5_figures+mapfiles

R-Markdown file. This contains the in house scripts used to process raw data files and run all downstream analyses reported in our paper. The script includes code to smooth recombination maps, generate motif density files, test correlations and and fit linear models to examine the relationship between motif density and recombination rate, at different smoothing scales, in Dmel and Dsim. Details can be found in our paper

2_recombination_maps_mimicrEE_ZIP

Recombination map files for D. simulans and D. melanogaster, at different smoothing resolutions. This set of files is the same as the CSV files, except that they formatted for use with MimicrEE simulation software. Also, we provide “Dsim_recombination_map_LOESS_100kb_1.txt”, in which LOESS smoothing equivalent to 100 kb windows is applied through an alternative R algorithm. The standard files provided are, again, the moving median and LOESS smoothed maps. For Dsim, moving median files are provided at resolutions: 5, 25, 101, 501, and 2501 kb. For Dmel, the moving median files are provided at resolutions: 501, and 2501 kb, due to a lower resolution initial map. For Dsim the LOESS files are at 0.001, 0.005, 0.02, 0.10. These levels are equivalent to moving median windows of 25, 101, 501, and 2501 kb. For Dmel, the LOESS smoothing parameter is set at: 0.02, 0.10. A raw recombination map is provided for Dsim, in 1 kb windows and for Dmel in 101 kb windows. Details for how this raw map was produced can be found in our paper, Howie et et al. 2019. The R script used to produce differently smoothed recombination maps is provided as an R-Markdown file

1_recombination_maps_csv_ZIP

Recombination map files for D. simulans and D. melanogaster, at different smoothing resolutions. We provide moving median and LOESS smoothed maps. For Dsim, the moving median files are provided at the following resolutions: 5, 25, 101, 501, and 2501 kb. For Dmel, the moving median files are provided at the following resolutions: 501, and 2501 kb, due to a lower resolution initial map. For Dsim the LOESS files are provided with the LOESS smoothing parameter set at the following levels: 0.001, 0.005, 0.02, 0.10. These levels are equivalent to moving median windows of 25, 101, 501, and 2501 kb. For Dmel, the LOESS smoothing parameter is set at: 0.02, 0.10. Finally, a raw unsmoothed recombination map is provided for Dsim, in 1 kb windows, and for Dmel at 101 kb. Details for how this raw Dsim map was produced are in our paper, Howie et et al. 2019. The R script used to produce differently smoothed recombination maps for both species is also provided as an R-Markdown file

3_dmel-fimo_ZIP.tsv

Motif density files for D. melanogaster, which are output from FIMO. These can be used to plot motif density along the genome or, in combination with the recombination maps, to test the relationship between recombination rates and motif density. The script is provided in the R Markdown file

4-dsim-fimo_ZIP.tsv

Motif density files for D. simulans, which are output from FIMO. These can be used to plot motif density along the genome or, in combination with the recombination maps, to test the relationship between recombination rates and motif density. The script is provided in the R Markdown file

6_PrepareFasta_X

Phased Haplotypes - that is, SNP and genomic location - used to produce the Dsim Recombination Map, for the X chromosome. We crossed focal males from 189 isofemale lines, from Florida, to virgin “reference” females, and then individually sequenced the F1 progeny. From the raw BAM files, we produced phased haplotype files, in which reference alleles are removed and SNPs called. This was done in FreeBayes: segment size 1kb, alpha 0.05, theta 0.04. Full details are provided in our paper. Here, we provide 189 phased haplotypes for the X chromosome. This is essentially information about SNPs and their genomic positions

Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species.

Meiotic recombination is crucial for chromosomal segregation, and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease towards centromeres and telomeres, with a dramatic impact on levels of variation in natural populations. Two close sister species, D. simulans and D. mauritiana do not only have higher recombination rates, but also exhibit a much more homogeneous recombination rate that only drops sharply very close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation in D. melanogaster, we tested whether the difference in recombination landscape between D. melanogaster and D. simulans can be explained by the genomic distribution of recombination-rate associated sequence motifs. We constructed the first high-resolution recombination map for D. simulans based on 189 haplotypes from a natural D. simulans population, and searched for short sequence motifs linked with higher than average recombination in both sister species. We identified five consensus motifs significantly associated with higher than average chromosome-wide recombination rates in at least one species and present in both. Testing fine resolution associations between motif density and recombination, we found strong and positive associations genome-wide over a range of scales in D. melanogaster, while the results were equivocal in D. simulans. Despite the strong association in D. melanogaster, we did not find a decreasing density of these short-repeat motifs towards centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape in D. melanogaster, nor the differences to D. simulans. The strong association seen for the sequence motifs in D. melanogaster likely reflects their impact influencing local differences in recombination rates along the genome

21. Recreational food:if legal highs are in the kitchen 39th International Congress of the European Association of Poisons Centres and Clinical Toxicologists (EAPCCT) 21-24 May 2019, Naples, Italy

