Warming signals in temperate reef communities following more than a decade of ecological stability.

Ecosystem structure and function are increasingly threatened by changing climate, with profound effects observed globally in recent decades. Based on standardized visual censuses of reef biodiversity, we describe 27 years of community-level change for fishes, mobile macroinvertebrates and macroalgae in the Tasmanian ocean-warming hotspot. Significant ecological change was observed across 94 reef sites (5-10 m depth range) spanning four coastal regions between three periods (1992-95, 2006-07, 2017-19), which occurred against a background of pronounced sea temperature rise (+0.80°C on average). Overall, fish biomass increased, macroinvertebrate species richness and abundance decreased and macroalgal cover decreased, particularly during the most recent decade. While reef communities were relatively stable and warming was slight between the 1990s and mid-2000s (+0.12°C mean temperature rise), increased abundances of warm affinity fishes and invertebrates accompanied warming during the most recent decade (+0.68°C rise). However, significant rises in the community temperature index (CTI) were only found for fishes, invertebrates and macroalgae in some regions. Coastal warming was associated with increased fish biomass of non-targeted species in fished zones but had little effect on reef communities within marine reserves. Higher abundances of larger fishes and lobsters inside reserves appeared to negate impacts of 'thermophilization'.

Plasma lipidome reveals critical illness and recovery from human Ebola virus disease.

Ebola virus disease (EVD) often leads to severe and fatal outcomes in humans with early supportive care increasing the chances of survival. Profiling the human plasma lipidome provides insight into critical illness as well as diseased states, as lipids have essential roles as membrane structural components, signaling molecules, and energy sources. Here we show that the plasma lipidomes of EVD survivors and fatalities from Sierra Leone, infected during the 2014-2016 Ebola virus outbreak, were profoundly altered. Focusing on how lipids are associated in human plasma, while factoring in the state of critical illness, we found that lipidome changes were related to EVD outcome and could identify states of disease and recovery. Specific changes in the lipidome suggested contributions from extracellular vesicles, viremia, liver dysfunction, apoptosis, autophagy, and general critical illness, and we identified possible targets for therapies enhancing EVD survival.

Production of mobile invertebrate communities on shallow reefs from temperate to tropical seas.

Primary productivity of marine ecosystems is largely driven by broad gradients in environmental and ecological properties. By contrast, secondary productivity tends to be more variable, influenced by bottom-up (resource-driven) and top-down (predatory) processes, other environmental drivers, and mediation by the physical structure of habitats. Here, we use a continental-scale dataset on small mobile invertebrates (epifauna), common on surfaces in all marine ecosystems, to test influences of potential drivers of temperature-standardized secondary production across a large biogeographic range. We found epifaunal production to be remarkably consistent along a temperate to tropical Australian latitudinal gradient of 28.6°, spanning kelp forests to coral reefs (approx. 3500 km). Using a model selection procedure, epifaunal production was primarily related to biogenic habitat group, which explained up to 45% of total variability. Production was otherwise invariant to predictors capturing primary productivity, the local biomass of fishes (proxy for predation pressure), and environmental, geographical, and human impacts. Highly predictable levels of epifaunal productivity associated with distinct habitat groups across continental scales should allow accurate modelling of the contributions of these ubiquitous invertebrates to coastal food webs, thus improving understanding of likely changes to food web structure with ocean warming and other anthropogenic impacts on marine ecosystems.

Activated ClpP kills persisters and eradicates a chronic biofilm infection.

Chronic infections are difficult to treat with antibiotics but are caused primarily by drug-sensitive pathogens. Dormant persister cells that are tolerant to killing by antibiotics are responsible for this apparent paradox. Persisters are phenotypic variants of normal cells and pathways leading to dormancy are redundant, making it challenging to develop anti-persister compounds. Biofilms shield persisters from the immune system, suggesting that an antibiotic for treating a chronic infection should be able to eradicate the infection on its own. We reasoned that a compound capable of corrupting a target in dormant cells will kill persisters. The acyldepsipeptide antibiotic (ADEP4) has been shown to activate the ClpP protease, resulting in death of growing cells. Here we show that ADEP4-activated ClpP becomes a fairly nonspecific protease and kills persisters by degrading over 400 proteins, forcing cells to self-digest. Null mutants of clpP arise with high probability, but combining ADEP4 with rifampicin produced complete eradication of Staphylococcus aureus biofilms in vitro and in a mouse model of a chronic infection. Our findings indicate a general principle for killing dormant cells-activation and corruption of a target, rather than conventional inhibition. Eradication of a biofilm in an animal model by activating a protease suggests a realistic path towards developing therapies to treat chronic infections.

