Value of sharing cow reference population between countries on reliability of genomic prediction for milk yield traits

Increasing the reliability of genomic prediction (GP) of economic traits in the pasture-based dairy production systems of New Zealand (NZ) and Australia (AU) is important to both countries. This study assessed if sharing cow phenotype and genotype data of NZ and AU improves the reliability of GP for NZ bulls. Data from approximately 32,000 NZ genotyped cows and their contemporaries were included in the May 2018 routine genetic evaluation of the Australian Dairy cattle in an attempt to provide consistent phenotypes for both countries. After the genetic evaluation, deregressed proofs of cows were calculated for milk yield traits. The April 2018 multiple across-country evaluation of Interbull was also used to calculate deregressed proofs for bulls on the NZ scale. Approximately 1,178 Jersey (Jer) and 6,422 Holstein (Hol) bulls had genotype and phenotype data. In addition to NZ cows, phenotype data of close to 60,000 genotyped Australian (AU) cows from the same genetic evaluation run as NZ cows were used. All AU and NZ females were genotyped using low-density SNP chips (<10K SNP) and were imputed first to 50K and then to ∼600K (referred to as high density; HD). We used up to 98,000 animals in the reference populations, both by expanding the NZ reference set (cow, bull, single breed to multi-breed set) and by adding AU cows. Reliabilities of GP were calculated for 508 Jer and 1,251 Hol bulls whose sires are not included in the reference set (RS) to ensure that real differences are not masked by close relationships. The GP was tested using 50K or high-density SNP chip using genomic BLUP in bivariate (considering country as a trait) or single trait models. The RS that gave the highest reliability for each breed were also tested using a hybrid GP method that combines expectation maximization with Bayes R. The addition of the AU cows to an NZ RS that included either NZ cows only, or cows and bulls, improved the reliability of GP for both NZ Hol and Jer validation bulls for all traits. Using single breed reference populations also increased reliability when NZ crossbred cows were added to reference populations that included only purebred NZ bulls and cows and AU cows. The full multi-breed RS (all NZ cows and bulls and AU cows) provided similar reliabilities in NZ Hol bulls, when compared with the single breed reference with crossbred NZ cows. For Jer validation bulls, the RS that included Jer cows and bulls and crossbred cows from NZ and Jer cows from AU was marginally better than the all-breed, all-country RS. In terms of reliability, the advantage of the HD SNP chip was small but captured more of the genomic variance than the 50K, particularly for Hol. The expectation maximization Bayes R GP method was slightly (up to 3 percentage points) better than genomic BLUP. We conclude that GP of milk production traits in NZ bulls improves by up to 7 percentage points in reliability by expanding the NZ reference population to include AU cows.

SIL1 deficiency causes degenerative changes of peripheral nerves and neuromuscular junctions in fish, mice and human

BACKGROUND

Marinesco-Sjögren Syndrome (MSS) is a rare neuromuscular condition caused by recessive mutations in the SIL1 gene resulting in the absence of functional SIL1 protein, a co-chaperone for the major ER chaperone, BiP. As BiP is decisive for proper protein processing, loss of SIL1 results in the accumulation of misshaped proteins. This accumulation likely damages and destroys cells in vulnerable tissues, leading to congenital cataracts, cerebellar ataxia, vacuolar myopathy and other MSS phenotypes. Whether the peripheral nervous system (PNS) is affected in MSS has not been conclusively shown.

METHODS

To study PNS vulnerability in MSS, intramuscular nerves fibres from MSS patients and from SIL1-deficient mice (woozy) as well as sciatic nerves and neuromuscular junctions (NMJ) from these mice have been investigated via transmission electron microscopic and immunofluorescence studies accompanied by transcript studies and unbiased proteomic profiling. In addition, PNS and NMJ integrity were analyzed via immunofluorescence studies in an MSS-zebrafish model which has been generated for that purpose.

RESULTS

Electron microscopy revealed morphological changes indicative of impaired autophagy and mitochondrial maintenance in distal axons and in Schwann cells. Moreover, changes of the morphology of NMJs as well as of transcripts encoding proteins important for NMJ function were detected in woozy mice. These findings were in line with a grossly abnormal structure of NMJs in SIL1-deficient zebrafish embryos. Proteome profiling of sciatic nerve specimens from woozy mice revealed altered levels of proteins implicated in neuronal maintenance suggesting the activation of compensatory mechanisms.

