Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.

BACKGROUND: The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS: We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS: In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS: To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.

A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer.

BACKGROUND: miR-346 was identified as an activator of Androgen Receptor (AR) signalling that associates with DNA damage response (DDR)-linked transcripts in prostate cancer (PC). We sought to delineate the impact of miR-346 on DNA damage, and its potential as a therapeutic agent. METHODS: RNA-IP, RNA-seq, RNA-ISH, DNA fibre assays, in vivo xenograft studies and bioinformatics approaches were used alongside a novel method for amplification-free, single nucleotide-resolution genome-wide mapping of DNA breaks (INDUCE-seq). RESULTS: miR-346 induces rapid and extensive DNA damage in PC cells - the first report of microRNA-induced DNA damage. Mechanistically, this is achieved through transcriptional hyperactivation, R-loop formation and replication stress, leading to checkpoint activation and cell cycle arrest. miR-346 also interacts with genome-protective lncRNA NORAD to disrupt its interaction with PUM2, leading to PUM2 stabilisation and its increased turnover of DNA damage response (DDR) transcripts. Confirming clinical relevance, NORAD expression and activity strongly correlate with poor PC clinical outcomes and increased DDR in biopsy RNA-seq studies. In contrast, miR-346 is associated with improved PC survival. INDUCE-seq reveals that miR-346-induced DSBs occur preferentially at binding sites of the most highly-transcriptionally active transcription factors in PC cells, including c-Myc, FOXA1, HOXB13, NKX3.1, and importantly, AR, resulting in target transcript downregulation. Further, RNA-seq reveals widespread miR-346 and shNORAD dysregulation of DNA damage, replication and cell cycle processes. NORAD drives target-directed miR decay (TDMD) of miR-346 as a novel genome protection mechanism: NORAD silencing increases mature miR-346 levels by several thousand-fold, and WT but not TDMD-mutant NORAD rescues miR-346-induced DNA damage. Importantly, miR-346 sensitises PC cells to DNA-damaging drugs including PARP inhibitor and chemotherapy, and induces tumour regression as a monotherapy in vivo, indicating that targeting miR-346:NORAD balance is a valid therapeutic strategy. CONCLUSIONS: A balancing act between miR-346 and NORAD regulates DNA damage and repair in PC. miR-346 may be particularly effective as a therapeutic in the context of decreased NORAD observed in advanced PC, and in transcriptionally-hyperactive cancer cells.

Effects of different types of zinc supplement on the growth, incidence of diarrhea, immune function, and rectal microbiota of newborn dairy calves.

Neonatal diarrhea in dairy calves causes huge economic and productivity losses in the dairy industry. Zinc is an effective anti-diarrheal agent, but high doses may pose a threat to the environment. Therefore, we aimed to evaluate the effects of low-dose zinc supplementation on the growth, incidence of diarrhea, immune function, and rectal microbiota of newborn Holstein dairy calves. Thirty newborn calves were allocated to either a control group (without extra zinc supplementation), or groups supplemented with either 104 mg of zinc oxide (ZnO, equivalent to 80 mg of zinc/d) or 457 mg of zinc methionine (Zn-Met, equivalent to 80 mg of zinc/d) and studied them for 14 d. The rectal contents were sampled on d 1, 3, 7, and 14, and blood samples were collected at the end of the study. Supplementation with ZnO reduced the incidence of diarrhea during the first 3 d of life, and increased serum IgG and IgM concentrations. The Zn-Met supplementation increased growth performance and reduced the incidence of diarrhea during the first 14 d after birth. The results of fecal microbiota analysis showed that Firmicutes and Proteobacteria were the predominant phyla, and Escherichia and Bacteroides were the dominant genera in the recta of the calves. As the calves grew older, rectal microbial diversity and composition significantly evolved. In addition, dietary supplementation with ZnO reduced the relative abundance of Proteobacteria in 1-d-old calves, and increased that of Bacteroidetes, Lactobacillus, and Faecalibacterium in 7-d-old calves, compared with the control group. Supplementation with Zn-Met increased the relative abundance of the phylum Actinobacteria and the genera Faecalibacterium and Collinsella on d 7, and that of the genus Ruminococcus after 2 wk, compared with the control group. Thus, the rectal microbial composition was not affected by zinc supplementation but significantly evolved during the calves' early life. Zinc supplementation reduced the incidence of diarrhea in young calves. In view of their differing effects, we recommend ZnO supplementation for dairy calves during their first 3 d of life and Zn-Met supplementation for the subsequent period. These findings suggest that zinc supplementation may be an alternative to antibacterial agents for the treatment of newborn calf diarrhea.

