Full sib pens of pigs are not suitable to identify variance component of associative effect: a simulation study using Gibbs Sampling

<p>Abstract</p> <p>Background</p> <p>Accounting for and quantifying the associative effect of each animal could improve both welfare of animals and response to selection. Because of the limitation of REML, Gibbs Sampling could be an alternative technique to estimate the variance component of the associative effect. The objective of this study was to investigate the estimation accuracy of the variance component of associative effect by using simulation via Gibbs Sampling. The simulated data comprised five generations of pigs. The breeding animals of each generation were selected randomly. In the simulation, variations were introduced for the methods of assigning pens (random, mixed sib and full sib), the number of pigs per pen (5 or 10), the number of breeding animals per generation (162 or 324) and the correlation between genetic direct effect and genetic associative effect (-0.5, 0.1 or +0.5). Each set of simulation was run for 30 replications.</p> <p>Results</p> <p>Random assignment or mixed sib assignment resulted in bias of estimated variance components in only 3 of 24 combinations. Furthermore, these 3 cases occurred with 162 breeding animals. With full sib assignment, 9 out of 12 groups of estimates significantly deviated from the true parameter value. The Root Mean Square Errors obtained with the full sib assignment were higher than with the other two methods of pen assignment in most of the cases. The Root Mean Square Errors obtained with datasets with 324 breeding animals were notably smaller than the datasets from 162 breeding animals. Within each method of pen assignment, the relative bias of the associative effect was significantly smaller with group size 10 than with group size 5.</p> <p>Conclusion</p> <p>Full sib assignment caused difficulties to estimate variance components in most of the cases, due to a lack of identifiability. With random and mixed assignment, most data structures yielded unbiased results but increasing the number of breeding animals or group size improves the estimation. Thus to get identifiable and unbiased estimates of the genetic associative effect, it is recommended to avoid close genetic relationship between animals within one pen and to use sufficient numbers of breeding animals and sufficient group sizes.</p

Single-cell copy number variation detection

Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition and recurrent genome artifact corrections. We demonstrate that the proposed channel clone normalization significantly improves the copy number variation detection in both simulated and real single-cell array CGH data

Immunophenotyping in BK Virus Allograft Nephropathy Distinct from Acute Rejection

Differentiating BK virus nephropathy (BKVN) from acute rejection (AR) is crucial in clinical practice, as both of them have interstitial inflammation in the grafts. The purpose of the study is to describe the inflammatory cellular constituents of BKVN and to determine the clinical utility of immunophenotyping findings in distinguishing BKVN from AR. In addition, the expression of the HLA-DR was investigated. Sixty-five renal allograft recipients were included in this study, including 22 cases of BKVN, 31 cases of AR, and 12 cases of stable allograft. Immunostaining for infiltrating lymphocytes showed that the number of CD20 cells (P<0.001) and the percentages of CD3 (P<0.001), CD4 (P=0.004), CD8 (P=0.005), and CD20 (P=0.002) cells were all significantly different between BKVN and AR. Moreover, there were no statistically significant differences in tubule cell HLA-DR expression (P=0.156). This observation suggests that the number of CD20 cells and the percentages of CD3, CD4, CD8, and CD20 cells in renal biopsies would aid the distinction between BKVN and AR. On the other hand, the presence of HLA-DR upregulation may not only be specific for acute rejection but also be a response to BKVN

Proteinuria, Estimated Glomerular Filtration Rate and Urinary Retinol-Binding Protein as Clinical Predictors of Long-Term Allograft Outcomes in Transplant Glomerulopathy

