Mapping the semi-nested community structure of 3D chromosome contact networks.

Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights derive from chromosome capture methods, such as Hi-C, which allow researchers to construct contact maps depicting 3D interactions among all DNA segment pairs. These maps show a complex cross-scale organization spanning megabase-pair compartments to short-ranged DNA loops.

The path to immortalization of cells starts by managing stress through gene duplications.

The genomes of immortalized cell lines (and cancer cells) are characterized by multiple types of aberrations, ranging from single nucleotide polymorphisms (SNPs) to structural rearrangements that have accumulated over time. Consequently, it is difficult to estimate the relative impact of different aberrations, the order of events, and which gene functions were under selective pressure at the early stage towards cellular immortalization. Here, we have established novel cell cultures derived from Drosophila melanogaster embryos that were sampled at multiple time points over a one-year period.

Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities.

Background: Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co-occurring metacommunities of bacteria, and environmental factors driving such patterns.

Methods: The water sources were different regarding nutrient composition, water quality, and climate characteristics, and displayed various degrees of anthropogenic impact.

Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.

Background: Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure.

FlexTaxD: flexible modification of taxonomy databases for improved sequence classification.

Summary: The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Availability And Implementation: Source code is freely available at https://github.

Zinc as a modulator of transglutaminase activity - Laboratory and pathophysiological aspects.

For a whole century, citrate has been used as an anticoagulant via chelation of calcium. Later, also EDTA was introduced as an anticoagulant. An often overlooked fact is that zinc is bound to citrate and EDTA with affinities much greater than that for calcium, imposing problems in biomedical research.

Airborne microbial biodiversity and seasonality in Northern and Southern Sweden.

Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities.

Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis.

Challenges of investigating a suspected bio attack include establishing if microorganisms have been cultured to produce attack material and to identify their source. Addressing both issues, we have investigated genetic variations that emerge during laboratory culturing of the bacterial pathogen Francisella tularensis. Key aims were to identify genetic variations that are characteristic of laboratory culturing and explore the possibility of using biological amplification to identify genetic variation present at exceedingly low frequencies in a source sample.

Biological characterization of new inhibitors of microsomal PGE synthase-1 in preclinical models of inflammation and vascular tone.

Background And Purpose: Microsomal PGE synthase-1 (mPGES-1), the inducible synthase that catalyses the terminal step in PGE biosynthesis, is of high interest as therapeutic target to treat inflammation. Inhibition of mPGES-1 is suggested to be safer than traditional NSAIDs, and recent data demonstrate anti-constrictive effects on vascular tone, indicating new therapeutic opportunities. However, there is a lack of potent mPGES-1 inhibitors lacking interspecies differences for conducting in vivo studies in relevant preclinical disease models.

A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations.

A common objective in microbial forensic investigations is to identify the origin of a recovered pathogenic bacterium by DNA sequencing. However, there is currently no consensus about how degrees of belief in such origin hypotheses should be quantified, interpreted, and communicated to wider audiences. To fill this gap, we have developed a concept based on calculating probabilistic evidential values for microbial forensic hypotheses.

Mapping the spectrum of 3D communities in human chromosome conformation capture data.

Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales.

Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins.

In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes.

Ligand hyperfine interactions at silicon vacancies in 4H-SiC.

The negative silicon vacancy ([Formula: see text]) in SiC has recently emerged as a promising defect for quantum communication and room-temperature quantum sensing. However, its electronic structure is still not well characterized. While the isolated Si vacancy is expected to give rise to only two paramagnetic centers corresponding to two inequivalent lattice sites in 4H-SiC, there have been five electron paramagnetic resonance (EPR) centers assigned to [Formula: see text] in the past: the so-called isolated no-zero-field splitting (ZFS) [Formula: see text] center and another four axial configurations with small ZFS: T , T , T , and T .

The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster.

Environmental perturbations induce transcriptional changes, some of which may be inherited even in the absence of the initial stimulus. Previous studies have focused on transfers through the germline although microbiota is also passed on to the offspring. Thus, we inspected the involvement of the gut microbiome in transgenerational inheritance of environmental exposures in Drosophila melanogaster.

Genomic 3D compartments emerge from unfolding mitotic chromosomes.

The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge.

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking.

Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic units (OTUs) that are unique to a certain source. However, no clear guidelines for how to incorporate OTU overlap or natural variation in the raw water bacterial community into MST analyses exist.

PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 () oncogene.

Polycomb group proteins are essential epigenetic repressors. They form multiple protein complexes of which two kinds, PRC1 and PRC2, are indispensable for repression. Although much is known about their biochemical properties, how mammalian PRC1 and PRC2 are targeted to specific genes is poorly understood.

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II.

Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide.

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data.

Cardiovascular and thermal strain during 3-4 days of a metabolically demanding cold-weather military operation.

Background: Cardiovascular (CV) and thermal responses to metabolically demanding multi-day military operations in extreme cold-weather environments are not well described. Characterization of these operations will provide greater insights into possible performance capabilities and cold injury risk.

Methods: Soldiers from two cold-weather field training exercises (FTX) were studied during 3-day (study 1,  = 18, age: 20 ± 1 year, height: 182 ± 7 cm, mass: 82 ± 9 kg) and 4-day (study 2,  = 10, age: 20 ± 1 year, height: 182 ± 6 cm, mass: 80.

Estimation of leaf area index and its sunlit portion from DSCOVR EPIC data: Theoretical basis.

This paper presents the theoretical basis of the algorithm designed for the generation of leaf area index and diurnal course of its sunlit portion from NASA's Earth Polychromatic Imaging Camera (EPIC) onboard NOAA's Deep Space Climate Observatory (DSCOVR). The Look-up-Table (LUT) approach implemented in the MODIS operational LAI/FPAR algorithm is adopted. The LUT, which is the heart of the approach, has been significantly modified.

Atrophin controls developmental signaling pathways via interactions with Trithorax-like.

Mutations in human , a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. () mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets.

Erratum to: CBP binding outside of promoters and enhancers in Drosophila melanogaster.

[This corrects the article DOI: 10.1186/s13072-015-0042-4.].