Leccese sheep breed from Apulia: evidence of genetic substructuring from STR loci

Leccese is an originally triple-purpose sheep breed from Southern Italy. Due to major changes in rural society and livestock production, the breed has experienced in the last decades a drastic population size reduction. Nowadays roughly one thousand animals are reared in about ten farms located in Apulia. In order to evaluate the genetic variability within the Leccese breed, a total of 97 animals, sampled from five different farms in the provinces of Bari, Taranto, Brindisi, and Lecce were genotyped at 19 microsatellite loci belonging to the ISAG-FAO panel for Domestic Animal Diversity. Samples were chosen according to genealogical records in order to minimize relatedness among animals. Although being a local bottlenecked breed, the Leccese sample displayed a valuable number of alleles (187 over 19 loci, with a minimum of 4 in BM1824 and OarFCB193 and a maximum of 16 in MAF70 and MCM140). A high proportion of private alleles was observed for each farm (7.7 alleles on average). In addition, a high level of linkage disequilibrium was observed in the total sample, also among non syntenic locus pairs, suggesting the presence of population sub-structuring. To test the hypothesis of a genetic partitioning at the farm hierarchical level we first calculated the pair-wise FST between the different farms, which highlighted significant (P<0.001) though moderate values (0.055 to 0.065). Then, we performed both a likelihood-based and a Bayesian population assignment test, respectively implemented in the Arlequin and Structure software packages, in order to verify the degree of differentiation between the five farms. A correct allocation was obtained for 96.9% of animals by using the Arlequin software and 92.8% when using Structure, thus highlighting a clear genetic differentiation at the farm level, counterbalanced by a marked within-herd genetic similarity. These results suggest that reproductive isolation and/or different selection strategies across farms contributed to the observed pattern of genetic sub-structuring; this should be seriously taken into consideration, due to the critical implications for the breed conservation

Haplotype recostruction from unphased genotype data at the bovine PRKAG3 gene

Haplotype analysis has became an area of intense research, both for population genetics studies and for molecular dissection of complex phenotypes. Haplotypes provide increased informativeness with respect to single nucleotide polymorphisms and allow to condense information on genomic variation, with a sensible gain of power in association studies. Direct haplotyping via molecular analysis provides more exact information per individual, but is much more expensive and labour-intensive than indirectly inferring haplotypes from genotypes. Several methods have been proposed so far to indirectly reconstruct haplotypes from unphased genotypes. In the present study, we adopted four different approaches (implemented in the computer programs ARLEQUIN, HELIXTREE, HAP and PHASE) to infer phase information from genotypic data on 197 subjects at 14 polymorphic sites of the bovine PRKAG3 gene. In the whole, twelve different haplotypes had been inferred by all the four different methods, although at slightly varying frequencies. Other three haplotypes were inferred by at least two different approaches and some haplotypes were unique to a single method. No dramatic differences among the four selected approaches were observed for the considered genomic target. This is probably due to the linkage-disequilibrium structure of the analysed region and to the moderate amount of missing genotype data

Nutritional Regimes Enriched with Antioxidants as an Efficient Adjuvant for IBD Patients under Infliximab Administration, a Pilot Study

Antioxidants are privileged candidates for the development of adjuvants able to improve the efficiency of pharmacological therapies, particularly for chronic inflammatory syndromes. During the last 20 years, anti-TNFα (tumor necrosis factor alpha) monoclonal antibodies infusion has been the biological therapy most frequently administered but there is still large space for improvement in disease remission rates and maintenance. In this context, nutritional bioactive compounds contained in dietary patterns or included as supplements, may act as adjuvants for the induction and maintenance of IBD (inflammatory bowel diseases) remission. To verify this possibility, a single-center preliminary study (SI-CURA, Soluzioni Innovative per la gestione del paziente e il follow up terapeutico della Colite UlceRosA) was designed and carried out to evaluate whether a daily administration of purple corn supplement could improve the response to Infliximab (IFX) infusion of IBD patients with both Crohn’s disease (CD) and ulcerative colitis (UC). A cohort of 47 patients was enrolled in the study. Biological samples were collected before the first and the third IFX infusion. All patients received nutritional guidelines, 27 of them received commercial red fruit tea with low anthocyanins content, while 20 received a purple corn supplement with a high anthocyanin content. Results show that the administration of an antioxidant-enriched purple corn supplement could improve IFX-mediated disease remission in terms of circulating inflammatory markers. Comparison between CD and UC patients revealed that, at this anthocyanin dosage, the purple corn extract administration improved the IFX response in CD but not in UC patients. Our results may pave the way for a new metacentric study of CD patients, recruiting a wider cohort and followed-up over a longer observational time

