Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally > 10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

Fatigue behavior of laser-welded NiTi wires in small-strain cyclic bending

NiTi wires and their weldments are commonly used in micro-electro-mechanical systems (MEMS), and in such applications, cyclic loading are commonly encountered. In this paper, the bending-rotation fatigue (BRF) test was used to study the bending fatigue behavior of NiTi wire laser weldment in the small-strain regime. The fracture mechanism, which includes crack initiation, crack growth and propagation of the weldment in the BRF test, was investigated with the aid of SEM fractography and discussed in terms of the microstructure. It was found that crack initiation was primarily surface-condition dependent. The cracks were found to initiate at the surface defects at the weld zone (WZ) surface, and the crack propagation was assisted by the gas inclusions in the WZ. The weldment was finally fractured in a ductile manner. The fatigue life was found to decrease with increasing surface strain and also with increasing bending frequency (controlled by the rotational speed in the BRF test). In comparison, the fatigue life of the unwelded NiTi wires was higher than their welded counterparts at all strain levels and bending frequencies. The decrease in fatigue resistance of the weldment could be attributed to the surface and microstructural defects introduced during laser welding.

Discovery of WASP-65b and WASP-75b: Two hot Jupiters without highly inflated radii

We report the discovery of two transiting hot Jupiters, WASP-65b (M_pl = 1.55 ± 0.16 M_J; R_pl = 1.11 ± 0.06 R_J), and WASP-75b (M_pl = 1.07 ± 0.05 M_J; R_pl = 1.27 ± 0.05 R_J). They orbit their host star every ∼2.311, and ∼2.484 days, respectively. The planet host WASP-65 is a G6 star (T_eff = 5600 K, [Fe/H] = −0.07 ± 0.07, age 8 Gyr); WASP-75 is an F9 star (T_eff = 6100 K, [Fe/H] = 0.07 ± 0.09, age ∼ 3 Gyr). WASP-65b is one of the densest known exoplanets in the mass range 0.1 and 2.0 MJ (ρpl = 1.13 ± 0.08 ρJ), a mass range where a large fraction of planets are found to be inflated with respect to theoretical planet models. WASP-65b is one of only a handful of planets with masses of ∼1.5 MJ, a mass regime surprisingly underrepresented among the currently known hot Jupiters. The radius of WASP-75b is slightly inflated (10%) as compared to theoretical planet models with no core, and has a density similar to that of Saturn (ρpl = 0.52 ± 0.06 ρJ). Key words. planetary systems – stars: individual:

Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis

Tuberculosis (TB) caused by Mycobacterium bovis is a re-emerging disease of livestock that is of major economic importance worldwide, as well as being a zoonotic risk there is significant heritability for host resistance to bovine TB (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein-Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin test and lesion positive vs skin test negative on multiple occasions, respectively these animals were genotyped with the Illumina BovineHD 700K BeadChip. Genome-wide rapid association using linear and logistic mixed models and regression (GRAMMAR), regional heritability mapping (RHM) and haplotype-sharing analysis identified two novel resistance loci that attained chromosome-wise significance, protein tyrosine phosphatase receptor T (PTPRT; P=4.8 × 10 -7) and myosin IIIB (MYO3B; P=5.4 × 10 -6). We estimated that 21% of the phenotypic variance in TB resistance could be explained by all of the informative single-nucleotide polymorphisms, of which the region encompassing the PTPRT gene accounted for 6.2% of the variance and a further 3.6% was associated with a putative copy number variant in MYO3B the results from this study add to our understanding of variation in host control of infection and suggest that genetic marker-based selection for resistance to bTB has the potential to make a significant contribution to bTB control.

