Pancreatic ductal adenocarcinomas from Mexican patients present a distinct genomic mutational pattern

Molecular Biology Reports - Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers in humans, with less than 5% 5-year survival rate. PDAC is characterized by a small number of...     

Biochemical markers of vascular calcification in elderly hemodialysis patients

The increased vascular calcification, cardiovascular morbidity, and mortality in chronic kidney disease (CKD) patients has been associated with disturbances in mineral-bone metabolism. In order to determine markers of the vascular calcification frequently observed in these patients, blood samples of elderly male and female hemodialysis CKD patients were used to measure serum levels of: osteoprotegerin (OPG), total soluble receptor activator of nuclear factor-κB ligand (sRANKL), and fetuin-A by enzyme immunoassay; tartrate-resistant acid phosphatase (TRACP-5b), and bone-specific alkaline phosphatase (BAP) by immunoenzymometric assay; osteocalcin (OC) by ELISA; iPTH by immunoradiometric assay; 25(OH)D₃ and 1,25(OH)₂D₃, by I¹²⁵ radioimmunoassay; and calcium and phosphorus by photometric assay. Serum OPG, BAP, iPTH, phosphorus, and OC levels were higher and serum 25(OH)D₃, 1,25(OH)₂D₃, and fetuin-A levels lower in both male and female CKD patients than in their respective controls. Our results indicate that the bone formation and resorption parameters are altered in elderly male and female hemodialysis CKD patients. These changes may lead to vascular calcifications and cardiovascular complications, given that elevated OPG and OC levels and reduced fetuin-A levels are associated with cardiovascular events.     

Conjugative Transfer and cis-Mobilization of a Genomic Island by an Integrative and Conjugative Element of Streptococcus agalactiae

Putative integrative and conjugative elements (ICEs), i.e., genomic islands which could excise, self-transfer by conjugation, and integrate into the chromosome of the bacterial host strain, were previously identified by in silico analysis in the sequenced genomes of Streptococcus agalactiae (M. Brochet et al., J. Bacteriol. 190:6913–6917, 2008). We investigated here the mobility of the elements integrated into the 3′ end of a tRNA^Lys gene. Three of the four putative ICEs tested were found to excise but only one (ICE_515_tRNA^Lys) was found to transfer by conjugation not only to S. agalactiae strains but also to a Streptococcus pyogenes strain. Transfer was observed even if recipient cell already carries a related resident ICE or a genomic island flanked by attL and attR recombination sites but devoid of conjugation or recombination genes (CIs-Mobilizable Element [CIME]). The incoming ICE preferentially integrates into the 3′ end of the tRNA^Lys gene (i.e., the attR site of the resident element), leading to a CIME-ICE structure. Transfer of the whole composite element CIME-ICE was obtained, showing that the CIME is mobilizable in cis by the ICE. Therefore, genomic islands carrying putative virulence genes but lacking the mobility gene can be mobilized by a related ICE after site-specific accretion.     

Engineering the Pattern of Protein Glycosylation Modulates the Thermostability of a GH11 Xylanase

Protein glycosylation is a common post-translational modification, the effect of which on protein conformational and stability is incompletely understood. Here we have investigated the effects of glycosylation on the thermostability of Bacillus subtilis xylanase A (XynA) expressed in Pichia pastoris. Intact mass analysis of the heterologous wild-type XynA revealed two, three, or four Hex_8–16GlcNAc₂ modifications involving asparagine residues at positions 20, 25, 141, and 181. Molecular dynamics (MD) simulations of the XynA modified with various combinations of branched Hex₉GlcNAc₂ at these positions indicated a significant contribution from protein-glycan interactions to the overall energy of the glycoproteins. The effect of glycan content and glycosylation position on protein stability was evaluated by combinatorial mutagenesis of all six potential N-glycosylation sites. The majority of glycosylated enzymes expressed in P. pastoris presented increased thermostability in comparison with their unglycosylated counterparts expressed in Escherichia coli. Steric effects of multiple glycosylation events were apparent, and glycosylation position rather than the number of glycosylation events determined increases in thermostability. The MD simulations also indicated that clustered glycan chains tended to favor less stabilizing glycan-glycan interactions, whereas more dispersed glycosylation patterns favored stabilizing protein-glycan interactions.     

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F_2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R ² of 31.7 %, was confirmed using a BC₂F₃ population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.     

Does fin damage allow discrimination among wild,escaped and farmed Sparus aurata (L.) and Dicentrarchus labrax (L.)?

