Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.     

HIVE-COTE 2.0: a new meta ensemble for time series classification

Machine Learning - The Hierarchical Vote Collective of Transformation-based Ensembles (HIVE-COTE) is a heterogeneous meta ensemble for time series classification. HIVE-COTE forms its ensemble from...     

Selected extended papers of NFM 2018

Innovations in Systems and Software Engineering -     

Free Fatty Acids Reduction in Waste Cooking Oil by Rhodosporidium toruloides and Simultaneous Carotenoids,Lipids, and PAL Enzyme Production in a Two-Phase Culture System

Waste cooking oil (WCO) is a problematic waste product that contains free fatty acids (FFAs), preventing it from being valorized easily as biodiesel and poses an environmental hazard if incorrectly disposed. The use of WCO as a carbon source for Rhodosporidium toruloides (R. toruloides) using a two-phase culture system is developed. The normal growth of R. toruloides when cultured in WCO (OD₆₀₀ 52) reveals its ability to use a hydrophobic substrate as the carbon source compared to glucose (OD₆₀₀ 51.9). Interestingly, the extracellular lipase activity when R. toruloides is grown on WCO is 14.4 U mL⁻¹ compared to when grown on glucose (2.4 U mL⁻¹). Additionally, FFA levels in WCO are reduced from 2% to 0.2% at end of fermentation, suggesting that R. toruloides can consume FFA. Furthermore, higher yield of beneficial products: β-carotene (4.57 µg mL⁻¹), torularhodin (4.2 µg mL⁻¹), fatty acids (1 mg mL⁻¹), and phenylalanine ammonia-lyase (PAL) enzyme (0.12 µmol mg⁻¹) are produced when WCO is the carbon source, compared to glucose (4.1 µg mL⁻¹ β-carotene, 3.0 µg mL⁻¹ torularhodin, 1 mg mL⁻¹ of fatty acids, and 0.096 µmol mg⁻¹ PAL enzyme). This is a first study that shows R. toruloides can grow on hydrophobic carbon source.     

Characterization of Listeria monocytogenes isolates from lactating dairy cows in a Wisconsin farm: Antibiotic resistance,mammalian cell infection,and effects on the fecal microbiota

Listeria monocytogenes is an invasive foodborne pathogen that is ubiquitously present in the dairy farm environment. Although cattle are a reservoir of L. monocytogenes, most adult animals do not exhibit clinical symptoms, suggesting a homeostasis between this pathogen and the bovine gastrointestinal ecosystem. Nevertheless, substantial prevalence of L. monocytogenes fecal shedding by dairy cattle has been reported in many studies, posing threats of transmission within the herd and contamination of the human food supply. Accordingly, understanding the L. monocytogenes ecology within the bovine gastrointestinal tract is important to prevent clinical illness in the animal host, reduce transmission, and guide intervention strategies. In this study, we conducted a longitudinal sampling of fecal samples from 20 lactating dairy cows in one Wisconsin farm over a 29-d period and found a strikingly high incidence of L. monocytogenes shedding, in 90% of sampled animals. The L. monocytogenes isolates were genetically diverse, representing all common serotypes previously identified from cattle. Additionally, most tested isolates were resistant to ampicillin, and a few were also resistant to gentamicin or trimethoprim/sulfamethoxazole. Most isolates effectively infected human epithelial cells (Caco-2) and murine fibroblasts (L2), suggesting that they are all capable of causing systemic infection if the intestinal barrier is breached. Finally, we investigated the effects of L. monocytogenes colonization on the gastrointestinal tract microbiota by analyzing the fecal bacterial communities of some shedding and nonshedding cows. Whereas L. monocytogenes did not affect the α and β diversity of tested animals, a subset of shedding cows exhibited different abundances of certain operational taxonomic units within the Bacteroidetes and Firmicutes phyla compared with nonshedding cows. Overall, our findings highlight the threat of antibiotic resistance among some L. monocytogenes isolates, emphasize the need for a strain-specific approach in listeriosis treatment, and suggest the potential negative influence of subclinical L. monocytogenes carriage on animal gut health.