Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population

The fatty acid composition and melting point of fatty tissue are among the most important economic traits in pig breeding because of their influence on the eating quality of meat. Identifying the quantitative trait locus (QTL) of these traits may help reveal the genetic structure of fatty acid composition and the melting point of fatty tissue and improve meat-quality traits by marker-assisted selection. We conducted whole-genome QTL analysis for fatty acid composition and melting point of inner and outer subcutaneous fat and inter- and intramuscular fat in a purebred Duroc population. A total of 129 markers were genotyped and used for QTL analysis. For fatty acid compositions of inner and outer subcutaneous fat, three significant QTL and 17 suggestive QTL were detected on SSC2, 4, 6, 8, 9, 10, 11, 12, 14 and 18. For the melting point of inner and outer subcutaneous fat, two significant QTL were detected on the same region of SSC14. For fatty acid compositions of inter- and intramuscular fat, five significant QTL and 13 suggestive QTL were detected on SSC2, 4, 6, 8, 9, 10, 14 and 15. On SSC14, significant QTL for C18:0 and C18:1 of outer subcutaneous fat and intramuscular fat, and melting point of subcutaneous fat, which had high likelihood of odds (LOD) scores (2.67-5.78), were detected in the same region. This study determined QTL affecting fatty acid composition and melting point of different fat tissues in purebred Duroc pigs.     

Orthotopic Small Bowel Transplantation in Rats

Small bowel transplantation has become an accepted clinical option for patients with short gut syndrome and failure of parenteral nutrition (irreversible intestinal failure). In specialized centers improved operative and managing strategies have led to excellent short- and intermediate term patient and graft survival while providing high quality of life ^1,3. Unlike in the more common transplantation of other solid organs (i.e. heart, liver) many underlying mechanisms of graft function and immunologic alterations induced by intestinal transplantation are not entirely known^6,7. Episodes of acute rejection, sepsis and chronic graft failure are the main obstacles still contributing to less favorable long term outcome and hindering a more widespread employment of the procedure despite a growing number of patients on home parenteral nutrition who would potentially benefit from such a transplant. The small intestine contains a large number of passenger leucocytes commonly referred to as part of the gut associated lymphoid system (GALT) this being part of the reason for the high immunogenity of the intestinal graft. The presence and close proximity of many commensals and pathogens in the gut explains the severity of sepsis episodes once graft mucosal integrity is compromised (for example by rejection). To advance the field of intestinal- and multiorgan transplantation more data generated from reliable and feasible animal models is needed. The model provided herein combines both reliability and feasibility once established in a standardized manner and can provide valuable insight in the underlying complex molecular, cellular and functional mechanisms that are triggered by intestinal transplantation. We have successfully used and refined the described procedure over more than 5 years in our laboratory ^8-11. The JoVE video-based format is especially useful to demonstrate the complex procedure and avoid initial pitfalls for groups planning to establish an orthotopic rodent model investigating intestinal transplantation.     

Mass spectrometry of Alternaria mali toxins and related cyclodepsipeptides

The structures of AM-toxins I, II and III, host specific phytotoxic metabolites of Alternaria mali, can be readily deduced from low and high resolution mass spectral data, since the amino acids and their sequences are demonstrated by this technique. Additionally, the general fragmentation of these compounds by electron impact is discussed by comparing the spectra of analogous synthetic compounds.     

GLP-1 receptor signaling protects pancreatic beta cells in intraportal islet transplant by inhibiting apoptosis

To clarify the cytoprotective effect of glucagon-like peptide-1 receptor (GLP-1R) signaling in conditions of glucose toxicity in vivo, we performed murine isogenic islet transplantation with and without exendin-4 treatment. When a suboptimal number of islets (150) were transplanted into streptozotocin-induced diabetic mice, exendin-4 treatment contributed to the restoration of normoglycemia. When 50 islets expressing enhanced green fluorescent protein (EGFP) were transplanted, exendin-4 treatment reversed loss of both the number and mass of islet grafts one and 3 days after transplantation. TUNEL staining revealed that exendin-4 treatment reduced the number of apoptotic beta cells during the early posttransplant phase, indicating that GLP-1R signaling exerts its cytoprotective effect on pancreatic beta cells by inhibiting their apoptosis. This beneficial effect might be used both to ameliorate type 2 diabetes and to improve engraftment rates in clinical islet transplantation.     

