Genomic sequence analysis reveals diversity of Australian Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli.

BACKGROUND: The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity. RESULTS: Phylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria. Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads. CONCLUSIONS: The phylogeny presented here confirmed X. vesicatoria, X. arboricola, X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations.

Towards area wide management of insect vectored viruses of tomatoes in the Bowen district.

The Bowen region of Northern Queensland is an important winter production area for tomatoes in Australia. There are three economically important viruses in the region that affect tomato, Tomato yellow leaf curl virus (TYLCV), Tomato spotted wilt virus (TSWV) and Potato leafroll virus (PLRV), which are vectored by whiteflies, thrips and aphids, respectively. An area wide management approach is required to lower the primary inoculum throughout the district. To this end, we undertook investigations into the virus incidence and alternative hosts for the virus and vectors in different cropping regions throughout the district, as well as local management options such as insecticide application and possible non-host cover crops for the wet-season break in production. The initial incidence of Potato leafroll virus was very high, most probably due to abnormal weather patterns for the district, and has ceased to be a problem. Tomato yellow leaf curl virus is a continual problem even at the beginning of the season, indicating large reservoir host(s) in the environment. Only four alternative hosts have been identified: Stachytarpheta jamaicensis (TSWV), Solanum americanum (PLRV and TYLCV) Trianthema portulacastrum (TYLCV), and Amaranthus viridis(TLYCV). Different insecticide and application options were trialled for protection against Tomato yellow leaf curl virus, with the best possible option yielding marketable fruit more than ninety percent of a resistant hybrid. A trial of yield vs time of infection of TYLCV found that whitefly exclusion for 6 weeks post-transplant yielded an average increase of nearly three kilograms of marketable fruit per plant. A number of pulse crops have been confirmed as non-hosts of tomato yellow leaf curl for use as cover crops in the wet-season break. Most of the production has moved to dual resistant TYLCV/TSWV hybrids, though an area wide management program still needs to be established to reduce the primary inoculum throughout the district, giving growers more varietal options, especially early in the season.

Impact of CFTR Modulation on Intestinal pH, Motility, and Clinical Outcomes in Patients With Cystic Fibrosis and the G551D Mutation.

OBJECTIVES: A defect in bicarbonate secretion contributes to the pathophysiology of gastrointestinal complications in patients with cystic fibrosis (CF). We measured gastrointestinal pH, clinical outcomes, and intestinal transit profiles in patients with the G551D mutation before and after treatment with ivacaftor, a CF transmembrane regulator channel (CFTR) potentiator. METHODS: Observational studies of ivacaftor effectiveness were conducted in the United States and Canada. A subset of subjects ingested a wireless motility capsule (n=10) that measures in vivo pH, both before therapy with ivacaftor and 1 month after treatment; values obtained were compared for mean pH and area under the pH curve, and regional intestinal motility. We also queried subjects about abdominal pain and recorded body weight before and after treatment. RESULTS: One month after administering ivacaftor, a significant increase in mean pH was observed after gastric emptying (P<0.05). Area under the pH curve analyses indicate increased bicarbonate mass (P<0.05 for select 5 min intervals and all segments >30 min); mean weight gain was 1.1 kg (P=0.08). No difference in abdominal pain or regional transit times was seen. CONCLUSIONS: CFTR modulation improves the proximal small intestinal pH profile in patients with the G551D CFTR mutation and we observed clinically relevant, contemporaneous weight gain, although it did not reach statistical significance. These data provide in vivo evidence that CFTR is an important regulator of bicarbonate secretion, which may be a translational link between CFTR function and clinical improvement.

Sex difference in the risk of recurrent venous thrombosis: a detailed analysis in four European cohorts.

BACKGROUND: Previous analyses reported a higher risk of recurrent venous thrombosis in men than women. OBJECTIVES: We aimed to assess the risk of recurrence in men compared with women whilst taking female reproductive risk factors (oral contraception, postmenopausal hormone therapy and pregnancy) into account. In addition, we hypothesized that the sex difference in venous thrombosis was related to F9 Malmö, an X-linked prothrombotic factor. METHODS: In four pooled European cohorts (CARROT study, Glasgow, UK; CVTE study, Cambridge, UK; AUREC study, Vienna, Austria; and LETS follow-up study, Leiden, the Netherlands), the risk of recurrent venous thrombosis was calculated in men, women with reproductive risk factors and women without reproductive risk factors at the time of their first venous thrombosis. F9 Malmö was genotyped and carriers and non-carriers contrasted. RESULTS: In total, 2185 patients with a first venous thrombosis, 1043 men and 1142 women, were included. Overall, men had a 2.8-fold (95% confidence interval [CI], 2.2-3.4) higher risk of recurrent venous thrombosis than women. This risk was 5.2-fold (95% CI, 3.5-7.7) higher in men than in women with reproductive risk factors, and 2.3-fold (95% CI, 1.7-3.2) higher in men than in women without reproductive risk factors. No difference in risk of recurrence was found for carriers vs. non-carriers of F9 Malmö. CONCLUSION: Men experienced a recurrent venous thrombosis twice as often as women without reproductive risk factors. These findings indicate that men have a higher intrinsic risk of venous thrombosis than women, which is partly masked by female reproductive risk factors. The sex difference cannot be explained by F9 Malmö.

