Enhancing production of bio-isoprene using hybrid MVA pathway and isoprene synthase in E. coli

The depleting petroleum reserve, increasingly severe energy crisis, and global climate change are reigniting enthusiasm for seeking sustainable technologies to replace petroleum as a source of fuel and chemicals. In this paper, the efficiency of the MVA pathway on isoprene production has been improved as follows: firstly, in order to increase MVA production, the source of the "upper pathway" which contains HMG-CoA synthase, acetyl-CoA acetyltransferase and HMG-CoA reductase to covert acetyl-CoA into MVA has been changed from Saccharomyces cerevisiae to Enterococcus faecalis; secondly, to further enhance the production of MVA and isoprene, a alanine 110 of the mvaS gene has been mutated to a glycine. The final genetic strain YJM25 containing the optimized MVA pathway and isoprene synthase from Populus alba can accumulate isoprene up to 6.3 g/L after 40 h of fed-batch cultivation.     

A “yellow” laccase with “blue” spectroscopic features,from Sclerotinia sclerotiorum

Reported here are the production, purification and characterization of a laccase from the phytophathogenic fungus Sclerotinia sclerotiorum. This laccase is identified by mass spectrometry with a sequence coverage of 74.9% (458/577 AA) revealing that the protein is identical or highly homologous to a predicted oxidoreductase from this species (A7EM18 in the Uniprot database); the closest homologous protein previously isolated from a fungus is the Melanocarpus albomyces, with only 35% identity. The UV–vis spectral features of this laccase classify it as a “yellow” one. The EPR spectrum nevertheless demonstrates resemblance to blue laccases – including the type 1 center not detectable in UV–vis spectra. The presence of type 3 coppers was proven by fluorescence spectrum and by 330 nm band in UV–vis. The purified laccase has an apparent molecular mass of 70 kDa and appears as a monomer. The values of K_M and k_cat were determined for ABTS, 2,6-dimethoxyphenol, p-phenylenediamine and guaicol and are typical of a laccase. The optimal pH value is around 4 except for ABTS, for which activity is linearly increasing with acidity. The high laccase activity in liquid culture makes S. sclerotiorum a useful source of laccase for practical applications.     

Anti‐Campylobacter and resistance‐modifying activity of Alpinia katsumadai seed extracts

Aims

We tested extracts from Alpinia katsumadai seeds for anti‐Campylobacter activity and investigated the roles of the CmeABC and CmeDEF efflux pumps in Campylobacter resistance to these natural phenolics. Additionally, we investigated an A. katsumadai ethanolic extract (AlpE) and other plant extracts as putative efflux pump inhibitors on Campylobacter isolates and mutants in efflux pump genes.

Methods and Results

AlpE showed antimicrobial activity against sensitive and multidrug‐resistant Campylobacter isolates. CmeB inactivation resulted in the greatest reduction in resistance, while cmeF and cmeR mutations produced only moderate effects on minimal inhibitory concentrations (MICs). The chemical efflux pump inhibitors additionally reduced MICs in isolates and mutants, confirming that active efflux is an important mechanism in resistance to AlpE, with additional contributions of other efflux systems. A notable decrease in resistance to tested antimicrobials in the presence of subinhibitory concentrations of AlpE confirms its modifying activity in Campylobacter spp.

Conclusions

AlpE is important anti‐Campylobacter source of antimicrobial compounds with resistance‐modifying activity. At least two of the efflux systems are involved in the resistance to A. katsumadai antimicrobial seed extracts.

Significance and Impact of the Study

This is the first report of antimicrobial and resistance‐modifying activity of AlpE from A. katsumadai seeds, demonstrating its potential in the control of Campylobacter in the food chain.     

OCRL1 Modulates Cilia Length in Renal Epithelial Cells

Lowe syndrome is an X-linked disorder characterized by cataracts at birth, mental retardation and progressive renal malfunction that results from loss of function of the OCRL1 (oculocerebrorenal syndrome of Lowe) protein. OCRL1 is a lipid phosphatase that converts phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 4-phosphate. The renal pathogenesis of Lowe syndrome patients has been suggested to result from alterations in membrane trafficking, but this cannot fully explain the disease progression. We found that knockdown of OCRL1 in zebrafish caused developmental defects consistent with disruption of ciliary function, including body axis curvature, pericardial edema, hydrocephaly and impaired renal clearance. In addition, cilia in the proximal tubule of the zebrafish pronephric kidney were longer in ocrl morphant embryos. We also found that knockdown of OCRL1 in polarized renal epithelial cells caused elongation of the primary cilium and disrupted formation of cysts in three-dimensional cultures. Calcium release in response to ATP was blunted in OCRL1 knockdown cells, suggesting changes in signaling that could lead to altered cell function. Our results suggest a new role for OCRL1 in renal epithelial cell function that could contribute to the pathogenesis of Lowe syndrome.     

