Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial.

Reduced-representation sequencing methods have wide utility in conservation genetics of non-model species. Several methods are now available that reduce genome complexity to examine a wide range of markers in a large number of individuals. We produced two datasets collected using different laboratory techniques, comprising a common set of samples from the greater bilby (Macrotis lagotis). We examined the impact of differing data filtering thresholds on downstream population inferences. We found that choice of restriction enzyme and data filtering thresholds, especially the rate of allowable missing data, impacted our ability to detect population structure. Estimates of FST were robust to alterations in laboratory and bioinformatic protocols while principal coordinates and STRUCTURE analyses showed variation according to the number of loci and percent missing data. We advise researchers using reduced-representation sequencing in conservation projects to examine a range of data thresholds, and follow these through to downstream population inferences. Multiple measures of population differentiation should be used in order to fully understand how data filtering thresholds influence the final dataset, paying particular attention to the impact of allowable missing data. Our results indicate that failure to follow these checks could impact conclusions drawn, and conservation management decisions made.

A Tasmanian devil breeding program to support wild recovery.

Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an 'insurance population' to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.

Apelin-13 analogues show potent in vitro and in vivo insulinotropic and glucose lowering actions.

Nine structurally modified apelin-13 analogues were assessed for their in vitro and acute in vivo antidiabetic potential. Stability was assessed in mouse plasma and insulinotropic efficacy tested in cultured pancreatic BRIN-BD11 cells and isolated mouse pancreatic islets. Intracellular Ca2+ and cAMP production in BRIN-BD11 cells was determined, as was glucose uptake in 3T3-L1 adipocytes. Acute antihyperglycemic effects of apelin analogues were assessed following i.p. glucose tolerance tests (ipGGT, 18 mmol/kg) in normal and diet-induced-obese (DIO) mice and on food intake in normal mice. Apelin analogues all showed enhanced in vitro stability (up to 5.8-fold, t½â€¯= 12.8 h) in mouse plasma compared to native apelin-13 (t½â€¯= 2.1 h). Compared to glucose controls, stable analogues exhibited enhanced insulinotropic responses from BRIN-BD11 cells (up to 4.7-fold, p < 0.001) and isolated mouse islets (up to 5.3-fold) for 10-7 M apelin-13 amide (versus 7.6-fold for 10-7 M GLP-1). Activation of APJ receptors on BRIN-BD11 cells increased intracellular Ca2+ (up to 3.0-fold, p < 0.001) and cAMP (up to 1.7-fold, p < 0.01). Acute ipGTT showed improved insulinotropic and glucose disposal responses in normal and DIO mice (p < 0.05 and p < 0.01, respectively). Apelin-13 amide and (pGlu)apelin-13 amide were the most effective analogues exhibiting acute, dose-dependent and persistent biological actions. Both analogues stimulated insulin-independent glucose uptake by differentiated adipocytes (2.9-3.3-fold, p < 0.05) and inhibited food intake (26-33%, p < 0.001), up to 180 min in mice, versus saline. In contrast, (Ala13)apelin-13 and (Val13)apelin-13 inhibited insulin secretion, suppressed beta-cell signal transduction and stimulated food intake in mice. Thus, stable analogues of apelin-13 have potential for diabetes/obesity therapy.

Primary Ciliary Dyskinesia Due to Microtubular Defects is Associated with Worse Lung Clearance Index.

PURPOSE: Primary ciliary dyskinesia (PCD) is characterised by repeated upper and lower respiratory tract infections, neutrophilic airway inflammation and obstructive airway disease. Different ultrastructural ciliary defects may affect lung function decline to different degrees. Lung clearance index (LCI) is a marker of ventilation inhomogeneity that is raised in some but not all patients with PCD. We hypothesised that PCD patients with microtubular defects would have worse (higher) LCI than other PCD patients. METHODS: Spirometry and LCI were measured in 69 stable patients with PCD. Age at testing, age at diagnosis, ethnicity, ciliary ultrastructure, genetic screening result and any growth of Pseudomonas aeruginosa was recorded. RESULTS: Lung clearance index was more abnormal in PCD patients with microtubular defects (median 10.24) than those with dynein arm defects (median 8.3, p = 0.004) or normal ultrastructure (median 7.63, p = 0.0004). Age is correlated with LCI, with older patients having worse LCI values (p = 0.03, r = 0.3). CONCLUSION: This study shows that cilia microtubular defects are associated with worse LCI in PCD than dynein arm defects or normal ultrastructure. The patient's age at testing is also associated with a higher LCI. Patients at greater risk of obstructive lung disease should be considered for more aggressive management. Differences between patient groups may potentially open avenues for novel treatments.