Differential risks in men and women for first and recurrent venous thrombosis: the role of genes and environment.

Men have a higher risk of first and recurrent venous thrombosis than do women. However, the pathophysiology underlying this phenomenon is as yet unknown. In this review article, we assessed the prevalence and strength of genetic and acquired risk factors for venous thrombosis for men and women separately, because it is likely that either a difference in effect or distribution of a risk factor explains the risk difference between the sexes. We also summarized the sex-specific results of previous studies on the risk of first and recurrent venous thrombosis. Few explanations for the sex difference were found. The major factor, explaining about 20% difference in population-attributable fraction, was body height. No difference in prevalence or strength for other venous thrombosis risk factors was observed, such as plaster cast immobilization, hospitalization, surgery, trauma, malignancy, hyperhomocysteinemia, factor V Leiden, prothrombin G20210A, or blood group non-O. Alternative explanations for the sex difference are hypothesized in this review, including X- or Y-linked mutations or a mutation on a gene with a sex-specific effect. Future studies should focus on the sex-specific risk of venous thrombosis to unravel the pathophysiology and thereby improve sex-specific treatment and prevention strategies. Even so, male sex can be used as a tool through which individuals at increased risk of first or recurrent venous thrombosis may be identified.

AltitudeOmics: exercise-induced supraspinal fatigue is attenuated in healthy humans after acclimatization to high altitude.

AIMS: We asked whether acclimatization to chronic hypoxia (CH) attenuates the level of supraspinal fatigue that is observed after locomotor exercise in acute hypoxia (AH). METHODS: Seven recreationally active participants performed identical bouts of constant-load cycling (131 ± 39 W, 10.1 ± 1.4 min) on three occasions: (i) in normoxia (N, PI O2 , 147.1 mmHg); (ii) in AH (FI O2 , 0.105; PI O2 , 73.8 mmHg); and (iii) after 14 days in CH (5260 m; PI O2 , 75.7 mmHg). Throughout trials, prefrontal-cortex tissue oxygenation and middle cerebral artery blood velocity (MCAV) were assessed using near-infrared-spectroscopy and transcranial Doppler sonography. Pre- and post-exercise twitch responses to femoral nerve stimulation and transcranial magnetic stimulation were obtained to assess neuromuscular and corticospinal function. RESULTS: In AH, prefrontal oxygenation declined at rest (Δ7 ± 5%) and end-exercise (Δ26 ± 13%) (P < 0.01); the degree of deoxygenation in AH was greater than N and CH (P < 0.05). The cerebral O2 delivery index (MCAV × Ca O2 ) was 19 ± 14% lower during the final minute of exercise in AH compared to N (P = 0.013) and 20 ± 12% lower compared to CH (P = 0.040). Maximum voluntary and potentiated twitch force were decreased below baseline after exercise in AH and CH, but not N. Cortical voluntary activation decreased below baseline after exercise in AH (Δ11%, P = 0.014), but not CH (Δ6%, P = 0.174) or N (Δ4%, P = 0.298). A twofold greater increase in motor-evoked potential amplitude was evident after exercise in CH compared to AH and N. CONCLUSION: These data indicate that exacerbated supraspinal fatigue after exercise in AH is attenuated after 14 days of acclimatization to altitude. The reduced development of supraspinal fatigue in CH may have been attributable to increased corticospinal excitability, consequent to an increased cerebral O2 delivery.

Inferring animal population distributions from individual tracking data: theoretical insights and potential pitfalls.

Animal population-level phenomena are often inferred from large tracking data sets obtained from only a few individuals. Two key challenges are to understand how these two scales are related, and to identify the factors that influence the extent to which small samples consisting of a few individuals can predict spatial patterns at the population scale. We used a simple spatially explicit theoretical model to explore some of the factors that affect inferences made at the population level from individual tracking data. We adopted a 'mixtures of correlated random walks' approach to simulate two discrete movement modes with different step lengths and turning angles in a hypothetical ungulate population with contrasting population sizes and sampling intensities. Movement state was assumed to be influenced by habitat type (patch or matrix) and social cues. We explored the predictive power of a tracked population subsample by regressing the space-use map generated by a few randomly chosen individuals against the map generated by the entire population (the 'true' map) for different scenarios (e.g. random and clumped habitat distributions) and parameter values. We show that the predictive power of the tracking sample varies nonlinearly and often counter-intuitively with factors such as habitat preference, the spatial context of the landscape and the importance of social interactions. We suggest that movement models coupled with individual tracking data can be used with Monte Carlo simulations to improve tracking studies by better understanding the links between detailed individual movement data and population distributions.

