Biology subjects

Milanesi, M.

Publications and source records attributed to Milanesi, M..

10 recordsLinked to original sources

bioRxiv2026

Linking geography and mutation profiles across goat species

Recent studies have characterised the mutational profile across multiple mammalian species, highlighting substantial differences across lineages. However, none of these studies investigated whether mutation profiles and geography are significantly correlated. In this study, we present a multi-genome alignment spanning several Capra taxa, reconstruct the ancestral genome of Capra hircus and use it to characterize the mutational profiles across multiple Capra species by using the 1000 genomes VarGoats dataset. Results confirmed that the scale of differences among Capra species largely reflects their phylogenetic relationships, in particular with the Bezoar being genetically closer to domestic goats than to other wild species. Subsequently, we correlated the mutational profile and the geographical origin of the different individuals. In particular, ACG>ATG changes have the strongest correlation with longitude (r = -0.79, P-value = 3.02*10-204), while TCA>TGA are strongly correlated with latitude (r = -0.51, P-value = 4.30*10-63). We highlight how sequential dinucleotide mutations (SDMs) place cosmopolitan breeds closer to the sampling location, rather than the country of origin, showing how the recent relocation of cosmopolitan breeds to new continents is reshaping the genome of these animals. Finally, we used the mutational profile to predict the coordinate of origin of each animal in the dataset. In conclusion, we show the important role that geography had in shaping the genomes of domestic goats.

genomics↗

bioRxiv2025

A tailored variant filtering procedure for multi-breed and multi-species unbalanced animal SNP collections

Technological advancements and decreasing costs of whole-genome sequencing have generated a huge amount of resequencing data. Large-sized datasets, spanning several species and/or populations can now be assembled easily. However, they vary widely in geographical provenance, and sample sizes, with taxonomic groups varying from single to hundreds of entries. Consequently, standard filtering approaches may bias the representation of groups or gene pools. Commonly adopted variant filters relying on minor allele frequency (MAF) and linkage disequilibrium (LD) are not adequate because LD patterns and allele frequencies differ substantially within datasets representing both local and global diversity of multiple populations and species. Thus, by using the VarGoats 1000 goat genome project, we devised a novel approach which avoids the biases of the standard filtering procedures by adopting within-population subsampling, minor allele count (MAC) and marker spacing (bp-space) as filters. Starting from a quality-filtered dataset of >28M SNPs from 1372 animals, we generated a dataset of <14M markers and 750 individuals, complying with the initial requirements and facilitating further computational steps.

bioinformatics↗

bioRxiv2025

The variability of goat microRNA genes is strongly shaped by functional constraints

BackgroundMicroRNAs (miRNAs) are a type of small non-coding RNAs involved in the post-transcriptional repression of target mRNA transcripts, and responsible for the fine-tuning of numerous molecular mechanisms regulating cell metabolism. In goats, multiple miRNAs are involved in coordinating the expression of networks of genes with key roles on the phenotypic variation of milk and meat traits. Although a comprehensive set of goat miRNAs has been annotated, their levels of polymorphism have not been characterized yet. Such information would be relevant in order to explore the effects of miRNA variants on phenotypes of economic interest in goats. ResultsBy using whole-genome sequencing data from 770 domestic goats with African, Asian, and European origins, we have identified polymorphic sites located within miRNA genes as well as in their flanking regions. In doing so, we have found that miRNA polymorphisms are rare (median alternative allele frequency of 0.46%) and that the distribution of polymorphic sites within and around miRNA loci is uneven. Remarkably, the stem, loop and neighbouring regulatory regions of precursor miRNA hairpins show a significantly higher polymorphism density compared to the miRNA seed, which determines the binding affinity to target mRNAs. Moreover, we have detected a differential segregation of miRNA variants across and within continental regions, with an enriched segregation of putatively high impact polymorphisms, i.e. those located in the seed and other biologically relevant regions of miRNA genes, in isolated goat populations with a low census and elevated content of runs of homozygosity. ConclusionGoat miRNA genes display low levels of variation particularly in the seed region, likely due to the action of strong purifying selection removing mutations with potential effects on gene regulatory networks linked to miRNA function. Moreover, miRNA polymorphisms tend to be more abundant in goat breeds with high levels of homozygosity, likely because purifying selection is less efficient in populations of limited size. The information provided in the current work could be useful to identify miRNA polymorphisms contributing to phenotypic variation through the disruption of gene regulatory networks in domestic goats, as well as to assess their potential impact on adaptation and fitness.

