Accounting for genomic pre-selection in national BLUP evaluations in dairy cattle

<p>Abstract</p> <p>Background</p> <p>In future Best Linear Unbiased Prediction (BLUP) evaluations of dairy cattle, genomic selection of young sires will cause evaluation biases and loss of accuracy once the selected ones get progeny.</p> <p>Methods</p> <p>To avoid such bias in the estimation of breeding values, we propose to include information on all genotyped bulls, including the culled ones, in BLUP evaluations. Estimated breeding values based on genomic information were converted into genomic pseudo-performances and then analyzed simultaneously with actual performances. Using simulations based on actual data from the French Holstein population, bias and accuracy of BLUP evaluations were computed for young sires undergoing progeny testing or genomic pre-selection. For bulls pre-selected based on their genomic profile, three different types of information can be included in the BLUP evaluations: (1) data from pre-selected genotyped candidate bulls with actual performances on their daughters, (2) data from bulls with both actual and genomic pseudo-performances, or (3) data from all the genotyped candidates with genomic pseudo-performances. The effects of different levels of heritability, genomic pre-selection intensity and accuracy of genomic evaluation were considered.</p> <p>Results</p> <p>Including information from all the genotyped candidates, i.e. genomic pseudo-performances for both selected and culled candidates, removed bias from genetic evaluation and increased accuracy. This approach was effective regardless of the magnitude of the initial bias and as long as the accuracy of the genomic evaluations was sufficiently high.</p> <p>Conclusions</p> <p>The proposed method can be easily and quickly implemented in BLUP evaluations at the national level, although some improvement is necessary to more accurately propagate genomic information from genotyped to non-genotyped animals. In addition, it is a convenient method to combine direct genomic, phenotypic and pedigree-based information in a multiple-step procedure.</p

Diabetic foot complications among Indigenous peoples in Canada: A scoping review through the PROGRESS-PLUS equity lens

Introduction Indigenous peoples in Canada face a disproportionate burden of diabetes-related foot complications (DRFC), such as foot ulcers, lower extremity amputations (LEA), and peripheral arterial disease. This scoping review aimed to provide a comprehensive understanding of DRFC among First Nations, Métis, and Inuit peoples in Canada, incorporating an equity lens Methods A scoping review was conducted based on Arksey and O’Malley refined by the Joanna Briggs Institute. The PROGRESS-Plus framework was utilized to extract data and incorporate an equity lens. A critical appraisal was performed, and Indigenous stakeholders were consulted for feedback. We identified the incorporation of patient-oriented/centered research (POR). Results Of 5,323 records identified, 40 studies were included in the review. The majority of studies focused on First Nations (92%), while representation of the Inuit population was very limited populations (< 3% of studies). LEA was the most studied outcome (76%). Age, gender, ethnicity, and place of residence were the most commonly included variables. Patient-oriented/centered research was mainly included in recent studies (16%). The overall quality of the studies was average. Data synthesis showed a high burden of DRFC among Indigenous populations compared to non-Indigenous populations. Indigenous identity and rural/remote communities were associated with the worse outcomes, particularly major LEA. Discussion This study provides a comprehensive understanding of DRFC in Indigenous peoples in Canada of published studies in database. It not only incorporates an equity lens and patient-oriented/centered research but also demonstrates that we need to change our approach. More data is needed to fully understand the burden of DRFC among Indigenous peoples, particularly in the Northern region in Canada where no data are previously available. Western research methods are insufficient to understand the unique situation of Indigenous peoples and it is essential to promote culturally safe and quality healthcare. Conclusion Efforts have been made to manage DRFC, but continued attention and support are necessary to address this population’s needs and ensure equitable prevention, access and care that embraces their ways of knowing, being and acting

Decreased Neutrophil Apoptosis in Quiescent ANCA-Associated Systemic Vasculitis

Background: ANCA-Associated Systemic Vasculitis (AASV) is characterized by leukocytoclasis, accumulation of unscavenged apoptotic and necrotic neutrophils in perivascular tissues. Dysregulation of neutrophil cell death may contribute directly to the pathogenesis of AASV. less thanbrgreater than less thanbrgreater thanMethods: Neutrophils from Healthy Blood Donors (HBD), patients with AASV most in complete remission, Polycythemia Vera (PV), Systemic Lupus Erythematosus (SLE), Rheumatoid Arthritis (RA) and renal transplant recipients (TP) were incubated in vitro, and the rate of spontaneous apoptosis was measured by FACS. Plasma levels of cytokines and sFAS were measured with cytometric bead array and ELISA. Expression of pro/anti-apoptotic factors, transcription factors C/EBP-alpha, C/EBP-beta and PU.1 and inhibitors of survival/JAK2-pathway were measured by real-time-PCR. less thanbrgreater than less thanbrgreater thanResults: AASV, PV and RA neutrophils had a significantly lower rate of apoptosis compared to HBD neutrophils (AASV 50 +/- 14% vs. HBD 64 +/- 11%, p andlt; 0.0001). In RA but not in AASV and PV, low apoptosis rate correlated with increased plasma levels of GM-CSF and high mRNA levels of anti-apoptotic factors Bcl-2A1 and Mcl-1. AASV patients had normal levels of G-CSF, GM-CSF and IL-3. Both C/EBP-alpha, C/EBP-beta were significantly higher in neutrophils from AASV patients than HBD. Levels of sFAS were significantly higher in AASV compared to HBD. less thanbrgreater than less thanbrgreater thanConclusion: Neutrophil apoptosis rates in vitro are decreased in AASV, RA and PV but mechanisms seem to differ. Increased mRNA levels of granulopoiesis-associated transcription factors and increased levels of sFAS in plasma were observed in AASV. Additional studies are required to define the mechanisms behind the decreased apoptosis rates, and possible connections with accumulation of dying neutrophils in regions of vascular lesions in AASV patients.Funding Agencies|Swedish Research Council|71X-15152|Crafoord Foundation||</p