Genomic prediction for tuberculosis resistance in dairy cattle

Background: The increasing prevalence of bovine tuberculosis (bTB) in the UK and the limitations of the currently available diagnostic and control methods require the development of complementary approaches to assist in the sustainable control of the disease. One potential approach is the identification of animals that are genetically more resistant to bTB, to enable breeding of animals with enhanced resistance. This paper focuses on prediction of resistance to bTB. We explore estimation of direct genomic estimated breeding values (DGVs) for bTB resistance in UK dairy cattle, using dense SNP chip data, and test these genomic predictions for situations when disease phenotypes are not available on selection candidates. Methodology/Principal Findings: We estimated DGVs using genomic best linear unbiased prediction methodology, and assessed their predictive accuracies with a cross validation procedure and receiver operator characteristic (ROC) curves. Furthermore, these results were compared with theoretical expectations for prediction accuracy and area-under-the-ROC- curve (AUC). The dataset comprised 1151 Holstein-Friesian cows (bTB cases or controls). All individuals (592 cases and 559 controls) were genotyped for 727,252 loci (Illumina Bead Chip). The estimated observed heritability of bTB resistance was 0.23±0.06 (0.34 on the liability scale) and five-fold cross validation, replicated six times, provided a prediction accuracy of 0.33 (95% C.I.: 0.26, 0.40). ROC curves, and the resulting AUC, gave a probability of 0.58, averaged across six replicates, of correctly classifying cows as diseased or as healthy based on SNP chip genotype alone using these data. Conclusions/Significance: These results provide a first step in the investigation of the potential feasibility of genomic selection for bTB resistance using SNP data. Specifically, they demonstrate that genomic selection is possible, even in populations with no pedigree data and on animals lacking bTB phenotypes. However, a larger training population will be required to improve prediction accuracies. © 2014 Tsairidou et al.

Assessment of commercial sand barge radar for detecting overwintering diving ducks at Lough Neagh

Overwintering diving ducks at Lough Neagh have declined dramatically in recent years, but it has been suggested that on-to-offshore redistribution may have led to an underestimate of numbers. Most species feed nocturnally and their distribution at night is unknown. We used radar and visual observations from on board commercial sand barges to determine the diurnal distribution of diving duck flocks in an effort to assess the feasibility of using standard
boat-mounted radar to describe their nocturnal feeding distribution. Sand barge radar was poor in identifying flocks compared to independent visual observations as it was sensitive to interference by waves during windy conditions. However, visual observations were useful in describing diurnal distribution. Sand barges were on average 1.5km from shore when a flock of diving ducks was observed and the probability of detection declined with distance from shore. This supports the reliability of shore-based counts in monitoring and surveillance. Given the poor performance of commercially available boatmounted radar systems, we recommend the use of specialised terrestrial Bird Detecting Radar to determine the movements of diving ducks at Lough Neagh.

Three new distal tephras in sediments spanning the Last Glacial-Interglacial Transition in Scotland

Three new microtephras are reported from a number of lake sites from the Inner Hebrides and Scottish mainland. One occurs stratigrapically in the middle of Greenland Interstadial 1 (GI-1) and has been named the Penifiler Tephra. It is rhyolitic and possesses a geochemical signature that is very similar to that of the Borrobol Tephra, which also occurs in three of the sequences reported here, but which lies close to the lower boundary of GI-1. The second occurs stratigraphically in the early Holocene below the Saksunarvatn Ash and is named the Ashik Tephra. This tephra is geochemically bimodal, with a rhyolitic component comparable to the An Druim Tephra that occurs later in the Holocene, and a basaltic component which is similar to the Saksunarvatn Ash. A third tephra occurs stratigraphically above the Saksunarvatn Ash and is provisionally named the Breakish Tephra. The consistent inter-site correlation demonstrated for these new tephras at several sites enhances the regional tephrostratigraphic framework, and increases the potential for correlating palaeoenvironmental events during GI-1 and the early Holocene. However, the occurrence of multiple tephras with similar geochemistry in close stratigraphic and temporal proximity has implications for the rigour with which tephrostratigraphic investigations must be performed.

A population-based study of adverse physical effects following prostate cancer treatments: Results from the PiCTure (Prostate cancer treatment – your experience) study

Background:

Men and clinicians need reliable population based information when making decisions about investigation and treatment of prostate cancer. In the absence of clearly preferred treatments, differences in outcomes become more important.

Aim:

To investigate rates of adverse physical effects among prostate cancer survivors 2-15 years post diagnosis by treatment, and estimate population burden.

