A versatile clearing agent for multi-modal brain imaging

Extensive mapping of neuronal connections in the central nervous system requires high-throughput um-scale imaging of large volumes. In recent years, different approaches have been developed to overcome the limitations due to tissue light scattering. These methods are generally developed to improve the performance of a specific imaging modality, thus limiting comprehensive neuroanatomical exploration by multimodal optical techniques. Here, we introduce a versatile brain clearing agent (2,2'-thiodiethanol; TDE) suitable for various applications and imaging techniques. TDE is cost-efficient, water-soluble and low-viscous and, more importantly, it preserves fluorescence, is compatible with immunostaining and does not cause deformations at sub-cellular level. We demonstrate the effectiveness of this method in different applications: in fixed samples by imaging a whole mouse hippocampus with serial two-photon tomography; in combination with CLARITY by reconstructing an entire mouse brain with light sheet microscopy and in translational research by imaging immunostained human dysplastic brain tissue.Comment: in Scientific Reports 201

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.Peer reviewe

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

The Role of miRNA Expression Profile in Sudden Cardiac Death Cases

Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a SCD case and the available methods used for diagnosis cannot always give an exhaustive answer. In addition, the molecular analysis of genes does not lead to a clear conclusion, but it could be interesting to focus attention on the expression level of miRNAs, a class of non-coding RNA of about 22 nucleotides. The role of miRNAs is to regulate the gene expression through complementary binding to 3′-untraslated regions of miRNAs, leading to the inhibition of translation or to mRNA degradation. In recent years, several studies were performed with the aim of exploring the use of these molecules as biomarkers for SCD cases, and to also distinguish the causes that lead to cardiac death. In this review, we summarize experiments, evidence, and results of different studies on the implication of miRNAs in SCD cases. We discuss the different biological starting materials with their respective advantages and disadvantages, studying miRNA expression on tissue (fresh-frozen tissue and FFPE tissue), circulating cell-free miRNAs in blood of patients affected by cardiac disease at high risk of SCD, and exosomal miRNAs analyzed from serum of people who died from SCD

The population genetic structure of Y chromosomes in 1338 Italians

A collaborative study was carried out by the Italian ISFG Working Group in order to improve the data on Y-STR mutations at the loci mostly used in forensic analysis, following recommendations of the ISFG DNA Commission. The knowledge on Y-STR mutation rates needs to be considered in the paternity probabilities, especially in deficiency cases of disputed paternity involving male offspring where the alleged father is not available for DNA analysis. Furthermore, the mutation rate represents a precious tool to estimate the local and temporal origin of a given Y-SNP based haplogroup. The sample consisted of 433 father/son pairs from paternity cases in 15 different laboratories from Italy. The biological relationship of all father/son pairs was previously confirmed by using autosomal microsatellites. The laboratories used AmpFlSTR YFiler kit (AB) and PowerPlex Y System (Promega); DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, GATA C4, and GATA H4.1 data were collected. The participants were also asked to provide the age of the biological father and, if possible, male descendants beyond the first generation. 20 mutations were observed among all of the allele transfers in the sample (19 single step and 1 double step), and mutations in the same father/son pair were found in three cases. Locus-specific mutation rates were calculated. Forensic implication of the average age of the father as well as the number of locus deletions and amplifications were discussed

The effect of fire on the dormancy break of annual legume seeds

Fire is a common phenomenon in the Mediterranean environment and strongly influences vegetal population dynamics through its impact on vegetation and the soil seed bank. Fire is able to break down the seed coat of hard-seeded legumes within the soil and trigger germination. To evaluate the effect of fire on the dormancy break in Medicago ciliaris , Medicago rugosa and S corpiurus muricatus subsp. subvillosus , the seeds were placed at three different depths (surface, 25 mm and 50 mm) and subjected to fires at two different intensities (high and low). As a control sample, a batch of seeds was buried at 25 mm for the duration of the trial and not subjected to fire. Soil temperatures during the fire were compared directly to stubble quantity and indirectly related to soil depth. The two Medicago species survived exposure to 90°C for a few minutes and displayed a significant increase in germination with exposure to high temperatures (over 70°C) for several minutes. On the other hand, no germination occurred in Scorpiurus, irrespective of treatment. In conclusion, fire had a significant and positive effect in triggering germination of the Medicago species, but the dispersal strategies of these hard-seeded legumes are only partially interrupted by fire as a large number of seeds (>50%) remained non-germinated in the soil