Background/Aims: We aimed to explore the associations between clinical parameters and long-term allograft outcomes in transplant glomerulopathy (TG) in a large retrospective cohort with long follow-up. Methods: Clinical and laboratory data at biopsy from 180 cases of TG with an estimated glomerular filtration rate (eGFR)&#x3e; 15ml/min/1.73m2 from January 2004 to December 2016 at our center were retrospectively analyzed. The main outcome of this study was initiation of replacement therapy or an eGFR declined to &#x3c; 15 ml/min/1.73m2. Results: During a median follow-up of 5 years (interquartile range 2.6-8.2 years), 117 cases (65.0%) achieved the combined event. Kaplan-Meier method yielded the 1-year and 5-year cumulative renal allograft survival rates after a histopathologic diagnosis of TG were 84% (95% confidence interval [CI] 81-87%) and 33% (95% CI 27–39%) respectively. In univariate analysis, allograft outcome differed significantly by eGFR, proteinuria, blood hemoglobin level, urinary retinol-binding protein (urRBP) and urinary N-acetyl-β-D-glucosaminidase (urNAG) level at the time of biopsy. Multivariate Cox analysis revealed that a higher level of eGFR was the most powerful predictor of allograft survival. Compared with those with eGFR≥60, the hazard ratio (HR) increased from 4.50 (95% CI: 1.03-19.71, p=0.0462) for patients with eGFR between 30 and 59 ml/min/1.73m2 to 9.14 (95% CI 1.97-42.45, P=0.0047) when eGFR decreased to 15 to 29 ml/min/1.73m2. Additionally, proteinuria and higher urRBP values (≥2.85mg/dl) were found to confer much worse survival rates for TG patients in multivariate Cox analysis. Male sex (HR 0.48, P=0.02) and HCV infection (HR 1.78, P=0.0499) were also found to be independent risk factors for worse allograft survival. Conclusion: Five clinical features—impaired renal function, higher proteinuria, higher urRBP level, male sex and HCV infection—are independent predictors of an unfavorable renal allograft outcome. urRBP is a simple and useful parameter that can add invaluable information for the clinical follow-up of patients with TG

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

Background: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.Methods: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.Results: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P &lt; 0.001). The LPC mice had significantly longer wire and grid hanging time (P &lt; 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P &lt; 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P &lt; 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.Conclusions: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.</p

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

Background: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.Methods: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.Results: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P &lt; 0.001). The LPC mice had significantly longer wire and grid hanging time (P &lt; 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P &lt; 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P &lt; 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.Conclusions: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.</p

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

Background: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.Methods: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.Results: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P &lt; 0.001). The LPC mice had significantly longer wire and grid hanging time (P &lt; 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P &lt; 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P &lt; 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.Conclusions: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.</p

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

Background: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.Methods: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.Results: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P &lt; 0.001). The LPC mice had significantly longer wire and grid hanging time (P &lt; 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P &lt; 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P &lt; 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.Conclusions: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.</p

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

Background: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.Methods: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.Results: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P &lt; 0.001). The LPC mice had significantly longer wire and grid hanging time (P &lt; 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P &lt; 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P &lt; 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.Conclusions: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.</p

The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models.

BACKGROUND: Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even with germline mutated p53, these engineered melanomas present with variable onset and pathology, implicating additional somatic mutations in a multi-hit tumorigenic process. RESULTS: To decipher the genetics of these melanomas, we sequence the protein coding exons of 53 primary melanomas generated from several BRAF(V600E) or NRAS(Q61K) driven transgenic zebrafish lines. We find that engineered zebrafish melanomas show an overall low mutation burden, which has a strong, inverse association with the number of initiating germline drivers. Although tumors reveal distinct mutation spectrums, they show mostly C > T transitions without UV light exposure, and enrichment of mutations in melanogenesis, p53 and MAPK signaling. Importantly, a recurrent amplification occurring with pre-configured drivers BRAF(V600E) and p53-/- suggests a novel path of BRAF cooperativity through the protein kinase A pathway. CONCLUSION: This is the first analysis of a melanoma mutational landscape in the absence of UV light, where tumors manifest with remarkably low mutation burden and high heterogeneity. Genotype specific amplification of protein kinase A in cooperation with BRAF and p53 mutation suggests the involvement of melanogenesis in these tumors. This work is important for defining the spectrum of events in BRAF or NRAS driven melanoma in the absence of UV light, and for informed exploitation of models such as transgenic zebrafish to better understand mechanisms leading to human melanoma formation