Short communication: Decrease of lipid profiles in cow milk by ultra-high-temperature treatment but not by pasteurization.

Triglyceride (TG) and fatty acid profiles of raw (RM), pasteurized (PM, 85°C for 15 s), and indirect UHT-treated (UM, 135°C for 15 s) cow milk were investigated by a lipidomics approach. Ninety-four TG were identified and all were present at significantly lower concentrations in UM than in RM or PM, and free fatty acid contents were significantly higher in UM than in RM and PM, indicating that TG lipolysis occurred to a greater degree in UM than in RM and PM. In addition, UM contained significantly fewer unsaturated fatty acids (14 types) than those in RM and PM, including C14:1n-5, C15:1n-5, C16:1n-7, C17:1n-7, C18:1n9 cis, C18:2n-6 cis, C18:3n-3, C18:3n-6, C20:1, C20:2, C20:3n-6, C20:3n-3, C20:4n-6, and C20:5n-3. However, we detected no significant differences between RM and PM in these fatty acids. In conclusion, UHT treatment, but not pasteurization, caused loss of the nutritional quality and bioactivity of cow milk lipid profiles.

Determination of sulbactam in raw bovine milk by isotope dilution-ultra-high-performance liquid chromatography-tandem mass spectrometry.

We developed a sensitive and selective isotope dilution ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the determination of sulbactam residue in raw bovine milk. Sulbactam and internal standard, sulbactam-d5, were extracted from raw bovine milk via liquid-liquid extraction and enriched with strong anion exchange solid-phase extraction cartridges and finally analyzed by using UPLC-MS/MS with multiple reaction monitoring mode. The method was validated according to European regulations. The calibration curve showed good linearity, with a correlation coefficient of 0.9998. Decision limit and detection capability of sulbactam were determined by matrix calibration curve and were 0.0445 and 0.0517 µg/L, respectively. The recoveries of sulbactam in fortified raw bovine milk ranged from 72.1 to 91.5%, with the intra- and interday relative standard deviations ranging from 3.0 to 18.9%. Furthermore, the developed method was applied to analyzing real raw bovine milk samples collected from dairy farms in Beijing, China. Sulbactam was not determined in all samples. The proposed method could ultimately serve as a methodological foundation for the determination of sulbactam in different types of raw milk and dairy products.

A metabolomics approach to characterize raw, pasteurized, and ultra-high temperature milk using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry and multivariate data analysis.

We developed a metabolomics workflow using ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry to determine the effect of thermal treatment on milk composition and metabolites based on multivariate data analysis. We analyzed raw, pasteurized, and UHT milk samples. The samples were first centrifuged to remove the fat layer and mixed with methanol to precipitate proteins. Subsequently, the supernatant was analyzed by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry in electrospray negative mode. Mass spectral data were acquired in MSE mode, a technique whereby both precursor and fragment mass spectral are simultaneously acquired by alternating between low and high collision energy (CE) during a single analytical run, to enable metabolite identification. Based on multivariate data analysis, these markers were significantly affected by thermal treatment. Among the 8 potential markers, we identified 7 oxylipids (9-hydroxydecanoic acid, 12-hydroxydodecanoic acid, 2-hydroxymyristic acid, 3-hydroxytetradecanoic acid, 5-hydroxyeicosatetraenoic acid, 3-hydroxyhexadecanoic acid, and 10-hydroxyoctadecanoic acid) and 1 phospholipid (LysoPE, hexadecanoyl-lysophosphatidylethanolamine). The oxylipids seemed to be adequate for distinguishing UHT milk from raw and pasteurized milk. The structures of the 8 potential markers were identified and characterized using informatics software. Our metabolomics workflow provides a fast approach for the identification of various types of milk.

