Nanopore sequencing simulator for DNA data storage

The exponential increase of digital data and the limited capacity of current storage devices have made clear the need for exploring new storage solutions. Thanks to its biological properties, DNA has proven to be a potential candidate for this task, allowing the storage of information at a high density for hundreds or even thousands of years. With the release of nanopore sequencing technologies, DNA data storage is one step closer to become a reality. Many works have proposed solutions for the simulation of this sequencing step, aiming to ease the development of algorithms addressing nanopore-sequenced reads. However, these simulators target the sequencing of complete genomes, whose characteristics differ from the ones of synthetic DNA. This work presents a nanopore sequencing simulator targeting synthetic DNA on the context of DNA data storage

Organoleptic and Quality Characteristics of Malagousia Variety, Grapes Fermented with Selected Indigenous Yeast Strains

Commercial Malagousia varietal wines, which are produced in almost all Greek viticultural zones, representa relatively important part of Greek wine activity. This study presents the results of a profile compilation ofvolatile aroma compounds of Malagousia musts fermented under identical conditions with selected yeaststrains. In total, 62 volatile aroma compounds were identified and separated into their chemical classes(aldehydes, higher alcohols, volatile phenols, terpenes, C13-norisoprenoids, lactones, esters, fatty acids,sulphur compounds, other compounds, and other alcohols). Alcohols and higher alcohols, such as cis-hexen-1-ol and geraniol, terpenes like linalool, esters such as ethyl isovalerate, ketones such us betadamascenone,beta-ionone and zingerone, and fatty acids such as geranic acid and phenylacetaldehyde, were found inall the samples. Among them, linalool and phenylacetaldehyde had the strongest effect on the volatilecompound profile of Malagousia wines. The same wine samples were subjected to sensorial analysis by atrained panel of 10 wine tasters, and a statistical analysis of both analyses presents similarities betweenthe two analysis approaches. It is hoped that the results will contribute to a better understanding of thequality potential of the Malagousia variety so as to evaluate possible differences on the basis of the detectedaroma concentrations

Exopolysaccharides producing lactic acid bacteria in wine and other fermented beverages: For better or for worse?

Lactic acid bacteria (LAB) from fermented beverages such as wine, cider and beer produce a wide range of exopolysaccharides (EPS) through multiple biosynthetic pathways. These extracellular polysaccharides constitute key elements for bacterial species adaptation to such anthropic processes. In the food industry, LAB polysaccharides have been widely studied for their rheological, functional and nutritional properties; however, these have been poorly studied in wine, beer and cider until recently. In this review, we have gathered the information available on these specific polysaccharide structure and, biosynthetic pathways, as well as the physiology of their production. The genes associated with EPS synthesis are also presented and compared. Finally, the possible role of EPS for bacterial survival and spread, as well as the risks or possible benefits for the winemaker and the wine lover, are discussed

Techno-Economic Assessment of Polysaccharide Extraction from Baobab: A Scale Up Analysis

This research studied the commercial exploitation of an indigenous African crop in order to formulate high value products, with a potential significant impact on the local economy. More specifically, the present work investigated the extraction of polysaccharides from baobab in a bench-scale unit, focusing on the overall yield and the techno-economic assessment of the extraction process. Preliminary technoeconomic analysis for two scenarios (with and without ethanol recycling) was performed to determine the economic viability of the process and the development of the baobab market both in Nigeria and the UK. A full economic analysis was undertaken for each of the two scenarios, considering all operating and capital costs, and the production cost of baobab polysaccharides was estimated based on a constant return on investment. Combining the operating cost with the average polysaccharide yield, the minimum profitable selling price in the UK was estimated to be between £23 and £35 per 100 g of polysaccharide, which is comparable to the commercial selling price of high purity polysaccharides. An assessment of a scaled-up plant was also performed under Nigerian conditions and the results showed that such an investment is potentially viable and profitable, with a minimum profitable selling price of £27 per 100 g, a value comparable to the UK-based scenarios

A transcriptomic approach for evaluating the relative potency and mechanism of action of azoles in the rat Whole Embryo Culture.

We evaluated the effect of six azoles on embryonic development in the rat whole embryo culture (WEC). Using the total morphological scoring system (TMS), we calculated the ID10concentration (effective dose for 10% decrease in TMS). For evaluating gene specific responses, we combined previously and newly collected transcriptomics data of rat WEC exposed to a total of twelve azoles at their ID10for 4h. Results revealed shared expressions responses in genes involved in the retinoic acid (RA) and sterol biosynthesis pathways, which are respectively representatives of developmental toxicity and targeted fungicidal action of the azoles. Azoles with more pronounced effects on the regulation of RA-associated genes were generally characterized as more potent embryotoxicants. Overall, compounds with strong sterol biosynthesis related responses and low RA related responses were considered as more favourable candidates, as they specifically regulated genes related to a desired target response. Among the identified sterol associated genes, we detected that methylsterol monooxygenase 1 (Msmo1) was more sensitively induced compared to Cyp51, a classical biomarker of this pathway. Therefore, we suggest that Msmo1 could be a better biomarker for screening the fungicidal value of azoles. In summary, we conclude that the embryonic regulation of RA and sterol metabolic pathways could be indicators for ranking azoles as embryotoxicants and determining their drug efficacy