Short communication: An association analysis between one missense polymorphism at the SREBF1 gene and milk yield and composition traits in goats

Sterol regulatory element binding transcription factor 1 (SREBF1) regulates the expression of genes involved in the biosynthesis of fatty acids and cholesterol. Herewith, we have sequenced the near-complete coding region and part of the 3?UTR of the goat SREBF1 gene. In doing so, we have detected a missense c.353CT polymorphism causing a proline to leucine substitution at position 118 (P118L). An association analysis with milk composition traits recorded in MurcianoGranadina goats only revealed a statistical tendency linking SREBF1 genotype and milk omega-3 fatty acid content. The lack of significant associations suggests that the P118L substitution does not involve a functional change.Le facteur de transcription de´nomme´ Sterol regulatory element binding transcription factor 1 (SREBF1) re´gule l’expression des ge`nes implique´s dans la biosynthe`se des acides gras et du choleste´rol. Dans cette e´tude, nous avons se´quence´ la quasi-totalite´ de la re´gion codante et une partie du la re´gion 3?UTR du ge`ne SREBF1 de la che`vre. Ce travail, nous a permis d’identifier un polymorphisme non-synonyme c.353CT causant la substitution d’une Proline en Leucine a` la position 118. L’e´tude d’association avec la composition du lait enregistre´e en che`vres Murciano-Granadina, a re´ve´le´ seulement une tendance statistique reliant SREBF1 ge´notype et l’acide gras ome´ga-3 du lait. L’absence d’associations significatives sugge`re que la substitution P118L n’implique pas un changement fonctionnel

Detoxification processes from vanadate at the root apoplasm activated by caffeic and polygalacturonic acids

In the root apoplasm, V(V) and V(IV) toxicity can be alleviated through redox and complexation reactions involving phenolic substances and the polyuronic components. In such context we report the role of polygalacturonic acid (PGA) on the reducing activity of caffeic acid (CAF) towards V(V). The redox reaction was particularly effective at pH 2.8 leading to the formation of oxidation products with redox activity towards V(V). An o-quinone was identified as the first product of the reaction which is further involved in the formation of CAF dimers. At pH ≥ 3.6 the redox activity decreased and a yield in V(IV) equal to 38, 31, 21 and 14% was found at pH 3.6, 4.0. 5.0 and 6.0 respectively compared with that obtained at pH 2.8. The redox reaction was faster in the presence of PGA and a higher yield of V(IV) was found in the 4.0–6.0 pH range with respect to the CAF-V(V) binary system. The higher efficiency of the redox reaction in the presence of PGA was related with the ability of PGA to bind V(IV). The biological significance of the redox reaction between CAF and V(V), as well as the role of PGA in such reaction, was established “in vivo” using triticale plants. Results showed that PGA reduced significantly the phytotoxic effects of the V(V)-CAF system.In the root apoplasm, V(V) and V(IV) toxicity can be alleviated through redox and complexation reactions involving phenolic substances and the polyuronic components. In such context we report the role of polygalacturonic acid (PGA) on the reducing activity of caffeic acid (CAF) towards V(V). The redox reaction was particularly effective at pH 2.8 leading to the formation of oxidation products with redox activity towards V(V). An o-quinone was identified as the first product of the reaction which is further involved in the formation of CAF dimers. At pH - 3.6 the redox activity decreased and a yield in V(IV) equal to 38, 31, 21 and 14% was found at pH 3.6, 4.0. 5.0 and 6.0 respectively compared with that obtained at pH 2.8. The redox reaction was faster in the presence of PGA and a higher yield of V(IV) was found in the 4.0-6.0 pH range with respect to the CAF-V(V) binary system. The higher efficiency of the redox reaction in the presence of PGA was related with the ability of PGA to bind V(IV). The biological significance of the redox reaction between CAF and V(V), as well as the role of PGA in such reaction, was established "in vivo" using triticale plants. Results showed that PGA reduced significantly the phytotoxic effects of the V(V)-CAF system. © 2015 Garau et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north–south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction

Onderzoek voor de Commissie Winsemius

Dit onderzoek betreft de volgende twee kernvragen:Welke mededingingsrechtelijke ruimte biedt de bestaande wet- en regelgeving het NFI om aan commerciële derden diensten of producten te leveren?Welke mededingingsrechtelijke risico's zijn verbonden aan het leveren van producten en diensten door het NFI aan commerciële derden?Dit onderzoek dient als input voor het advies van de Commissie Winsemius - een onafhankelijke commissie ingesteld door de minister van V&J - dat betrekking zal hebben op de toekomst van de Nederlandse markt voor forensisch onderzoek en de rol van het NFI hierin. INHOUD: 1. Inleiding 2. Feitelijk en juridisch kader NFI 3. Essentiële begrippen: onderneming en diensten van algemeen economisch belang 4. Mededingingsrecht 5. Overheid en mededinging: de EU-regels betreffende staatssteun 6. Het NFI als onderneming en de kwalificatie van activiteiten als diensten van algemeen economisch belang 7. Toepassing van de mededingingsregels op activiteiten van het NFI 8. Toepassing van de staatssteunregels op activiteiten van het NFI 9. Conclusie: bevindingen en advie

A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean F ST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds

Authoritarian neoliberalism and democratic backsliding in Turkey: beyond the narratives of progress

Unpacking the core themes that are discussed in this collection, this article both offers a research agenda to re-analyse Turkey’s ‘authoritarian turn’ and mounts a methodological challenge to the conceptual frameworks that reinforce a strict analytical separation between the ‘economic’ and the ‘political’ factors. The paper problematises the temporal break in scholarly analyses of the AKP period and rejects the argument that the party’s methods of governance have shifted from an earlier ‘democratic’ model – defined by ‘hegemony’ – to an emergent ‘authoritarian’ one. In contrast, by retracing the mechanisms of the state-led reproduction of neoliberalism since 2003, the paper demonstrates that the party’s earlier ‘hegemonic’ activities were also shaped by authoritarian tendencies which manifested at various levels of governance

Ethiopian indigenous goats offer insights into past and recent demographic dynamics and localadaptation in sub-Saharan African goats

Abstract Knowledge on how adaptive evolution and human socio‐cultural and economic interests shaped livestock genomes particularly in sub‐Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio‐climatic conditions. Using 52K genome‐wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome‐wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi‐Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub‐Saharan Africa indigenous goats

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background: Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods: The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results: A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion: Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)