CONCLUSION

Taken together, our combined data expand the spectrum of tissues affected by SIL1-loss and suggest that impaired neuromuscular transmission might be part of MSS pathophysiology.

Identifying factors that influence the '6-hour target' in the Emergency Department by applying Regression Analysis

AIM

To determine factors within the Emergency Department (ED) that have maximum influence on the '6-hour target'.

METHODS

Regression Analysis methodology employed to analyse the influence of 9 ED variables on the '6-hour target' compliance.

RESULTS

The number of patients waiting to be seen an ED physician at 8pm exerts maximum influence on the '6-hour target' (r = -0.581, p<0.05).

CONCLUSION

The '6-hour target' compliance rises with lesser number of patients waiting to be seen by an ED physician at 8pm. Also, the '6-hour target' compliance rises by increasing the number of ED Registrar working hours and the number of ED SHO working hours per day.

Clinical and research strategies for limb-girdle congenital myasthenic syndromes

Congenital myasthenic syndromes (CMS) are a group of rare disorders that cause fatigable muscle weakness due to defective signal transmission at the neuromuscular junction, a specialized synapse between peripheral motor neurons and their target muscle fibers. There are now over 30 causative genes that have been reported for CMS. Of these, there are 10 that are associated with a limb-girdle pattern of muscle weakness and are thus classed as LG-CMS. Next-generation sequencing and advanced methods of data sharing are likely to uncover further genes that are associated with similar clinical phenotypes, contributing to better diagnosis and effective treatment of LG-CMS patients. This review highlights clinical and pathological hallmarks of LG-CMS in relation to the underlying genetic defects and pathways. Tailored animal and cell models are essential to elucidate the exact function and pathomechanisms at the neuromuscular synapse that underlie LG-CMS. The integration of genomics and proteomics data derived from these models and patients reveals new and often unexpected insights that are relevant beyond the rare genetic disorder of LG-CMS and may extend to the functioning of mammalian synapses in health and disease more generally.

Palliative and end of life care in solid organ transplantation

Palliative care is an interprofessional approach that focuses on quality of life of patients who are facing life-threatening illness. Palliative care is consistently associated with improvements in advance care planning, patient and caregiver satisfaction, quality of life, symptom burden, and lower healthcare utilization. Most transplant patients have advanced chronic disease, significant symptom burden, and mortality awaiting transplant. Transplantation introduces new risks including perioperative death, organ rejection, infection, renal insufficiency, and malignancy. Numerous publications over the last decade identify that palliative care is well-suited to support these patients and their caregivers, yet access to palliative care and research within this population are lacking. This review describes palliative care and summarizes existing research supporting palliative intervention in advanced organ failure and transplant populations. A proposed model to provide palliative care in parallel with disease-directed therapy in a transplant program has the potential to improve symptom burden, quality of life, and healthcare utilization. Further studies are needed to elucidate specific benefits of palliative care for this population. In addition, there is a tremendous need for education, specifically for clinicians, patients, and families, to improve understanding of palliative care and its benefits for patients with advanced disease.

A quantitative study of neurochemically defined populations of inhibitory interneurons in the superficial dorsal horn of the mouse spinal cord

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Neurochemistry of lamina I–II inhibitory neurons in mouse is similar to that in rat.

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Five neurochemical classes account for all lamina I–II inhibitory neurons in mouse.

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Excitatory dynorphin cells are largely restricted to glabrous skin territory.

Around a quarter of neurons in laminae I–II of the dorsal horn are inhibitory interneurons. These play an important role in modulating somatosensory information, including that perceived as pain or itch. Previous studies in rat identified four largely non-overlapping neurochemical populations among these cells, defined by expression of galanin, neuropeptide Y (NPY), neuronal nitric oxide synthase (nNOS) or parvalbumin. The galanin cells were subsequently shown to coexpress dynorphin. Several recent studies have used genetically modified mice to investigate the function of different interneuron populations, and it is therefore important to determine whether the same pattern applies in mouse, and to estimate the relative sizes of these populations. We show that the neurochemical organization of inhibitory interneurons in mouse superficial dorsal horn is similar to that in the rat, although a larger proportion of these neurons (33%) express NPY. Between them, these four populations account for ∼75% of inhibitory cells in laminae I–II. Since ∼25% of inhibitory interneurons in this region belong to a novel calretinin-expressing type, our results suggest that virtually all inhibitory interneurons in superficial dorsal horn can be assigned to one of these five neurochemical populations. Although our main focus was inhibitory neurons, we also identified a population of excitatory dynorphin-expressing cells in laminae I–II that are largely restricted to the medial part of the mid-lumbar dorsal horn, corresponding to glabrous skin territory. These findings are important for interpretation of studies using molecular-genetic techniques to manipulate the functions of interneuron populations to investigate their roles in somatosensory processing.