Methods:

A cross sectional, postal survey to 6,559 survivors (all ages) diagnosed with primary, invasive prostate cancer (ICD10-C61), identified in Northern Ireland and the Republic of Ireland via cancer registries. Questions included symptoms at diagnosis, treatments received and adverse physical effects (impotence, urinary incontinence, bowel problems, breast changes, libido loss, hot flashes, fatigue) experienced ‘ever’ and ‘current’ i.e. at questionnaire completion. Physical effect levels were weighted by age, country and time since diagnosis for all prostate cancer survivors. Bonferroni corrections were applied to account for multiple comparisons.

Results:

Adjusted response rate 54%, (n=3,348). 75% reported at least one current physical effect (90% ever), with 29% reporting at least three. These varied by treatment. Current impotence was reported by 76% post-prostatectomy, 64% post-external beam radiotherapy with hormone therapy, with average for all survivors of 57%. Urinary incontinence (overall current level: 16%) was highest post-prostatectomy (current 28%, ever 70%). 42% of brachytherapy patients reported no current adverse physical effects; however 43% reported current impotence and 8% current incontinence. Current hot flashes (41%), breast changes (18%) and fatigue (28%) were reported more commonly by patients on hormone therapy.

Conclusions:

This study provides evidence that adverse physical effects following prostate cancer represent a significant public health burden; an estimated 1.6% of men over 45 is a prostate cancer survivor with a current adverse physical effect. This information should facilitate investigation and treatment decision-making and follow-up care of patients.

Preserving arteriovenous fistula outcomes during surgical training

PURPOSE: Arteriovenous fistulae (AVFs) are the preferred option for vascular access, as they are associated with lower mortality in hemodialysis patients than in those patients with arteriovenous grafts (AVGs) or central venous catheters (CVCs). We sought to assess whether vascular access outcomes for surgical trainees are comparable to fully trained surgeons.

METHODS: A prospectively collected database of patients was created and information recorded regarding patient demographics, past medical history, preoperative investigations, grade of operating surgeon, type of AVF formed, primary AVF function, cumulative AVF survival and functional patency.

RESULTS: One hundred and sixty-two patients were identified as having had vascular access procedures during the 6 month study period and 143 were included in the final analysis. Secondary AVF patency was established in 123 (86%) of these AVFs and 89 (62.2%) were used for dialysis. There was no significant difference in survival of AVFs according to training status of surgeon (log rank x2 0.506 p=0.477) or type of AVF (log rank x2 0.341 p=0.559). Patency rates of successful AVFs at 1 and 2 years were 60.9% and 47.9%, respectively.

CONCLUSION: We have demonstrated in this prospective study that there are no significant differences in outcomes of primary AVFs formed by fully trained surgeons versus surgical trainees. Creation of a primary AVF represents an excellent training platform for intermediate stage surgeons across general and vascular surgical specialties.

Patient-reported 'ever had' and 'current' long term physical symptoms following prostate cancer treatments

OBJECTIVE: To document prostate cancer patient reported 'ever experienced' and 'current' prevalence of disease specific physical symptoms stratified by primary treatment received.
PATIENTS: 3,348 prostate cancer survivors 2-15 years post diagnosis.
METHODS: Cross-sectional, postal survey of 6,559 survivors diagnosed 2-15 years ago with primary, invasive PCa (ICD10-C61) identified via national, population based cancer registries in Northern Ireland and Republic of Ireland. Questions included symptoms at diagnosis, primary treatments and physical symptoms (impotence/urinary incontinence/bowel problems/breast changes/loss of libido/hot flashes/fatigue) experienced 'ever' and at questionnaire completion ("current"). Symptom proportions were weighted by age, country and time since diagnosis. Bonferroni corrections were applied for multiple comparisons.
RESULTS: Adjusted response rate 54%; 75% reported at least one 'current' physical symptom ('ever':90%), with 29% reporting at least three. Prevalence varied by treatment; overall 57% reported current impotence; this was highest following radical prostatectomy (RP)76% followed by external beam radiotherapy with concurrent hormone therapy (HT); 64%. Urinary incontinence (overall 'current' 16%) was highest following RP ('current'28%, 'ever'70%). While 42% of brachytherapy patients reported no 'current' symptoms; 43% reported 'current' impotence and 8% 'current' incontinence. 'Current' hot flashes (41%), breast changes (18%) and fatigue (28%) were reported more often by patients on HT.
CONCLUSION: Symptoms following prostate cancer are common, often multiple, persist long-term and vary by treatment. They represent a significant health burden. An estimated 1.6% of men over 45 is a prostate cancer survivor currently experiencing an adverse physical symptom. Recognition and treatment of physical symptoms should be prioritised in patient follow-up. This information should facilitate men and clinicians when deciding about treatment as differences in survival between radical treatments is minimal.

