Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license

Gene rearrangements in bone marrow cells of patients with acute myelogenous leukemia

At diagnosis, clonal gene rearrangement probes {[}retinoic acid receptor (RAR)-alpha, major breakpoint cluster region (M-bcr), immunoglobulin (Ig)-JH, T cell receptor (TcR)-beta, myeloid lymphoid leukemia (MLL) or cytokine genes (GM-CSF, G-CSF, IL-3)] were detected in bone marrow samples from 71 of 153 patients with acute myelogenous leukemia (AML) (46%): in 41 patients with primary AML (pAML) (58%) and in 30 patients with secondary AML (42%). In all cases with promyelocytic leukemia (AML-M3) RAR-alpha gene rearrangements were detected (n = 9). Gene rearrangements in the Ig-JH or the TcR-beta or GM-CSF or IL-3 or MLL gene were detected in 12, 10, 16 and 12% of the cases, respectively, whereas only few cases showed gene rearrangements in the M-bcr (6%) or G-CSF gene (3%). Survival of pAML patients with TcR-beta gene rearrangements was longer and survival of pAML patients with IL-3 or GM-CSF gene rearrangement was shorter than in patients without those rearrangements. No worse survival outcome was seen in patients with rearrangements in the MLL, Ig-JH or M-bcr gene. In remission of AML (CR), clonal gene rearrangements were detected in 23 of 48 cases (48%) if samples were taken once in CR, in 23 of 26 cases (88%) if samples were taken twice in CR and in 23 of 23 cases (100%) if samples were studied three times in CR. All cases with gene rearrangements at diagnosis showed the same kind of rearrangement at relapse of the disease (n = 12). Our data show that (1) populations with clonal gene rearrangements can be regularly detected at diagnosis, in CR and at relapse of AML. (2) Certain gene rearrangements that are detectable at diagnosis have a prognostic significance for the patients' outcome. Our results point out the significance of gene rearrangement analyses at diagnosis of AML in order to identify `poor risk' patients - independently of the karyotype. Moreover, the persistence of clonal cells in the further course of AML can be studied by gene rearrangement analysis. Copyright (C) 2000 S. Karger AG, Basel

Soil Microclimate and Chemistry of Spruce–Fir Tree Islands in Northern Utah

The objective was to investigate differences in soil properties in high-elevation tree islands composed of subalpine fir [Abies lasiocarpa (Hook.) Nutt.] and Engelmann spruce [Picea engelmannii Parry ex Engelm.] relative to semiarid meadows in Northern Utah. We compared snow depths, surface soil temperature and moisture, and soil chemical properties (0–30 cm) between tree islands and the surrounding meadow. Snow accumulated evenly around the tree islands. Snow depth differences developed during snowmelt when shaded areas to the north of the islands retained snow longer. Less snow accumulated inside and at the edge of the tree islands. In summer, canopy shading inside the islands slowed soil moisture loss and decreased the magnitude and fluctuation of soil temperatures relative to the exposed meadow. Tree islands affected O horizon mass and chemistry: 6 to 10 kg m-2 of O material, with higher macronutrient concentrations and lower C/N ratio, had accumulated under tree canopies; 3 kg m-2 in the island interior; and /N ratio. The pH of meadow soils was constant with depth (6.22–5.95). Below the trees, the pH in the upper soil was 0.1 to 0.3 units higher than in the meadow and decreased 0.8 to 0.9 pH units with depth. The presence of tree islands significantly modified the soil microclimate and nutrient distribution relative to the surrounding meadows

Characterization of Antibiotic and Biocide Resistance Genes and Virulence Factors of Staphylococcus Species Associated with Bovine Mastitis in Rwanda