A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species

Background

High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual.

Results

We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6–9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases.

Conclusions

We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-017-2654-1) contains supplementary material, which is available to authorized users.

Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions

Background

Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population.

Results

The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence.

Conclusions

Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0997-9) contains supplementary material, which is available to authorized users.

Study of the apoptotic effect of urine as a diagnostic biomarker in patients with interstitial cystitis

INTRODUCTION

The main objective of the study was to assess the apoptotic effect of urine from patients with interstitial cystitis (IC) in cell cultures and to study its value as a diagnostic biomarker for IC.

MATERIAL AND METHODS

A prospective study was conducted between January 2010 and January 2015 and included 57 patients diagnosed with IC and 50 healthy patients from the Hospital Clinic of Barcelona and the La Paz University Hospital. The urine of these patients was exposed to cell cultures, and its ability to induce apoptosis in the cultures was analysed. Using flow cytometry, we then measured the degree of apoptosis, quantified by the percentage of cells of the cell cycle in phase sub G0.

RESULTS

The cell cultures exposed to the urine of patients with IC had a sub G1 peak and a G2 phase, which was significantly greater than that of the control group, and a significantly lower percentage in the S phase than the control group. The mean apoptosis values in the urine cultures from patients with IC were significantly higher than those of the control group. Using a value >10% of the apoptosis test as a positive result, we observed a specificity of 96% and a positive predictive value of 92%.

CONCLUSIONS

The urine of patients with IC exerts an apoptotic effect on tumour cell cultures that is significantly greater than that exerted by the urine of healthy control patients. A≥10% cutoff for the apoptosis test presented very low sensitivity (40%) but had a very high specificity (96%), thereby able to confirm the diagnosis of IC when positive.

Identification of mutations in the MYO9A gene in patients with congenital myasthenic syndrome

Congenital myasthenic syndromes are a group of rare and genetically heterogenous disorders resulting from defects in the structure and function of the neuromuscular junction. Patients with congenital myasthenic syndrome exhibit fatigable muscle weakness with a variety of accompanying phenotypes depending on the protein affected. A cohort of patients with a clinical diagnosis of congenital myasthenic syndrome that lacked a genetic diagnosis underwent whole exome sequencing in order to identify genetic causation. Missense biallelic mutations in the MYO9A gene, encoding an unconventional myosin, were identified in two unrelated families. Depletion of MYO9A in NSC-34 cells revealed a direct effect of MYO9A on neuronal branching and axon guidance. Morpholino-mediated knockdown of the two MYO9A orthologues in zebrafish, myo9aa/ab, demonstrated a requirement for MYO9A in the formation of the neuromuscular junction during development. The morphants displayed shortened and abnormally branched motor axons, lack of movement within the chorion and abnormal swimming in response to tactile stimulation. We therefore conclude that MYO9A deficiency may affect the presynaptic motor axon, manifesting in congenital myasthenic syndrome. These results highlight the involvement of unconventional myosins in motor axon functionality, as well as the need to look outside traditional neuromuscular junction-specific proteins for further congenital myasthenic syndrome candidate genes.

Assessing the quality of life of non–Hodgkin lymphoma survivors: A population-based study

