Cohesin causes replicative DNA damage by trapping DNA topological stress

DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae, we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological-stress-linked damage in these regions. At cohesin-enriched centromeres, cohesin activity causes the accumulation of DNA damage, RF rotation, and pre-catenation, confirming that cohesin-dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA, cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that, as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress

Modelling environmental factors correlated with podoconiosis: a geospatial study of non-filarial elephantiasis

Introduction The precise trigger of podoconiosis — endemic non-filarial elephantiasis of the lower legs — is unknown. Epidemiological and ecological studies have linked the disease with barefoot exposure to red clay soils of volcanic origin. Histopathology investigations have demonstrated that silicon, aluminium, magnesium and iron are present in the lower limb lymph node macrophages of both patients and non-patients living barefoot on these clays. We studied the spatial variation (variations across an area) in podoconiosis prevalence and the associated environmental factors with a goal to better understanding the pathogenesis of podoconiosis. Methods Fieldwork was conducted from June 2011 to February 2013 in 12 kebeles (administrative units) in northern Ethiopia. Geo-located prevalence data and soil samples were collected and analysed along with secondary geological, topographic, meteorological and elevation data. Soil data were analysed for chemical composition, mineralogy and particle size, and were interpolated to provide spatially continuous information. Exploratory, spatial, univariate and multivariate regression analyses of podoconiosis prevalence were conducted in relation to primary (soil) and secondary (elevation, precipitation, and geology) covariates. Results Podoconiosis distribution showed spatial correlation with variation in elevation and precipitation. Exploratory analysis identified that phyllosilicate minerals, particularly clay (smectite and kaolinite) and mica groups, quartz (crystalline silica), iron oxide, and zirconium were associated with podoconiosis prevalence. The final multivariate model showed that the quantities of smectite (RR = 2.76, 95% CI: 1.35, 5.73; p = 0.007), quartz (RR = 1.16, 95% CI: 1.06, 1.26; p = 0.001) and mica (RR = 1.09, 95% CI: 1.05, 1.13; p < 0.001) in the soil had positive associations with podoconiosis prevalence. Conclusions More quantities of smectite, mica and quartz within the soil were associated with podoconiosis prevalence. Together with previous work indicating that these minerals may influence water absorption, potentiate infection and be toxic to human cells, the present findings suggest that these particles may play a role in the pathogenesis of podoconiosis and acute adenolymphangitis, a common cause of morbidity in podoconiosis patients

The causes and consequences of topological stress during DNA replication

The faithful replication of sister chromatids is essential for genomic integrity in every cell division. The replication machinery must overcome numerous difficulties in every round of replication, including DNA topological stress. Topological stress arises due to the double-stranded helical nature of DNA. When the strands are pulled apart for replication to occur, the intertwining of the double helix must also be resolved or topological stress will arise. This intrinsic problem is exacerbated by specific chromosomal contexts encountered during DNA replication. The convergence of two replicons during termination, the presence of stable protein-DNA complexes and active transcription can all lead to topological stresses being imposed upon DNA replication. Here we describe how replication forks respond to topological stress by replication fork rotation and fork reversal. We also discuss the genomic contexts where topological stress is likely to occur in eukaryotes, focusing on the contribution of transcription. Finally, we describe how topological stress, and the ways forks respond to it, may contribute to genomic instability in cell

MMP-9 Microsatellite Polymorphism and Susceptibility to Carotid Arteries Atherosclerosis

