CRISPR Associated Diversity within a Population of Sulfolobus islandicus

Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats) are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations.We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population.The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population

Patient-Reported Outcomes in Free-Flap Breast Reconstructive Surgery over Time (PRO-BREST)

INTRODUCTION Patient-reported outcomes (PROMs) are increasingly relevant to assess surgical quality and guide decisions in breast reconstruction (BR). Satisfaction with outcomes may change as time progresses. We assessed satisfaction in patients who underwent free-flap BR in the last 12 years. METHODS All patients who underwent free-flap BR from 2006 to 2018 were invited to complete the validated BREAST-Q for reconstruction. The BREAST-Q comprises 6 domains covering various aspects of satisfaction. Unadjusted linear regression assessed the relationship between different domains of the BREAST-Q and time since BR. Two-sample t tests assessed differences in satisfaction between patients who underwent BR ≥5 years versus <5 years prior. RESULTS Forty-three women with primary or secondary free-flap BR between 2006 and 2018 were included in the study. Most patients (n = 33, 76.7%) underwent DIEP flap BR. Overall satisfaction with breasts and with outcomes improved as time since BR increased (p = 0.031 and p = 0.017, respectively). Overall satisfaction with outcomes scored higher in patients with BR ≥5 years prior (≥5 years vs. <5 years: breast score 88.6 (SD 12.5) versus 66.9 (SD 21.8); p = 0.005). Satisfaction with breasts and psychosocial well-being also scored higher in these patients. There was no difference in results between primary and secondary BR. Patients who underwent additional surgery (refinements) reported higher satisfaction with outcomes and abdominal well-being. CONCLUSIONS PROMs concerning satisfaction with breast and with outcomes following BR improve as time since treatment progresses. This study demonstrates that time since diagnosis may be an important factor in satisfaction. It underlines the importance of long-term PROMs related to BR, to help provide patients and health care professionals in decision-making and in managing expectations related to BR

Patellar Tendon Shear Wave Velocity Is Higher and has Different Regional Patterns in Elite Competitive Alpine Skiers than in Healthy Controls

Competitive alpine skiers are exposed to enormous forces acting on their bodies-particularly on the knee joint and hence the patellar tendon - during both the off-season preparation and in-season competition phases. However, factors influencing patellar tendon adaptation and regional pattern differences between alpine skiers and healthy controls are not yet fully understood, but are essential for deriving effective screening approaches and preventative countermeasures. Thirty elite competitive alpine skiers, all members of the Swiss Alpine Ski Team, and 38 healthy age-matched controls were recruited. A set of two-dimensional shear wave elastography measurements of the PT was acquired and projected into three-dimensional space yielding a volumetric representation of the shear wave velocity profile of the patellar tendon. Multivariate linear models served to quantify differences between the two cohorts and effects of other confounding variables with respect to regional shear wave velocity. A significant (p < 0.001) intergroup difference was found between skiers (mean ± SD = 10.4 ± 1.32 m/s) and controls (mean ± SD = 8.9 ± 1.59 m/s). A significant sex difference was found within skiers (p = 0.024), but no such difference was found in the control group (p = 0.842). Regional SWV pattern alterations between skiers and controls were found for the distal region when compared to the mid-portion (p = 0.023). Competitive alpine skiers exhibit higher SWV in all PT regions than healthy controls, potentially caused by long-term adaptations to heavy tendon loading. The presence of sex-specific differences in PT SWV in skiers but not in controls indicates that sex effects have load-dependent dimensions. Alterations in regional SWV patterns between skiers and controls suggest that patellar tendon adaptation is region specific. In addition to the implementation of 3D SWE, deeper insights into long-term tendon adaptation and normative values for the purpose of preventative screening are provided

Lack of growth enhancement by exogenous growth hormone treatment in yellow perch (Perca flavescens) in four separate experiments

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B. V. for personal use, not for redistribution. The definitive version was published in Aquaculture 250 (2005): 471-479, doi:10.1016/j.aquaculture.2005.03.019.The effect of exogenous growth hormone (GH) treatment on the growth of juvenile yellow perch (Perca flavescens) was investigated in four experiments. In the first two experiments, juvenile yellow perch were reared at either 13°C or 21°C, and injected weekly with bovine GH (bGH) at 0.1, 1.0 or 10.0 μg/g body weight for 84 days. No significant growth enhancement in GH-treated fish was measured in fish in either of the experiments. In the third experiment, juvenile yellow perch were treated with estradiol-17β (E2, 15 μg/g of diet), bGH (1.0 μg/g body weight) injected weekly or both hormones for 70 days at 21°C. E2 alone stimulated growth, but no further growth stimulation occurred in the E2 + bGH-treated fish. In addition, no growth enhancement was found in fish treated with bGH alone. We measured no difference in serum insulin-like growth factor-I (IGF-I) levels between the treatment groups at 12 and 24 h after the final injection of GH; however, a drop in IGF-I levels after 24 h was observed. In a fourth study, the effect of recombinant yellow perch GH (rypGH, 0.2 or 1.0 μg/g body weight) injected weekly was evaluated in yellow perch juveniles. The fish were reared for 42 days at 18°C. Neither GH dosages improved growth compared to control-injected and non-injected fish. Taken together, the lack of effect of mammalian GH or rypGH in our experiments suggests (1) low binding affinity between these hormones and the GH receptor in yellow perch, (2) that the endogenous GH levels were already at biologically maximal levels or (3) that other endocrine factors are needed in order for GH to promote yellow perch growth. The reduction in IGF-I levels 24 h after handling suggests a negative effect of handling stress on the GH-IGF-I axis in yellow perch.This work was supported by the University of Wisconsin-Madison College of Agricultural and Life Sciences and School of Natural Resources; the Wisconsin Department of Natural Resources; the University of Wisconsin Sea Grant College Program, National Oceanic and Atmospheric Administration, US Department of Commerce; the State of Wisconsin (Federal Grant NA46RG0481, Project No. R/AQ-38); and the USDA NOAA Project R/A-05-99, grant #NA86RG0048 to FG and SR. This study was also funded by the Norwegian Research Council (NFR)

