Quinol Oxidase Encoded by \u3cem\u3ecyoABCD\u3c/em\u3e in \u3cem\u3eRhizobium etli\u3c/em\u3e CFN42 is Regulated by ActSR and is Crucial for Growth at Low pH or Low Iron Conditions

Rhizobium etli aerobically respires with several terminal oxidases. The quinol oxidase (Cyo) encoded by cyoABCD is needed for efficient adaptation to low oxygen conditions and cyo transcription is upregulated at low oxygen. This study sought to determine how transcription of the cyo operon is regulated. The 5′ sequence upstream of cyo was analysed in silico and revealed putative binding sites for ActR of the ActSR two-component regulatory system. The expression of cyo was decreased in an actSR mutant regardless of the oxygen condition. As ActSR is known to be important for growth under low pH in another rhizobial species, the effect of growth medium pH on cyo expression was tested. As the pH of the media was incrementally decreased, cyo expression gradually increased in the WT, eventually reaching ∼10-fold higher levels at low pH (4.8) compared with neutral pH (7.0) conditions. This upregulation of cyo under decreasing pH conditions was eliminated in the actSR mutant. Both the actSR and cyo mutants had severe growth defects at low pH (4.8). Lastly, the actSR and cyo mutants had severe growth defects when grown in media treated with an iron chelator. Under these conditions, cyo was upregulated in the WT, whereas cyo was not induced in the actSR mutant. Altogether, the results indicated cyo expression is largely dependent on the ActSR two-component system. This study also demonstrated additional physiological roles for Cyo in R. etli CFN42, in which it is the preferred oxidase for growth under acidic and low iron conditions

A Quinol Oxidase, Encoded by \u3cem\u3ecyoABCD\u3c/em\u3e, Is Utilized to Adapt to Lower O\u3csub\u3e2\u3c/sub\u3e Concentrations in \u3cem\u3eRhizobium etli\u3c/em\u3e CFN42

Bacteria have branched aerobic respiratory chains that terminate at different terminal oxidases. These terminal oxidases have varying properties such as their affinity for oxygen, transcriptional regulation and proton pumping ability. The focus of this study was a quinol oxidase encoded by cyoABCD. Although this oxidase (Cyo) is widespread among bacteria, not much is known about its role in the cell, particularly in bacteria that contain both cytochrome c oxidases and quinol oxidases. Using Rhizobium etli CFN42 as a model organism, a cyo mutant was analysed for its ability to grow in batch cultures at high (21 % O2) and low (1 and 0.1 % O2) ambient oxygen concentrations. In comparison with other oxidase mutants, the cyo mutant had a significantly longer lag phase under low-oxygen conditions. Using a cyo :: lacZ transcriptional fusion, it was shown that cyo expression in the wild type peaks between 1 and 2.5 % O2. In addition, it was shown with quantitative reverse transcriptase PCR that cyoB is upregulated approximately fivefold in 1 % O2 compared with fully aerobic (21 % O2) conditions. Analysis of the cyo mutant during symbiosis with Phaseolous vulgaris indicated that Cyo is utilized during early development of the symbiosis. Although it is commonly thought that Cyo is utilized only at higher oxygen concentrations, the results from this study indicate that Cyo is important for adaptation to and sustained growth under low oxygen

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses

Dystrophic calcification and heterotopic ossification in fibrocartilaginous tissues of the spine in diffuse idiopathic skeletal hyperostosis (DISH)