Objective— The aims of this study were to compare a microsatellite polymorphism (PM) of matrix metalloproteinase (MMP)-9 in patients with carotid atherosclerosis and control population, and to assess the relationship between this PM and plaque structure. Methods and Results— One hundred fifty patients referring to vascular diagnostic centers for suspected carotid atherosclerosis (at ultrasound examination: 110 positive, 40 negative) and controls (n=110) have been genotyped for MMP-9 PM. After controlling for risk factors, allelic and genotype frequencies were significantly different among the groups, with significant prevalence of long microsatellites in patients with carotid atherosclerosis. Long microsatellites (settled as 22 to 27 repeats) were associated with carotid atherosclerosis (odds ratio [OR], 5.2; 95% confidence interval [CI], 2.9 to 9.2), compared with controls; an independent case control study on patients with coronary atherosclerosis confirmed such result. Binary logistic regression showed that hypertension, long microsatellites in MMP-9 PM and smoking habits were variables accounting for the difference between ultrasound-positive patients and controls. Long microsatellites were also associated to plaques with thin fibrous cap and echolucent core (OR, 13.1; 95% CI, 1.6 to 100). These alleles were slightly more represented in female patients (χ 2 test=0.019; OR, 2.7; 95% CI, 1.2 to 6) but not associated with other risk factors. Plasma MMP-9 levels were related neither to MMP-9 PM nor to plaque type, and were related to gender and extension of atherosclerosis in carotid arteries. Conclusions— The number of repeats (≥22 CA) in the microsatellite of MMP-9 promoter, but not MMP-9 plasma levels, is associated to carotid atherosclerosis and particularly to plaques with a thin fibrous cap

Factors contributing to high performance of sows in free farrowing systems

BackgroundPressure to abolish farrowing crates is increasing, and producers are faced with decisions about which alternative system to adopt. For sow welfare, well designed free farrowing systems without close confinement are considered optimal but producers have concerns about increased piglet mortality, particularly crushing by the sow. Reporting accurate performance figures from commercial farms newly operating such systems could inform the transition process. This study investigated performance on three commercial farms operating four different zero-confinement systems, three of which were newly installed. A total of 3212 litters from 2920 sows were followed from farrowing to weaning over a three-year period with key performance indicators (KPIs) recorded. Mixed Models (LMMs, GLMMs) determined the influence of different factors (e.g. farrowing system, sow parity, management aspects) and litter characteristics on performance, including levels and causes of piglet mortality.ResultsPiglet mortality was significantly influenced by farm/system. Live-born mortality ranged from 10.3 to 20.6% with stillbirths ranging from 2.5 to 5.9%. A larger litter size and higher parity resulted in higher levels of mortality regardless of system. In all systems, crushing was the main cause of piglet mortality (59%), but 31% of sows did not crush any piglets, whilst 26% crushed only one piglet and the remaining sows (43%) crushed two or more piglets. System significantly influenced crushing as a percentage of all deaths, with the system with the smallest spatial footprint (m2) compared to the other systems, recording the highest levels of crushing. Time from the start of the study influenced mortality, with significant reductions in crushing mortality (by ~ 4%) over the course of the three-year study. There was a highly significant effect of length of time (days) between moving sows into the farrowing accommodation and sows farrowing on piglet mortality (P &lt; 0.001). The less time between sows moving in and farrowing, the higher the levels of piglet mortality, with ~ 3% increase in total mortality every five days. System effects were highly significant after adjusting for parity, litter size, and days pre-farrowing.ConclusionThese results from commercial farms demonstrate that even sows that have not been specifically selected for free farrowing are able, in many cases, to perform well in these zero-confinement systems, but that a period of adaptation is to be expected for overall farm performance. There are performance differences between the farms/systems which can be attributed to individual farm/system characteristics (e.g. pen design and management, staff expertise, pig genotypes, etc.). Higher parity sows and those producing very large litters provide a greater challenge to piglet mortality in these free farrowing systems (just as they do in crate systems). Management significantly influences performance, and ensuring sows have plenty of time to acclimatise between moving in to farrowing accommodation and giving birth is a critical aspect of improving piglet survival

Analytical solution for capacitance calculation of a curved patch capacitor that conforms to the curvature of a homogeneous cylindrical dielectric rod

This Letter presents an analytical expression for the capacitance of a curved patch capacitor whose electrodes conform to the curvature of a long, homogeneous, cylindrical dielectric rod. The capacitor is composed of two infinitely long curved electrodes, symmetrically placed about a diameter of the cylinder cross-section. The resulting capacitance per unit length depends on both the dielectric properties of the material under test and the capacitor configuration. A practical capacitance measurement is also presented, with appropriately guarded finite electrodes. Very good agreement between measured and theoretically predicted capacitances were observed, to within 2.4 percent. The analytical result presented in this Letter can be applied for extremely rapid evaluation of rod permittivity from measured capacitance