Anticancer efficacy of p-dodecylaminophenol against high-risk and refractory neuroblastoma cells in vitro and in vivo

Neuroblastoma is an aggressive and drug-resistant refractory cancer. The human high-risk neuroblastoma cell line, SK-N-AS (non-amplified N-myc) is derived from stromal cells and it is resistant to treatment with retinoic acid (1, RA), which is a chemotherapeutic agent used to induce neuronal cellular differentiation of neuroblastomas. We have developed p-dodecylaminophenol (3, p-DDAP), based on N-(4-hydroxyphenyl)retinamide (2, 4-HPR), a synthetic amide of 1, since 1 and 2 are associated with the side-effect of nyctalopia. In order to evaluate the effects of 3 on high-risk neuroblastomas, we employed SK-N-AS cells as well as a second high-risk human neuroblastoma cell line, IMR-32, which is derived from neuronal cells (amplified N-myc, drug sensitive). Compound 3 suppressed cell growth of SK-N-AS and IMR-32 cells more effectively than 1, 2, p-decylaminophenol (4, p-DAP), N-(4-hydroxyphenyl)dodecananamide (5, 4-HPDD) or N-(4-hydroxyphenyl)decananamide (6, 4-HPD). In SK-N-AS cells, 3 induced G₀/G₁ arrest and apoptosis to a greater extent than 1 and 2. In IMR-32 cells, 3 induced apoptosis to a similar extent as 1 and 2, potentially by inhibiting N-myc expression. In addition, i.p. administration of 3 suppressed tumor growth in SK-N-AS-implanted mice in vivo. Since 3 showed no effects on blood retinol concentrations, in contrast to reductions following the administration of 2, it exhibited excellent anticancer efficacy against high-risk neuroblastoma SK-N-AS and IMR-32 expressing distinct levels of N-myc. Compound 3 may have potential for clinical use in the treatment of refractory neuroblastoma with reduced side effects.     

Reduction of Selenium Oxyanions in Wastewater Using Two Bacterial Strains

The biological reduction of selenium oxyanions is capable of reducing both selenate and selenite to insoluble elemental selenium. In this process, however, bacteria inevitably require expensive chemicals such as yeast extract in almost all cases. Therefore, the reduction of selenium oxyanions with inexpensive alcohol would be more practical. A Pseudomonas sp. strain 4C‐C isolated from a sludge in a wastewater treatment facility was able to reduce selenate to selenite using ethanol as an electron donor for its anaerobic respiration, but could not reduce selenite to elemental selenium. Paracoccus denitrificans JCM‐6892, on the other hand, was observed to be able to reduce selenite to elemental selenium in the presence of ethanol, but not selenate to selenite. Therefore, a mixture containing a suspension of Pseudomonas sp. strain 4C‐C and P. denitrificans JCM‐6892 cells allowed selenate to be reduced to insoluble elemental selenium via selenite in the presence of ethanol and was also capable of reducing nitrate to nitrogen gas. Aiming at simplicity of the recovery process of insoluble elemental selenium, a polymeric gel immobilized mixture of the two bacterial strains was examined using ethanol as an electron donor. The immobilized mixture could therefore reduce not only selenate to elemental selenium, but also nitrate to nitrogen gas in a single step. The gel that immobilized the microbial mixture changed its color during the process to bright red and no red elemental selenium was left in the wastewater. This indicates that the reduced elemental selenium was completely absorbed in the gel. This simple bacterial combination would therefore be effective in the presence of ethanol to reduce selenium oxyanions in various wastewaters containing selenium and the other oxyanions.     

