Biology subjects

Pozzi, A.

Publications and source records attributed to Pozzi, A..

15 recordsLinked to original sources

bioRxiv2025

α-Parvin regulation of cell re-arrangement is critical for ureteric bud branching morphogenesis

All branched tubular structures, including the kidney collecting system, are formed by branching morphogenesis, a process that includes tip branching and trunk narrowing. Tight control of cell movement and rearrangements is a prerequisite for branching morphogenesis. The role of integrin-associated adhesion proteins in coordinating actin dynamics and cell rearrangements during branching morphogenesis is poorly understood. Here we used 3D live imaging of mouse ureteric bud branching to show that -parvin, a component of the integrin binding ILK-PINCH-Parvin (IPP) complex, regulates tip branching and tubule thinning by inhibiting excessive cell adhesion and actin polymerization. Mechanistically, -parvin promotes actin turnover by inhibiting activation of the small GTPases RhoA and Cdc42, which in turn enhances the severing function of the actin regulatory protein, cofilin. These results underscore the importance of adhesion protein-regulated actin dynamics in the critical process of cell rearrangement, which is required for branching morphogenesis. TeaserScaffold protein -parvin limits cell adhesion and actin polymerization, enabling cell rearrangements that drive kidney branching

developmental biology↗

bioRxiv2025

Alpha Parvin Promotes Glucose Uptake and Metabolism in Skeletal Muscle with Minimal Influence on Hepatic Insulin Sensitivity

Skeletal muscle and liver insulin resistance are early features in the sequelae of type 2 diabetes. Integrins are extracellular matrix receptors expressed on skeletal muscle cells and hepatocytes and have been implicated in modulating obesity-associated insulin resistance. Integrins regulate cell function through intracellular proteins including the ILK-PINCH-Parvin (IPP) complex. ILK promotes skeletal muscle and liver insulin resistance in diet-induced obesity in mice but the role of Parvin is unexplored. Here we demonstrate that hepatocyte specific deletion of -Parvin had only minimal influence on endogenous glucose production or whole-body insulin sensitivity. In contrast, deletion of -Parvin in skeletal muscle caused a striking reduction in muscle glucose uptake during an insulin clamp in lean mice which was not exacerbated by diet-induced obesity. Insulin-mediated GLUT4 membrane recruitment was impaired in mutant muscles which displayed significant morphological abnormalities due to actin cytoskeleton dysfunction. Consistent with severe muscular dysfunction, mitochondrial oxidative capacity and aerobic exercise capacity were blunted in muscle -Parvin-null mice. Thus, -Parvin has a minor role in liver insulin action but is required for insulin-stimulated glucose uptake in skeletal muscle due to its role in actin cytoskeleton regulation. These data suggest that individual IPP complex proteins link cell structure to metabolism via distinct mechanisms in a tissue-specific fashion.

physiology↗

bioRxiv2025

Diploid genomes of the booklouse reveal evolutionary consequences ofasexuality

The "Meselson Effect"--a cornerstone of evolutionary theory predicting that asexual organisms accumulate mutations independently across haplotypes due to the absence of recombination--has long eluded robust empirical validation. Here, we address this gap using three high-quality diploid genome assemblies of the obligately parthenogenetic booklouse Liposcelis bostrychophila, a species characterized by apomictic meiosis and striking intraspecific variation. Combining Illumina, PacBio, and Hi-C sequencing, we generated three diploid genomes of three populations (Lb_1, Lb_2, Lb_3), revealing exceptionally high heterozygosity rates (1.67-3.92%) and minimal recombination--hallmarks of prolonged asexuality. Critically, in population Lb_2, intra-individual SNP divergence surpassed inter-population levels, directly demonstrating the Meselson Effect. Phylogenetic analyses of 7,029 genes revealed that while haplotypes within populations clustered as expected under sexual reproduction, nearly 15% of gene trees exhibited topologies consistent with asexual divergence--a signature of incipient Meselson-driven evolution. Comparative genomic analyses further uncovered a twofold expansion of repetitive elements in asexual lineages relative to their sexual relatives (L. brunnea) and widespread relaxation of purifying selection, particularly affecting transcription factor activities. We propose that relaxed selection on transcriptional regulators may act as a compensatory mechanism, buffering the functional consequences of escalating heterozygosity in non-recombining genomes. By integrating population genomics, phylogenomics, and selection analyses, this work not only provides the clearest evidence to date of the Meselson Effect but also establishes L. bostrychophila as a pivotal model for unraveling the genomic paradox of parthenogenesis. Significance StatementThe Meselson Effect, a theoretical prediction that asexual organisms should accumulate mutations independently in their two haplotypes, has been difficult to confirm empirically due to limited genomic data and contradictory findings in prior studies. Here, we provide strong evidence for the Meselson Effect in the parthenogenetic booklouse Liposcelis bostrychophila, using high-quality diploid genomes from three populations. We show that one population exhibits higher genetic divergence within individuals than between populations, a key signature of the Meselson Effect. Additionally, we found a possible novel compensatory mechanism for maintaining genomic stability in the face of increased heterozygosity. These findings advance our understanding of the genomic impacts under asexuality and establish L. bostrychophila as a model for studying the evolutionary consequences of parthenogenesis.