Lung Clearance Index (LCI) is Stable in Most Primary Ciliary Dyskinesia (PCD) Patients Managed in a Specialist Centre: a Pilot Study.

Primary ciliary dyskinesia is a condition in which abnormal cilia structure or function leads to reduced mucociliary clearance and obstructive lung disease. Twenty-nine patients had lung clearance index (LCI) measured in 2009 and we attempted to perform a 5-year follow-up. Only 12 patients could be re-recruited, but in this small group LCI was stable over the 5 years, which confirms previous data showing that spirometry is also stable in these patients over the medium term. The two patients with the highest LCI in 2009 had since died, despite one having relatively preserved spirometry at the time. These data may be used to inform sample size calculations of future studies.

European Respiratory Society guidelines for the diagnosis of primary ciliary dyskinesia

The diagnosis of primary ciliary dyskinesia is often confirmed with standard, albeit complex and expensive, tests. In many cases, however, the diagnosis remains difficult despite the array of sophisticated diagnostic tests. There is no "gold standard" reference test. Hence, a Task Force supported by the European Respiratory Society has developed this guideline to provide evidence-based recommendations on diagnostic testing, especially in light of new developments in such tests, and the need for robust diagnoses of patients who might enter randomised controlled trials of treatments. The guideline is based on pre-defined questions relevant for clinical care, a systematic review of the literature, and assessment of the evidence using the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) approach. It focuses on clinical presentation, nasal nitric oxide, analysis of ciliary beat frequency and pattern by high-speed video-microscopy analysis, transmission electron microscopy, genotyping and immunofluorescence. It then used a modified Delphi survey to develop an algorithm for the use of diagnostic tests to definitively confirm and exclude the diagnosis of primary ciliary dyskinesia; and to provide advice when the diagnosis was not conclusive. Finally, this guideline proposes a set of quality criteria for future research on the validity of diagnostic methods for primary ciliary dyskinesia

Testicular parameters and spermatogenesis in different birthweight boars.

The present study investigated the effect of birthweight on testicular development and spermatogenesis in boars. Twenty-four pairs of littermate boars were selected: one piglet with the highest birthweight (HW) and the other with the lowest birthweight (LW) within the litter. Two subsets of 12 pairs of male littermates from each birthweight group were obtained after selection: one subset was orchiectomised at 8 days and the other at 8 months of age. HW boars had higher body and testicular weights at both ages (P<0.05). Testosterone concentrations and the relative expression of 17α-hydroxylase in the testis were similar between birthweight groups. Birthweight affected somatic and germ cell numbers in the neonatal testis, which were higher in HW boars (P<0.05). Moreover, a significant reduction in the number of pachytene spermatocytes and round spermatids was observed in LW boars (P<0.05) at 8 months of age, which caused a decrease in the total number of elongated spermatids and daily sperm production (P<0.05). Hence, HW boars have the potential to produce more spermatozoa and consequently more semen doses per ejaculate, and would be very valuable to an industry that relies on AI.

DNA double-strand breaks caused by new and contemporary endodontic sealers.