Protective Effect of Immobilized Ammonia Oxidizers and Phenol‐degrading Bacteria on Nitrification in Ammonia– and Phenol‐containing Wastewater

Phenol present in wastewaters from various industries has an inhibitory effect on nitrification even at low concentrations. Hence, the biological treatment of wastewater containing both phenol and ammonia involves a series of treatment steps. It is difficult to achieve nitrification capability in an activated sludge system that contains phenol at concentrations above the inhibitory level. Batch treatment of wastewater containing various concentrations of phenol showed that the ammonia oxidation capability of suspended Nitrosomonas europaea cells, an ammonia oxidizer, was completely inhibited in the presence of more than 5.0 mg/L phenol. To protect the ammonia oxidizer from the inhibitory effect of phenol and to achieve ammonia oxidation capability in the wastewater containing phenol at concentrations above the inhibitory level, a simple bacterial consortium composed of an ammonia oxidizer (N. europaea) and a phenol‐degrading bacterial strain (Acinetobacter sp.) was used. Ammonia oxidation did not occur in the presence of phenol at concentrations above the inhibitory level when suspended or immobilized N. europaea and Acinetobacter sp. cells were used in batch treatment. Following the acclimatization of the immobilized cells, accumulation of nitrite was observed, even when the wastewater contained phenol at concentrations above the inhibitory level. These results showed that immobilization was effective in protecting N. europaea cells from the inhibitory effect of phenol present in the wastewater.     

Nitrogen removal by tubular gel containing Nitrosomonas europaea and Paracoccus denitrificans.

A new bioreactor for the removal of nitrogen from wastewater is described which consists of a tubular polymeric gel containing Nitrosomonas europaea and Paracoccus denitrificans. The outer surface of the tube is in aerobic contact with wastewater containing ammonia, while the inside of the tube is in anaerobic contact with ethanol flowing through the tube. N. europaea oxidizes ammonia to nitrite in the gel, and then P. denitrificans reduces the nitrite to nitrogen gas in the same gel. This concept would be effective for simplifying nitrogen removal systems requiring aerobic and anaerobic operations.     

Accuracy of high‐density genotype imputation in Japanese Black cattle

Genotype imputation facilitates the identification of missing genotypes on a high‐density array using low‐density arrays and has great potential for reducing genotyping costs for cattle populations. However, the imputation quality varies across breeds, which have different effective population sizes. Therefore, the accuracy of genotype imputation must be evaluated in each breed. The Japanese Black cattle population has a unique genetic background, and this study aimed to investigate different factors affecting imputation quality in this population. A total of 1368 animals were genotyped using the Illumina BovineHD BeadChip, and the accuracy of imputation was evaluated using information from four lower density arrays. The extent of linkage disequilibrium for this population was relatively higher than that in other beef breeds but lower than that in dairy breeds. The accuracy of arrays with more than 20 000 single nucleotide polymorphisms (SNPs) was similar to or higher than that of lower density arrays. In addition, the minor allele frequency of SNPs in the reference population affected the accuracy. The accuracy increased as the size of the reference population increased, up to 400 animals, beyond which there was little increase. A higher genetic relationship between the reference and test populations increased imputation accuracy. These results indicate that high imputation accuracy can be achieved using high‐density arrays, having enough reference animals and including relatives in the reference population.     

Mechanisms of Genomic Instabilities Underlying Two Common Fragile-Site-Associated Loci, PARK2 and DMD, in Germ Cell and Cancer Cell Lines

Common fragile sites (CFSs) are specific chromosome regions that exhibit an increased frequency of breaks when cells are exposed to a DNA-replication inhibitor such as aphidicolin. PARK2 and DMD, the causative genes for autosomal-recessive juvenile Parkinsonism and Duchenne and Becker muscular dystrophy, respectively, are two very large genes that are located within aphidicolin-induced CFSs. Gross rearrangements within these two genes are frequently observed as the causative mutations for these diseases, and similar alterations within the large fragile sites that surround these genes are frequently observed in cancer cells. To elucidate the molecular mechanisms underlying this fragility, we performed a custom-designed high-density comparative genomic hybridization analysis to determine the junction sequences of approximately 500 breakpoints in germ cell lines and cancer cell lines involving PARK2 or DMD. The sequence signatures where these breakpoints occur share some similar features both in germ cell lines and in cancer cell lines. Detailed analyses of these structures revealed that microhomologies are predominantly involved in rearrangement processes. Furthermore, breakpoint-clustering regions coincide with the latest-replicating region and with large nuclear-lamina-associated domains and are flanked by the highest-flexibility peaks and R/G band boundaries, suggesting that factors affecting replication timing collectively contribute to the vulnerability for rearrangement in both germ cell and somatic cell lines.