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Background: Non-Hodgkin Lymphoma survival in Ireland has improved significantly over recent years. However, little survivorship research has been conducted in this country. The aim of this study is to assess the quality of life (QOL) in an Irish population of Non-Hodgkin Lymphoma (NHL) survivors. Methods: High–grade NHL survivors treated in 2 University Hospitals participated in this cross–sectional study by completing the validated Lymphoma specific Functional Assessment of Cancer Therapy (FACT–Lym) questionnaire and Symptom Index–18. Scales were measured using a score from 1 (not at all) to 4 (very much). Raw data was transformed to linear scores, with high scores indicating a higher level of functioning. Linear regression analysis was used to compare scores according to time since diagnosis. Results: Of 87 questionnaires, 47 were completed and returned by NHL survivors (54% response rate). QOL scores improved from time of diagnosis, with the exception of 4–5 years where scores decreased before again improving in the following years. After adjusting for age and sex, statistically significant differences were identified 5+ years after diagnosis in emotional, functional wellbeing and global FACT-Lym scores when compared to 1-2 years after diagnosis. Conclusions: QOL improves post diagnosis with a transient decrease at year 4-5 which may represent anxiety prior to being declared ‘cured’ or being discharged from follow–up. Our small, mostly private patient population reported higher QOL than larger government insured American groups (Smith et. al. Health status and quality of life among Non-Hodgkin lymphoma survivors. Cancer. 2009.). Patients reported on–going symptoms after treatment ended. These findings may help to develop a focused cancer survivorship programme in the future. [Table: see text]

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.

Prevalence of bone metastases and bone-targeting agent use among solid tumor patients in the United States

Purpose

Patients with bone metastases are at an increased risk of experiencing morbidity due to bone complications, and bone-targeting agents (BTA) are indicated for the prevention of these complications. Population-based estimates of the prevalence of bone metastases associated with solid tumors, and current treatment patterns for these patients, are limited. This study was undertaken to estimate the prevalence of bone metastases from solid tumors and to describe recent trends in the use of BTA in the US.

Methods

We estimated the prevalence of bone metastases in the US in 2012 using data from Medicare fee-for-service and PharMetrics Plus, a large commercial claims database. We evaluated the proportion of patients with bone metastases who were treated with BTA in 2012, timing of initiation of BTA relative to bone metastasis diagnosis, and persistence on BTA, overall and by primary tumor type and treatment.

Results

There were ~330,000 (168,063 Medicare fee-for-service; 162,239 other) patients aged ≥18 years living with solid tumors and bone metastases in 2012. BTA were used by 43% (Commercial) to 47% (Medicare) of patients in 2012, with the greatest use among breast cancer patients. Over half (Medicare: 57%; Commercial: 53%) of BTA-treated patients initiated BTA after experiencing a bone complication.

Conclusion

Of the estimated 330,000 solid tumor patients living with bone metastases in the US in 2012, many may have received less than optimal care to prevent bone complications during the calendar year.

Daytime CO2 urban surface fluxes from airborne measurements, eddy-covariance observations and emissions inventory in Greater London

Airborne measurements within the urban mixing layer (360 m) over Greater London are used to quantify CO(2) emissions at the meso-scale. Daytime CO(2) fluxes, calculated by the Integrative Mass Boundary Layer (IMBL) method, ranged from 46 to 104 μmol CO(2) m(-2) s(-1) for four days in October 2011. The day-to-day variability of IMBL fluxes is at the same order of magnitude as for surface eddy-covariance fluxes observed in central London. Compared to fluxes derived from emissions inventory, the IMBL method gives both lower (by 37%) and higher (by 19%) estimates. The sources of uncertainty of applying the IMBL method in urban areas are discussed and guidance for future studies is given.

The interpretation of perioperative lactate abnormalities in patients undergoing cardiac surgery

Hyperlactataemia and lactic acidosis are commonly encountered during and after cardiac surgery. Perioperative lactate production increases in the myocardium, skeletal muscle, lungs and in the splanchnic circulation during cardiopulmonary bypass. Hyperlactataemia has a bimodal distribution in the perioperative period. An early increase in lactate levels, arising intraoperatively or soon after intensive care unit admission, is a familiar and concerning finding for most clinicians. It is highly suggestive of tissue ischaemia and is associated with a prolonged intensive care unit stay, a prolonged requirement for respiratory and cardiovascular support and increased postoperative mortality. Its presence should prompt a thorough search for potential causes of tissue hypoxia. In contrast, late-onset hyperlactataemia, a less well recognised complication, occurs 4 to 24 hours after completion of surgery and is typically associated with preserved cardiac output and oxygen delivery. Risk factors for late-onset hyperlactataemia include hyperglycaemia, long cardiopulmonary bypass time and elevated endogenous catecholamines. Although patients with this complication may have a longer duration of ventilation and intensive care unit length of stay than those with normolactataemia, an association with increased mortality has not been demonstrated. The discovery of late-onset hyperlactataemia should not delay the postoperative progress of an otherwise stable patient following cardiac surgery.