The response of tenocytes to commercial scaffolds used for rotator cuff repair.

Surgical repairs of rotator cuff tears have high re-tear rates and many scaffolds have been developed to augment the repair. Understanding the interaction between patients' cells and scaffolds is important for improving scaffold performance and tendon healing. In this in vitro study, we investigated the response of patient-derived tenocytes to eight different scaffolds. Tested scaffolds included X-Repair, Poly-Tape, LARS Ligament, BioFiber (synthetic scaffolds), BioFiber-CM (biosynthetic scaffold), GraftJacket, Permacol, and Conexa (biological scaffolds). Cell attachment, proliferation, gene expression, and morphology were assessed. After one day, more cells attached to synthetic scaffolds with dense, fine and aligned fibres (X-Repair and Poly-Tape). Despite low initial cell attachment, the human dermal scaffold (GraftJacket) promoted the greatest proliferation of cells over 13 days. Expression of collagen types I and III were upregulated in cells grown on non-cross-linked porcine dermis (Conexa). Interestingly, the ratio of collagen I to collagen III mRNA was lower on all dermal scaffolds compared to synthetic and biosynthetic scaffolds. These findings demonstrate significant differences in the response of patient-derived tendon cells to scaffolds that are routinely used for rotator cuff surgery. Synthetic scaffolds promoted increased cell adhesion and a tendon-like cellular phenotype, while biological scaffolds promoted cell proliferation and expression of collagen genes. However, no single scaffold was superior. Our results may help understand the way that patients' cells interact with scaffolds and guide the development of new scaffolds in the future.

Comparison of reliability, construct validity and responsiveness of the IPAQ-SF and PASE in adults with osteoarthritis.

BACKGROUND: This study assessed the measurement properties of two commonly used self-report physical activity (PA) measures: the International Physical Activity Questionnaire-Short Form (IPAQ-SF) and the Physical Activity Scale for the elderly (PASE) in adults with osteoarthritis. METHODS: Secondary analysis of the MOSAICS cluster randomised controlled trial baseline and 3-month follow-up questionnaires, total scores and subdomains of the IPAQ-SF and PASE were compared. Intra-class correlations (ICC) were used to assess test-retest reliability, measurement error was assessed using standard error of measurement (SEM), smallest detectable change (SDC) and 95% limits of agreement (LoA). Responsiveness was assessed using effect size (ES), standard responsive measurement (SRM) and response ratio (RR). RESULTS: There was moderate correlation (r = 0.56) between the total IPAQ-SF scores (score ranges 0-16,398) and the total PASE scores (score ranges 0-400). Subdomain correlations were also moderate (ranges 0.39-0.57). The PASE showed greater reliability compared to the IPAQ-SF (ICC = 0.68; 0.61-0.74 95% CI and ICC = 0.64; 0.55-0.72, respectively). Measurement errors in both measures were large: PASE SEM = 46.7, SDC = 129.6 and 95% LoA ranges = -117 to 136, the IPAQ-SF SEM = 3532.2 METS-1 min-1 week , SDC = 9790.8 and 95% LoA ranges = -5222 to 5597. Responsiveness was poor: ES -0.14 and -0.16, SRM -0.21 and -0.21, and RR 0.12 and 0.09 for the IPAQ-SF and PASE, respectively. DISCUSSION: The IPAQ-SF and PASE appear limited in reliability, measurement error and responsiveness. Researchers and clinicians should be aware of these limitations, particularly when comparing different levels of PA and monitoring PA levels changes over time in those with osteoarthritis.

Developmental changes in the germinability, desiccation tolerance, hardseededness, and longevity of individual seeds of Trifolium ambiguum.