The risk of venous thrombosis in women over 50 years old using oral contraception or postmenopausal hormone therapy.

BACKGROUND: Oral contraception (OC) and postmenopausal hormone therapy (HT) can be used to alleviate menopausal symptoms. However, the risk of venous thrombosis (VT) associated with OC use in women over 50 years old has never been assessed and the two preparations have not been directly compared. OBJECTIVES: To determine and compare the risk of VT associated with OC and HT use. METHODS: From a large case-control study, 2550 women aged over 50 years old, 1082 patients with a first VT and 1468 controls, were included. Odds ratios (ORs) and 95% confidence intervals for VT were calculated for OC-users (164 patients and 54 controls) and HT-users (88 patients and 102 controls) compared with non-hormone users (823 patients and 1304 controls). RESULTS: OC-users had a 6.3-fold (4.6-9.8) increased risk of VT. This ranged from 5.4 (3.3-8.9) for preparations containing levonorgestrel to 10.2 (4.8-21.7) for desogestrel. The VT-risk associated with oral HT use was 4.0 (1.8-8.2) for conjugated equine estrogen combined with medroxyprogesterone acetate and 3.9 (1.5-10.7) for micronized estradiol combined with norethisterone acetate. Non-oral HT did not increase the risk of VT: OR 1.1 (0.6-1.8). Relative risk estimates were further increased in hormone users with factor V Leiden, prothrombin G20210A or blood group non-O and hormone users with a family history of VT. CONCLUSIONS: In this study, non-oral HT seemed to be the safest hormonal preparation in women over 50 years old. OC use increased the VT risk the most, especially in women with inherited thrombophilia or a family history of VT.

Coffee consumption is associated with a reduced risk of venous thrombosis that is mediated through hemostatic factor levels.

BACKGROUND: Coffee consumption is associated with a lower risk of venous thrombosis, but the role of confounding and the pathophysiology behind these findings are unclear. OBJECTIVE: To assess the role of hemostatic factors in the relationship between coffee consumption and venous thrombosis. METHODS: From a large case-control study, 1803 patients with a first venous thrombosis and 1803 partner controls were included. With conditional logistic regression, odds ratios (ORs) and 95% confidence intervals (CIs) for venous thrombosis were calculated for coffee consumption vs. no coffee consumption. In addition, mean differences in hemostatic factor levels between these groups were calculated in the controls. RESULTS: Coffee consumption yielded a 30% lower risk of venous thrombosis than no coffee consumption (OR 0.7, 95% CI 0.5-0.9). Adjustment for several putative confounders (age, sex, body mass index, smoking, hormonal factors, statin, aspirin, alcohol, malignancy, and chronic disease) yielded an OR of 0.8 (95% CI 0.6-1.1). Results were similar for provoked and unprovoked events, and for deep vein thrombosis and pulmonary embolism. In controls, von Willebrand factor levels were 11 (3-19) IU dL(-1) lower and factor (F) VIII levels were 11 (1-21) IU dL(-1) lower in coffee consumers than in non-consumers. After adjustment of the risk estimates for these hemostatic factors, the inverse association between coffee consumption and venous thrombosis diminished (OR 1.0, 95% CI 0.7-1.4). There was no association between coffee consumption and anticoagulant proteins, fibrinogen levels, or fibrinolytic markers. CONCLUSIONS: Coffee consumption is associated with a lower risk of venous thrombosis, which seems to be mediated through von Willebrand factor and FVIII.

Stem cell biology in the lung and lung cancers: using pulmonary context and classic approaches.

Classic stem cell biology approaches tailored specifically with lung biology in mind are needed to bring the field of lung stem cell biology up to speed with that in other tissues. The infrequent cellular turnover, the diversity of cell types, and the necessity of daily cell function in this organ must be considered in stem cell studies. Previous work has created a base from which to explore transplantation, label retention, and more sophisticated lineage-tracing schemes to identify and characterize stem cell populations in the normal lung. These approaches are also imperative for building on precedents set in other tissues in the exploration of the cancer stem cell hypothesis in lung cancers. Additionally, recent studies provide key leads to further explore the molecular mechanisms that regulate lung homeostasis. Here, we discuss strategies to advance the field of lung stem cell biology with an emphasis on developing new, lung-specific tools.

Optic nerve sheath diameter, intracranial pressure and acute mountain sickness on Mount Everest: a longitudinal cohort study.

