Lovelindhardt9572

S. even though they (especially Europe) do not face anywhere near the level of crisis as the U.S. In the long-run, upstream measures (tackling the social determinants of health) are more effective public health strategies to control the epidemic. In the meantime, however, harm reduction strategies have to be employed to mitigate the harm from addiction and overdose deaths.The junction between the double-stranded and single-stranded telomeric DNA (ds-ss junction) is fundamental in the maintenance of the telomeric chromatin, as it directs the assembly of the telomere binding proteins. In budding yeast, multiple Rap1 proteins bind the telomeric dsDNA, while ssDNA repeats are bound by the Cdc13 protein. Here, we aimed to determine, for the first time, the telomeric 5' end nucleotide in a budding yeast. To this end, we developed a permutation-specific PCR-based method directed towards the regular 8-mer telomeric repeats in Naumovozyma castellii. We find that, in logarithmically growing cells, the 320 ± 30 bp long telomeres mainly terminate in either of two specific 5' end permutations of the repeat, both corresponding to a terminal adenine nucleotide. Strikingly, two permutations are completely absent at the 5' end, indicating that not all ds-ss junction structures would allow the establishment of the protective telomere chromatin cap structure. Using in vitro DNA end protection assays, we determined that binding of Rap1 and Cdc13 around the most abundant ds-ss junction ensures the protection of both 5' ends and 3' overhangs from exonucleolytic degradation. Our results provide mechanistic insights into telomere protection, and reveal that Rap1 and Cdc13 have complementary roles.In C. elegans, PUF proteins promote germline stem cell self-renewal. Their functions hinge on partnerships with two proteins that are redundantly required for stem cell maintenance. Here we focus on understanding how the essential partner protein, LST-1, modulates mRNA regulation by the PUF protein, FBF-2. LST-1 contains two nonidentical sites of interaction with FBF-2, LST-1 A and B. Our crystal structures of complexes of FBF-2, LST-1 A, and RNA visualize how FBF-2 associates with LST-1 A versus LST-1 B. One commonality is that FBF-2 contacts the conserved lysine and leucine side chains in the KxxL motifs in LST-1 A and B. A key difference is that FBF-2 forms unique contacts with regions N- and C-terminal to the KxxL motif. Consequently, LST-1 A does not modulate the RNA-binding affinity of FBF-2, whereas LST-1 B decreases RNA-binding affinity of FBF-2. The N-terminal region of LST-1 B, which binds near the 5' end of RNA elements, is essential to modulate FBF-2 RNA-binding affinity, while the C-terminal residues of LST-1 B contribute strong binding affinity to FBF-2. We conclude that LST-1 has the potential to impact which mRNAs are regulated depending on the precise nature of engagement through its functionally distinct FBF binding sites.

Protein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult task and requires extensive efforts to qualify a given interaction as an eligible target. To this end, besides the evident need to determine the role of PPIs in disease-associated pathways and their experimental characterization as therapeutics targets, prediction of their capacity to be bound by other protein partners or modulated by future drugs is of primary importance.

We present InDeep, a tool for predicting functional binding sites within proteins that could either host protein epitopes or future drugs. Leveraging deep learning on a curated data set of PPIs, this tool can proceed to enhanced functional binding site predictions either on experimental structures or along molecular dynamics trajectories. The benchmark of InDeep demonstrates that our tool outperforms state of the art ligandable binding sites predictors when assessing PPI targets but also conventional targets. This offers new opportunities to assist drug design projects on PPIs by identifying pertinent binding pockets at or in the vicinity of PPI interfaces.

The tool is available on GitLab at https//gitlab.pasteur.fr/InDeep/InDeep.