BACKGROUND AND AIMS: Using two parental clones of outcrossing Trifolium ambiguum as a potential model system, we examined how during seed development the maternal parent, number of seeds per pod, seed position within the pod, and pod position within the inflorescence influenced individual seed fresh weight, dry weight, water content, germinability, desiccation tolerance, hardseededness, and subsequent longevity of individual seeds. METHODS: Near simultaneous, manual reciprocal crosses were carried out between clonal lines for two experiments. Infructescences were harvested at intervals during seed development. Each individual seed was weighed and then used to determine dry weight or one of the physiological behaviour traits. KEY RESULTS: Whilst population mass maturity was reached at 33-36 days after pollination (DAP), seed-to-seed variation in maximum seed dry weight, when it was achieved, and when maturation drying commenced, was considerable. Individual seeds acquired germinability between 14 and 44 DAP, desiccation tolerance between 30 and 40 DAP, and the capability to become hardseeded between 30 and 47 DAP. The time for viability to fall to 50 % (p(50)) at 60 % relative humidity and 45 degrees C increased between 36 and 56 DAP, when the seed coats of most individuals had become dark orange, but declined thereafter. Individual seed f. wt at harvest did not correlate with air-dry storage survival period. Analysing survival data for cohorts of seeds reduced the standard deviation of the normal distribution of seed deaths in time, but no sub-population showed complete uniformity of survival period. CONCLUSIONS: Variation in individual seed behaviours within a developing population is inherent and inevitable. In this outbreeder, there is significant variation in seed longevity which appears dependent on embryo genotype with little effect of maternal genotype or architectural factors.

Primary sequence information from intact proteins by electrospray ionization tandem mass spectrometry.

Tandem mass spectrometry has been used to obtain information related to portions of the primary sequence for an intact protein, bovine ribonuclease A. Multiply charged molecular ions, generated by electrospray ionization, were collisionally dissociated at low energies in a triple quadrupole mass spectrometer to yield singly and multiply charged fragment ions that can be assigned to the known sequence of the protein. Dissociation of the highly charged molecular ions resulted in pairs of complementary product ions. The higher order (gas-phase) protein structure affects the dissociation processes, as observed in comparisons of tandem mass spectra of the native and disulfide-reduced forms of ribonuclease A.

Bovine babesiosis: protection of cattle with culture-derived soluble Babesia bovis antigen.

Adult Hereford (Bos taurus) cattle were protected from severe reactions and death caused by the tick-borne protozoan hemoparasite Babesia bovis, 3 months after vaccination with a cell culture--derived immunogen. The immunogen consisted of filtered, freeze-dried supernatant fluid collected from long-term cultures of Babesia bovis in vitro. It was reconstituted with saponin adjuvant and injected twice subcutaneously at 2-week intervals. Serum collected from vaccinated cattle caused thickening of the merozoite surface coat, aggregation, and lysis of merozoites in vitro. This reaction was identical to that caused by serum from immune carrier cattle suggesting that the protective antigen present in culture fluids is merozoite surface coat antigen. No mortality occurred among vaccinated cattle, whereas mortality among unvaccinated cattle and Babesia bigemina--immune cattle was 62.5 percent indicating that immunity to bovine babesiosis is species-specific.

Interaction of a protein phosphatase with an Arabidopsis serine-threonine receptor kinase.

A protein phosphatase was cloned that interacts with a serine-threonine receptor-like kinase, RLK5, from Arabidopsis thaliana. The phosphatase, designated KAPP (kinase-associated protein phosphatase), is composed of three domains: an amino-terminal signal anchor, a kinase interaction (KI) domain, and a type 2C protein phosphatase catalytic region. Association of RLK5 with the KI domain is dependent on phosphorylation of RLK5 and can be abolished by dephosphorylation. KAPP may function as a signaling component in a pathway involving RLK5.

Post-abscission, pre-dispersal seeds of Digitalis purpurea remain in a developmental state that is not terminated by desiccation ex planta.

