Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients.

Tensor-product kernel-based representation encoding joint MRI view similarity

To support 3D magnetic resonance image (MRI) analysis, a marginal image similarity (MIS) matrix holding MR inter-slice relationship along every axis view (Axial, Coronal, and Sagittal) can be estimated. However, mutual inference from MIS view information poses a difficult task since relationships between axes are nonlinear. To overcome this issue, we introduce a Tensor-Product Kernel-based Representation (TKR) that allows encoding brain structure patterns due to patient differences, gathering all MIS matrices into a single joint image similarity framework. The TKR training strategy is carried out into a low dimensional projected space to get less influence of voxel-derived noise. Obtained results for classifying the considered patient categories (gender and age) on real MRI database shows that the proposed TKR training approach outperforms the conventional voxel-wise sum of squared differences. The proposed approach may be useful to support MRI clustering and similarity inference tasks, which are required on template-based image segmentation and atlas construction.

Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe

Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors.

Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001.

Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0.

Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones.

Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.

Association between subjective evaluation and physical parameters for radiographic images optimization

PURPOSE

The purpose of this study was to develop a methodology to optimize computed radiographic techniques to image the skull, chest, and pelvis of a standard patient.

METHODS

Optimization was performed by varying exposure levels with different tube voltages to generate images of an anthropomorphic phantom. Image quality was evaluated using visual grading analysis and measuring objective parameters such as the effective detective quantum efficiency and the contrast-to-noise ratio. Objective and subjective evaluations were compared to obtain an optimized technique for each anatomic region.

RESULTS

Gold standard techniques provided a significant reduction in X-ray doses compared to the techniques used in our radiology service, without compromising diagnostic accuracy. They were chosen as follows 102 kVp/1.6 mAs for skull; 81 kVp/4.5 mAs for pelvis and 90 kVp/3.2 mAs for chest.

CONCLUSION

There is a range of acceptable techniques that produce adequate images for diagnosis in computed radiography systems. This aspect allows the optimization process to be focused on the patient dose without compromising diagnostic capabilities. This process should be performed through association of quantitative and qualitative parameters, such as effective detective quantum efficiency, contrast-to-noise ratio, and visual grading analysis.

Trichinella pseudospiralis in the Iberian peninsula

Nematode worms of the genus Trichinella are zoonotic parasites circulating in most continents, including Europe. In Spain, Trichinella spiralis and Trichinella britovi are highly prevalent in wildlife but seldom in domestic pigs. In Portugal, only T. britovi was documented in wild carnivores. In the period 2006-2013 in Spain, 384 (0.0001%) pigs and 1399 (0.20%) wild boars (Sus scrofa) were positive for Trichinella spp. larvae, which were identified as T. spiralis or T. britovi. In 2014, Trichinella pseudospiralis larvae were isolated from a wild boar hunted in the Gerona province, Cataluña region, North-East of Spain, near the border to France. This is the first report of T. pseudospiralis in the Iberian peninsula, which suggests a broad distribution area of this zoonotic nematode in Europe. Since larvae of this Trichinella species do not encapsulate in the host muscles, they can be detected only by artificial digestion of muscle samples. T. pseudospiralis is the only Trichinella species infecting both mammals and birds. Birds can spread this pathogen over great distances including islands triggering new foci of infections in areas previously considered at low risk for this pathogen.

Effect of a Chlorhexidine Mouthwash on the Risk of Postextraction Bacteremia

Objective.

To investigate the prevalence, duration, and etiology of bacteremia following dental extractions performed after a single administration of Chlorhexidine mouthwash.

Design and Setting.

A randomized, controlled trial performed in a university hospital.

Methods.

A series of 106 patients with mental and behavioral disabilities who underwent dental extractions under general anesthesia were randomly assigned to a control group or Chlorhexidine group. The exclusion criteria applied were use of antibiotics in the previous 3 months, use of oral antiseptics, any type of congenital or acquired immunodeficiency, and disease that predisposes the patient to infections or bleeding. The Chlorhexidine group had 0.2% Chlorhexidine mouthwash administered for 30 seconds before any dental manipulation. Blood samples were collected at baseline, 30 seconds, 15 minutes, and 1 hour after the dental extractions. Subculture and further identification of the isolated bacteria were performed by conventional microbiological techniques.

Results.

The prevalence of bacteremia after dental extraction in the control and Chlorhexidine groups were 96% and 79%, respectively, at 30 seconds (P = .008), 64% and 30% at 15 minutes (P <.001), and 20% and 2% at 1 hour (P = .005). The most frequently identified bacteria were Streptococcus species in both the control and Chlorhexidine groups (64% and 68%, respectively), particularly viridans group streptococci.

Conclusion.

We recommend the routine use of a 0.2% Chlorhexidine mouthwash before dental extractions to reduce the risk of postextraction bacteremia.

