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.

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.

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.

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.

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.

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.

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.

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.

Association between polymorphisms of the swine MHC-DQA gene and diarrhoea in three Chinese native piglets.

Swine leucocyte antigen (SLA) is a highly polymorphic multigene family that plays a crucial role in swine immune response and disease resistance. Here, we identified polymorphisms and gene variations of SLA-DQA exon 2 using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing analysis, and further investigated the correlation between the polymorphisms and piglet diarrhoea in three Chinese native pig breeds (Bamei, Juema and Gansu Black pigs). Consequently, 12 genotypes and 8 alleles including two novel alleles were detected. Nucleotide polymorphism was compared with the actual functional polymorphism in the peptide-binding region (PBR), binding pockets P1, P6 and P9, and the antigen-binding groove, variations in the antigen-binding groove of alleles DQA*01xa01, DQA*01xa03, DQA*01xb01, DQA*We02, DQA*03xb03 and DQA*wy06 were higher than alleles DQA*03xa01 and DQA*03xa03, while amino acid variations in peptide-binding pockets of allele DQA*03xa03 were most abundant among all alleles. The results of association analysis showed the diarrhoea score of Gansu Black pigs (-0.08 ± 0.78) was significantly higher than Bamei and Juema pigs (P < 0.01), and genotype DQA*03xa0103xa01 (0.39 ± 0.54) was significantly higher relative to other genotypes (P < 0.01), while that of genotype DQA*03xa0303xa03 (-1.31 ± 0.88) was markedly lower than scores obtained with genotypes DQA*03xa0103xa01 and DQA*03xa0101xa01 (P < 0.01), as well as DQA*01xa0101xa01 (P < 0.05), indicating that amino acid variations in the peptide-binding pockets play a more important role than the antigen-binding groove in piglet diarrhoea resistance. Further studies on other SLA molecules of native pigs are required to validate the link between this gene complex and diarrhoea.

Association between Genetic Polymorphism in the Swine Leukocyte Antigen-DRA Gene and Piglet Diarrhea in Three Chinese Pig Breeds.

The swine leukocyte antigen (SLA)-DRA locus is noteworthy among other SLA class II loci for its limited variation and has not been investigated in depth. This study was investigated to detect polymorphisms of four exons of SLA-DRA gene and its association with piglet diarrhea in Landrace, Large White and Duroc pigs. No polymorphisms were detected in exon 3, while 2 SNPs (c.178G>A and c.211T>C), 2 SNPs (c.3093A>C and c.3104C>T) and 5 SNPs (c.4167A>G, c.4184A>G, c.4194A>G, c.4246A>G and c.4293G>A) were detected in exon 1, exon 2 and exon 4 respectively, and 1 SNP (c.4081T>C) in intron 3. Statistical results showed that genotype had significant effect on piglet diarrhea, individuals with genotype BC had a higher diarrhea score when compared with the genotypes AA, AB, AC and CC. Futhermore, genotype AC had a higher diarrhea score than the genotype CC in exon 1 (p<0.05); diarrhea scores of genotype AA and BB were higher than those of genotypes AC and CC in exon 2 (p<0.05); individuals with genotype AA had a higher diarrhea score than individuals with genotype AB and BB in exon 4 (p<0.05). Fourteen common haplotypes were founded by haplotype constructing of all SNPs in the three exons, its association with piglet diarrhea appeared that Hap2, 5, 8, 10, and 14 may be the susceptible haplotypes and Hap9 may be the resistant haplotype to piglet diarrhea. The genetic variations identified of the SLA-DRA gene may potentially be functional mutations related to piglet diarrhea.

Impact of MTHFR polymorphisms on methylation of MGMT in glioma patients from Northeast China with different folate levels.