The present study compares fin damages in gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax) according to their wild, escaped or farmed origins. In addition, the potential applicability of fin condition indices (Fin Erosion Index ‘FEI’ and Fin Splitting Index ‘FSI’) as identification tools is discussed. Farmed seabream fins evidenced more erosion and splitting (FEI ± SD: 2.1 ± 0.3; FSI ± SD: 1.9 ± 0.6) than wild seabream fins (FEI: 0.8 ± 0.6; FSI: 1.2 ± 0.9), a result of farming conditions in open‐sea cages. Escaped seabream fin erosion was between that of farmed and wild seabream (FEI: 1.6 ± 0.4), which could indicate that fins in farmed fish recover over time from farming abrasions once they are in the wild. However, the fins of escaped seabream seem to be weaker than those of the wild fish, and therefore might be more susceptible to suffer other types of erosion such as splitting or nipping (FSI: 2.3 ± 0.7). No significant differences were found in seabass FEI according to their origins, although wild seabass presented significantly more split caudal fins (FSI: 3.3 ± 2.8) than the farmed seabass (FSI: 1.2 ± 1.1) and escapees (FSI: 2.5 ± 1.6). Therefore, FEI for seabream could be used as tools not only to distinguish between wild and farmed fish, but also to identify recent escapees, improving further assessments on the contribution of seabream escapees in fishery landings. However, the healing potential of damaged fins must be considered for the proper identification of escapees. Use of fin condition indices from both species could be helpful for aquaculture management, to assess fish welfare in fish farms stocks, and improve the knowledge of handling, stock densities and open‐sea cage environment conditions.     

Discovery of aryl ureas and aryl amides as potent and selective histamine H3 receptor antagonists for the treatment of obesity (Part I)

A series of structurally novel aryl ureas was derived from optimization of the HTS lead as selective histamine H₃ receptor (H₃R) antagonists. The SAR was explored and the data obtained set up the starting point and foundation for further optimization. The most potent tool compounds, as exemplified by compounds 2l, 5b, 5d, and 5e, displayed antagonism potencies in the subnanomolar range in in vitro human-H₃R FLIPR assays and rhesus monkey H₃R binding assays.     

Synthesis,docking, and biological studies of phenanthrene β-diketo acids as novel HIV-1 integrase inhibitors

In the present study we report the synthesis of halogen-substituted phenanthrene β-diketo acids as new HIV-1 integrase inhibitors. The target phenanthrenes were obtained using both standard thermal- and microwave-assisted synthesis. 4-(6-Chlorophenanthren-2-yl)-2,4-dioxobutanoic acid (18) was the most active compound of the series, inhibiting both 3′-end processing (3′-P) and strand transfer (ST) with IC₅₀ values of 5 and 1.3 μM, respectively. Docking studies revealed two predominant binding modes that were distinct from the binding modes of raltegravir and elvitegravir, and suggest a novel binding region in the IN active site. Moreover, these compounds are predicted not to interact significantly with some of the key amino acids (Q148 and N155) implicated in viral resistance. Therefore, this series of compounds can further be investigated for a possible chemotype to circumvent resistance to clinical HIV-1 IN inhibitors.     

Heating and microwave assisted SPPS of C-terminal acid peptides on trityl resin: the truth behind the yield

Despite correct purity of crude peptides prepared on trityl resin by Fmoc/tBu microwave assisted solid phase peptide synthesis, surprisingly, lower yields than those expected were obtained while preparing C-terminal acid peptides. This could be explained by cyclization/cleavage through diketopiperazine formation during the second amino acid deprotection and third amino acid coupling. However, we provide here evidence that this is not the case and that this yield loss was due to high temperature promoted hydrolysis of the 2-chlorotrityl ester, yielding premature cleavage of the C-terminal acid peptides.     

Disturbances, elevation, topography and spatial proximity drive vegetation patterns along an altitudinal gradient of a top biodiversity hotspot

The correlation between vegetation patterns (species distribution and richness) and altitudinal variation has been widely reported for tropical forests, thereby providing theoretical basis for biodiversity conservation. However, this relationship may have been oversimplified, as many other factors may influence vegetation patterns, such as disturbances, topography and geographic distance. Considering these other factors, our primary question was: is there a vegetation pattern associated with substantial altitudinal variation (10–1,093 m a.s.l.) in the Atlantic Rainforest—a top hotspot for biodiversity conservation—and, if so, what are the main factors driving this pattern? We addressed this question by sampling 11 1-ha plots, applying multivariate methods, correlations and variance partitioning. The Restinga (forest on sandbanks along the coastal plains of Brazil) and a lowland area that was selectively logged 40 years ago were floristically isolated from the other plots. The maximum species richness (>200 spp. per hectare) occurred at approximately 350 m a.s.l. (submontane forest). Gaps, multiple stemmed trees, average elevation and the standard deviation of the slope significantly affected the vegetation pattern. Spatial proximity also influenced the vegetation pattern as a structuring environmental variable or via dispersal constraints. Our results clarify, for the first time, the key variables that drive species distribution and richness across a large altitudinal range within the Atlantic Rainforest.