Using mobile devices to improve the safety of medication administration processes

Within preventable medical errors, those related to medications are frequent in every stage of the prescribing cycle. Nursing is responsible for maintaining each patients safety and care quality. Moreover, nurses are the last people who can detect an error in medication before its administration. Medication administration is one of the riskiest tasks in nursing. The use of information and communication technologies is related to a decrease in these errors. Including mobile devices related to 2D code reading of patients and medication will decrease the possibility of error when preparing and administering medication by nurses. A cross-platform software (iOS and Android) was developed to ensure the five Rights of the medication administration process (patient, medication, dose, route and schedule). Deployment in November showed 39% use.

Human recombinant cementum attachment protein (hrPTPLa/CAP) promotes hydroxyapatite crystal formation in vitro and bone healing in vivo

Cementum extracellular matrix is similar to other mineralized tissues; however, this unique tissue contains molecules only present in cementum. A cDNA of these molecules, cementum attachment protein (hrPTPLa/CAP) was cloned and expressed in a prokaryotic system. This molecule is an alternative splicing of protein tyrosine phosphatase-like A (PTPLa). In this study, we wanted to determine the structural and functional characteristics of this protein. Our results indicate that hrPTPLa/CAP contains a 43.2% α-helix, 8.9% β-sheet, 2% β-turn and 45.9% random coil secondary structure. Dynamic light scattering shows that this molecule has a size distribution of 4.8 nm and aggregates as an estimated mass of 137 kDa species. AFM characterization and FE-SEM studies indicate that this protein self-assembles into nanospheres with sizes ranging from 7.0 to 27 nm in diameter. Functional studies demonstrate that hrPTPLa/CAP promotes hydroxyapatite crystal nucleation: EDS analysis revealed that hrPTPLa/CAP-induced crystals had a 1.59 ± 0.06 Ca/P ratio. Further confirmation with MicroRaman spectrometry and TEM confirm the presence of hydroxyapatite. In vivo studies using critical-size defects in rat cranium showed that hrPTPLa/CAP promoted 73% ± 2.19% and 87% ± 1.97% new bone formation at 4 and 8 weeks respectively. Although originally identified in cementum, PTPLa/CAP is very effective at inducing bone repair and healing and therefore this novel molecule has a great potential to be used for mineralized tissue bioengineering and tissue regeneration.

Salvaging urospermic ejaculates from brown bear (Ursus arctos)

The objective of this study was to reverse the osmotic stress of sperm in urine contaminated bear ejaculates that were obtained by electroejaculation using pre-freezing washing or density gradient centrifugation isolation. In Experiment 1, ejaculates were divided into six aliquots, five were diluted in each washing extender: 200, 300, 400, 500 and 700 mOsm/kg (prepared from a Tes-Tris-Fructose base, adding water or fructose as corresponds), at a 1:2 ratio (raw semen: washing solution, v/v); and the other aliquot was handled without washing (Control group). Samples were centrifuged at 600 × g for 6 min prior to freezing. In Experiment 2, ejaculates were divided into two aliquots: one was diluted 1:1 with TCG (Tris-Citric acid-Glucose) and centrifuged at 600 × g for 6 min (Centrifugation Control; C-Control); the other was treated with PureSperm density gradient column. After treatments, samples were cryopreserved. Sperm motility, viability (SYBR-14/propidium iodide (PI)) and acrosomal status (peanut agglutinin-fluorescein isothiocyanate (PNA-FITC)/PI) were analyzed before and after freezing. Ejaculates with an initial osmolality of less than 120 mOsm/kg treated with pre-freezing washing, and the Control sample had greater pre-freezing sperm motility than the raw ejaculate, but sperm viability was not different among these groups. The samples washed with 700 mOsm/kg solutions had the least pre-freezing viability. In the post-thawing evaluation, pre-freezing washing treatments did not provide any improvement in comparison with the Control sample, and treatment with 700 mOsm/kg extender had deleterious effects in all urospermic samples. PureSperm density gradient centrifugation applied to urospermic raw semen was suitable for improving sperm motility and viability of pre-freezing samples and the selected spermatozoa had greater freezing capacity.

Suppression of cooling by strong magnetic fields in white dwarf stars

Isolated cool white dwarf stars more often have strong magnetic fields than young, hotter white dwarfs, which has been a puzzle because magnetic fields are expected to decay with time but a cool surface suggests that the star is old. In addition, some white dwarfs with strong fields vary in brightness as they rotate, which has been variously attributed to surface brightness inhomogeneities similar to sunspots, chemical inhomogeneities and other magneto-optical effects. Here we describe optical observations of the brightness and magnetic field of the cool white dwarf WD 1953-011 taken over about eight years, and the results of an analysis of its surface temperature and magnetic field distribution. We find that the magnetic field suppresses atmospheric convection, leading to dark spots in the most magnetized areas. We also find that strong fields are sufficient to suppress convection over the entire surface in cool magnetic white dwarfs, which inhibits their cooling evolution relative to weakly magnetic and non-magnetic white dwarfs, making them appear younger than they truly are. This explains the long-standing mystery of why magnetic fields are more common amongst cool white dwarfs, and implies that the currently accepted ages of strongly magnetic white dwarfs are systematically too young.