evolutionary biology↗

bioRxiv2025

Beyond single-trait GxE: higher-order environmental interactions and clonal diversity govern trait relationships in yeast

Predicting organismal responses to complex ecological change requires understanding how multiple environmental stressors (E) and genetic background (G) interact on phenotypic variation (P). Here, we investigate how temperature (ET) and salinity (ES) shape growth (PG) and flocculation (PF) in multiple strains of the fission yeast, Schizosaccharomyces pombe. We find that environmental interactions are critical, with the effect of temperature on flocculation being inverted by changes in salinity (P[~]ExE). Multi-stress reaction norms are genotype-dependent (P[~]GxExE), revealing that evolution can adopt diverse strategies to deal with ExE interactions. We further show that the covariation between traits (PxP) is itself a plastic and evolvable feature. The relationship between growth and flocculation changed from negative to positive or completely uncoupled, depending on the specific GxExE context. This context-dependent covariation suggests that clonal variability and stochastic processes modulate phenotypic outcomes beyond deterministic genotypic effects. Our findings demonstrate that higher-order interactions govern not only individual traits but also their interrelationships, highlighting the necessity of integrating GxExE effects and phenotypic covariation into models of adaptation.

evolutionary biology↗

bioRxiv2025

Database for extended ligand-target analyses (DELTA): a new balanced resource for AI applications in drug discovery

We here present the DELTA resource, a database including balanced and annotated datasets of ligands for about 500 therapeutically relevant targets specifically collected for developing AI-based predictive models. For each target, DELTA comprises an optimized protein structure plus 200 experimentally tested ligands equally distributed between active and inactive molecules. All ligands are prepared by considering unspecified isomeric elements and combining semi-empirical calculations with MD simulations to explore their conformational space. The so-collected molecules allowed extended analyses of both ligands and targets, and the study presents some preliminary results. The performed analyses revealed that on average active ligands are larger than inactive molecules, while possessing a similar polarity. The scaffold analysis emphasized the expected and crucial role of aromatic systems, even though with some relevant differences between active and inactive molecules. Moreover, similar targets often show conserved binding sites and there is a limited but not negligible relationship between the similarity of binding sites and ligands suggesting that similar pockets tend to bind rather similar ligands. Finally, the collected biological data also allowed the analysis of the polypharmacological profile of the ligands endowed with more than one biological value. Most ligands bind two or three targets with diverse activities and almost always the bound targets belong to the same biological class. All the collected data are available for download at delta.unimi.it.

bioinformatics↗

bioRxiv2025

Agonistic behavior and fear response during consecutive encounters in female fish

While consecutive agonistic encounters modulating aggressive behavior are well studied in males, the extent to which social behavior can be altered by fear sensing during consecutive agonistic encounters remains unexplored. A well-established paradigm to assess fear sensing is the exposure to alarm substances (AS) from conspecifics in Ostariophysi fish, such as zebrafish, which causes several physiological and behavioral changes associated to distress. Considering that the exposure to AS induces changes in individual behavior associated to fear response, the aim of the present work is to examine whether repeated exposure to AS alters both agonistic behavior and fear response in female zebrafish. Moreover, since female aggression is understudied when compared to males, this study also assesses possible differences according to the reproductive stage. We performed intrasexual dyadic encounters between female zebrafish to determine if agonistic behavior is altered during two consecutive contests and by the presence of AS. When comparing agonistic behavior in different reproductive stages, results suggest there are no differences in latency and in freezing. Regarding time of aggression, while there are no differences between contests in prespawning or postspawning, significant differences are detected between postspawning dyads and mixed dyads with both females in different reproductive stages. Results suggest that exposure to AS reduces female motivation to engage in an agonistic encounter while aggressive behavior is still maintained despite sensing AS as potential threat, regardless of corresponding to the first or second contest. Finally, similar to agonistic behavior, the effect of fear sensing on individual behavioral parameters such as distance, mean velocity and freezing is also observed during a first and also a second exposure to AS. To the best of our knowledge, this is the first evidence assessing how consecutive agonistic encounters with a real opponent can be altered by repeated exposure to AS. Summary statementWe assess whether repeated exposure to distress alters both agonistic behavior and fear response in female zebrafish, by performing consecutive agonistic encounters with a real opponent exposed to alarm substances.