Outcome of postmastectomy radiotherapy after primary systemic treatment in patients with clinical T1-2N1 breast cancer.

PURPOSE: The role of postmastectomy radiotherapy following primary systemic treatment in patients with clinical T1-2N1 breast cancer remains a controversial issue. The purpose of this study was to evaluate the benefit of postmastectomy radiotherapy following primary systemic treatment. PATIENTS AND METHODS: Between 2005 and 2012, in two independent institutions, female patients with T1-2N1 breast cancer receiving primary systemic treatment followed by mastectomy and lymph node dissection because bad response, then treated with or without chest wall and regional lymph node irradiation have been studied retrospectively. The patients received normofractionated radiotherapy using 3D conformal photons or electron techniques. Locoregional recurrence-free survival, distant metastasis-free survival and disease-free survival were calculated using Kaplan-Meier method. Univariate analysis of potential prognostic factors was performed using log-rank test. RESULTS: Eighty-eight patients have been studied. Of them, 75 patients received postmastectomy radiotherapy. At surgery, 53 patients achieved ypN0. Median follow-up was 67 months. Postmastectomy radiotherapy significantly improved locoregional recurrence-free survival, with a 5-year rate of 96.9% versus 78.6% in the group that did not have postmastectomy radiotherapy. In the subgroup of 53 patients achieving ypN0, postmastectomy radiotherapy improved locoregional recurrence-free survival (a 5-year rate of 94.7% vs. 72.9%), distant metastasis-free survival (a 5-year rate of 92.8% vs. 75%) and disease-free survival (a 5-year rate of 92.9% vs. 62.5%). By univariate analysis, postmastectomy radiotherapy was the only significant prognostic factor affecting locoregional recurrence-free survival. CONCLUSIONS: For patients with clinical T1-2N1 disease, postmastectomy radiotherapy could significantly improve locoregional recurrence-free survival after primary systemic treatment and be even more therapeutic in the subgroup of patients with good response for primary systemic treatment by improving locoregional recurrence-free, distant metastasis-free and disease-free survival. Larger prospective studies are needed to confirm our findings.

d-Glucose and amino acid deficiency inhibits casein synthesis through JAK2/STAT5 and AMPK/mTOR signaling pathways in mammary epithelial cells of dairy cows.

Amino acids and energy deficiency lead to lower milk protein content in dairy cows. However, the known mechanisms involved in this process do not adequately explain the variability of milk protein concentration in the mammary gland. We hypothesized that a deficiency in d-glucose (d-Glc) or AA would inhibit casein synthesis by regulating signaling pathways in mammary epithelial cells. Cow mammary epithelial cells (CMEC) were subjected to combinations of 1 of 3 concentrations of d-Glc (0, 2.50, or 17.5 mM) and 1 of 3 concentrations of AA (0, 1.03, or 7.20 mM). The effect of each mixture on cell cycle stage was assessed by flow cytometry. The expression levels of ß-casein and κ-casein (encoded by CSN2 and CSN3) were measured by quantitative real-time PCR and Western blotting. Phosphorylation of Janus kinase 2 (Jak2), signal transducer and activator of transcription 5a (Stat5a), AMP-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), ribosomal protein S6 kinase 1 (S6K1), and eukaryotic factor 4E-binding protein 1 (4EBP1) were analyzed by Western blotting. The percentages of cells in the DNA postsynthetic (G2) and DNA synthesis (S) phases would decrease, with the level of d-Glc or AA declining individually, but no interaction was observed between the d-Glc and AA effects. The CSN2 and CSN3 mRNA and protein were downregulated when d-Glc or AA decreased individually from 17.5 to 2.50 mM or from 7.20 to 1.03 mM, but d-Glc deficiency had a greater effect according to the regression analysis. The phosphorylation ratio of Jak2 (Tyr1007/1008), Stat5a (Tyr694), mTOR (Ser2448), S6K1 (Thr389), and 4EBP1 (Thr37) was downregulated with the level of d-Glc or AA decline, whereas the phosphorylation ratio of AMPK (Thr183/172) was upregulated. And the change of d-Glc level had a more marked effect than AA in regulating the activity of these signaling protein above according to the regression analysis. Thus, d-Glc or AA deficiency likely reduced casein transcription via inhibition of the Jak2/Stat5 pathway, and reduced translation via suppression of the mTOR pathway by activation of AMPK, but d-Glc deficiency had a more marked effect. These indicated that deficiency of AA, and especially Glc, suppressed proliferation of CMEC and casein gene and protein expression, associated with inhibition of JAK2/STAT5 and AMPK/mTOR signaling pathways.