Disturbed Expression of Splicing Factors in Renal Cancer Affects Alternative Splicing of Apoptosis Regulators, Oncogenes, and Tumor Suppressors

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer. One of the processes disturbed in this cancer type is alternative splicing, although phenomena underlying these disturbances remain unknown. Alternative splicing consists of selective removal of introns and joining of residual exons of the primary transcript, to produce mRNA molecules of different sequence. Splicing aberrations may lead to tumoral transformation due to synthesis of impaired splice variants with oncogenic potential. In this paper we hypothesized that disturbed alternative splicing in ccRCC may result from improper expression of splicing factors, mediators of splicing reactions. METHODOLOGY/PRINCIPAL FINDINGS: Using real-time PCR and Western-blot analysis we analyzed expression of seven splicing factors belonging to SR proteins family (SF2/ASF, SC35, SRp20, SRp75, SRp40, SRp55 and 9G8), and one non-SR factor, hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1) in 38 pairs of tumor-control ccRCC samples. Moreover, we analyzed splicing patterns of five genes involved in carcinogenesis and partially regulated by analyzed splicing factors: RON, CEACAM1, Rac1, Caspase-9, and GLI1. CONCLUSIONS/SIGNIFICANCE: We found that the mRNA expression of splicing factors was disturbed in tumors when compared to paired controls, similarly as levels of SF2/ASF and hnRNP A1 proteins. The correlation coefficients between expression levels of specific splicing factors were increased in tumor samples. Moreover, alternative splicing of five analyzed genes was also disturbed in ccRCC samples and splicing pattern of two of them, Caspase-9 and CEACAM1 correlated with expression of SF2/ASF in tumors. We conclude that disturbed expression of splicing factors in ccRCC may possibly lead to impaired alternative splicing of genes regulating tumor growth and this way contribute to the process of carcinogenesis

Similarity, precedent and argument from analogy

In this paper, it is shown (1) that there are two schemes for argument from analogy that seem to be competitors but are not, (2) how one of them is based on a distinctive type of similarity premise, (3) how to analyze the notion of similarity using story schemes illustrated by some cases, (4) how arguments from precedent are based on arguments from analogy, and in many instances arguments from classification, and (5) that when similarity is defined by means of episode schemes, we can get a clearer idea of how it integrates with the use of argument from classification and argument from precedent in case-based reasoning by using a dialogue structure

Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation

Introduction The prolactin-Janus-kinase-2-signal transducer and activator of transcription-5 (JAK2-STAT5) pathway is essential for the development and functional differentiation of the mammary gland. The pathway also has important roles in mammary tumourigenesis. Prolactin regulated target genes are not yet well defined in tumour cells, and we undertook, to the best of our knowledge, the first large genetic screen of breast cancer cells treated with or without exogenous prolactin. We hypothesise that the identification of these genes should yield insights into the mechanisms by which prolactin participates in cancer formation or progression, and possibly how it regulates normal mammary gland development. Methods We used subtractive hybridisation to identify a number of prolactin-regulated genes in the human mammary carcinoma cell line SKBR3. Northern blotting analysis and luciferase assays identified the gene encoding heat shock protein 90-alpha (HSP90A) as a prolactin-JAK2-STAT5 target gene, whose function was characterised using apoptosis assays. Results We identified a number of new prolactin-regulated genes in breast cancer cells. Focusing on HSP90A, we determined that prolactin increased HSP90A mRNA in cancerous human breast SKBR3 cells and that STAT5B preferentially activated the HSP90A promoter in reporter gene assays. Both prolactin and its downstream protein effector, HSP90&#945;, promote survival, as shown by apoptosis assays and by the addition of the HSP90 inhibitor, 17-allylamino-17-demethoxygeldanamycin (17-AAG), in both untransformed HC11 mammary epithelial cells and SKBR3 breast cancer cells. The constitutive expression of HSP90A, however, sensitised differentiated HC11 cells to starvation-induced wild-type p53-independent apoptosis. Interestingly, in SKBR3 breast cancer cells, HSP90&#945; promoted survival in the presence of serum but appeared to have little effect during starvation. Conclusions In addition to identifying new prolactin-regulated genes in breast cancer cells, we found that prolactin-JAK2-STAT5 induces expression of the HSP90A gene, which encodes the master chaperone of cancer. This identifies one mechanism by which prolactin contributes to breast cancer. Increased expression of HSP90A in breast cancer is correlated with increased cell survival and poor prognosis and HSP90&#945; inhibitors are being tested in clinical trials as a breast cancer treatment. Our results also indicate that HSP90&#945; promotes survival depending on the cellular conditions and state of cellular transformation

Activation of Akt Is Essential for the Propagation of Mitochondrial Respiratory Stress Signaling and Activation of the Transcriptional Coactivator Heterogeneous Ribonucleoprotein A2

This article shows that mitochondrial respiratory dysfunction activates a stress signaling that induces Akt1 activation. Akt1 activation occurs through calcineurin-mediated IGF1R/PI3-K pathway. Akt1-mediated phosphorylation of hnRNPA2 is a key requirement for the propagation of stress signaling and activation of nuclear target genes