Inversion variants in human and primate genomes

For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited. Here, we performed a genome-wide comparison between human, great ape, and macaque genomes using the net alignments for the most recent releases of genome assemblies. We identified a total of 156 putative inversions, between 103 kb and 91 Mb, corresponding to 136 human loci. Combining literature, sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one or multiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated with human disease. This work doubles the number of validated primate inversions larger than 100 kb, beyond what was previously documented. We identified 74 sites of errors, where the sequence has been assembled in the wrong orientation, in the reference genomes analyzed. Our data serve two purposes: First, we generated a map of evolutionary inversions in these genomes representing a resource for interrogating differences among these species at a functional level; second, we provide a list of misassembled regions in these primate genomes, involving over 300 Mb of DNA and 1978 human genes. Accurately annotating these regions in the genome references has immediate applications for evolutionary and biomedical studies on primates

Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain.

Bacillus coagulans GBI-30, 6086 is a safe strain, already available on the market, and characterized by certified beneficial effects.The draft genome sequence presented here constitutes the first pillar toward the identification of the molecular mechanisms responsiblefor its positive features and safety

Characteristics and patterns of care of endometrial cancer before and during COVID-19 pandemic

Objective: Coronavirus disease 2019 (COVID-19) outbreak has correlated with the disruption of screening activities and diagnostic assessments. Endometrial cancer (EC) is one of the most common gynecological malignancies and it is often detected at an early stage, because it frequently produces symptoms. Here, we aim to investigate the impact of COVID-19 outbreak on patterns of presentation and treatment of EC patients. Methods: This is a retrospective study involving 54 centers in Italy. We evaluated patterns of presentation and treatment of EC patients before (period 1: March 1, 2019 to February 29, 2020) and during (period 2: April 1, 2020 to March 31, 2021) the COVID-19 outbreak. Results: Medical records of 5,164 EC patients have been retrieved: 2,718 and 2,446 women treated in period 1 and period 2, respectively. Surgery was the mainstay of treatment in both periods (p=0.356). Nodal assessment was omitted in 689 (27.3%) and 484 (21.2%) patients treated in period 1 and 2, respectively (p<0.001). While, the prevalence of patients undergoing sentinel node mapping (with or without backup lymphadenectomy) has increased during the COVID-19 pandemic (46.7% in period 1 vs. 52.8% in period 2; p<0.001). Overall, 1,280 (50.4%) and 1,021 (44.7%) patients had no adjuvant therapy in period 1 and 2, respectively (p<0.001). Adjuvant therapy use has increased during COVID-19 pandemic (p<0.001). Conclusion: Our data suggest that the COVID-19 pandemic had a significant impact on the characteristics and patterns of care of EC patients. These findings highlight the need to implement healthcare services during the pandemic

Practice patterns and 90-day treatment-related morbidity in early-stage cervical cancer

To evaluate the impact of the Laparoscopic Approach to Cervical Cancer (LACC) Trial on patterns of care and surgery-related morbidity in early-stage cervical cancer

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Draft genome sequence of Bacillus coagulans GBI-30, a widely used sporeforming probiotic strain

Introduction: Bacillus coagulans strain GBI-30 (ATCC Designation Number PTA-6086) is a safe strain, authorized for human consumption and it is already available in a wide choice of functional foods or as dietary supplement (Cutting, 2011). This strain is characterized by certified beneficial effects in gastrointestinal disorders, such as Irritable Bowel Syndrome, intestinal gas, rheumatoid arthritis, and in common viral infections of the respiratory tract (Jurenka, 2012). Due to its wide use, the goal of the present study is the whole genome sequencing of B. coagulans GBI-30 in order to unveil the genetic basis of its safety and probiosis. Methods Whole genome sequencing was performed using the Illumina GAIIx platform; the obtained sequences were de novo assembled using the CLC Genomic Workbench v. 7.0. with an average coverage of 840 7. Finally, RAST annotation server was employed to perform annotation (Aziz et al., 2008). Results A total of 14,500,000 paired end reads of 110 bp length were assembled into 224 contigs (N50 length of 44,706 bp) with the largest assembled contig of 125,999 kb length. The draft genome consists of 3,458,655 bp with GC % content of 46.38. About 3,890 coding sequences (CDS) and a total of 90 RNAs were predicted. According to the annotation, the probiotic strain is predicted to possess 491 proteins involved in carbohydrate utilization, including glycolysis, the citrate cycle, and the pentose phosphate pathway. As expected, a total of 82 genes regarding dormancy and sporulation were annotated: seven of them are involved in spore DNA protection, while the others are associated directly to the sporulation mechanism, spore core dehydration, and spore germination. Regarding the safety of this strain, 44 CDS were included in the RAST subsystem related to virulence, disease and defense. Detailed analysis of these genes revealed that one of them is involved in adhesion (which is also a probiotic feature), while the majority are associated to copper homeostasis and cobalt-zinc-cadmium resistance. Discussion As more probiotic strains are used in the food and drug industry, more attention should be paid to confirm the safety of these strains using complete genome analysis as a tool (Zhang et al., 2012). In this perspective, the complete genome of B. coagulans GBI-30 obtained in the present study has contributed to a wider and deeper insight into the positive features of this strain. Furthermore, the comparative genomic analysis with other Bacillus strains genomes might shed new light on the molecular mechanisms at the basis of its probiotic and beneficial properties. Acknowledgements This research was funded by the Italian Ministry for Development in the framework of the project \u201cPass-World - pasta e salute nel mondo - Industria 2015\u201d

Metabolomics characterization of colostrum in three sow breeds and its influences on piglets' survival and litter growth rates

Background: Colostrum is the first secretion produced by mammary glands during the hours immediately preceding and succeeding parturition. This secretion differs from milk and represents an essential vehicle of passive immunity, prebiotic compounds and growth factors involved in intestinal development. Most of the literature concerning colostrum composition refers mainly to human and cow; and little is known about pig colostrum metabolome and how it varies between pig breeds and different farrowing parity. Thus, the aim of the present research is to provide new information about pig colostrum composition and the associations between metabolites, the sows' breed and the survival and growth rates of their litters. Results: Colostrum samples were gathered from 58 parturitions of sows belonging to three different breeds chosen for their importance in Italian heavy pig production: 31 Large White, 15 Landrace and 12 Duroc respectively. The defatted and ultrafiltered colostrum samples were analysed using1H-NMR spectroscopy. Principal Components Analysis (PCA) was assessed on the obtained spectra. In addition, using a Stepwise Regression and a Linear Regression analyses the metabolites named after the signals assignment were tested for their associations with piglets' performances. Twenty-five metabolites were identified, comprehending monosaccharides, disaccharides (such as lactose), organic acids (lactate, citrate, acetate and formate), nitrogenous organic acids (such as creatine) and other compounds, including nucleotides. PCA results evidence a clustering due to breed and season effects. Lactose was the main compound determining the assignment of the samples into different clusters according to the sow breed. Furthermore, some metabolites showed to be associated with piglets' performance and survival traits: acetate and taurine were positively related to litter weight gain and piglets' survival rate, respectively, while dimethylamine and cis-aconitate were linked to new-borns' impaired ability to survive. Conclusions: The results obtained suggest that colostrum composition is affected by breed, which, together with environmental conditions, may cause changes in colostrum metabolites content with possible consequences on piglets' performances. Among the identified metabolites, acetate, taurine, dimethylamine and cis-aconitate showed consistent associations with piglets' survival rate and litter weight gain, implying that these compounds may affect new-borns' ability to survive