Hypomethylation of the O6-methylguanine-DNA-methyltransferase (MGMT) promoter in glioma cells has been associated with temozolomide resistance. S-adenosylmethionine (SAM), which is produced during folate metabolism, is the main source of methyl groups during DNA methylation. As a key enzyme during folate metabolism, polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR) may regulate folate end-products. We investigated the effect of typical polymorphisms of MTHFR (C677T and A1298C) on MGMT methylation based on different serum folate levels in patients with glioma from Northeast China. A total of 275 patients with glioma and 329 without malignant tumors were tested. Serum folate concentration was assayed by using the electrochemiluminescence immunoassay. MTHFR polymorphisms were detected by Taqman-Fluorescence quantitative polymerase chain reaction (PCR). Methylation-specific PCR was used to assess MGMT methylation. The constituent ratio of glioma patients below the serum folate biological reference value was significantly higher than that of the control population (P < 0.001). In patients with oligodendroglioma and glioblastoma, heterozygotes for the A1298C mutation were found in higher frequency than homozygotes or wild types (oligodendroglioma, P < 0.001; glioblastoma, P < 0.01). When grouped by the median or biological reference value of serum folate, only homozygotes for C677T with low levels of folate were significantly associated with decreased methylation of MGMT (median, P < 0.001; biological reference value, P = 0.036). These data suggest that, in combination with a negative folate balance in glioma patients, T/T genotypes in MTHFR C677T may be associated with MGMT demethylation.

Swine Leukocyte Antigen-DQA Gene Variation and Its Association with Piglet Diarrhea in Large White, Landrace and Duroc.

The swine leukocyte antigen class II molecules are possibly associated with the induction of protective immunity. The study described here was to investigate the relationship between polymorphisms in exon 2 of the swine DQA gene and piglet diarrhea. This study was carried out on 425 suckling piglets from three purebred pig strains (Large White, Landrace and Duroc). The genetic diversity of exon 2 in swine DQA was detected by PCR-SSCP and sequencing analysis, eight unique SSCP patterns (AB, BB, BC, CC, CD, BD, BE and DD) representing five specific allele (A to E) sequences were detected. Sequence analysis revealed 21 nucleotide variable sites and resulting in 12 amino acid substitutions in the populations. A moderate level polymorphism and significant deviations from Hardy-Weinberg equilibrium of the genotypes distribution were observed in the populations (p<0.01). The association analysis indicated that there was a statistically significant difference in the score of piglet diarrhea between different genotypes, individuals with genotype CC showed a lower diarrhea score than genotypes AB (0.98±0.09), BB (0.85±0.77) and BC (1.25±0.23) (p<0.05), and significantly low than genotype BE (1.19±0.19) (p<0.01), CC genotype may be a most resistance genotype for piglet diarrhea.

Cloning and bioinformatic analysis of an acidophilic beta-mannanase gene, Anman5A, from Aspergillus niger LW-1.

Using 3' and 5' rapid amplification of cDNA ends (RACE) techniques, the full-length cDNA sequence of the AnmanSA, a gene that encodes an acidophilic beta-mannanase of Aspergillus niger LW-1 (abbreviated to AnMan5A), was identified from the total RNA. The cDNA sequence was 1417 bp in length, harboring 5'- and 3'-untranslated regions, as well as an open reading frame (ORF) which encodes a 21-aa signal peptide, a 17-aa propeptide and a 345-aa mature peptide. Based on the topology of the phylogenetic tree of beta3-mannanases from glycoside hydrolase (GH) family 5, the AnMan5A belongs to the subfamily 7 of the GH family 5. Its 3D structure was modeled by the bitemplate-based method using both MODELLER 9.9 and SALIGN programs, based on the known beta-mannanase crystal structures of Trichoderma reesei (1QNO) and Lycopersicon esculentum (1RH9) from the GH family 5. In addition, the complete DNA sequence of the Anman5A was amplified from the genomic DNA using the pUCm-T vector-mediated PCR and conventional PCR methods. The DNA sequence was 1825 bp in length, containing a 5'-flanking regulatory region, 2 introns and 3 exons when compared with the full-length cDNA.