BACKGROUND AND AIMS: Seed quality may be compromised if seeds are harvested before natural dispersal (shedding). It has been shown previously that slow or delayed drying can increase potential quality compared with immediate rapid drying. This study set out to investigate whether or not there is a critical moisture content, below which drying terminates maturation events for seeds harvested after mass maturity but before dispersal. METHODS: Seeds of foxglove (Digitalis purpurea) in the post-abscission pre-dispersal phase were held at between 15 and 95 % RH for 4 or 8 d, with or without re-hydration to 95 % RH for a further 4 d, before drying to equilibrium at 15 % RH. In addition, dry seeds were primed for 48 h at -1 MPa. Subsequent seed longevity was assessed at 60 % RH and 45 degrees C. KEY RESULTS: Rate of germination and longevity were improved by holding seeds at a wide range of humidities after harvest. Longevity was further improved by re-hydration at 95 % RH. Priming improved the longevity of the seeds dried immediately after harvest, but not of those first held at 95 % RH for 8 d prior to drying. CONCLUSIONS: Maturation continued ex planta in these post-abscission, pre-dispersal seeds of D. purpurea dried at 15-80 % RH at a rate correlated positively with RH (cf. ageing of mature seeds). Subsequent re-hydration at 95 % RH enabled a further improvement in quality. Priming seeds initially stored air-dry for 3 months also allowed maturation events to resume. However, once individual seeds within the population had reached maximum longevity, priming had a negative impact on their subsequent survival.

Priming and re-drying improve the survival of mature seeds of Digitalis purpurea during storage.

BACKGROUND AND AIMS: Most priming studies have been conducted on commercial seed lots of unspecified uniformity and maturity, and subsequent seed longevity has been reported to both increase and decrease. Here a seed lot of Digitalis purpurea L. with relatively uniform maturity and known history was used to analyse the effects of priming on seed longevity in air-dry storage. METHODS: Seeds collected close to natural dispersal and dried at 15% relative humidity (RH), 15 degrees C, were placed into experimental storage (60% RH, 45 degrees C) for 14 or 28 d, primed for 48 h at 0, -1, -2, -5, -10 or -15 MPa, re-equilibrated (47% RH, 20 degrees C) and then returned to storage. Further seed samples were primed for 2 or 48 h at -1 MPa and either dried at 15% RH, 15 degrees C or immediately re-equilibrated for experimental storage. Finally, some seeds were given up to three cycles of experimental storage and priming (48 h at -1 MPa). KEY RESULTS: Priming at -1 MPa had a variable effect on subsequent survival during experimental storage. The shortest lived seeds in the control population showed slightly increased life spans; the longer lived seeds showed reduced life spans. In contrast, seeds first stored for 14 or 28 d before priming had substantially increased life spans. The increase tended to be greatest in the shortest lived fraction of the seed population. Both the period of rehydration and the subsequent drying conditions had significant effects on longevity. Interrupting air-dry storage with additional cycles of priming also increased longevity. CONCLUSIONS: The extent of prior deterioration and the post-priming desiccation environment affect the benefits of priming to the subsequent survival of mature seeds. Rehydration-dehydration treatments may have potential as an adjunct or alternative to the regeneration of seed accessions maintained in gene banks for plant biodiversity conservation or plant breeding.

Case selection for urological input in planned laparoscopic rectovaginal endometriosis surgery.

BACKGROUND: Surgery for deep endometriosis often requires input from urological surgeons. This study aims to determine pre-operative and intra-operative factors that influence the need for urological input in laparoscopic resection of rectovaginal endometriosis and to assess the usefulness of a scoring system to predict this. METHODS: We conducted a retrospective cohort study of 230 patients undergoing laparoscopic excision of deep endometriosis, at a tertiary referral centre for endometriosis in London UK, 2011 to 2015. Data from pre-operative assessment, surgery and post-operative follow up were analysed and patients were categorised according to their pre-operative and intra-operative risk factors. The primary outcome measure was the requirement of intra-operative input by urological surgeons. RESULTS: The median age was 35 years. In addition to the excision of endometriosis, 19.6% patients (45 patients) underwent hysterectomy, 14.8% (34 patients) required JJ stent placement, 6.1% (14 patients) had bowel resections and 2.6% (6 patients) required an ileostomy. 93.9% (216 patients) were considered normal-risk pre-operatively, of whom 89.4% (193/216) did not require any intra-operative urological input. 10.6% of this normal-risk group (23/216) required JJ stents, of whom 69.6% (16/23) also required a hysterectomy or bowel resection. Post operative complications occurred in 0.9% (2/216) of normal-risk patients, with none having required intra-operative urological reconstruction.Six percent (14 patients) were deemed to be increased-risk pre-operatively, of whom 78.6% (11/14) required JJ stent insertion. Thirty-six percent of increased-risk patients (5/14) had pre-operative renal dysfunction demonstrated on MAG3/DMSA and 80.0% of these (4/5) required intra-operative ureteric reconstruction. CONCLUSIONS: Patients considered normal-risk pre-operatively, planned for excision, without hysterectomy or bowel resection, can be safely managed without specific urology input. Patients with risk-features are highly likely to require urological input, particularly for JJ stent insertion. Patients with pre-operative renal dysfunction, demonstrated on MAG3/DMSA, have a high chance of requiring intra-operative ureteric reconstruction and are best managed with pre-planned reconstructive urologist input.

