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Sequencing databases contain enormous amounts of functional genomics data, making them an extensive resource for genome-scale analysis. Reanalyzing publicly available data, and integrating it with new, project-specific data sets, can be invaluable. With current technologies, genomic experiments have become feasible for virtually any species of interest. However, using and integrating this data comes with its challenges, such as standardized and reproducible analysis. Seq2science is a multi-purpose workflow that covers preprocessing, quality control, visualization, and analysis of functional genomics sequencing data. It facilitates the downloading of sequencing data from all major databases, including NCBI SRA, EBI ENA, DDBJ, GSA, and ENCODE. Furthermore, it automates the retrieval of any genome assembly available from Ensembl, NCBI, and UCSC. It has been tested on a variety of species, and includes diverse workflows such as ATAC-, RNA-, and ChIP-seq. It consists of both generic as well as advanced steps, such as differential gene expression or peak accessibility analysis and differential motif analysis. Seq2science is built on the Snakemake workflow language and thus can be run on a range of computing infrastructures. It is available at https://github.com/vanheeringen-lab/seq2science.

Solid-state fermentation is widely used in traditional food production, but most of the complex processes involved were designed and are carried out without a scientific basis. Often, mathematical models can be established to describe mass and heat transfer with the assistance of chemical engineering tools. However, due to the complex nature of solid-state fermentation, mathematical models alone cannot explain the many dynamic changes that occur during these processes. For example, it is hard to identify the most important variables influencing product yield and quality fluctuations. Here, using solid-state fermentation of Chinese liquor as a case study, we established statistical models to correlate the final liquor yield with available industrial data, including the starting content of starch, water and acid; starting temperature; and substrate temperature profiles throughout the process. Models based on starting concentrations and temperature profiles gave unsatisfactory yield predictions. Although the most obvious factor is the starting month, ambient temperature is unlikely to be the direct driver of differences. A lactic-acid-inhibition model indicates that lactic acid from lactic acid bacteria is likely the reason for the reduction in yield between April and December. Further integrated study strategies are necessary to confirm the most crucial variables from both microbiological and engineering perspectives. Our findings can facilitate better understanding and improvement of complex solid-state fermentations.

Objectives It is well-known that long-term osteoarthritis prognosis is not improved by corticosteroid treatments. Here we investigate what could underlie this phenomenon by measuring the short term corticosteroid response of osteoarthritic joint synovial macrophages (OA-Mf). Methods We determined the genome-wide transcriptomic response to corticosteroids of end-stage OA-Mf. This was compared with lipopolysaccharide-tolerized and β-glucan-trained circulating blood monocyte-derived macrophage models. Results Upon corticosteroid stimulation, the trained and tolerized macrophages significantly altered the abundance of 201 and 257 RNA transcripts, respectively. By contrast, by the same criteria, OA-Mf had a very restricted corticosteroid response of only 12 RNA transcripts. Furthermore, while metalloproteinases 1, 2, 3 and 10 expression clearly distinguish OA-Mf from both the tolerized and trained macrophage models, OA-Mf IL-1, chemokine (CXCL) and cytokine (CCL) family member profiles resembled the tolerized macrophage model, with the exception that OA-Mf showed high levels of CCL20. Conclusion Terminal osteoarthritis joints harbour macrophages with an inflammatory state that closely resembles the tolerized macrophage state, and this is compounded by a weak corticosteroid response capacity that may explain the lack of positive long-term effects of corticosteroid treatment for osteoarthritis patients. [ABSTRACT FROM AUTHOR]

Abstract Carcass decomposition largely depends on vertebrate scavengers. However, how behavioral differences between vertebrate scavenger species, the dominance of certain species, and the diversity of the vertebrate scavenger community affect the speed of carcass decomposition is poorly understood. As scavenging is an overlooked trophic interaction, studying the different functional roles of vertebrate species in the scavenging process increases our understanding about the effect of the vertebrate scavenger community on carcass decomposition. We used motion‐triggered infrared camera trap footages to profile the behavior and activity of vertebrate scavengers visiting carcasses in Dutch nature areas. We grouped vertebrate scavengers with similar functional roles. We found a clear distinction between occasional scavengers and more specialized scavengers, and we found wild boar (Sus scrofa) to be the dominant scavenger species in our study system. We showed that these groups are functionally different within the scavenger community. We found that overall vertebrate scavenger diversity was positively correlated with carcass decomposition speed. With these findings, our study contributes to the understanding about the different functional roles scavengers can have in ecological communities.

Polyol accumulation and metabolism were examined in Aspergillus oryzae cultured on whole wheat grains or on wheat dough as a model for solid-state culture. In solid-state fermentation (SSF), water activity ([a.sub.w]) is typically low resulting in osmotic stress. In addition to a high level of mannitol, which is always present in the cells, A. oryzae accumulated high concentrations of glycerol, erythritol and arabitol at relatively low [a.sub.w] (0.96-0.97) in SSF. Accumulation of such a mixture of polyols is rather unusual and might be typical for SSF. A. oryzae mycelium accumulating various polyols at low [a.sub.w] contained at least four distinct polyol dehydrogenases with highest activities toward glycerol, erythritol, D-arabitol and mannitoL NAD[P.sup.+]-dependent glycerol dehydrogenase activity correlated very well with glycerol accumulation. A similar correlation was observed for erythritol and NAD[P.sup.+]-erythritol dehydrogenase suggesting that NAD[P.sxup.+]-dependent glycerol and erythritol dehydrogenases are involved in biosynthesis of glycerol and erythritol, respectively, and that these enzymes are induced by osmotic stress.