86,555 research outputs found
Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets
No full textPolymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions
Population genomics from a food matrix: estimating csd variability using next generation sequencing on Apis mellifera DNA present in honey
No full textThe complementary sex determiner (csd) gene is a crucial genetic factor in the sex determination of Apis mellifera L. Females only develop if fertilized eggs have functional heterozygous genotypes at this gene. Males, being haploids, are emizygous. Two identical csd alleles result in non-viable males. Given the recent decline in honey bee populations, it is imperative to monitor allele variability at this gene to prevent negative effects of high inbreeding levels. In this study, we evaluated the use of next generation sequencing in conjunction with environmental honey DNA as a source of honey bee genomic information to obtain extensive sequencing data for analysing variability at the hypervariable region (HVR) of the csd gene. DNA was extracted from several honey samples directly collected from oneycombs of various colonies. A bioinformatic pipeline was utilised to analyse approx. 1.5 million reads, identifying a total of 160 different csd alleles, 55% of which were novel. The average number of alleles per sample corresponded with the expected number of patrilines per colony, based on queen mating behaviour. The diversity of alleles at the csd gene could also offer valuable information for reconstructing the honey bee population genetic history
Impact of Residual Setup Error on Parotid Gland Dose in Intensity-Modulated Radiation Therapy with or without Planning Organ-at-Risk Margin
No full textPurpose: To estimate the dosimetric impact of residual setup errors on parotid sparing in head-and-neck (H&N) intensity-modutated treatments and to evaluate the effect of employing an PRV (planning organ-at-risk volume) margin for the parotid gland. Patients and Methods: Ten patients treated for H&N cancer were considered. A nine-beam intensity-modutated radiotherapy (IMRT) was planned for each patient. A second optimization was performed prescribing dose constraint to the PRV of the parotid gland. Systematic setup errors of 2 mm, 3 mm, and 5 mm were simulated. The dose-volume histograms of the shifted and reference plans were compared with regard to mean parotid gland dose (MPD), normal-tissue complication probability (NTCP), and coverage of the clinical target volume (V(95%) and equivalent uniform dose [EUD]); the sensitivity of parotid sparing on setup error was evaluated with a probability-based approach. Results: MPD increased by 3.4%/mm and 3.0%/mm for displacements in the craniocaudal and lateral direction and by 0.7%/mm for displacements in the anterior-posterior direction. The probability to irradiate the parotid with a mean dose > 30 Gy was > 50%, for setup errors in cranial and lateral direction and < 10% in the anterior-posterior direction. The addition of a PRV margin improved parotid sparing, with a relative reduction in NTCP of 14%. The PRV margin compensates for setup errors of 3 mm and 5 mm (MPD <= 30 Gy in 87% and 60% of cases), without affecting clinical target volume coverage (V(95%) and EUD variations < 1% and < 1 Gy). Conclusion: The parotid gland is more sensitive to craniocaudal and lateral displacements. A setup error of 2 mm guarantees an MPD : 30 Gy in most cases, without adding a PRV margin. If greater displacements are expected/accepted, an adequate PRV margin could be used to meet the clinical parotid gland constraint of 30 Gy, without affecting target volume coverage
Untargeted metabolomics describes genetic factors that influence pig metabolism for adaptation traits in a Duroc line
No full textTo enhance selection programs and develop novel breeding strategies, the pig production sector continuously explores new phenotypic traits, expanding the traditional phenotypic landscape, which has typically focused on final phenotypes such as production and performance traits. Final phenotypes are complex, influenced by many external and molecular interactions at the organismal level. These influences can be broken down by studying molecular layers or intermediate phenotypes, such as the metabolome. This study aims to genetically dissect pig metabolism to identify markers associated with the adaptation to heat-stress conditions. About 700 blood plasma metabolites were quantified through an untargeted metabolomic platform on 300 growing male Duroc pigs. Additionally, genotypes for ~40,000 single nucleotide polymorphisms were obtained for the same animals. The pigs were from two groups with extreme and divergent values for feed intake under heat-stress conditions. Genomic heritability estimates and genome wide associations for the level of metabolites were calculated using GEMMA. Heritability estimates ranged from 0.0 to 0.83 (average = 0.18; s.d. = 0.15). We found suggestive (P < 5.5×10-05) and significant (P < 1.3×10-06) marker associations for 400 and 102 metabolites, respectively. Most of these associations were between markers in enzyme-encoding genes and metabolites that either serve as substrates or final products of the corresponding genes. Overall, these newly identified genetic determinants of pig metabolism serve as (i) a novel source of information for indirectly explaining complex traits, including resilience to heat stress, proxied using feed intake measures; and (ii) new genetic markers for fine-tuning selection programs to enhance the sustainability and resilience of pig production. Acknowledgments: This study received funding from the European Union’s Horizon Europe research and innovation program under grant agreement No. 01059609 (Re-Livestock project)