The tool is available on GitLab at https//gitlab.pasteur.fr/InDeep/InDeep.Dysfunction caused by mGluR5 expression or activation is an important mechanism in the development of Parkinson's disease (PD). Early clinical studies on mGluR5 negative allosteric modulators have shown some limitations. It is therefore necessary to find a more specific approach to block mGluR5-mediated neurotoxicity. Here, we determined the role of NMDA receptor subunit NR2B in mGluR5-mediated ER stress and DNA damage. In vitro study, rotenone-induced ER stress and DNA damage were accompanied by an increase in mGluR5 expression, and overexpressed or activated mGluR5 with agonist CHPG induced ER stress and DNA damage, while blocking mGluR5 with antagonist MPEP alleviated the effect. Furthermore, the damage caused by CHPG was blocked by NMDA receptor antagonist MK-801. Additionally, rotenone or CHPG increased the p-Src and p-NR2B, which was inhibited by MPEP. Blocking p-Src or NR2B with PP2 or CP101,606 alleviated CHPG-induced ER stress and DNA damage. Overactivation of mGluR5 accompanied with the increase of p-Src and p-NR2B in the ER stress and DNA damage was found in rotenone-induced PD rat model. These findings suggest a new mechanism wherein mGluR5 induces ER stress and DNA damage through the NMDA receptor and propose NR2B as the molecular target for therapeutic strategy for PD.Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. selleck In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.Tepidimonas taiwanensis is a moderately thermophilic, Gram-negative, rod-shaped, chemoorganoheterotrophic, motile bacterium. The alkaline protease producing type strain T. taiwanensis LMG 22826T was recently reported to also be a promising producer of polyhydroxyalkanoates (PHAs)-renewable and biodegradable polymers representing an alternative to conventional plastics. Here, we present its first complete genome sequence which is also the first complete genome sequence of the whole species. The genome consists of a single 2,915,587-bp-long circular chromosome with GC content of 68.75%. Genome annotation identified 2,764 genes in total while 2,634 open reading frames belonged to protein-coding genes. Although functional annotation of the genome and division of genes into Clusters of Orthologous Groups (COGs) revealed a relatively high number of 694 genes with unknown function or unknown COG, the majority of genes were assigned a function. Most of the genes, 406 in total, were involved in energy production and conversion, and amino acid transport and metabolism. Moreover, particular key genes involved in the metabolism of PHA were identified. Knowledge of the genome in connection with the recently reported ability to produce bioplastics from the waste stream of wine production makes T. taiwanensis LMG 22826T, an ideal candidate for further genome engineering as a bacterium with high biotechnological potential.

Single-cell RNA sequencing determines RNA copy numbers per cell for a given gene. However, technical noise poses the question how observed distributions (output) are connected to their cellular distributions (input).

We model a single-cell RNA sequencing setup consisting of PCR amplification and sequencing, and derive probability distribution functions for the output distribution given an input distribution. We provide copy number distributions arising from single transcripts during PCR amplification with exact expressions for mean and variance. We prove that the coefficient of variation of the output of sequencing is always larger than that of the input distribution. Experimental data reveals the variance and mean of the input distribution to obey characteristic relations, which we specifically determine for a HeLa data set. We can calculate as many moments of the input distribution as are known of the output distribution (up to all). This, in principle, completely determines the input from the output distribution.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.The 3D structure of Taka-amylase A was determined by X-ray crystal analysis at 3 Å resolution by Masao Kakudo's laboratory at the Institute for Protein Research, Osaka University, in 1980. Seven kinds of heavy atom derivatives were used for phase determination. There are three copies of Taka-amylase molecules in the asymmetric unit, which improved the quality of electron density maps, leading to the completion of a molecular model with 478 amino acids. The structure determination process in those days is described briefly.The rate-limiting step for skeletal muscle glucose uptake is transport from microcirculation to muscle interstitium. Capillary endothelium poses a barrier that delays the onset of muscle insulin action. Defining physiological barriers that control insulin access to interstitial space is difficult because of technical challenges that confront study of microscopic events in an integrated physiological system. Two physiological variables determine muscle insulin access. These are the number of perfused capillaries and the permeability of capillary walls to insulin. Disease states associated with capillary rarefaction are closely linked to insulin resistance. Insulin permeability through highly resistant capillary walls of muscle poses a significant barrier to insulin access. Insulin may traverse the endothelium through narrow intercellular junctions or vesicular trafficking across the endothelial cell. Insulin is large compared with intercellular junctions, making this an unlikely route. Transport by endothelial vesicular trafficking is likely the primary route of transit. Studies in vivo show movement of insulin is not insulin receptor dependent. This aligns with single-cell transcriptomics that show the insulin receptor is not expressed in muscle capillaries. Work in cultured endothelial cell lines suggest that insulin receptor activation is necessary for endothelial insulin transit. Controversies remain in the understanding of transendothelial insulin transit to muscle. These controversies closely align with experimental approaches. Control of circulating insulin accessibility to skeletal muscle is an area that remains ripe for discovery. Factors that impede insulin access to muscle may contribute to disease and factors that accelerate access may be of therapeutic value for insulin resistance.