AIM: To investigate the cytotoxicity and genotoxicity of a new silicate-based BioRoot RCS® sealer in comparison with contemporary sealers. METHODOLOGY: A periodontal ligament cell line using lentiviral gene transfer of human telomerase reverse transcriptase (hTERT) was used and exposed to subtoxic concentrations of 24-h eluates from two epoxy resin-based (AH Plus Jet® and Acroseal® ), four various methacrylate-based endodontic sealers (EndoREZ® , RealSeal® , RealSeal SE® and Hybrid Root SEAL® ) and three silicate-based sealers (BioRoot RCS® , iRootSP® and MTA Fillapex® ). The XTT-based cell viability assay was used for cytotoxicity screening of materials. The γ-H2AX assay was used for genotoxicity screening. In the γ-H2AX immunofluorescence assay, PDL-hTERT cells were exposed to eluates of the substances for 6 h and DNA double-strand breaks (DSB) were detected microscopically. Induced foci represented DSBs, which can induce ATM-dependent phosphorylation of the histone H2AX. The statistical significance of the differences between the experimental groups was compared using the Student's t-test (P < 0.05). RESULTS: The cytotoxicity of the 24-h eluates could be ranked in the following order: Hybrid Root SEAL® >RealSeal® >Acroseal® >RealSeal SE® ≥ AH Plus Jet® > EndoREZ® >MTA Fillapex® > iRoot SP® >BioRoot RCS® . In negative controls (cells which received medium only) 4.08 ± 0.53 DSB foci (mean ± SEM) whilst in positive controls 10.76 ± 4.05 DSB foci/cell were found. BioRoot RCS® and RealSeal SE® exhibited significant differences in foci formation at 1/3 EC50 compared with their 1/10 EC50 concentration (P < 0.05). Both concentrations (1/10 and 1/3 of EC50) of AH Plus Jet® , Acroseal® , RealSeal® and MTA Fillapex® sealers were not significantly different when compared with the medium control (P < 0.05). CONCLUSIONS: New BioRoot RCS® was not toxic whilst Hybrid Root SEAL® demonstrated more toxicity and DNA double-strand breaks when compared with other resin- and silicate-based root canal sealers.

Should any workplace be exempt from smoke-free law: the Irish experience.

BACKGROUND: In 2004, the Irish Government introduced national legislation banning smoking in workplaces; with exemptions for "a place of residence". This paper summarises three Irish studies of exempted premises; prisons, psychiatric hospitals and nursing homes. METHODS: PM(2.5) and nicotine were measured in nursing homes and psychiatric hospitals, in addition to ultrafine particles in the hospitals. In the prisons, officers (n = 30) completed exhaled breath Carbon Monoxide (CO) measurements. Questionnaires determined officers' opinion on introducing smoking prohibitions in prisons. Nursing home smoking policies were examined and questionnaires completed by staff regarding workplace secondhand smoke (SHS) exposure. FINDINGS: Ultrafine particle concentrations in psychiatric hospitals averaged 130,000 cm(3), approximately 45% higher than Dublin pub (35.5 µg/m(3)) pre ban. PM(2.5) levels in psychiatric hospitals (39.5 µg/m(3)) were similar to Dublin pubs (35.5 µg/m(3)) pre ban. In nursing homes permitting smoking, similar PM(2.5) levels (33 µg/m(3)) were measured, with nicotine levels (0.57 µg/m(3)) four times higher than "non-smoking" nursing homes (0.13 µg/m(3)). In prisons, 44% of non-smoking officers exhibited exhaled breath CO criteria for light to heavy smokers. CONCLUSIONS: With SHS exposure levels in some exempted workplaces similar to Dublin pubs levels pre ban, policies ensuring full protection must be developed and implemented as a right for workers, inmates and patients.

Identification of miRNAs associated with the follicular-luteal transition in the ruminant ovary.

Little is known about the involvement of microRNAs (miRNAs) in the follicular-luteal transition. The aim of this study was to identify genome-wide changes in miRNAs associated with follicular differentiation in sheep. miRNA libraries were produced from samples collected at defined stages of the ovine oestrous cycle and representing healthy growing follicles, (diameter, 4.0-5.5  mm), pre-ovulatory follicles (6.0-7.0  mm), early corpora lutea (day 3 post-oestrus) and late corpora lutea (day 9). A total of 189 miRNAs reported in sheep or other species and an additional 23 novel miRNAs were identified by sequencing these libraries. miR-21, miR-125b, let-7a and let-7b were the most abundant miRNAs overall, accounting for 40% of all miRNAs sequenced. Examination of changes in cloning frequencies across development identified nine different miRNAs whose expression decreased in association with the follicular-luteal transition and eight miRNAs whose expression increased during this transition. Expression profiles were confirmed by northern analyses, and experimentally validated targets were identified using miRTarBase. A majority of the 29 targets identified represented genes known to be actively involved in regulating follicular differentiation in vivo. Finally, luteinisation of follicular cells in vitro resulted in changes in miRNA levels that were consistent with those identified in vivo, and these changes were temporally associated with changes in the levels of putative miRNA targets in granulosa cells. In conclusion, this is the first study to characterise genome-wide miRNA profiles during different stages of follicle and luteal development. Our data identify a subset of miRNAs that are potentially important regulators of the follicular-luteal transition.