Clinical Features, Cardiovascular Risk Profile, and Therapeutic Trajectories of Patients with Type 2 Diabetes Candidate for Oral Semaglutide Therapy in the Italian Specialist Care

Introduction: This study aimed to address therapeutic inertia in the management of type 2 diabetes (T2D) by investigating the potential of early treatment with oral semaglutide. Methods: A cross-sectional survey was conducted between October 2021 and April 2022 among specialists treating individuals with T2D. A scientific committee designed a data collection form covering demographics, cardiovascular risk, glucose control metrics, ongoing therapies, and physician judgments on treatment appropriateness. Participants completed anonymous patient questionnaires reflecting routine clinical encounters. The preferred therapeutic regimen for each patient was also identified. Results: The analysis was conducted on 4449 patients initiating oral semaglutide. The population had a relatively short disease duration (42%  60% of patients, and more often than sitagliptin or empagliflozin. Conclusion: The study supports the potential of early implementation of oral semaglutide as a strategy to overcome therapeutic inertia and enhance T2D management

Comparative evaluation of the efficiency of low-cost adsorbents and ligninolytic fungi to remove a combination of xenoestrogens and pesticides from a landfill leachate and abate its phytotoxicity

In this study, two widely available low-cost adsorbents, almond shells and a green compost, and two ligninolytic fungi, Pleurotus ostreatus and Stereum hirsutum, were used to remove organic contaminants from a landfill leachate (LLe) and abate its phytotoxicity. The methodology adopted was based on the occurrence of two simultaneous processes, such as adsorption and bioremoval. The leachate was artificially contaminated with a mixture of the xenoestrogens bisphenol A (BPA), ethynilestadiol (EE2) and 4-n-nonylphenol (NP), the herbicide linuron and the insecticide dimethoate at concentrations of 10, 1, 1, 10 and 10 mg L¡1 , respectively. Three adsorption substrates were prepared: potato dextrose agar alone or the same incorporating each adsorbent. The substrates were either not inoculated or inoculated with each fungus, separately, before to be superimposed on LLe. After 2 months, the residual amount of each contaminant, the electrical conductivity, the pH and the content of total phenols were measured in treated LLe. Germination assays using lettuce, ryegrass and radish were performed to evaluate LLe phytotoxicity. The combination substrateCP. ostreatus showed the best results with average removals of 88, 96, 99, 58 and 46% for BPA, EE2, NP, linuron and dimethoate, respectively. The same treatment considerably reduced the phenol content in LLe compared to no treatment. The combination substrateCS. hirsutum produced average removals of 39, 71, 100, 61 and 32% for BPA, EE2, NP, linuron and dimethoate, respectively. Also uninoculated substrates showed relevant adsorption capacities towards the five contaminants. Most treatments significantly reduced LLe phytotoxicity, especially on lettuce. The best results were obtained with the treatment compostCS. hirsutum, which produced root and shoot lengths and seedling biomass of lettuce, respectively, 2.3, 3.3, and 1.9 times those measured in untreated LLe. In general, germination results were negatively correlated with LLe properties like the residual amount of the contaminants, the electrical conductivity and the pH. These results show that the methodology adopted in the study, i.e., combined adsorption/biodegradation, is suitable not only to remove xenobiotic contaminants from the leachate but also to reduce considerably its inhibition on seed germinatio