animal behavior and cognition↗

bioRxiv2025

Remembering the opponent: neuronal activation associated with social memory in Zebrafish

Learning and remembering an opponent and the characteristics of a previous encounter may allow individuals to modify their behavior based on that acquired information. In the present study, using a long-term memory paradigm associated with social interactions, we aimed to evaluate the neuronal activation underlying individual recognition and memory of a previous agonistic encounter in male zebrafish. By quantifying a marker of neuronal activation, the immediate early gene c-fos, we compared the activation in different telencephalic nuclei belonging to the social decision-making network. Two dorsal nuclei, the medial (Dm) and the lateral (Dl), and two ventral nuclei, the ventral (Vv) and the dorsal (Vd), were evaluated by quantifying c-fos protein by immunohistochemical techniques. Two agonistic encounters between the same pair of opponents were performed, and the number of c-fos-immunopositive cells was quantified immediately after the second encounter in fish that had been treated with an amnesic agent after the first encounter (MK-801) and untreated individuals (Water), as well as a Control group with no physical interaction. We found that the Vv nucleus showed lower activation in individuals not exposed to physical interaction than those exposed (MK-801 and Water treatment). The Dl nucleus showed a higher activation only in individuals previously treated with MK-801, who would face an unremembered opponent, but not in those treated with water, which recognized the opponent. Our study provides evidence as a first step to understanding the neuronal processes underlying individual recognition and retrieval of an opponent. Summary statementOur study provides new information about the neuronal activation related to individual recognition and social interaction in zebrafish

animal behavior and cognition↗

bioRxiv2024

Pedigree Painter (PePa): a tool for the visualization of genetic inheritance in chromosomal context

BackgroundData visualization is increasingly important in genomics, enabling researchers to uncover inheritance and recombination patterns across generations. While most existing tools focus on ancestry prediction, they lack functionality for analyzing known ancestries in controlled settings, such as determining parental contributions to offspring genomes. To address this gap, I developed pepa, a lightweight, modular tool that visualizes and quantifies genomic inheritance, designed for beginner and advanced users. Resultspepa is a program for processing VCF files, assigning ancestries to SNPs, and clustering them into biologically meaningful regions. It generates human-readable comparison tables and visualizes inheritance patterns with chromosome paintings through R. Tested on fission yeast, pepa revealed non-uniform recombination patterns, with chromosomes largely inherited from one parent and seemingly random recombination. Quantitative analyses showed differences in parental contributions at the nucleotide and gene levels, with some offspring inheriting similar percentages from parents. However, the painted chromosomes revealed that even offspring with similar percentages from one parent rarely inherit the same genomic region, highlighting the importance of this tool in drawing biologically meaningful insights. Conclusionpepa provides an accessible and powerful solution for analyzing genomic inheritance, bridging experimental and computational biology. Its modular design and minimal dependencies allow adaptation to diverse organisms, facilitating intuitive visualization and quantitative insights into recombination dynamics.

bioinformatics↗

bioRxiv2024

Integrin alpha1 beta1 promotes interstitial fibrosis in a mouse model of polycystic kidney disease

Fibrosis is the cause of end-stage kidney failure in patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD). The molecular and cellular mechanisms involved in fibrosis are complex and anti-fibrotic therapies have so far failed to make an impact on patient welfare. Using unbiased proteomics analysis on the Pkd1nl/nl mouse, we found that expression of the integrin 1 subunit is increased in this model of ADPKD. In human ADPKD tissue and two single cell RNA kidney disease datasets, ITGA1 was also upregulated. To investigate the functional role of this integrin subunit in ADPKD, we generated a Pkd1nl/nlItga1-/- mouse. We observed a significant reduction in kidney volume and kidney dysfunction in mice lacking the integrin 1 subunit. Kidneys from Pkd1nl/nlItga1-/- mice had smaller cysts and reduced interstitial expansion and tubular atrophy. Picrosirius red staining identified a restriction in collagen staining in the interstitium and the myofibroblast marker smooth muscle actin was also downregulated. Myofibroblast cell proliferation was reduced in Pkd1nl/nlItga1-/- mice and primary fibroblast cultures demonstrated an abrogated fibrogenic phenotype in integrin 1-depleted fibroblasts. These results highlight a previously unrecognised role for the integrin 1 subunit in kidney fibrosis.

pathology↗

bioRxiv2024

Endothelial β1 Integrins are Necessary for Microvascular Function and Glucose Uptake