Use of cohort data to estimate national prevalence of transmitted drug resistance to antiretroviral drugs in Spain (2007-2012)

Prevalence of transmitted drug resistance (pTDR) to antiretroviral drugs in Spain (2007-2012) was estimated using the CoRIS cohort, adjusting its territorial distribution and transmission route to the reference population from the Spanish Information System on New human immunodeficiency virus diagnoses. A total of 2702 patients from ten autonomous communities and with naive FASTA sequence within 6 months of human immunodeficiency virus diagnosis were selected. Weighted pTDR, estimated using the inverse probability of selection in the sample by autonomous communities and transmission group, was 8.12% (95% CI 6.44-9.80), not significantly different from unweighted pTDR. We illustrate how proportional weighting can maximize representativeness of cohort-based data, and its value to monitor pTDR at country level.

Transmitted drug resistance to rilpivirine in newly diagnosed antiretroviral naive adults

We characterized transmitted drug resistance to rilpivirine and the predicted efficacy of first-line rilpivirine-containing regimens in antiretroviral-naive Spanish patients. International Antiviral Society-USA mutations were detected in 138 of 2781 patients (4.9%), E138A (3.4%) being the most prevalent. Using the Stanford Algorithm, 121 patients (4.4%) showed low-level or intermediate resistance. No differences in the predicted efficacy of first-line non-nucleoside reverse transcriptase inhibitor-based regimens were observed. As rilpivirine becomes more widely used in clinical practice, the evolution of its transmitted drug resistance will need to be monitored. In addition, the exact role of E138A singletons on rilpivirine activity as part of first-line regimens merits further evaluation.

Alternative procedures for the cryopreservation of brown bear ejaculates depending on the flexibility of the "in cooling" period (5°C)

The adaptability of cryopreservation protocols for brown bear spermatozoa collected under field conditions and frozen in a nearby laboratory (transported for a few hours) or shipped to a reference laboratory for sex sorting (transported for a few days) was evaluated. Forty-nine electroejaculates from 15 mature brown bears were extended to 100×10(6) sperm/mL in a TES-Tris-Fructose based extender and cryopreserved (-20°C/min to -100°C and stored at -196°C). After thawing, the quality of the seminal samples was assessed for total (TM), progressive (PM) motility and kinetic parameters - by CASA -, and viability (VIAB), viable and non-apoptotic status (YOPRO-), high membrane mitochondrial potential (MIT) and intact acrosomes (iACR) - by flow cytometry -. In Experiment 1, we assessed different storage times (0, 0.5, 1 - control -, 4-5, 7-8 and 11-12 h) at 5°C from final dilution to freezing. After thawing, non-equilibrated samples (0 h) showed lower values of iACR, TM and PM. No significant differences were found for the different periods of equilibration tested. In Experiment 2, we evaluated three long-term storage times (24, 48 and 72 h) at 5°C before freezing using storage for 1h as control. The post-thawing quality of brown bear spermatozoa declined markedly after 48-72 h of pre-freezing. In conclusion, our findings suggest the possibility of extending the pre-freezing cooling period up to 24h post-collection without freezing. This knowledge should enable the adaptation of the freezing protocols for when a special handling conditions are required such as the shipment of seminal samples to technological centers for the pre-freezing application of enhancer spermatic biotechnologies.

Skeletal muscle plasticity induced by seasonal acclimatization involves IGF1 signaling: implications in ribosomal biogenesis and protein synthesis

One of the most fundamental biological processes in living organisms that are affected by environmental fluctuations is growth. In fish, skeletal muscle accounts for the largest proportion of body mass, and the growth of this tissue is mainly controlled by the insulin-like growth factor (IGF) system. By using the carp (Cyprinus carpio), a fish that inhabits extreme conditions during winter and summer, we assessed the skeletal muscle plasticity induced by seasonal acclimatization and the relation of IGF signaling with protein synthesis and ribosomal biogenesis. The expression of igf1 in muscle decreased during winter in comparison with summer, whereas the expression for both paralogues of igf2 did not change significantly between seasons. The expression of igf1 receptor a (igf1ra), but not of igf1rb, was down-regulated in muscle during the winter as compared to the summer. A decrease in protein contents and protein phosphorylation for IGF signaling molecules in muscle was observed in winter-acclimatized carp. This was related with a decreased expression in muscle for markers of myogenesis (myoblast determination factor (myod), myogenic factor 5 (myf5), and myogenin (myog)); protein synthesis (myosin heavy chain (mhc) and myosin light chain (mlc3 and mlc1b)); and ribosomal biogenesis (pre-rRNA and ribosomal proteins). IGF signaling, and key markers of ribosomal biogenesis, protein synthesis, and myogenesis were affected by seasonal acclimatization, with differential regulation in gene expression and signaling pathway activation observed in muscle between both seasons. This suggests that these molecules are responsible for the muscle plasticity induced by seasonal acclimatization in carp.