Dry versus wet aging of beef: Retail cutting yields and consumer palatability evaluations of steaks from US Choice and US Select short loins.

Paired beef short loins from US Choice (n=48) and US Select (n=48) carcasses were assigned to be dry or wet aged for 14, 21, 28 or 35d. After aging, short loins were processed to determine retail yields and processing times. Upon completion of cutting tests, steaks were served to consumers to assess palatability characteristics. Retail cutting tests showed that dry-aged short loins had reduced yields and increased cutting times when compared to wet-aged short loins. Consumers were unable to determine differences between dry- and wet-aged steaks and for aging periods; however, USDA quality grade had a significant impact on consumer perception of palatability attributes.

Dry versus wet aging of beef: Retail cutting yields and consumer sensory attribute evaluations of steaks from ribeyes, strip loins, and top sirloins from two quality grade groups.

Top Choice (n=48) and Select (n=48) paired bone-in ribeye rolls, bone-in strip loins, and boneless top sirloin butts were assigned randomly to one of two aging treatments, dry or wet, and were aged for 14, 21, 28 or 35d. Cutting tests, performed to determine retail yields and processing times, showed dry-aged subprimals had lower total saleable yield percentages and increased processing times compared to wet-aged subprimals. Sensory and Warner-Bratzler shear evaluation was conducted to determine palatability characteristics. For the most part, aging treatment and aging period did not affect consumer sensory attributes. However, ribeye and top loin steaks from the Top Choice quality grade group received higher sensory ratings than their Select counterparts. For top sirloin steaks, no consumer sensory attributes were affected by aging treatment, aging period, or quality grade group.

Pollution signature for temperate reef biodiversity is short and simple.

Pollution increasingly impacts healthy functioning of marine ecosystems globally. Here we quantify concentrations of major pollutant types (heavy metals/sewage/petrochemicals/plastics) as accumulated within marine sediments on and/or immediately adjacent to shallow reefs for 42 sites spanning coastal population centres across south-eastern Australia. Gradients in pollutants were revealed, but few pollutants co-varied, while increasing wave exposure ostensibly diluted concentrations of all pollutants except microplastics. Examination of reef biodiversity indicators revealed that maximum size of fauna and flora, a key life-history parameter summarised by the Community shortness index, plus declining functional and species richness, were the most sensitive bioindicators of pollutants - for which heavy metals and nutrient-enrichment were most pervasive. Results indicate that assemblages of biogenic habitat formers and associated fauna collapse from "long and complicated" to "short and simplified" configurations in response to increasing pollution, and this community signature may form an effective bioindicator to track human-driven degradation.

Isolation of the galactose-binding lectin that mediates the in vitro adherence of Entamoeba histolytica.

Entamoeba histolytica adheres to human colonic mucus, colonic epithelial cells, and other target cells via a galactose (Gal) or N-acetyl-D-galactosamine (GalNAc) inhibitable surface lectin. Blockade of this adherence lectin with Gal or GalNAc in vitro prevents amebic killing of target cells. We have identified and purified the adherence lectin by two methods: affinity columns derivatized with galactose monomers or galactose terminal glycoproteins, and affinity columns and immunoblots prepared with monoclonal antibodies that inhibit amebic adherence. By both methods the adherence lectin was identified as a 170-kD secreted and membrane-bound amebic protein. The surface location of the lectin was confirmed by indirect immunofluorescence. Purified lectin competitively inhibited amebic adherence to target cells by binding to receptors on the target Chinese hamster ovary cells in a Gal-inhibitable manner.