OBJECTIVE: To investigate the association of optic nerve sheath diameter (ONSD), as a correlate of intracranial pressure (ICP), with acute mountain sickness (AMS). DESIGN: Longitudinal cohort study of mountaineers from sea level to 6400 m. SETTING: Mount Everest (North side). PARTICIPANTS: 13 mountaineers (10 men, 3 women; aged 23-52 years) on a British expedition to climb Mount Everest. INTERVENTIONS: ONSD was measured ultrasonically, 3 mm behind the globe using B scans recorded with an OTI-Scan 3D scanner (Ophthalmic Technologies, Canada). Serial binocular scans were recorded at sea level, and 2000, 3700, 5200 and 6400 m. All ONSDs were measured by a blinded observer. MAIN OUTCOME MEASURES: ONSD, AMS score (using the Lake Louise scoring system), heart rate, and oxygen saturation levels. RESULTS: All results were analysed by regression analysis with adjustment. ONSD was positively associated with increasing altitude above sea level (0.10 mm increase in ONSD per 1000 m, 95% CI 0.05 to 0.14 mm) and AMS score (0.12 mm per score, 95% CI 0.06 to 0.18 mm); further associations were found with resting heart rate (0.29 mm per 20 beats/min, 95% CI 0.17 to 0.41 mm) and oxygen saturations (0.20 mm per 10% decrease, 95% CI 0.11 to 0.29 mm). CONCLUSIONS: ONSD increases at high altitude, and this increase is associated with more severe symptoms of AMS. Given the linkage between ONSD and ICP, these results strongly suggest that intracranial pressure plays an important role in the pathophysiology of AMS.

Cerebral vasoreactivity in Andeans and headache at sea level.

Headache is common in Cerro de Pasco (CP), Peru (altitude 4338 m) and was present in all patients with chronic mountain sickness (CMS) in CP reported here. Forty-seven percent of inhabitants report headache. Twenty-four percent of men have migraine with aura, with an average of 65 attacks a year. We assessed vasoreactivity of the cerebral vessels to CO2 by rebreathing and to NO by the administration of isosorbite dinitrate (IDN), a nitric oxide (NO) donor, using transcranial Doppler ultrasound in the middle cerebral artery (MCA) in natives of CP, some of whom suffered from CMS. We repeated the measurements in Lima (altitude 150 m) in the same subjects within 24 h of arrival. Vasodilatation in the middle cerebral artery supply territory in response to CO2 and NO, both physiologic vasodilators, is defective in Andean natives at altitude and in the same subjects at sea level. Incapacitating migraine can occur with impaired cerebral vasoreactivity to physiologic vasodilators. We propose that susceptibility to migraine might depend in part on gene expression with consequent alterations of endothelial function.

Doppler ultrasound determination of the distribution of human cardiac output: effects of age and physical stresses.

Due to its high spatial, temporal, and dynamic resolution, noninvasive Doppler ultrasound can be used to determine the distribution of phasic cardiac output in humans. The effects of ageing and various common physical stresses on combined human major central and regional blood flows have not been reported. We tested the hypothesis that there are no significant age-related differences in steady-state human central and regional hemodynamics during leg exercise, hypoxia, eating, and standing. We used noninvasive, image-guided Doppler flowmetry (approximately 7% linearity, approximately 11% accuracy) to measure absolute values and percent changes (%C) in phasic blood flows in the following major arteries: ascending aorta (CO, cardiac output), common carotid (CQ, brain), subclavian (SQ, arm), renal (RQ, kidney), superior mesenteric (MQ, gut), and common femoral (FQ, leg). Mean arm cuff blood pressure (BP), heart rate (HR), stroke volume (SV), and total peripheral resistance (PR) were also determined. We studied 16 young (Y, 24/3 years, 8 males) and 16 elderly (E, 73/2 years, 7 males) healthy, lean adults during separate experiments of: 50% submaximal leg exercise; 12% oxygen breathing; ~700 calorie meal; and 70 degrees upright tilt. Exercise results (X/SD) are given as Y(%C) then E(%C) where (+) represents p<0.05 vs resting, fasting control: HR: 78/8+,66/7+; BP: 6/5,8/6; SV: - 15/5+,21/4+; CO: 96/11+,87/9+; PR: -83/13+,- 76/10+; CQ: 16/8+,14/6+; SQ: -6/8,-12/8; MQ: -21/11+,-15/11; RQ: -14/8/-12/7; FQ: 919/88+,898/74 Importantly, there were no significant (p<0.05) age-related differences in the percentage changes in any of these hemodynamic variables. Similar results were found during hypoxia, eating, and standing. We conclude that although physical stresses significantly (p<0.05) affects various central and regional hemodynamics, there are no significant age-related differences in these variables between healthy, successfully aged, 20 and 70 year old cohorts. These data suggest that given an appropriate genetic template and behavior free of significant trauma and disease states, cardiovascular control mechanisms and the distributions of cardiac output during common, daily, physical stresses are maintained with age through 70 years of life.