Haplotype reconstruction from unphased genotype data at the bovine PRKAG3 gene

SUMMARY Haplotype analysis has became an area of intense research, both for population genetics studies and for molecular dissection of complex phenotypes. Haplotypes provide increased informativeness with respect to single nucleotide polymorphisms and allow to condense information on genomic variation, with a sensible gain of power in association studies. Direct haplotyping via molecular analysis provides more exact information per individual, but is much more expensive and labour-intensive than indirectly inferring haplotypes from genotypes. Several methods have been proposed so far to indirectly reconstruct haplotypes from unphased genotypes. In the present study, we adopted four different approaches (implemented in the computer programs ARLEQUIN, HELIXTREE, HAP and PHASE) to infer phase information from genotypic data on 197 subjects at 14 polymorphic sites of the bovine PRKAG3 gene. In the whole, twelve different haplotypes had been inferred by all the four different methods, although at slightly varying frequencies. Other three haplotypes were inferred by at least two different approaches and some haplotypes were unique to a single method. No dramatic differences among the four selected approaches were observed for the considered genomic target. This is probably due to the linkage-disequilibrium structure of the analysed region and to the moderate amount of missing genotype data. RIASSUNTO L’ambito di analisi degli aplotipi evidenzia un interesse crescente da parte della ricerca, sia in termini di studi di genetica delle popolazioni che per la comprensione delle basi molecolari di caratteri complessi. Gli aplotipi forniscono un livello maggiore di informatività rispetto alle mutazioni a carico di singole basi nucleotidiche e consentono di condensare l’informazione relativa alla variabilità genetica, permettendo, altresì, di acquisire un incremento nella potenza di analisi in studi di associazione. I metodi diretti di ricostruzione dell’aplotipo basati sull’analisi molecolare forniscono un livello di informazione più accurato ma presentano il grosso inconveniente di essere estremamente costosi e laboriosi rispetto ai metodi indiretti di inferenza. Molteplici approcci sono stati proposti ad oggi per la ricostruzione indiretta degli aplotipi a partire da dati genotipici a fase gametica ignota. Nel presente lavoro, sono stati adottati quattro diversi metodi (implementati nei programmi ARLEQUIN, HELIXTREE, HAP e PHASE) per l’inferenza della fase gametica a partire dai dati genotipici di 197 soggetti relativi a 14 siti polimorfici del gene PRKAG3 bovino. Complessivamente, dodici diversi aplotipi sono stati inferiti da tutti i quattro metodi adottati, sebbene con frequenze relativamente divergenti. Altri tre aplotipi sono stati inferiti da almeno due dei quattro diversi approcci mentre alcuni aplotipi sono stati inferiti esclusivamente da uno dei quattro metodi. Complessivamente, non sono state osservate differenze sostanziali tra i diversi approcci adottati relativamente alla regione genomica di interesse. Ciò è presumibilmente ascrivibile al profilo di linkage disequilibrium della regione analizzata ed alla presenza molto contenuta di dati genotipici mancanti

A Two-Step Approach to Eliminate Pesticides and Estrogens from a Wastewater and Reduce Its Phytotoxicity: Adsorption onto Plant-Derived Materials and Fungal Degradation

In this study, adsorption and biodegradation were exploited sequentially to remove the herbicide fenuron, the insecticide carbaryl and the estrogens 17β-estradiol (E2) and 4-tert-octylphenol (OP) from a municipal landfill leachate (MuLL). In the first step, we used spent coffee grounds, almond shells, a biochar and potato dextrose agar to adsorb the compounds spiked in MuLL at a concentration of 1 mg L−1. After only 3 days, any adsorbent removed from MuLL the totality of E2 and OP, averagely more than 95 % of carbaryl and 62 % of fenuron (81 % after 7 days). In the second step, the adsorbents collected from MuLL after 7 days were inoculated with the fungi Bjerkandera adusta and Irpex lacteus, separately. After 7 days, the maximum degradation occurred for OP in any treatment being averagely 78 and 74 % using B. adusta and I. lacteus, respectively. After 15 days, the average percentages of fenuron, carbaryl, E2 and OP degraded were, respectively, 75, 76, 88 and 88 % using B. adusta, and 74, 79, 85 and 89 % using I. lacteus. Residual estrogenicity in the adsorbents, tested with the recombinant yeast assay, was strictly related to residual E2, thus indicating a negligible contribution from the other contaminants and/or degradation products. The 7-day treatment of MuLL with the adsorbents caused a significant abatement of MuLL phytotoxicity on flax (2.5 times seedling elongation with coffee grounds, compared to MuLL) and a huge stimulation of rapeseed respect to water (biomass almost doubled), thus suggesting a possible worthwhile recycling of this wastewater in agriculture