© 2020, The Author(s). Diffuse idiopathic skeletal hyperostosis (DISH) is a prevalent noninflammatory spondyloarthropathy characterized by ectopic mineral formation along the anterolateral aspect of the vertebral column, yet little is known about its underlying pathogenesis. Our objective was to evaluate the histopathological features and composition of ectopic mineral within spinal tissues affected by DISH in humans. Thoracic spine segments from six embalmed cadaveric donors (one female and five males; median age 82 years) meeting the radiographic diagnostic criteria for DISH were evaluated using radiological, histological, and physical analyses. Overall, the histological features of ectopic mineralization at individual motion segments were heterogeneous, including regions of heterotopic ossification and dystrophic calcification. Heterotopic ossifications were characterized by woven and lamellar bone, multifocal areas of metaplastic cartilage, and bony bridges along the anterior aspect of the intervertebral disc space. Dystrophic calcifications were characterized by an amorphous appearance, a high content of calcium and phosphorus, an X-ray diffraction pattern matching that of hydroxyapatite, and radiodensities exceeding that of cortical bone. Dystrophic calcifications were found within the anterior longitudinal ligament and annulus fibrosus in motion segments both meeting and not meeting the radiographic criteria for DISH. In summary, our findings indicate that in DISH, ectopic mineral forms along the anterior aspect of the spine by both heterotopic ossification and dystrophic calcification of fibrocartilaginous tissues. Although both types of ectopic mineralization are captured by current radiographic criteria for DISH, dystrophic calcification may reflect a distinct disease process or an early stage in the pathogenesis of DISH

HI in Arp72 and similarities with M51-type systems

We present neutral hydrogen (H{\sc i}) observations with the Giant Metrewave Radio Telescope ({\it GMRT}) of the interacting galaxies NGC5996 and NGC5994, which make up the Arp72 system. Arp72 is an M51-type system and shows a complex distribution of H{\sc i} tails and a bridge due to tidal interactions. H{\sc i} column densities ranging from 0.8$-1.8\times10^{20}$ atoms cm$^{-2}$ in the eastern tidal tail to 1.7$-2\times10^{21}$ atoms cm$^{-2}$ in the bridge connecting the two galaxies, are seen to be associated with star-forming regions. We discuss the morphological and kinematic similarities of Arp72 with M51, the archetypal example of the M51-type systems, and Arp86, another M51-type system studied with the {\it GMRT}, and suggest that a multiple passage model of Salo & Laurikainen may be preferred over the classical single passage model of Toomre & Toomre, to reproduce the H{\sc i} features in Arp72 as well as in other M-51 systems depicting similar optical and H{\sc i} features.Comment: 8 pages, 6 figures, accepted for publication in MNRA

CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the {\beta}-globin locus

The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional folding of a 1 Mbp region of human chromosome 11 containing the {\beta}-globin genes by integrating looping interactions of the insulator protein CTCF determined comprehensively by chromosome conformation capture (3C) into a polymer model of chromatin. We find that CTCF-mediated cell type specific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the {\beta}-globin locus control region (LCR) and genes. In these cells, the modeled {\beta}-globin domain folds into a globule with the LCR and the active globin genes on the periphery. By contrast, in non-erythroid cells, the globule is less compact with few but dominant CTCF interactions driving the genes away from the LCR. This leads to a decrease in contact frequencies that can exceed 1000-fold depending on the stiffness of the chromatin and the exact positioning of the genes. Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription.Comment: Full article, including Supp. Mat., is available at Nucleic Acids Research, doi: 10.1093/nar/gks53

Walking the walk: a phenomenological study of long distance walking

Evidence suggests that regular walking can elicit significant psychological benefits although little evidence exists concerning long distance walking. The purpose of this study was to provide detailed accounts of the experiences of long distance walkers. Phenomenological interviews were conducted with six long distance walkers. Data were transcribed verbatim before researchers independently analyzed the transcripts. Participants reported a cumulative effect with positive feelings increasing throughout the duration of the walk. Long distance walking elicited positive emotions, reduced the effects of life-stress, and promoted an increased sense of well-being and personal growth. Results are aligned to theories and concepts from positive psychology

Heavy Ion Microbeam and Broadbeam Transients in SiGe HBTs

SiGe HBT heavy ion current transients are measured using microbeam and both high- and low-energy broadbeam sources. These new data provide detailed insight into the effects of ion range, LET, and strike location