Cuspal deflection and microleakage in premolar teeth restored with bulk-fill flowable resin-based composite base materials.

OBJECTIVES: To assess the cuspal deflection and cervical microleakage of standardised Class II cavities incrementally filled with a dimethacrylate RBC or bulk-fill flowable RBC bases. METHODS: Twenty-four sound upper premolar teeth with Class II cavities were allocated to three groups (n=8). Restoration of the teeth involved the placement of an RBC (GrandioSO) in eight oblique increments (Group A) or Groups B and C were restored to within 2 mm of the palatal cusp in a single increment with bulk-fill flowable RBC bases (SDR and x-tra base) before the two occlusal cavity increments were placed with GrandioSO. Buccal and palatal cusp deflections were recorded postirradiation using a twin channel deflection measuring gauge. Following restoration, the teeth were thermocycled, immersed in 0.2% basic fuchsin dye for 24h, sectioned and examined for cervical microleakage. RESULTS: The mean total cuspal deflection for the oblique incremental restoration technique was 11.26 (2.56) µm (Group A) and 4.63 (1.19) µm (Group B) and 4.73 (0.99) µm (Group C) for the bulk-fill flowable RBC bases. A significant increase in the mean total cuspal deflection for the incrementally filled GrandioSO compared with the SDR (P=0.007) and x-tra base (P=0.005) restored teeth was evident. No significant difference in the cervical microleakage scores was recorded between groups AC (P>0.05). CONCLUSIONS: The bulk-fill flowable RBC bases significantly reduced cuspal deflection compared with a conventional RBC restored in an oblique incremental filling technique with no associated change in cervical microleakage recorded.

'Your good days and your bad days' an exploration and consideration of how lay people conceptualize depression.

Depression remains a significant public health issue globally; 121 million people are affected by depression health education campaigns. Regardless of the prevalence of depression and recent health education campaigns to reduce the burden of depression, many people are still stigmatized and sometimes excluded from the society in which they live. Using qualitative research, the aim of this study was to explore lay people's perceptions and attitudes of mental disorder and in particular depression. A purposive sample of 22 lay people were each asked to read a case scenario which was then followed up by the researcher using open-ended questions to explore their knowledge and attitudes and beliefs relating to depression. The data was analysed using Braun & Clarke's strategy of thematic analysis. The results revealed that many of the participants were familiar with the concept of depression, either through their own experiences of the disorder or through knowing people with depression. The participants also drew from psychosocial explanations of depression and located depression as part of the human condition. The paper suggests that lay people's concepts of depression offer rich complex and diverse perspectives that enhance professional views and may lead to a greater understanding of uptake and acceptance of care for depression.

Regression of early diabetic macular oedema is associated with prevention of dark adaptation.

HYPOTHESIS: Dark-adapted rods consume oxygen at high rates and light adaptation decreases this oxygen burden and can have therapeutic effects on diabetic macular oedema (DMO). METHODS: Patients with mild non-proliferative diabetic retinopathy (DR) and early, untreated non-sight-threatening DMO slept for 6 months wearing masks that illuminated the eyelid of one closed eye by 505 nm light. Exclusion criteria were any concomitant eye disease, DR >ETDRS grade 35, and other systemic diseases. PRIMARY OUTCOME: change of OCT retinal thickness in the local region where oedema was present. RESULTS: A total of 34 out of 40 patients completed the study. Mean baseline OCT macular cube thickness was equivalent for study and fellow eyes. But study eyes had a greater mean thickness in the central subfield zone 1 (282±53 µm) vs (256±19 µm) the fellow eyes. Twenty-eight study eyes showed intraretinal cysts compared with nine in the fellow eyes. At 6 months, only 19 study eyes had cysts while cysts were seen in 20 fellow eyes. After 6 months, the worst affected ETDRS zone and the central subfield zone 1 reduced in thickness in study eyes only by 12 µm (95% CI 20 to -7, P=0.01). The secondary outcomes of change in visual acuity, achromatic contrast sensitivity, and microperimetric thresholds improved significantly in study eyes and deteriorated in fellow eyes. CONCLUSIONS: Sleeping in dim light that can keep rods light adapted may reverse the changes of DMO.

Changes to colour vision on exposure to high altitude.

