A 3-hydroxy-3-methylglutaryl-CoA synthase-based probe for the discovery of the acyltransferase-less type I polyketide synthases

Acyltransferase (AT)-less type I polyketide synthases (PKSs) produce complex natural products due to the presence of many unique tailoring enzymes. The 3-hydroxy-3-methylglutaryl coenzyme A synthases (HCSs) are responsible for β-alkylation of the growing polyketide intermediates in AT-less type I PKSs. In this study, we discovered a large group of HCSs, closely associated with the characterized and orphan AT-less type I PKSs through in silico genome mining, sequence and genome neighbourhood network analyses. Using HCS-based probes, the survey of 1207 in-house strains and 18 soil samples from different geographic locations revealed the vast diversity of HCS-containing AT-less type I PKSs. The presence of HCSs in many AT-less type I PKSs suggests their co-evolutionary relationship. This study provides a new probe to study the abundance and diversity of AT-less type I PKSs in the environment and microbial strain collections. Our study should inspire future efforts to discover new polyketide natural products from AT-less type I PKSs.     

Lectin Binding Assays for In-Process Monitoring of Sialylation in Protein Production

Many therapeutic proteins require appropriate glycosylation for their biological activities and plasma half life. Coagulation factor VIII (FVIII) is a glycoprotein which has extensive post-translational modification by N-linked glycosylation. The terminal sialic acid in the N-linked glycans of FVIII is required for maximal circulatory half life. The extent of FVIII sialylation can be determined by high pH anion-exchange chromatography coupled with a pulse electrochemical detector (HPAEC-PED), but this requires a large amount of purified protein. Using FVIII as a model, the objective of the present study was to develop assays that enable detection and prediction of sialylation deficiency at an early stage in the process and thus prevent downstream product quality excursions. Lectin ECA (Erythrina Cristagalli) binds to unsialylated Galβ1-4 GlcNAc and the ECA-binding level (i.e., terminal Gal(β1-4) exposure) is inversely proportional to the level of sialylation. By using ECA, a cell-based assay was developed to measure the global sialylation profile in FVIII producing cells. To examine the Galβ1-4 exposure on the FVIII molecule in bioreactor tissue culture fluid (TCF), an ELISA-based ECA-FVIII binding assay was developed. The ECA-binding specificity in both assays was assessed by ECA-specific sugar inhibitors and neuraminidase digestion. The ECA-binding specificity was also independently confirmed by a ST3GAL4 siRNA knockdown experiment. To establish the correlation between Galβ1-4 exposure and the HPAEC-PED determined FVIII sialylation value, the FVIII containing bioreactor TCF and the purified FVIII samples were tested with ECA ELISA binding assay. The results indicated an inverse correlation between ECA binding and the corresponding HPAEC-PED sialylation value. The ECA-binding assays are cost effective and can be rapidly performed, thereby making them effective for in-process monitoring of protein sialylation.     

Genomic information infrastructure after the deluge

Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.     

Mitochondrial haplogroup N1a phylogeography,with implication to the origin of European farmers

Background  

Tracing the genetic origin of central European farmer N1a lineages can provide a unique opportunity to assess the patterns of the farming technology spread into central Europe in the human prehistory. Here, we have chosen twelve N1a samples from modern populations which are most similar with the farmer N1a types and performed the complete mitochondrial DNA genome sequencing analysis. To assess the genetic and phylogeographic relationship, we performed a detailed survey of modern published N1a types from Eurasian and African populations.     

Correlation of <Emphasis Type="Italic">trans</Emphasis>-Lycopene Measurements by the HPLC Method with the Optothermal and Photoacoustic Signals and the Color Readings of Fresh Tomato Homogenates

The trans-lycopene content of fresh tomato homogenates was assessed by means of the laser photoacoustic spectroscopy, the laser optothermal window, micro-Raman spectroscopy, and colorimetry; none of these methods require the extraction from the product matrix prior to the analysis. The wet chemistry method (high-performance liquid chromatography) was used as the absolute quantitative method. Analytical figures of merit for all methods were compared statistically; best linear correlation was achieved for the chromaticity index a* and chroma C*.     

A multi-criteria decision-making model for classifying wood products with respect to their impact on environment

Background, aim and scope  

Although life cycle assessment is frequently used in scientific studies of product comparison, many practitioners are looking for improvements in the normalisation, grouping and weighting of life cycle inventory results. Local conditions, which are well known to local experts, are very important to these steps. The goal of this work was to develop a computer-based decision support system for classifying wood products according to their influence on the environment in their whole life cycle. The model specifically addresses local conditions in the Republic of Slovenia and was developed by Slovenian experts.     

Inclusion of carbonation during the life cycle of built and recycled concrete: influence on their carbon footprint

Background, aim, and scope  

When the service life (or primary life) of built concrete infrastructure has elapsed, a common practice is that the demolished concrete is crushed and recycled, then incorporated into new construction. LCA studies of CO₂ emissions focus on the manufacturing and construction and occupancy/utilization phases, without consideration of the demolition and application of recycled concrete into a secondary construction application. Concrete has a documented ability to chemically react with airborne carbon dioxide (CO₂); however, carbon capture (or carbonation) by concrete during the primary and secondary life, is not considered in LCA models. This paper incorporates CO₂ capture during both primary and secondary life into an LCA model for built concrete.     

Rigorous proof of fuzzy error propagation with matrix-based LCI

Background, aim, and scope  

Propagation of parametric uncertainty in life cycle inventory (LCI) models is usually performed based on probabilistic Monte Carlo techniques. However, alternative approaches using interval or fuzzy numbers have been proposed based on the argument that these provide a better reflection of epistemological uncertainties inherent in some process data. Recent progress has been made to integrate fuzzy arithmetic into matrix-based LCI using decomposition into α-cut intervals. However, the proposed technique implicitly assumes that the lower bounds of the technology matrix elements give the highest inventory results, and vice versa, without providing rigorous proof.