Reproductive tissue-specific expression profiling and genetic variation across a 19 gene bovine β-defensin cluster

β-defensins are small cationic peptides, with potent immunoregulatory and antimicrobial activity which are produced constitutively and inducibly by eukaryotic cells. This study profiles the expression of a cluster of 19 novel defensin genes which spans 320 kb on chromosome 13 in Bos taurus. It also assesses the genetic variation in these genes between two divergently selected cattle breeds. Using quantitative real-time PCR (qRT-PCR), all 19 genes in this cluster were shown to be expressed in the male genital tract and 9 in the female genital tract, in a region-specific manner. These genes were sequenced in Norwegian Red (NR) and Holstein-Friesian (HF) cattle for population genetic analysis. Of the 17 novel single nucleotide polymorphisms (SNPs) identified, 7 were non-synonymous, 6 synonymous and 4 outside the protein coding region. Significant frequency differences in SNPs in bovine β-defensins (BBD) 115, 117, 121, and 122 were detected between the two breeds, which was also reflected at the haplotype level (P < 0.05). There was clear segregation of the haplotypes into two blocks on chromosome 13 in both breeds, presumably due to historical recombination. This study documents genetic variation in this β-defensin gene cluster between Norwegian Red and Holstein-Friesian cattle which may result from divergent selection for production and fertility traits in these two breeds. Regional expression in the epididymis and fallopian tube suggests a potential reproductive-immunobiology role for these genes in cattle.     

The integration of 'omic' disciplines and systems biology in cattle breeding

Enormous progress has been made in the selection of animals, including cattle, for specific traits using traditional quantitative genetics approaches. Nevertheless, considerable variation in phenotypes remains unexplained, and therefore represents potential additional gain for animal production. In addition, the paradigm shift in new disciplines now being applied to animal breeding represents a powerful opportunity to prise open the 'black box' underlying the response to selection and fully understand the genetic architecture controlling the traits of interest. A move away from traditional approaches of animal breeding toward systems approaches using integrative analysis of data from the 'omic' disciplines represents a multitude of exciting opportunities for animal breeding going forward as well as providing alternatives for overcoming some of the limitations of traditional approaches such as the expressed phenotype being an imperfect predictor of the individual's true genetic merit, or the phenotype being only expressed in one gender or late in the lifetime of an animal. This review aims to discuss these opportunities from the perspective of their potential application and contribution to cattle breeding. Harnessing the potential of this paradigm shift also poses some new challenges for animal scientists - and they will also be discussed.     

Immobilization of organophosphate hydrolase on an amyloid fibril nanoscaffold: towards bioremediation and chemical detoxification

Organophosphate hydrolase has potential as a bioremediation and chemical detoxification enzyme, but the problems of reusability and stability need to be addressed to use this enzyme on an industrial scale. Immobilizing the enzyme to a nanoscaffold may help to solve these problems. Amyloid fibrils generated from insulin and crystallin provided a novel nanoscaffold for the immobilization of organophosphate hydrolase, using glutaraldehyde as the crosslinking reagent. Electrophoretic, centrifugation, and temperature stability experiments, together with transmission electron microscopy were undertaken to verify that crosslinking had successfully occurred. The resulting fibrils remained active towards the substrate paraoxon and when immobilized to the insulin amyloid fibrils, the enzyme exhibited a significant (～ 300%) increase in the relative temperature stability at 40, 45, and 50°C (as measured by comparing the initial enzyme activity to the activity remaining after heating), compared to free enzyme. This confirms that amyloid fibrils could provide a new type of nanoscaffold for enzyme immobilization.     

Local adaptation across a complex bioclimatic landscape in two montane bumble bee species

Understanding evolutionary responses to variation in temperature and precipitation across species ranges is of fundamental interest given ongoing climate change. The importance of temperature and precipitation for multiple aspects of bumble bee (Bombus) biology, combined with large geographic ranges that expose populations to diverse environmental pressures, make these insects well‐suited for studying local adaptation. Here, we analyzed genome‐wide sequence data from two widespread bumble bees, Bombus vosnesenskii and Bombus vancouverensis, using multiple environmental association analysis methods to investigate climate adaptation across latitude and altitude. The strongest signatures of selection were observed in B. vancouverensis, but despite unique responses between species for most loci, we detected several shared responses. Genes relating to neural and neuromuscular function and ion transport were especially evident with respect to temperature variables, while genes relating to cuticle formation, tracheal and respiratory system development, and homeostasis were associated with precipitation variables. Our data thus suggest that adaptive responses for tolerating abiotic variation are likely to be complex, but that several parallels among species can emerge even for these complex traits and landscapes. Results provide the framework for future work into mechanisms of thermal and desiccation tolerance in bumble bees and a set of genomic targets that might be monitored for future conservation efforts.     

High Dynamic Range Processing for Magnetic Resonance Imaging

Purpose

To minimize feature loss in T₁- and T₂-weighted MRI by merging multiple MR images acquired at different T_R and T_E to generate an image with increased dynamic range.