The effect of energy restriction on fatty acid profiles of longissimus dorsi and tissue adipose depots in sheep.

Sheep production systems in northwest China depend mostly on natural grasslands. Seasonal growth and maturity fluctuations can cause periodical restrictions in food quality and quantity. These fluctuations, in turn, result in variability in fat deposition and fatty acid profiles in different fat depots. Consequently, the study objective was to compare fat deposition, intramuscular fat (IMF) percentage and fatty acid profiles of the longissimus dorsi (LD), kidney fat (KF), tail fat (TF), and subcutaneous fat (SF) in lambs under ME restrictions similar to seasonal changes observed in the natural grasslands of northwest China. Nineteen male Dorper × Small Tailed Han lambs were assigned to 2 treatments, a control (CON) fed at 1.0 MJ / W × d and restricted (RES) by restricting ME sequentially every 30 d (0.56 MJ / W × d, 0.84 / W × d, 1.0 MJ / W × d, 0.84 MJ / W × d, 0.56 MJ / W × d, 0.28 MJ / W × d). All lambs were harvested at the end of the 180 d experimental period. Compared to CON fed lambs, restricting ME resulted in lesser IMF, fat deposition indexes ( < 0.05) except testicular and heart fat and greater ( < 0.05) SFA in LD, KF, and TF depots. The RES fed lambs had greater ( < 0.05) -3 PUFA, eicosatrienoic acid (C20:3n3), eicosapentaenoic acid (C20:5n3, EPA), and trans-linolelaidic acid (C18:2n6t) in LD muscle. The conjugated linoleic acids (CLA) content was greater in the SF depots of the CON fed lambs compared to the RES fed lambs. Fatty acid ratios (unsaturated fatty acid; USFA:SFA, MUFA:SFA, PUFA:SFA), and percentage USFA in RES fed lambs were lesser in muscle and adipose tissue compared to CON fed lambs ( < 0.05), except SF depots. In RES fed lambs, EFA were less ( < 0.05) in LD and KF depots and the ratios of functional fatty acids were lesser in LD and some adipose tissues ( < 0.05), including lesser n-6:n-3 in KF and SF ( < 0.05) depots, lesser USFA, SFA, MUFA, SFA in LD, KF, and TF ( < 0.05) depots, and lesser PUFA and SFA in LD and TF ( < 0.05) depots. Results from this research demonstrate that sequential energy restriction, as might be experience during seasonal forage quality and quantity changes in natural grasslands, result in lesser intramuscular fat with associated lesser quality, as well as, changes in fatty acid composition in different fat depots, which has implications for both meat quality and animal physiological functions.

Combination of histidine, lysine, methionine, and leucine promotes ß-casein synthesis via the mechanistic target of rapamycin signaling pathway in bovine mammary epithelial cells.