Mass deposition fluxes of Saharan mineral dust to the tropical northeast Atlantic Ocean: an intercomparison of methods

Mass deposition fluxes of mineral dust to the tropical northeast Atlantic Ocean were determined within this study. In the framework of SOPRAN (Surface Ocean Processes in the Anthropocene), the interaction between the atmosphere and the ocean in terms of material exchange were investigated at the Cape Verde atmospheric observatory (CVAO) on the island Sao Vicente for January 2009. Five different methods were applied to estimate the deposition flux, using different meteorological and physical measurements, remote sensing, and regional dust transport simulations. The set of observations comprises micrometeorological measurements with an ultra-sonic anemometer and profile measurements using 2-D anemometers at two different heights, and microphysical measurements of the size-resolved mass concentrations of mineral dust. In addition, the total mass concentration of mineral dust was derived from absorption photometer observations and passive sampling. The regional dust model COSMO-MUSCAT was used for simulations of dust emission and transport, including dry and wet deposition processes. This model was used as it describes the AOD's and mass concentrations realistic compared to the measurements and because it was run for the time period of the measurements. The four observation-based methods yield a monthly average deposition flux of mineral dust of 12–29 ng m−2 s−1. The simulation results come close to the upper range of the measurements with an average value of 47 ng m−2 s−1. It is shown that the mass deposition flux of mineral dust obtained by the combination of micrometeorological (ultra-sonic anemometer) and microphysical measurements (particle mass size distribution of mineral dust) is difficult to compare to modeled mass deposition fluxes when the mineral dust is inhomogeneously distributed over the investigated area

Patterns of Gene Flow Define Species of Thermophilic Archaea

A genomic view of speciation in Archaea shows higher rates of gene flow within coexisting microbial species than between them

Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins

Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (∼12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication

Altered DNA Methylation in Leukocytes with Trisomy 21

The primary abnormality in Down syndrome (DS), trisomy 21, is well known; but how this chromosomal gain produces the complex DS phenotype, including immune system defects, is not well understood. We profiled DNA methylation in total peripheral blood leukocytes (PBL) and T-lymphocytes from adults with DS and normal controls and found gene-specific abnormalities of CpG methylation in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function. Validation of the microarray data by bisulfite sequencing and methylation-sensitive Pyrosequencing (MS-Pyroseq) confirmed strong differences in methylation (p<0.0001) for each of 8 genes tested: TMEM131, TCF7, CD3Z/CD247, SH3BP2, EIF4E, PLD6, SUMO3, and CPT1B, in DS versus control PBL. In addition, we validated differential methylation of NOD2/CARD15 by bisulfite sequencing in DS versus control T-cells. The differentially methylated genes were found on various autosomes, with no enrichment on chromosome 21. Differences in methylation were generally stable in a given individual, remained significant after adjusting for age, and were not due to altered cell counts. Some but not all of the differentially methylated genes showed different mean mRNA expression in DS versus control PBL; and the altered expression of 5 of these genes, TMEM131, TCF7, CD3Z, NOD2, and NPDC1, was recapitulated by exposing normal lymphocytes to the demethylating drug 5-aza-2′deoxycytidine (5aza-dC) plus mitogens. We conclude that altered gene-specific DNA methylation is a recurrent and functionally relevant downstream response to trisomy 21 in human cells

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses

To understand neurological complications of COVID-19 better both acutely and for recovery, we measured markers of brain injury, inflammatory mediators, and autoantibodies in 203 hospitalised participants; 111 with acute sera (1–11 days post-admission) and 92 convalescent sera (56 with COVID-19-associated neurological diagnoses). Here we show that compared to 60 uninfected controls, tTau, GFAP, NfL, and UCH-L1 are increased with COVID-19 infection at acute timepoints and NfL and GFAP are significantly higher in participants with neurological complications. Inflammatory mediators (IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) are associated with both altered consciousness and markers of brain injury. Autoantibodies are more common in COVID-19 than controls and some (including against MYL7, UCH-L1, and GRIN3B) are more frequent with altered consciousness. Additionally, convalescent participants with neurological complications show elevated GFAP and NfL, unrelated to attenuated systemic inflammatory mediators and to autoantibody responses. Overall, neurological complications of COVID-19 are associated with evidence of neuroglial injury in both acute and late disease and these correlate with dysregulated innate and adaptive immune responses acutely