Bioavailability of atrazine to soil microbes in the presence of the earthworm Lumbricus terrestrius (L.)

Experiments were conducted to investigate the interactions between an earthworm species (Lumbricus terrestrius) and soil microflora with respect to the bioavailability and mineralisation of ¹⁴C ring-labelled atrazine. Presence of earthworms had no affect on atrazine in soil solution (assayed by soil centrifugation). This soil solution pool was highly time dependent, decreasing considerably as the experiment proceeded. KCl-extractable label was, however, affected by the presence of earthworms, with this pool initially increasing in the presence of the worms. This pool was also highly time-dependent although, the pattern of this dependence did not follow that for label in soil solution. Mineralisation of the atrazine closely followed the KCl exchangeable pool and not that of the soil solution pool. However, label sorbed to the surface of the worms was closely correlated to the soil solution pool. Mineralisation in the presence of earthworms was double that of the controls. By the end of the experiment 6% of added radioactivity was present in the earthworm biomass.

Experimental study on PC hollow-core slab strengthened with bamboo plates

An experimental study on strengthening prestressed concrete (PC) hollow-core slabs was conducted. Nine PC hollow-core slabs were tested, including three unstrengthened reference slabs and six slabs strengthened with bamboo plates. The results show that compared with unreinforced slabs, the cracking loads of PC hollow-core slabs strengthened with bamboo plates increase by 5% to 96% (with an average of 41%), the loads at allowable deflection increase by 8% to 76% (with an average of 35%), and the ultimate loads increase by 83% to 184% (with an average of 123%), respectively. All the degrees of improvement in the crack load, allowable load and ultimate load increase with the increase in the thickness and width of the bamboo plates. With the increase in the loads, the strain distribution along the height of the strengthened slabs at the mid-span basically remains a plan-assumption. With the increase in the thickness and width of the bamboo plates, both the bamboo tensile strain on the tensile face and the concrete compressive strain on the compression face of the strengthened slabs decrease under the same load level.

Prevalence of the factor VR506Q mutation in two Irish control populations:use of a novel nested polymerase chain reaction approach

The prevalence of factor V (FV) Leiden among normal populations has primarily been determined using blood donors. This control group is carefully selected and therefore may not accurately reflect the true prevalence within the population. We assessed the prevalence of FV Leiden within the Irish population using Guthrie card samples randomly selected from all newborns. We compared this result with the prevalence of FV Leiden within blood donors. A novel nested polymerase chain reaction (PCR) method for FV Leiden was developed for analysis of the Guthrie card samples. There was no significant difference between the allele frequency within the Guthrie card samples and blood donors (2.07% vs. 2.35%, P = 0.66)

Atmospheric cold plasma process for vegetable leaf decontamination: A feasibility study on radicchio (red chicory, Cichorium intybus L.)

Cold plasma is an emerging non-thermal processing technology that could be used for large scale leaf decontamination as an alternative to chlorine washing. In this study the effect of an atmospheric cold plasma apparatus (air DBD, 15 kV) on the safety, antioxidant activity and quality of radicchio (red chicory, Cichorium intybus L.) was investigated after 15 and 30 min of treatment (in afterglow at 70 mm from the discharge, at 22 °C and 60% of RH) and during storage. Escherichia coli O157:H7 inoculated on radicchio leaves was significantly reduced after 15 min cold plasma treatment (-1.35 log MPN/cm²). However, a 30 min plasma treatment was necessary to achieve a significant reduction of Listeria monocytogenes counts (-2.2 log CFU/cm²). Immediately after cold plasma treatment, no significant effects emerged in terms of antioxidant activity assessed by the ABTS and ORAC assay and external appearance of the radicchio leaves. Significant changes between treated and untreated radicchio leaves are quality defects based on the cold plasma treatment. Atmospheric cold plasma appears to be a promising processing technology for the decontamination of leafy vegetables although some criticalities, that emerged during storage, need to be considered in future studies.