The functional significance of E-β-Farnesene: Does it influence the populations of aphid natural enemies in the fields?

Aphids cause much damage to Chinese cabbage in northern China. Over reliance on pesticides have large environmental and human health costs that compel researchers to seek alternative management tactics for aphid control. The component of aphid alarm pheromone, E-β-Farnesene (EβF), extracted from Matricaria chamomilla L., which attracts natural enemies in the laboratory, may have significant implications for the design of cabbage aphid control strategies. The purpose of this paper is to understand the effects of EβF on natural enemies to cabbage aphid control in Chinese cabbage fields. Ladybeetles on Chinese cabbage leaves in EβF released plots and Aphidiidae in EβF released yellow traps were significantly higher than those of in controls. No significant differences were detected in the interactions of different treatments and the two years for all natural enemies. More important, lower aphid densities were found in EβF released plots. Our results suggested that the EβF extracted from M. chamomilla L. could attract natural enemies to reduce cabbage aphids in the Chinese cabbage fields.     

PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences

The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct low-quality sequences. We have developed a program called PyroTrimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.     

MicroRNAome Comparison between Intramuscular and Subcutaneous Vascular Stem Cell Adipogenesis

Background

As an important factor affecting meat quality, intramuscular fat (IMF) content is a topic of worldwide concern. Emerging evidences indicate that microRNAs play important roles in adipocyte differentiation. However, miRNAome has neither been studied during porcine intramuscular preadipocyte differentiation, nor compared with subcutaneous preadipocytes. The objectives of this study were to identify porcine miRNAs involved in adipogenesis in primary preadipocytes, and to determine whether intramuscular and subcutaneous adipocytes differ in the expression and regulation of miRNAs.

Results

miRNAomes in primary intramuscular and subcutaneous adipocytes during differentiation were first sequenced using the Solexa deep sequencing method. The sequences and relative expression levels of 224 known (98.2% in miRbase 18.0) and 280 potential porcine miRNAs were identified. Fifty-four of them changed in similar pattern between intramuscular vascular stem cells (IVSC) and subcutaneous vascular stem cells (SVSC) differentiation, such as miR-210, miR-10b and miR-99a. Expression levels of 10 miRNAs were reversely up-or down-regulated between IVSC and SVSC differentiation, 19 were up-or down-regulated only during IVSC differentiation and 55 only during SVSC differentiation. Additionally, 30 miRNAs showed fat-depot specific expression pattern (24 in cells of intramuscular origin and 6 in cells of subcutaneous origin). These adipogenesis-related miRNAs mainly functioned by targeting similar pathways in adipogenesis, obesity and syndrome.

Conclusion

Comparison of miRNAomes in IVSC and SVSC during differentiation revealed that many different miRNAs are involved in adipogenesis, and they regulate SVSC and IVSC differentiation through similar pathways. These miRNAs may serve as biomarkers or targets for enhancing IMF content, and uncovering their function in IMF development will be of great value in the near future.     

Role of Toll Like Receptors in Irritable Bowel Syndrome: Differential Mucosal Immune Activation According to the Disease Subtype

Background

The irritable bowel syndrome (IBS) is a functional gastrointestinal disorder whose pathogenesis is not completely understood. Its high prevalence and the considerable effects on quality of life make IBS a disease with high social cost. Recent studies suggest that low grade mucosal immune activation, increased intestinal permeability and the altered host-microbiota interactions that modulate innate immune response, contribute to the pathophysiology of IBS. However, the understanding of the precise molecular pathophysiology remains largely unknown.

Methodology and Findings

In this study our objective was to evaluate the TLR expression as a key player in the innate immune response, in the colonic mucosa of IBS patients classified into the three main subtypes (with constipation, with diarrhea or mixed). TLR2 and TLR4 mRNA expression was assessed by real time RT-PCR while TLRs protein expression in intestinal epithelial cells was specifically assessed by flow cytometry and immunofluorescence. Mucosal inflammatory cytokine production was investigated by the multiplex technology. Here we report that the IBS-Mixed subgroup displayed a significant up-regulation of TLR2 and TLR4 in the colonic mucosa. Furthermore, these expressions were localized in the epithelial cells, opening new perspectives for a potential role of epithelial cells in host-immune interactions in IBS. In addition, the increased TLR expression in IBS-M patients elicited intracellular signaling pathways resulting in increased expression of the mucosal proinflammatory cytokines IL-8 and IL1β.

Conclusions

Our results provide the first evidence of differential expression of TLR in IBS patients according to the disease subtype. These results offer further support that microflora plays a central role in the complex pathophysiology of IBS providing novel pharmacological targets for this chronic gastrointestinal disorder according to bowel habits.