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Describing feed efficiency using metabolomic data in pigs
No full textFeed conversion ratio (FCR) is commonly used to determine production efficiency in pigs. However, the basic biological mechanisms of this complex trait are still largely unexplored. In this study, we aimed to describe FCR in Italian Large White pigs using metabolomic data. For 691 pigs, FCR random residuals (FCR-RR), untargeted plasma metabolomic data (constituted by about 1000 metabolites) and high-density single nucleotide polymorphisms were available. We first identified two extreme groups of pigs (100 with the lowest and 100 the highest FCR-RR) and compared their metabolomic data using Sparse Partial Least Squares Discriminant Analysis and Boruta algorithm. With the combination of these two approaches, we identified 12 metabolites that could discriminate the two extreme groups of pigs. These metabolites were involved in a few metabolomic pathways, including fatty acid oxidation, carnitine, alanine, and histidine metabolism. Genomic heritability of the selected metabolites ranged from 0.11 to 0.35. The obtained results can contribute to identify molecular proxies useful to describe feed efficiency and develop new breeding strategies in pigs. Acknowledgments: This study has received funding from the European Union – NextGenerationEU under the National Recovery and Resilience Plan (PNRR) – FEEDTHEPIG, proposal code P2022FZMJ9 – CUP J53D23018310001 and from the European Union’s Horizon Europe research and innovation programme under the grant agreement No. 01059609 (Re-Livestock)
HPLC analysis of HbA1c in dried blood spot samples (DBS): a reliable future for diabetes monitoring
No full textTo simplify collection and transport of blood for HbA1c measuring, we have studied the use of a special paper that absorbs a defined volume of capillary blood and quickly dries it (dried blood-spot, DBS). The DBS can be sent to a central laboratory using regular postal service and without temperature control. This system differs greatly from other proposed DBS methods for HbA1c because it overcomes the haemoglobin alterations during the drying and storing processes, that otherwise make this analysis unreliable. We have developed a special treatment of the paper before collection that stabilises the HbA1c molecule excellently in dried blood samples, allowing accurate HPLC analysis even two weeks after collection. This method has been applied in a "blind" study in which HbA1c values determined in 97 DBS coming from an hospital diabetes care centre were compared with those obtained from parallel venous blood samples
Metabolomics identifies novel biomarkers for fat deposition, feed efficiency and growth in Italian Large White pigs
No full textThe Italian heavy pig sector relies on key traits that need optimization: feed efficiency, as pigs are slaughtered at a heavier weight; growth, as they have a minimum slaughter age; and the right fat proportion, since their meat is used for high-quality dry-cured hams. Advances in omics suggest that plasma untargeted metabolomics may provide biomarkers to improve evaluation accuracy. This study analyzed over 700 Italian Large White pigs, with random residuals extracted from genetic indexes routinely collected for selection. Pigs were grouped into five pools based on the trait of interest: feed conversion ratio (FCR), average daily gain (ADG), backfat thickness (BFT), lean cut (LC), and ham weight (HW). Machine learning, including the Boruta algorithm, identified discriminant metabolites associated with these traits. The SNP-based heritability of key metabolites was estimated using GEMMA. Boruta analyses detected 8 to 26 discriminant metabolites per trait, with only partial overlap. The most common were sphingomyelins, leucine-, isoleucine-, valine-, and tyrosine-derived metabolites. The highest metabolite overlap was found between HW and LC, sharing ~50%, especially amino acids. The average heritability was 0.25(±0.11), with three metabolites exceeding 0.5. These findings highlight the trait interplay and demonstrate metabolomics’ potential in identifying biochemical markers for growth, feed efficiency, and fat deposition. Such metabolites could enhance selection precision for high-quality dry-cured ham production. The research was supported by the Italian PRIN2022 project FEEDTHEPIG, funded by the European Union – NextGenerationEU under the National Recovery and Resilience Plan (PNRR) – Mission 4 Education and research – Component 2 From research to business – Investment 1.1 Notice PRIN 2022 PNRR (DD N. 1409 del 14/09/2022), proposal code P2022FZMJ9 – CUP J53D23018310001
Biogenic amines in the taste organ
No full textThe presence and content of biogenic amines in taste disk-bearing fungiform papillae of the frog, Rana esculenta, the only available model of an isolated taste organ, were verified by means of HPLC. Fungiform papillae were found to contain measurable amounts of serotonin, epinephrine and norepinephrine. The amounts of serotonin and epinephrine were significantly higher in fungiform papillae than in the general mucosa of the tongue. Moreover, the epinephrine content of fungiform papillae was found to differ across the tongue, in accordance with previous physiological studies showing an inhomogeneous response of different tongue regions to taste stimuli. Ultrastructural and histochemical investigations confirmed the presence of catecholamine and serotonin. The latter was found to be contained mainly in the basal cells of the frog taste disk. These results extend previous qualitative data on the presence of biogenic amines in taste chemoreceptors
Determination of apomorphine in human plasma by alumina extraction and high-performance liquid chromatography with electrochemical detection
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