The present study was conducted from July to August 2018 on milk samples taken at dairy farms in the Northern Province and Kigali District of Rwanda in order to identify Staphylococcus spp. associated with bovine intramammary infection. A total of 161 staphylococcal isolates originating from quarter milk samples of 112 crossbred dairy cattle were included in the study. Antimicrobial susceptibility testing was performed and isolates were examined for the presence of various resistance genes. Staphylococcus aureus isolates were also analyzed for the presence of virulence factors, genotyped by spa typing and further phenotypically subtyped for capsule expression using Fourier Transform Infrared (FTIR) spectroscopy. Selected S. aureus were characterized using DNA microarray technology, multi-locus sequence typing (MLST) and whole-genome sequencing. All mecA-positive staphylococci were further genotyped using dru typing. In total, 14 different staphylococcal species were detected, with S. aureus being most prevalent (26.7%), followed by S. xylosus (22.4%) and S. haemolyticus (14.9%). A high number of isolates was resistant to penicillin and tetracycline. Various antimicrobial and biocide resistance genes were detected. Among S. aureus, the Panton–Valentine leukocidin (PVL) genes, as well as bovine leukocidin (LukM/LukF-P83) genes, were detected in two and three isolates, respectively, of which two also carried the toxic shock syndrome toxin gene tsst-1 bovine variant. t1236 was the predominant spa type. FTIR-based capsule serotyping revealed a high prevalence of non-encapsulated S. aureus isolates (89.5%). The majority of the selected S. aureus isolates belonged to clonal complex (CC) 97 which was determined using DNA microarray based assignment. Three new MLST sequence types were detected

Iso-maleimycin, a Constitutional Isomer of Maleimycin, fromStreptomycessp. QL37

Microbial Biotechnolog

Digital carbon footprint awareness among digital natives: an exploratory study

Changes in use practices due to COVID-19 have illustrated the potential of digital technology as a catalyst of more sustainable and pro-environmental behavior. At the same time, the energy consumption and environmental impact of digital applications and services has been put more firmly on the agenda. In this paper, we adopt a bottom-up approach to explore digital natives’ awareness of their digital carbon footprint, i.e., related to their use of digital services and applications. We present findings from 21 semi-structured in-depth interviews that were conducted to explore (1) to which extent digital natives are aware of and reflect on their digital carbon footprint, (2) what could motivate efforts to reduce this footprint and (3) which compromises they might be willing to make in this respect. The findings point to low awareness of the carbon footprint of digital applications and services. The lack of technological understanding, public information and social awareness about the topic were identified as important factors. In terms of the motivation for adopting pro-environmental digital habits, we found that several factors indirectly contribute to this goal, including the striving for personal wellbeing. Finally, the results indicate some willingness to change and make compromises, albeit not an unconditional one: the alignment with other goals (e.g., personal well-being) and nature of the perceived sacrifice and its impact play a key role. With this work, we aim to strengthen ongoing efforts to increase users’ awareness and to stimulate more sustainable and well-being supporting digital consumption

Submesoscale Kinematic Properties in Summer and Winter Surface Flows in the Northern Gulf of Mexico

Statistical properties of near-surface horizontal velocity gradients are obtained from four drifter experiments conducted in the Gulf of Mexico during Summer 2012 and Winter 2016. The data density provided by the near-simultaneous deployments of 90-326 surface drifters in each allows direct, drifter-based estimates of the scale dependence of velocity gradients at separation scales ranging from 200 m to 5 km. The robustness of these estimates, derived from uniquley sampled, nearly equilateral triplets, is confirmed by comparisons with estimates produced from larger drifter clusters, and with estimates based on concurrent Eulerian X-band radar observations. The winter launches were deployed above a ∼80 m deep mixed layer, one in a region with nearly homogeneous horizontal density structure, the other in a region of strong surface density gradients associated with filaments of fresh Mississippi River water. The summer launches occurred in a shallow (10m) mixed layer, one launched across a mesoscale frontal jet separating regions of horizontally homogeneous density and the other, similar to the corresponding winter launch, also in a region filamented by shallow lenses of cold, fresh water. Seasonal differences are observed, with larger velocity fluctuations and greater variance in divergence and vorticity, especially at the smallest scales, in winter. Differences between same-season launches are, however, as large as seasonal differences. In both seasons, observations sampling regions directly impacted by fresh water fluxes show strongly skewed vorticity distributions, with cyclonic vorticity dominating strain. For the other launches, one in each season, strain dominated minimally skewed vorticity