Synthesis of β-Peptide Standards for Use in Model Prebiotic Reactions

A one-pot method was developed for the preparation of a series of β-alanine standards of moderate size (2 to ≥12 residues) for studies concerning the prebiotic origins of peptides. The one-pot synthesis involved two sequential reactions: (1) dry-down self-condensation of β-alanine methyl ester, yielding β-alanine peptide methyl ester oligomers, and (2) subsequent hydrolysis of β-alanine peptide methyl ester oligomers, producing a series of β-alanine peptide standards. These standards were then spiked into a model prebiotic product mixture to confirm by HPLC the formation of β-alanine peptides under plausible reaction conditions. The simplicity of this approach suggests it can be used to prepare a variety of β-peptide standards for investigating differences between α- and β-peptides in the context of prebiotic chemistry.     

白茆塘戚浦塘流域维管束植物资源及群落

白茆塘和戚浦塘位于苏州市辖区,水生维管植物十分丰富.对其流域水生维管束植物资源进行了调查,发现共有水生植物99种,隶属于36科76属.同时对水生维管束植物的资源及群落进行了分析探讨,以期为水生植物资源的保护和合理利用等方面提供科学建议.     

Differential expression analysis for sequence count data

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.     

Chromogranin A and the Tumor Microenvironment

Chromogranin A (CgA) is an acidic glycoprotein belonging to a family of regulated secretory proteins stored in the dense core granules of the adrenal medulla and of many other neuroendocrine cells and neurons. This protein is frequently used as a diagnostic and prognostic serum marker for a range of neuroendocrine tumors. Circulating CgA is also increased in patients with other diseases, including subpopulations of patients with non-neuroendocrine tumors, with important prognostic implications. A growing body of evidence suggests that CgA is more than a diagnostic/prognostic marker for cancer patients. Indeed, results of in vitro experiments and in vivo studies in animal models suggest that this protein and its fragments can affect several elements of the tumor microenvironment, including fibroblasts and endothelial cells. In this article, recent findings implicating CgA as a modulator of the tumor microenvironment and suggesting that abnormal secretion of CgA could play important roles in tumor progression and response to therapy in cancer patients are reviewed and discussed.     

Comparing movement of four butterfly species in experimental grassland strips

In contrast to many studies on the habitat quality of road verges for butterflies in relation to management regimes, little is known about whether road verges also function as corridors linking fragmented grassland habitats. We experimentally compared movements of four model species, two small blues and two medium browns, with one habitat specialist and one habitat generalist in each size and phylogenetic category. A total of 425 individual butterflies were caught and translocated to an experimental arena with three 2 × 30 m grassland strips that approximated road verges; one with adult feeding resources, one sheltered from the wind, and one without food and shelter. Movements in grassland strips were compared to movements in continuous grassland habitat. Results indicated that (1) individuals did not use the low-quality strip, (2) only specialists used strips but not in the same way according to their size and phylogenic category, and (3) strip use could not be predicted from habitat selection. This finding supports the idea that corridors of intermediate quality are the most efficient to promote dispersal rates in fragmented landscapes. Road verges cover 250,000 ha in Sweden, which is nearly the total amount of seminatural grasslands. Our results suggest that, to benefit butterfly dispersal among grassland patches, road verges should be managed to create a more favourable microclimate (e.g. sheltered from wind, high temperatures).     

Analysis of rhamnolipid biosurfactants by methylene blue complexation

Rhamnolipids, produced by Pseudomonas aeruginosa, represent an important group of biosurfactants having various industrial, environmental, and medical applications. Current methods for rhamnolipid quantification involve the use of strong hazardous acids/chemicals, indirect measurement of the concentration of sugar moiety, or require the availability of expensive equipment (HPLC-MS). A safer, easier method that measures the whole rhamnolipid molecules would significantly enhance strain selection, metabolic engineering, and process development for economical rhamnolipid production. A semi-quantitative method was reported earlier to differentiate between the rhamnolipid-producing and non-producing strains using agar plates containing methylene blue and cetyl trimethylammonium bromide (CTAB). In this study, a rapid and simple method for rhamnolipid analysis was developed by systematically investigating the complexation of rhamnolipids and methylene blue, with and without the presence of CTAB. The method relies on measuring the absorbance (at 638 nm) of the rhamnolipid−methylene blue complex that partitions into the chloroform phase. With P. aeruginosa fermentation samples, the applicability of this method was verified by comparison of the analysis results with those obtained from the commonly used anthrone reaction technique.     

A computational algorithm to simulate disorganization of collagen network in injured articular cartilage

Cartilage defects are a known risk factor for osteoarthritis. Estimation of structural changes in these defects could help us to identify high risk defects and thus to identify patients that are susceptible for the onset and progression of osteoarthritis. Here, we present an algorithm combined with computational modeling to simulate the disorganization of collagen fibril network in injured cartilage. Several potential triggers for collagen disorganization were tested in the algorithm following the assumption that disorganization is dependent on the mechanical stimulus of the tissue. We found that tensile tissue stimulus alone was unable to preserve collagen architecture in intact cartilage as collagen network reoriented throughout the cartilage thickness. However, when collagen reorientation was based on both tensile tissue stimulus and tensile collagen fibril strains or stresses, the collagen network architecture was preserved in intact cartilage. Using the same approach, substantial collagen reorientation was predicted locally near the cartilage defect and particularly at the cartilage–bone interface. The developed algorithm was able to predict similar structural findings reported in the literature that are associated with experimentally observed remodeling in articular cartilage. The proposed algorithm, if further validated, could help to predict structural changes in articular cartilage following post-traumatic injury potentially advancing to impaired cartilage function.     

Phosphorylation of cardiac troponin I by mammalian sterile 20-like kinase 1

Mst1 (mammalian sterile 20-like kinase 1) is a ubiquitously expressed serine/threonine kinase and its activation in the heart causes cardiomyocyte apoptosis and dilated cardiomyopathy. Its myocardial substrates, however, remain unknown. In a yeast two-hybrid screen of a human heart cDNA library with a dominant-negative Mst1 (K59R) mutant used as bait, cTn [cardiac Tn (troponin)] I was identified as an Mst1-interacting protein. The interaction of cTnI with Mst1 was confirmed by co-immunoprecipitation in both co-transfected HEK-293 cells (human embryonic kidney cells) and native cardiomyocytes, in which cTnI interacted with full-length Mst1, but not with its N-terminal kinase fragment. in vitro phosphorylation assays demonstrated that cTnI is a sensitive substrate for Mst1. In contrast, cTnT was phosphorylated by Mst1 only when it was incorporated into the Tn complex. MS analysis indicated that Mst1 phosphorylates cTnI at Thr(31), Thr(51), Thr(129) and Thr(143). Substitution of Thr(31) with an alanine residue reduced Mst1-mediated cTnI phosphorylation by 90%, whereas replacement of Thr(51), Thr(129) or Thr(143) with alanine residues reduced Mst1-catalysed cTnI phosphorylation by approx. 60%, suggesting that Thr(31) is a preferential phosphorylation site for Mst1. Furthermore, treatment of cardiomyocytes with hydrogen peroxide rapidly induced Mst1-dependent phosphorylation of cTnI at Thr(31). Protein epitope analysis and binding assays showed that Mst1-mediated phosphorylation modulates the molecular conformation of cTnI and its binding affinity to TnT and TnC, thus indicating functional significances. The results of the present study suggest that Mst1 is a novel mediator of cTnI phosphorylation in the heart and may contribute to the modulation of myofilament function under a variety of physiological and pathophysiological conditions.