OBJECTIVE. Nutmeg is commonly used as a kitchen spice but for its psychotomimetic properties is also considered as legal high. Nitrous Oxide gained popularity among the youth and its misuse is alarming widespread. Hence, here are reported two cases of teenagers who gained easily these two legal highs for recreational and self-medication purpose. CASE SERIES.Case 1 The Poison Control Centre (PCC) of Policlinico Umberto I Hospital – Sapienza University of Rome, was alerted at 3:00 a.m. for a 16 years old boy, body weight 50 Kg, who ingested an amount of about 7 grams of nutmeg 14 hours before. He presented a clinical history of depressive mood and social isolation. After 6 hours from the ingestion he developed emesis, abdominal pain and headache. In particular, emesis was repeated and persistent. No psychotomimetic symptoms were reported. The PCC suggested the admission at the local Emergency Department (ED) to treat the emesis and to assess his suicidal risk. The boy revealed that he tried the nutmeg for its euphoria-inducing properties following some reports read on the Internet. Case 2 A 14 years old girl was admitted at the local ED as the result of inhaling nitrous oxide contained in a spray cream for recreational use. She reported nausea, dizziness, tachycardia (heart rate: 106 bpm) and anterograde amnesia. The PCC was alerted and suggested to monitor vital signs and to perform an Arterial Blood Gas (ABG) test to check the risk of methemoglobinemia. No abnormalities were detected and the patient was discharged without symptoms 6 hours later. She revealed to inhale the nitrous oxide with friends after reading the procedure on the Internet. CONCLUSIONS. Although these two cases have low clinical relevance because of the transient and minor symptoms presented, they allow some considerations: i) the lasting trend among the youth to search information on the Internet about substances usually sold and easily available, ii) the use of these substances even as self-medication, iii) the easy availability may underestimate the risks associated to their abuse mostly among the youth, iv) the variability in the psychopharmacological response as well as the concentrations of its active components not ensure a “safe” level of exposure in the context of nutmeg intoxication

Impact of the media on the Poison Control Centres: the false outbreak of Loxosceles Rufescens spider bite in Italy

Objective.To describe the increment of telephone calls to the Poison Control Centre (PCC) of Policlinico Umberto I Hospital – Sapienza University of Rome related to Loxosceles Rufescens (LR) spider bites following an alarming awareness campaign in the media. Methods.The telephone calls to the PCC on alleged LR bites from April 2016 to September 2018 were reviewed. The month of April 2018, when the lay press published the first alarming article, was identified as an index. Data were normalized for the increase in the overall consultations registered in 2018. Results.The recorded enquiries regarding LR bites were as follows: i) 22 calls over the two years period April 2016 - March 2018, of which 4 from Emergency Department (ED) and 18 from private citizens; ii) 79 calls from April 2018 to September 2018, of which 18 from ED and 61 from private citizens. The mean age of subjects was 49 years (range: 12 months - 86 years). Only 2 subjects presented a skin lesion suggestive of LR: i) a 3-year old child hospitalized for 1 day for a necrotic skin lesion and low-grade fever. ii) a 61-years old man who presented an ulcerative skin lesion and was already treated at home with oral antibiotic therapy.Conclusions.Irrational fears about insects and other arthropods are very common. LR rarely bites humans and, contrary to what often stated or claimed, its bite causes minor, transient effects. Currently, there is no known fatal case. The “lethal” reputation of LR is mostly predicated by the lay press. It is well-known that the increase in mass media coverage is associated with an increase in ED admissions.This report allows the follow considerations: i) the mass media play a pivotal role in public health behavior and may influence health care utilization, ii) medical news reports may cause alarm, often unjustified, and may have significant costs either in terms of public health or in terms of people’s quality of life, iii) diagnoses of LR bite are mostly incorrect or refer at least to non-verified bites

Prevalence, Pathogenesis and Management of Anemia in Inflammatory Bowel Disease: An IG-IBD Multicenter, Prospective, and Observational Study

Background: Anemia is a common extraintestinal manifestation of inflammatory bowel disease (IBD), with a 6% to 74% prevalence and a negative impact on patient survival and quality of life, although the prevalence is apparently declining due to improved disease treatment. We aimed to investigate the prevalence, pathogenesis, and clinical correlates of anemia in Italian patients with IBD. Methods: A multicenter, prospective, observational study, involving 28 Italian gastroenterology centers, was conducted to investigate the epidemiology and consequences of IBD-associated anemia. Clinical and laboratory data of anemic patients were obtained at study enrolment. Results: Anemia was diagnosed in 737 of 5416 adult IBD outpatients (prevalence 13.6%); females were more commonly affected than males (odds ratio, 1.5; 95% confidence interval [CI], 1.2-1.7) and had more severe anemia. In the majority of cases, anemia was due to iron deficiency (62.5% of cases; 95% CI, 58.3%-66.6%), either isolated or in association with inflammation and/or vitamin deficiencies; anemia of inflammation accounted for only 8.3% of cases. More severe anemia was associated with increasing fatigue and worse quality of life. Only 68.9% of anemic patients with iron deficiency (95% CI, 63.4%-73.8%) and 34.6% of those with vitamin deficiencies (95% CI, 26.2%-44.2%) were properly treated with supplementation therapy. Conclusions: In Italy, the prevalence of IBD-associated anemia is lower than previously reported. Anemia of IBD is most commonly due to iron deficiency and contributes to fatigue and poor quality of life, but remains untreated in a large proportion of patients with iron and/or vitamin deficiencies. This study is registered at clinicaltrials.gov as NCT02872376