Towards a Dataset of Activities for Action Recognition in Open Fields

In an agricultural context, having autonomous robots that can work side-by-side with human workers provide a range of productivity benefits. In order for this to be achieved safely and effectively, these autonomous robots require the ability to understand a range of human behaviors in order to facilitate task communication and coordination. The recognition of human actions is a key part of this, and is the focus of this paper. Available datasets for Action Recognition generally feature controlled lighting and framing while recording subjects from the front. They mostly reflect good recording conditions but fail to model the data a robot will have to work with in the field, such as varying distance and lighting conditions. In this work, we propose a set of recording conditions, gestures and behaviors that better reflect the environment an agricultural robot might find itself in and record a dataset with a range of sensors that demonstrate these conditions

Changes in tail posture detected by a 3D machine vision system are associated with injury from damaging behaviours and ill health on commercial pig farms

To establish whether pig tail posture is affected by injuries and ill health, a machine vision system using 3D cameras to measure tail angle was used. Camera data from 1692 pigs in 41 production batches of 42.4 (±16.6) days in length over 17 months at seven diverse grower/finisher commercial pig farms, was validated by visiting farms every 14(±10) days to score injury and ill health. Linear modelling of tail posture found considerable farm and batch effects. The percentage of tails held low (0°) or mid (1–45°) decreased over time from 54.9% and 23.8% respectively by -0.16 and -0.05%/day, while tails high (45–90°) increased from 21.5% by 0.20%/day. Although 22% of scored pigs had scratched tails, severe tail biting was rare; only 6% had tail wounds and 5% partial tail loss. Adding tail injury to models showed associations with tail posture: overall tail injury, worsening tail injury, and tail loss were associated with more pigs detected with low tail posture and fewer with high tails. Minor tail injuries and tail swelling were also associated with altered tail posture. Unexpectedly, other health and injury scores had a larger effect on tail posture- more low tails were observed when a greater proportion of pigs in a pen were scored with lameness or lesions caused by social aggression. Ear injuries were linked with reduced high tails. These findings are consistent with the idea that low tail posture could be a general indicator of poor welfare. However, effects of flank biting and ocular discharge on tail posture were not consistent with this. Our results show for the first time that perturbations in the normal time trends of tail posture are associated with tail biting and other signs of adverse health/welfare at diverse commercial farms, forming the basis for a decision support system

A pilot randomised controlled trial of cognitive behavioural therapy for antenatal depression.

BACKGROUND: Few trials have evaluated the effectiveness of psychological treatment in improving depression by the end of pregnancy. This is the first pilot randomised controlled trial (RCT) of individual cognitive behavioural therapy (CBT) looking at treating depression by the end of pregnancy. Our aim was to assess the feasibility of delivering a CBT intervention modified for antenatal depression during pregnancy. METHODS: Women in North Bristol, UK between 8-18 weeks pregnant were recruited through routine contact with midwives and randomised to receive up to 12 sessions of individual CBT in addition to usual care or to continue with usual care only. Women were eligible for randomisation if they screened positive on a 3-question depression screen used routinely by midwives and met ICD-10 criteria for depression assessed using the clinical interview schedule - revised version (CIS-R). Two CBT therapists delivered the intervention. Follow-up was at 15 and 33 weeks post-randomisation when assessments of mental health were made using measures which included the CIS-R. RESULTS: Of the 50 women assessed for the trial, 36 met ICD-10 depression criteria and were randomised: 18 to the intervention and 18 to usual care. Thirteen of the 18 (72%) women who were allocated to receive the intervention completed 9 or more sessions of CBT before the end of pregnancy. Follow-up rates at 15 and 33 weeks post-randomisation were higher in the group who received the intervention (89% vs. 72% at 15 weeks and 89% vs. 61% at 33 weeks post-randomisation). At 15 weeks post-randomisation (the end of pregnancy), there were more women in the intervention group (11/16; 68.7%) who recovered (i.e. no longer met ICD-10 criteria for depression), than those receiving only usual care (5/13; 38.5%). CONCLUSIONS: This pilot trial shows the feasibility of conducting a large RCT to assess the effectiveness of CBT for treating antenatal depression before the end of pregnancy. The intervention could be delivered during the antenatal period and there was some evidence to suggest that it could be effective. TRIAL REGISTRATION: ISRCTN44902048