genomics↗

bioRxiv2025

K5 polysaccharides inhibit SARS-CoV-2 infection by preventing spike-proteolytic priming

SARS-CoV-2 spike glycoprotein is a promising drug target due to its crucial role in viral infection. Heparin, a long linear polysaccharide that inhibits SARS-CoV-2 infection by acting on spike, has limited antiviral applications due to its anticoagulant effect. E. coli K5 polysaccharides share the same structure as the heparin precursor and can be chemically modified to devoid anticoagulant activity. Here, biochemical assays and computer simulations reveal that K5 with a high degree of sulfation at O-(K5OSH) or N- and O-positions (K5NOSH) bind spike with higher affinity than heparin, preventing its binding to ACE2 and cleavage by furin. This mechanism is supported by a cell syncytia assay showing that K5OSH and K5NOSH inhibit viral infection by blocking membrane fusion. Infection assays for SARS-CoV-2 Wuhan-Hu-1 and Omicron BA.1 variants corroborate their antiviral activity. These results support the therapeutic potential of K5OSH and K5NOSH against SARS-CoV-2, with K5OSH displaying the more promising activity profile.

biochemistry↗

bioRxiv2025

Inferring domestic goat demographic history through ancient genome imputation

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this we used published high coverage (>8x) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5x genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with [≥]0.5x coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes. SignificancePaleogenomics offers crucial insight into how animals were domesticated, but poor DNA preservation in ancient remains often limits the reach of genetic analyses. We utilise a cutting-edge technique, genotype imputation, to recover missing genetic information from ancient low coverage goat genomes and shine light on their domestication process. Early domestic goats showed low overall runs-of-homozygosity (ROH) and relatedness. We find that during the Neolithic, runs-of-homozygosity (ROH) and relatedness among goats increased, likely a consequence of the movement of herds beyond their natural range by humans. Inbreeding levels decline in more recent periods, potentially due to expanded herd sizes, animal trade networks, or improved husbandry practices. These findings challenge long-standing assumptions about domestication bottlenecks and highlight how ancient DNA can be used to uncover complex evolutionary histories, even from low coverage ancient samples.

genomics↗

bioRxiv2024

Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments

A wide range of human disorders, including Alzheimers disease (AD), are characterised by the aberrant formation of amyloid fibrils. Amyloid fibrils are filamentous structures characterized by the presence of a highly-ordered cross-{beta} core. In many cases, this core structure is flanked by disordered regions, often referred to as fuzzy coat. The structural properties of fuzzy coats, and the way in which they interact with their environments, however, have not been described in full detail to date. Here, we generated the conformational ensembles of two brain-derived amyloid filaments of A{beta}42, corresponding respectively to familial and sporadic forms of AD. The approach that we used, called metadynamic electron microscopy metainference (MEMMI), enabled us to provide a characterization of the transient interactions between the fuzzy coat and the cross-{beta} core of the filaments. These calculations indicated that the familial AD filaments are less soluble than the sporadic AD filaments, and that the fuzzy coat contributes to increasing the solubility of both types of filament. In addition, by analyzing the deviations between the density maps from cryo-EM and from the MEMMI structural ensembles, we observed a slowing down in the diffusion of water and sodium ions near the surface of the filaments, offering insight into the hydration dynamics of amyloid fibrils. These results illustrate how the metainference approach can help analyse cryo-EM maps for the characterisation of the properties of amyloid fibrils.

biophysics↗

bioRxiv2021

Phylogenetic analysis and in silico studies link spike Q675H mutation to SARS-CoV-2 adaptive evolution

Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region delimiting the conformational space of the highly flexible loop containing the furin cleavage site. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was found to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation is likely to confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we show an ongoing increase in the occurrence of Q675H spike mutation in the most common SARS-CoV-2 variants of concern (VOC). This finding highlights that, VOC are still evolving and start acquiring the Q675H mutation. At the same time, it suggests that our hypothesis of fitness advantage prompted by Q675H could be concrete.