Mechanical properties of all-suture anchors for rotator cuff repair.

OBJECTIVES: All-suture anchors are increasingly used in rotator cuff repair procedures. Potential benefits include decreased bone damage. However, there is limited published evidence for the relative strength of fixation for all-suture anchors compared with traditional anchors. MATERIALS AND METHODS: A total of four commercially available all-suture anchors, the 'Y-Knot' (ConMed), Q-FIX (Smith & Nephew), ICONIX (Stryker) and JuggerKnot (Zimmer Biomet) and a traditional anchor control TWINFIX Ultra PK Suture Anchor (Smith & Nephew) were tested in cadaveric human humeral head rotator cuff repair models (n = 24). This construct underwent cyclic loading applied by a mechanical testing rig (Zwick/Roell). Ultimate load to failure, gap formation at 50, 100, 150 and 200 cycles, and failure mechanism were recorded. Significance was set at p < 0.05. RESULTS: Overall, mean maximum tensile strength values were significantly higher for the traditional anchor (181.0 N, standard error (se) 17.6) compared with the all-suture anchors (mean 133.1 N se 16.7) (p = 0.04). The JuggerKnot anchor had greatest displacement at 50, 100 and 150 cycles, and at failure, reaching statistical significance over the control at 100 and 150 cycles (22.6 mm se 2.5 versus 12.5 mm se 0.3; and 29.6 mm se 4.8 versus 17.0 mm se 0.7). Every all-suture anchor tested showed substantial (> 5 mm) displacement between 50 and 100 cycles (6.2 to 14.3).All-suture anchors predominantly failed due to anchor pull-out (95% versus 25% of traditional anchors), whereas a higher proportion of traditional anchors failed secondary to suture breakage. CONCLUSION: We demonstrate decreased failure load, increased total displacement, and variable failure mechanisms in all-suture anchors, compared with traditional anchors designed for rotator cuff repair. These findings will aid the surgeon's choice of implant, in the context of the clinical scenario.Cite this article: N. S. Nagra, N. Zargar, R. D. J. Smith, A. J. Carr. Mechanical properties of all-suture anchors for rotator cuff repair. Bone Joint Res 2017;6:82-89. DOI: 10.1302/2046-3758.62.BJR-2016-0225.R1.

Quantitative analysis of globin gene induction in single human erythroleukemic cells.

The mechanisms involved in the normal developmental regulation of globin gene expression, and the response to pharmacological agents that elevate fetal hemoglobin, may be expected to involve either changes in each cell or a selection process affecting subsets of differentiating erythroid cells. To study these mechanisms we have developed assays to measure mRNA levels in single erythroid cells. The assay involved the use of globin-specific probes, with no detectable cross-reactivity, in real-time, fluorescence-based quantitative PCR (Q-PCR). We had previously used this Q-PCR method to measure globin mRNA levels in cultures of primary erythroid cells demonstrating that drugs like hydroxyurea, 5-azacytidine and butyric acid each yielded increases in gamma/( gamma + ss) mRNA ratios, with differential effects on ss-globin levels. We have now extended this approach to measure globin mRNA levels in single K562 cells, a human erythroleukemic cell line, with and without 30 microM hemin treatment. Hemin exposure increases total hemoglobin levels by approximately 9-fold and total alpha-, epsilon- and gamma-globin mRNA levels by 1.5-2.3-fold. Single cell analyses showed initial wide distributions of each of the three individual globin mRNA levels with most cells having detectable but very low levels of each globin transcript. Hemin induction shifted the distributions to higher levels, with a tendency to residual left skewing as some cells remained with very low expression levels despite the effect of hemin in increasing expression in most of these low expressing cells. Thus transcriptional heterogeneity remains a crucial variable, even in this extensively used model of human erythroid biology, and clearly influences strongly the response to inducing agents. These methods may enable us to define better possible molecular and/or cellular models of globin gene modulation.