The ratio of different AA in the diets of cows is vital to improve milk protein yield. ß-Casein is one of the important milk proteins with high nutritive value. However, the suitable ratio of essential amino acids (EAA) for the expression of ß-casein in the immortalized bovine mammary epithelial cell line is not fully characterized. This study employed response surface methodology to determine the optimal ratio of His, Lys, Met, and Leu on ß-casein expression level in vitro and clarified the effect of the 4 EAA on ß-casein via the mechanistic target of rapamycin (mTOR) signaling pathway. A central composite design containing 5 axial points per EAA and 28 combinations of the 4 EAA was used in our study. The results of response surface methodology and the changes of the mTOR-related signaling proteins were determined by western blot. The results showed that ß-casein level was significantly affected by all 4 EAA (R2 = 0.71). The optimum conditions for ß-casein expression are found to be 5.47 mM of His, 7.48 mM of Lys, 1.17 mM of Met, and 8.21 mM of Leu (His:Lys:Met:Leu = 5:6:1:7) in the designed scope of concentration. The interaction of Leu and Met significantly affected ß-casein expression (P < 0.01). The phosphorylation of mTOR (Ser2481), regulatory associated protein of target of rapamycin (Ser792), ribosomal protein S6 kinase 1 (Thr389), ribosomal protein S6 (Ser235/236), and eukaryotic elongation factor 2 (Thr56) was increased with the supplementation of either single EAA or an optimal combination of EAA. However, the phosphorylation of eukaryotic initiation factor 4E binding protein 1 (Thr37) was decreased with the addition of Lys, Met, or Leu alone. Furthermore, the phosphorylation (P) of eIF2α (Ser51) was decreased when Met was supplemented alone. Under the optimal mixture of 4 EAA, the phosphorylation of mechanistic target of rapamycin complex 1 signaling proteins was significantly greater than the single EAA supplementations and the expression of ß-casein was 98% as high as the positive control (i.e., medium with all AA). A similar trend was found with P-ribosomal protein S6 kinase 1 and P-ribosomal protein S6. In conclusion, the extracellular concentrations of His, Lys, Met, and Leu at a ratio of 5:6:1:7 maximized ß-casein expression in the immortalized bovine mammary epithelial cell line may occur via activation of the mechanistic target of rapamycin complex 1 signaling pathway.

Short communication: Microbiological quality of raw cow milk and its association with herd management practices in Northern China.

Contamination of raw milk with bacterial pathogens is potentially hazardous to human health. The aim of this study was to evaluate the total bacteria count (TBC) and presence of pathogens in raw milk in Northern China along with the associated herd management practices. A total of 160 raw milk samples were collected from 80 dairy herds in Northern China. All raw milk samples were analyzed for TBC and pathogens by culturing. The results showed that the number of raw milk samples with TBC <2 × 106 cfu/mL and <1 × 105 cfu/mL was 146 (91.25%) and 70 (43.75%), respectively. A total of 84 (52.50%) raw milk samples were Staphylococcus aureus positive, 72 (45.00%) were Escherichia coli positive, 2 (1.25%) were Salmonella positive, 2 (1.25%) were Listeria monocytogenes positive, and 3 (1.88%) were Campylobacter positive. The prevalence of S. aureus was influenced by season, herd size, milking frequency, disinfection frequency, and use of a Dairy Herd Improvement program. The TBC was influenced by season and milk frequency. The correlation between TBC and prevalence of S. aureus or E. coli is significant. The effect size statistical analysis showed that season and herd (but not Dairy Herd Improvement, herd size, milking frequency, disinfection frequency, and area) were the most important factors affecting TBC in raw milk. In conclusion, the presence of bacteria in raw milk was associated with season and herd management practices, and further comprehensive study will be powerful for effectively characterizing various factors affecting milk microbial quality in bulk tanks in China.

Cell cycle-coupled expansion of AR activity promotes cancer progression.