Materials and Methods

High Dynamic Range (HDR) processing techniques from the field of photography were applied to a series of acquired MR images. Specifically, a method to parameterize the algorithm for MRI data was developed and tested. T₁- and T₂-weighted images of a number of contrast agent phantoms and a live mouse were acquired with varying T_R and T_E parameters. The images were computationally merged to produce HDR-MR images. All acquisitions were performed on a 7.05 T Bruker PharmaScan with a multi-echo spin echo pulse sequence.

Results

HDR-MRI delineated bright and dark features that were either saturated or indistinguishable from background in standard T₁- and T₂-weighted MRI. The increased dynamic range preserved intensity gradation over a larger range of T₁ and T₂ in phantoms and revealed more anatomical features in vivo.

Conclusions

We have developed and tested a method to apply HDR processing to MR images. The increased dynamic range of HDR-MR images as compared to standard T₁- and T₂-weighted images minimizes feature loss caused by magnetization recovery or low SNR.     

Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study

Background

Host-associated microbial communities have important roles in tissue homeostasis and overall health. Severe perturbations can occur within these microbial communities during critical illness due to underlying diseases and clinical interventions, potentially influencing patient outcomes. We sought to profile the microbial composition of critically ill mechanically ventilated patients, and to determine whether microbial diversity is associated with illness severity and mortality.

Methods

We conducted a prospective, observational study of mechanically ventilated critically ill patients with a high incidence of pneumonia in 2 intensive care units (ICUs) in Hamilton, Canada, nested within a randomized trial for the prevention of healthcare-associated infections. The microbial profiles of specimens from 3 anatomical sites (respiratory, and upper and lower gastrointestinal tracts) were characterized using 16S ribosomal RNA gene sequencing.

Results

We collected 65 specimens from 34 ICU patients enrolled in the trial (29 endotracheal aspirates, 26 gastric aspirates and 10 stool specimens). Specimens were collected at a median time of 3?days (lower respiratory tract and gastric aspirates; interquartile range [IQR] 2–4) and 6?days (stool; IQR 4.25–6.75) following ICU admission. We observed a loss of biogeographical distinction between the lower respiratory tract and gastrointestinal tract microbiota during critical illness. Moreover, microbial diversity in the respiratory tract was inversely correlated with APACHE II score (r?=???0.46, p?=?0.013) and was associated with hospital mortality (Median Shannon index: Discharged alive; 1.964 vs. Deceased; 1.348, p?=?0.045).

Conclusions

The composition of the host-associated microbial communities is severely perturbed during critical illness. Reduced microbial diversity reflects high illness severity and is associated with mortality. Microbial diversity may be a biomarker of prognostic value in mechanically ventilated patients.

Trial registration

ClinicalTrials.gov ID NCT01782755. Registered February 4 2013.

     

Pharmacists' Perceptions of the Barriers and Facilitators to the Implementation of Clinical Pharmacy Key Performance Indicators

BackgroundIn hospitals around the world, there has been no consensus regarding which clinical activities a pharmacist should focus on until recently. In 2011, a Canadian clinical pharmacy key performance indicator (cpKPI) collaborative was formed. The goal of the collaborative was to advance pharmacy practice in order to improve patient outcomes and enhance the quality of care provided to patients by hospital pharmacists. Following a literature review, which indicated that pharmacists can improve patient outcomes by carrying out specific activities, and an evidence-informed consensus process, a final set of eight cpKPIs were established. Canadian hospitals leading the cpKPI initiative are currently in the early stages of implementing these indicators.ObjectiveTo explore pharmacists'' perceptions of the barriers and facilitators to the implementation of cpKPIs.MethodsClinical pharmacists employed by the Nova Scotia Health Authority were invited to participate in focus groups. Focus group discussions were audio-recorded and transcribed, and data was analyzed using thematic analysis.FindingsThree focus groups, including 26 pharmacists, were conducted in February 2015. Three major themes were identified. Resisting the change was comprised of documentation challenges, increased workload, practice environment constraints, and competing priorities. Embracing cpKPIs was composed of seeing the benefit, demonstrating value, and existing supports. Navigating the unknown was made up of quality versus quantity battle, and insights into the future.ConclusionsAlthough pharmacists were challenged by documentation and other changes associated with the implementation of cpKPIs, they demonstrated significant support for cpKPIs and were able to see benefits of the implementation. Pharmacists came up with suggestions for overcoming resistance associated with the implementation of cpKPIs and provided insights into the future of pharmacy practice. The identification of barriers and facilitators to cpKPI implementation will be used to inform the implementation process on a local and national level.     

Electron transfer in DNA: covalent attachment of spectroscopically unique donor and acceptor complexes

 The notion that DNA is capable of electron transfer (ET) has inspired several groups to investigate the nature of this intriguing process. While several factors modulate ET reaction rates, the distance dependence of ET in DNA is the focus of our current investigations. To this end we propose that several design criteria must be met to facilitate the collection of kinetic data corresponding to DNA-mediated ET reactions. These criteria include (1) covalent attachment of site-selective donor-acceptor pairs, (2) incorporation of donor-acceptor pairs that offer minimal structural perturbation of the DNA duplex, and (3) use of spectroscopically distinguishable donor and acceptor complexes that allow identification of kinetic intermediates. Received, accepted: 5 January 1998