bioinformatics↗

bioRxiv2018

Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.\n\nAuthor summaryThe tick-borne parasite Theileria parva parva infects cattle populations of eastern, central and southern Africa, by causing a highly fatal pathology called \"East Coast fever\". The disease is especially severe for the exotic breeds imported to Africa, as well as outside the endemic areas of East Africa. In these regions, indigenous cattle populations can survive to infection, and this tolerance might result from unique adaptations evolved to fight the disease. We investigated this hypothesis by using a method named \"landscape genomics\", with which we compared the genetic characteristics of indigenous Ugandan cattle coming from areas at different infection risk, and located genomic sites potentially attributable to tolerance. In particular, the method pinpointed two genes, one (PRKG1) involved into inflammatory response and potentially affecting East Coast fever vector attachment, the other (SLA2) involved into lymphocytes proliferation, a process activated by T. parva parva infection. Our findings can orientate future research on the genetic basis of East Coast fever-tolerance, and derive from a general method that can be applied to investigate adaptation in analogous host-vector-parasite systems. Characterization of the genetic factors underlying East Coast-fever-tolerance represents an essential step towards enhancing sustainability and productivity of local agroecosystems.

evolutionary biology↗

bioRxiv2018

Non-invasive Assessment of Liver Disease in Rats Using Multiparametric Magnetic Resonance Imaging: A Feasibility Study

Background & AimsNon-invasive quantitation of chronic liver disease using multiparametric MRI has the potential to refine clinical care pathways, trial design and preclinical drug development. The aim of the study was to evaluate the use of multiparametric liver MRI in experimental rat models of chronic liver disease. Methods: Liver injury was induced in male wild-type Sprague-Dawley rats using 4 or 12 weeks carbon tetrachloride (CCl4) intoxication and 4 or 8 weeks methionine and choline deficient (MCD) diet. Liver MRI was performed using a 7.0 Tesla small animal scanner at baseline and specified timepoints after liver injury. Multiparametric liver MRI parameters (T1 mapping, T2* mapping and proton density fat fraction (PDFF)) were correlated with gold standard histopathological measures, assessed by a blinded expert adjudicator. One-way analysis of variance with Tukeys post-hoc test was used to assess differences between groups and Spearmans rank-order correlation to examine associations.\n\nResultsMean hepatic T1 increased significantly in rats treated with CCl4 for 12 weeks compared to controls (1122{+/-}78 ms vs. 959{+/-}114 ms; d=162.7, 95% CI (11.92, 313.4), P=0.038) and correlated strongly with histological collagen content (rs=0.717, P=0.037). In MCD diet-treated rats, hepatic PDFF correlated strongly with histological fat content (rs=0.819, P<0.0001), steatosis grade (rs=0.850, P<0.0001) and steatohepatitis score (rs=0.818, P<0.0001). Although there was minimal histological iron, progressive fat accumulation in MCD diet-treated liver significantly shortened T2*.\n\nConclusionsIn preclinical models, quantitative MRI markers correlated with histopathological assessments, especially for fatty liver disease. Validation in longitudinal studies is required.\n\nKey pointsO_LINon-invasive quantitative measures of chronic liver injury are needed for stratification and monitoring of disease in clinical practice and in drug development\nC_LIO_LIWe adapted and applied a clinically-relevant non-contrast multiparametric MRI protocol in well-established preclinical liver disease models, for simultaneous quantitation of hepatic fat, fibro-inflammatory injury and iron\nC_LIO_LIMultiparametric liver MRI was feasible at 7.0 Tesla in experimental rat models and imaging parameters correlated with gold standard histopathological assessments, especially characteristics of fatty liver disease\nC_LIO_LIFurther development of multiparametric liver MRI could refine drug development strategies and impact upon trial design and clinical care pathways\nC_LI

pathology↗

bioRxiv2017

BITE: an R package for biodiversity analyses

Nowadays, molecular data analyses for biodiversity studies often require advanced bioinformatics skills, preventing many life scientists from analyzing their own data autonomously. BITE R package provides complete and user-friendly functions to handle SNP data and third-party software results (i.e. Admixture, TreeMix), facilitating their visualization, interpretation and use. Furthermore, BITE implements additional useful procedures, such as representative sampling and bootstrap for TreeMix, filling the gap in existing biodiversity data analysis tools.\n\nAvailabilityhttps://github.com/marcomilanesi/BITE

bioinformatics↗