The androgen receptor (AR) is required for prostate cancer (PCa) survival and progression, and ablation of AR activity is the first line of therapeutic intervention for disseminated disease. While initially effective, recurrent tumors ultimately arise for which there is no durable cure. Despite the dependence of PCa on AR activity throughout the course of disease, delineation of the AR-dependent transcriptional network that governs disease progression remains elusive, and the function of AR in mitotically active cells is not well understood. Analyzing AR activity as a function of cell cycle revealed an unexpected and highly expanded repertoire of AR-regulated gene networks in actively cycling cells. New AR functions segregated into two major clusters: those that are specific to cycling cells and retained throughout the mitotic cell cycle ('Cell Cycle Common'), versus those that were specifically enriched in a subset of cell cycle phases ('Phase Restricted'). Further analyses identified previously unrecognized AR functions in major pathways associated with clinical PCa progression. Illustrating the impact of these unmasked AR-driven pathways, dihydroceramide desaturase 1 was identified as an AR-regulated gene in mitotically active cells that promoted pro-metastatic phenotypes, and in advanced PCa proved to be highly associated with development of metastases, recurrence after therapeutic intervention and reduced overall survival. Taken together, these findings delineate AR function in mitotically active tumor cells, thus providing critical insight into the molecular basis by which AR promotes development of lethal PCa and nominate new avenues for therapeutic intervention.

Correlation of B7-H3 with androgen receptor, immune pathways and poor outcome in prostate cancer: an expression-based analysis.

BACKGROUND: B7-H3 (CD276), part of the B7 superfamily of immune checkpoint molecules, has been shown to have an immunomodulatory role. Its regulation, receptor and mechanism of action remain unclear. B7-H3 protein expression correlates with prostate cancer outcomes, and humanized monoclonal antibodies (that is, enoblituzumab) are currently being investigated for therapeutic use. Here we used genomic expression data to examine the relationship between B7-H3 mRNA expression and prostate cancer. METHODS: Prostatectomy tissue from 2781 patients were profiled using the Affymetrix HuEx 1.0 ST microarray. Pairwise comparisons were used to identify significant associations between B7-H3 expression and clinicopathologic variables, and survival analyses were used to evaluate the prognostic significance of B7-H3. Pearson's correlation analyses were performed to assess the relationship of B7-H3 expression with molecular subtypes and individual transcripts. Androgen receptor (AR) occupancy at the B7-H3 locus was determined using chromatin immunoprecipitation (ChIP), and androgen-dependent expression changes in B7-H3 was evaluated by quantitative reverse transcription PCR in LNCaP cell lines. Oncomine was queried to evaluate B7-H3 expression in metastatic disease. RESULTS: B7-H3 mRNA expression was positively associated with higher Gleason score (P<0.001), tumor stage (P<0.001), and castrate resistant metastatic disease (P<0.0001). High B7-H3 expression correlated with the development of metastasis and prostate cancer specific mortality, but this was not significant on multi-variable analysis. B7-H3 expression correlated with ERG-positive disease (r=0.99) and AR expression (r=0.36). ChIP revealed an AR-binding site upstream of B7-H3, and the presence of androgens decreased B7-H3 expression in LNCaP suggesting potential direct AR regulation. Gene set enrichment analysis demonstrated an association of B7-H3 with androgen signaling as well as immune regulatory pathways. CONCLUSIONS: Higher B7-H3 expression correlates with Gleason grade, prostate cancer stage and poor oncologic outcomes in prostatectomy cohorts. B7-H3 expression appears to be related to androgen signaling as well as the immune reactome.

Genetic association of sequence variation in exon 3 of the swine leukocyte antigen-DQA gene with piglet diarrhea in Large White, Landrace, and Duroc piglets.