OBJECTIVES: Several studies have shown deterioration in colour vision at altitudes above 3,000m. These studies have been conducted in photopic (bright daylight) conditions, whereas many military operations take place in mesopic (dim light) conditions. Data suggests that the tritan colour vision axis (blue cones, TA) are more susceptible to hypoxic insult than protan axis (red cones, PA). The objective of this study was to examine colour vision at high altitude, in mesopic conditions, and using a novel method of assessment to discriminate between the tritan and protan axis. METHODS: We examined 42 eyes (21 subjects, mean age 44, range 22-71), at sea level and within 12-36 hours of exposure to 3300m. This was done in a darkened room, with refractive error correction. Colour vision was studied using ChromaTest, a software programme that analyzes colour contrast threshold (CCT) of both TA and PA. We planned to repeat CCT measurement at 4,392m, but technology failure prevented this. Non-parametric paired data was examined using the Wilcoxon signed rank test. RESULTS: There was found to be no change to either the PA (p = 0.409) or the TA (p = 0.871) upon ascent. Within the PA 16 eyes had a lower CCT at high altitude, whilst 26 were higher. In the TA 20 eyes had a lower CCT and 22 were higher. At sea level, mean CCT for PA was 4.21 (SD 2.29) TA was 7.06 (SD 1.77). At 3,300m mean CCT for PA was 4.36 (SD 2.86) and TA was 6.93 (SD 2.39). CONCLUSIONS: This experiment revealed no changes to colour vision with exposure to 3,300m. This may be below the threshold altitude for cone dysfunction, alternatively colour vision deterioration may be less significant in mesopic conditions.

Toneburst-evoked auditory brainstem response in a leopard seal, Hydrurga leptonyx.

Toneburst-evoked auditory brainstem responses (ABRs) were recorded in a captive subadult male leopard seal. Three frequencies from 1 to 4 kHz were tested at sound levels from 68 to 122 dB peak equivalent sound pressure level (peSPL). Results illustrate brainstem activity within the 1-4 kHz range, with better hearing sensitivity at 4 kHz. As is seen in human ABR, only wave V is reliably identified at the lower stimulus intensities. Wave V is present down to levels of 82 dB peSPL in the right ear and 92 dB peSPL in the left ear at 4 kHz. Further investigations testing a wider frequency range on seals of various sex and age classes are required to conclusively report on the hearing range and sensitivity in this species.

Core-shell magnetic morphology of structurally uniform magnetite nanoparticles.

A new development in small-angle neutron scattering with polarization analysis allows us to directly extract the average spatial distributions of magnetic moments and their correlations with three-dimensional directional sensitivity in any magnetic field. Applied to a collection of spherical magnetite nanoparticles 9.0 nm in diameter, this enhanced method reveals uniformly canted, magnetically active shells in a nominally saturating field of 1.2 T. The shell thickness depends on temperature, and it disappears altogether when the external field is removed, confirming that these canted nanoparticle shells are magnetic, rather than structural, in origin.

A fatal case of cough.

Dysfunctional swallowing is an uncommon, but important cause of bronchiectasis. We describe a child with a brainstem tumor, who developed bronchiectasis caused by chronic aspiration secondary to a dysfunctional swallow. The case highlights the importance of thorough and repeated evaluation before a diagnosis of idiopathic bronchiectasis is made. If dysfunctional swallow is found further investigation to ascertain the cause is indicated.

Primary ciliary dyskinesia: a consensus statement on diagnostic and treatment approaches in children.

Primary ciliary dyskinesia (PCD) is associated with abnormal ciliary structure and function, which results in retention of mucus and bacteria in the respiratory tract, leading to chronic oto-sino-pulmonary disease, situs abnormalities and abnormal sperm motility. The diagnosis of PCD requires the presence of the characteristic clinical phenotype and either specific ultrastructural ciliary defects identified by transmission electron microscopy or evidence of abnormal ciliary function. Although the management of children affected with PCD remains uncertain and evidence is limited, it remains important to follow-up these patients with an adequate and shared care system in order to prevent future lung damage. This European Respiratory Society consensus statement on the management of children with PCD formulates recommendations regarding diagnostic and therapeutic approaches in order to permit a more accurate approach in these patients. Large well-designed randomised controlled trials, with clear description of patients, are required in order to improve these recommendations on diagnostic and treatment approaches in this disease.