we have performed concurrent genome-wide analyses of copy number variation and gene expression to identify genes reproducibly associated with tumorigenesis and survival in non-smoking female lung adenocarcinoma. The genomic landscape of frequent copy number variable regions (CNVRs) in at least 30% of samples was revealed, and their aberration patterns were highly similar to several studies reported previously. Further statistical analysis for genes located in the CNVRs identified 475 genes differentially expressed between tumor and normal tissues (p<10⁻⁵). We demonstrated the reproducibility of these genes in another lung cancer study (p = 0.0034, Fisher''s exact test), and showed the concordance between copy number variations and gene expression changes by elevated Pearson correlation coefficients. Pathway analysis revealed two major dysregulated functions in lung tumorigenesis: survival regulation via AKT signaling and cytoskeleton reorganization. Further validation of these enriched pathways using three independent cohorts demonstrated effective prediction of survival. In conclusion, by integrating gene expression profiles and copy number variations, we identified genes/pathways that may serve as prognostic biomarkers for lung tumorigenesis.