Piglet diarrhea is one of the primary factors that affects the benefits of the swine industry. Recent studies have shown that exon 2 of the swine leukocyte antigen-DQA gene is associated with piglet resistance to diarrhea; however, the contributions of additional exon coding regions of this gene remain unclear. Here, we detected and sequenced variants in the exon 3 region and examined their associations with diarrhea infection in 425 suckling piglets using the polymerase chain reaction-single-strand conformational polymorphism and sequencing analysis. The results revealed that exon 3 of the swine leukocyte antigen-DQA gene is highly polymorphic and pivotal to both diarrhea susceptibility and resistance in piglets. We identified 14 genotypes (AA, AB, BB, BC, CC, EE, EF, BE, BF, CF, DD, DH, GG, and GF) and eight alleles (A-H) that were generated by 14 nucleotide variants, eight of which were novel, and three nucleotide deletions. Statistical analyses revealed that the genotypes AB and EF were associated with resistance to diarrheal disease (P < 0.05), and the genotype DD may contribute to diarrhea susceptibility but was unique to Large White pigs (P > 0.05). These results elucidate the genetic and immunological background to piglet diarrhea, and provide useful information for resistance breeding programs.

Effect of swine leukocyte antigen-DQA gene variation on diarrhea in Large White, Landrace, and Duroc piglets.

Piglet diarrhea is one of the most common factors that affects the benefits of the swine industry. Although recent studies have shown that exon 2 of SLA-DQA is associated with piglet resistance to diarrhea, contributions of genetic variation in the additional exon coding regions of this gene remain unclear. Here, we investigated variation in exons 1, 3 and 4 of the SLA-DQA gene and evaluated their effects on diarrheal infection in 425 suckling piglets. No variation was identified in exon 1. In exon 3, there were eight alleles detected, generated by 14 single nucleotide polymorphisms (SNPs) and three nucleotide deletions, eight SNPs being newly identified. Four allele sequences and three SNPs were identified in exon 4, only one SNP being newly identified. Statistical analysis showed that the genotypes of exon 3 are significantly associated with piglet diarrhea; indeed, genotypes DQA*wb01/wb02 and wb04/wb05 are clearly associated with resistance to piglet diarrhea, as they have the lowest probabilities of infection (P < 0.05). However, no significant association was found between the genotypes of exon 4 and diarrhea (P > 0.05). These results provide important new information concerning the level of genetic diversity at the SLA-DQA locus and suggest that further genetic association studies of piglet diarrhea resistance should include analyses of both exons 2 and 3 of this locus.

Short communication: Influence of preserving factors on detection of ß-lactamase in raw bovine milk.

The refrigeration (4, 8, 24, or 48 d), freezing (1, 7, or 30 h), thawing (25, 40, or 60°C), and usage of preservatives (sodium azide, potassium dichromate, sodium thiocyanate, bronopol, and methanol), of raw bovine milk were investigated for ß-lactamase activity. The ß-lactamase activity in all samples was assessed by using the test strips, and the samples with the preservatives were further assessed for ß-lactamase activity using the cylinder plate method. Results showed that the refrigeration, freezing, and thawing of raw bovine milk samples had no influence on the assay of the ß-lactamase activity. The addition of sodium azide or potassium dichromate as a sample preservative failed the test of ß-lactamase activity, whereas the addition of sodium thiocyanate, bronopol, or methanol had no influence on the test. In conclusion, sodium azide and potassium dichromate were not suitable preservatives for assessing ß-lactamase activity in raw milk when the cylinder plate method was used.

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep.

Research on gene regulation has been made possible with the help of RNA sequencing applications such as RNA-Seq technology for high-throughput sequencing platforms. Recent studies have explored the transcriptomes from different tissues of domestic animals using RNA-Seq technology, but little research has been done to study the transcriptomes of breeds of sheep having different adipose tissue deposition mechanisms, such as Mongolian and Lanzhou fat-tailed sheep. In this study, Mongolian and Lanzhou fat-tailed sheep were selected as experimental breeds, and six libraries (three libraries per breed) were constructed. A total of 286 Mb of high-quality reads was obtained, and three-quarters of the reads were mapped to the reference genome per library. In addition, there were 16,257, 16,186, 16,254, 16,827, 16,437, and 15,761 known reference genes in the six constructed libraries (LCL1, LCL2, LCL3, MCL1, MCL2, and MCL3, respectively). Seven genes were differentially expressed: four were upregulated and three were downregulated in liver tissue between the MCL and LCL groups; 65,303, 65,442, 63,426, 76,267, 69,853, and 57,439 potential cSNPs were detected in the six libraries, respectively, with the G/R substitution occurring most commonly. There were 24,239, 22,283, 22,457, 26,635, 27,093, and 18,700 alternate splicing (AS) events in the six libraries. Intron retention was the most common AS event, followed by alternative 3' splice sites. These results indicate that there are many differences in the liver transcriptomes of Mongolian and Lanzhou fat-tailed sheep breeds. Such results may provide fundamental information for further research on defining the sheep genome.

Independent validation of the prognostic capacity of the ISUP prostate cancer grade grouping system for radiation treated patients with long-term follow-up.

BACKGROUND: There has been a recent proposal to change the grading system of prostate cancer into a five-tier grade grouping system. The prognostic impact of this has been demonstrated in regards only to biochemical recurrence-free survival (bRFS) with short follow-up (3 years). METHODS: Between 1990 and 2013, 847 consecutive men were treated with definitive external beam radiation therapy at a single academic center. To validate the new grade grouping system, bRFS, distant metastases-free survival (DMFS) and prostate cancer-specific survival (PCSS) were calculated. Adjusted Kaplan-Meier and multivariable Cox regression analyses were performed to assess the independent impact of the new grade grouping system. Discriminatory analyses were performed to compare the commonly used three-tier Gleason score system (6, 7 and 8-10) to the new system. RESULTS: The median follow-up of our cohort was 88 months. The 5-grade groups independently validated differing risks of bRFS (group 1 as reference; adjusted hazard ratio (aHR) 1.35, 2.16, 1.79 and 3.84 for groups 2-5, respectively). Furthermore, a clear stratification was demonstrated for DMFS (aHR 2.03, 3.18, 3.62 and 13.77 for groups 2-5, respectively) and PCSS (aHR 3.00, 5.32, 6.02 and 39.02 for groups 2-5, respectively). The 5-grade group system had improved prognostic discrimination for all end points compared with the commonly used three-tiered system (that is, Gleason score 6, 7 and 8-10). CONCLUSIONS: In a large independent radiotherapy cohort with long-term follow-up, we have validated the bRFS benefit of the proposed five-tier grade grouping system. Furthermore, we have demonstrated that the system is highly prognostic for DMFS and PCSS. Grade group 5 had markedly worse outcomes for all end points, and future work is necessary to improve outcomes in these patients.

Effects of tail docking on the expression of genes related to lipid metabolism in Lanzhou fat-tailed sheep.

To evaluate stearoyl-CoA desaturase (SCD), hormone-sensitive lipase (HSL), lipoprotein lipase (LPL), and peroxisome proliferator-activated receptor (PPARγ) expression in Lanzhou fat-tailed sheep (with and without docked tails), 18 rams were randomly divided into two equal groups (docked group, LT; control group, LC). These data were also used to increase the understanding of sheep fat deposition and metabolism. All animals were harvested at the age of 18 months, and expression was determined for 10 tissues. The results indicated that the fat weight of each tissue in LT was higher than in LC (P < 0.05). SCD expression in semitendinosus, omentum majus fat (OF), subcutaneous fat, kidney fat (KF), and subcutaneous rump fat was higher in LT than in LC rams (P < 0.05). Trends (P < 0.10) associated with higher HSL expression of LC in comparison to that of LT rams in intestinal fat, OF, and KF tissues were detected. Numerically, LPL expression was the highest in KF, OF, and kidney tissues, but there were few differences (P > 0.10). PPARγexpression was greater in LT than in LC rams in liver tissues (P < 0.05), but there were few differences in other tissues. No significant differences were found with regard to the regression analysis of expression and adipose tissue weights, but the two indices exhibited the same trend. The results indicated that changes in fatty deposits may be due to the common control of docking management and the minor effects associated with the regulation of SCD, HSL, LPL, and PPARγexpression.