Microvascular insulin delivery to myocytes is rate limiting for the onset of insulin-stimulated muscle glucose uptake. The structural integrity of capillaries of the microvasculature is regulated, in part, by a family of transmembrane adhesion receptors known as integrins, which are composed of an and {beta} subunit. The integrin {beta}1 (itg{beta}1) subunit is highly expressed in endothelial cells (EC). EC itg{beta}1 is necessary for the formation of capillary networks during embryonic during development and its knockdown in adult mice blunts the reactive hyperemia that manifests during ischemia reperfusion. In this study we investigated the contribution of skeletal muscle EC itg{beta}1 in microcirculatory function and glucose uptake. We hypothesized that loss of EC itg{beta}1 would impair microvascular hemodynamics and glucose uptake during insulin stimulation, creating delivery-mediated insulin resistance. An itg{beta}1 knockdown mouse model was developed to avoid lethality of embryonic gene knockout and the deteriorating health resulting from early post-natal inducible gene deletion. We found that mice with (itg{beta}1fl/flSCLcre) and without (itg{beta}1fl/fl) inducible stem cell leukemia cre recombinase (SLCcre) expression at 10 days post cre induction have comparable exercise tolerance and pulmonary and cardiac functions. We quantified microcirculatory hemodynamics using intravital microscopy and the ability of mice to respond to the high metabolic demands of insulin-stimulated muscle using a hyperinsulinemic-euglycemia clamp. We show that itg{beta}1fl/flSCLcre mice compared to itg{beta}1fl/fl littermates have, i) deficits in capillary flow rate, flow heterogeneity, and capillary density; ii) impaired insulin-stimulated glucose uptake despite sufficient transcapillary insulin efflux; and iii) reduced insulin-stimulated glucose uptake due to perfusion-limited glucose delivery. Thus, EC itg{beta}1 is necessary for microcirculatory function and to meet the metabolic challenge of insulin stimulation.

physiology↗

bioRxiv2023

Recognizing the opponent: the consolidation of long-term social memory in zebrafish males

Recognizing and remembering another individual in a social context could be beneficial for individual fitness. Especially in agonistic encounters, remembering an opponent and the previous fight could allow avoiding new conflicts. Considering this, we hypothesized that this type of social interaction forms a long-term recognition memory lasting several days. It has been shown that a second encounter 24 hours later between the same pair of zebrafish males is resolved with lower levels of aggression. Here, we evaluated if this behavioral change could last for longer intervals and a putative mechanism associated with memory storage: the recruitment of NMDA receptors. We found that if a pair of zebrafish males fight and 48 or 72 hours later fight again, they resolved the second encounter with lower levels of aggression. However, if immediately after the first encounter opponents were exposed to MK-801 (NMDA receptor antagonist), they resolve the second one with the same levels of aggression, that is, no reduction in aggressive behaviors was observed. These results suggest the formation of a long-term social memory related to recognizing a particular opponent and/or the outcome and features of a previous fight.

animal behavior and cognition↗

bioRxiv2022

The 5-LOX/COX-2 cross-over metabolite, hemiketal E2, enhances VEGFR2 activation and promotes angiogenesis

Consecutive oxygenation of arachidonic acid by 5-lipoxygenase (5-LOX) and cyclooxygenase-2 (COX-2) yields the hemiketal (HK) eicosanoids, HKE2 and HKD2. HKs stimulate angiogenesis by inducing endothelial cell tubulogenesis in culture; however, how this process is regulated has not been determined. Here, we identify vascular endothelial growth factor receptor 2 (VEGFR2) as a mediator of HKE2-induced angiogenesis in vitro and in vivo. HKE2 treatment of human umbilical vein endothelial cells dose-dependently increased phosphorylation of VEGFR2 and the downstream kinases ERK and Akt that mediated endothelial cell tubulogenesis. In vivo, HKE2 induced the growth of blood vessels into polyacetal sponges implanted in mice. HKE2-mediated effects in vitro and in vivo were blocked by the VEGFR2 inhibitor vatalanib, indicating that the pro-angiogenic effect of HKE2 was mediated by VEGFR2. We found that HKE2 covalently bound and inhibited PTP1B, a protein tyrosine phosphatase that dephosphorylates VEGFR2, thereby providing a possible molecular mechanism for how HKE2 induced pro-angiogenic signaling. Our studies indicate that biosynthetic cross-over of the 5-LOX and COX-2 pathways gives rise to a potent lipid autacoid that regulates endothelial cell function in vitro and in vivo. SignificanceAngiogenesis, the growth of new blood vessels from existing vessels, contributes to both physiological and pathological conditions, including tissue repair after injury and tumorigenesis. Novel approaches to control pathologic angiogenesis are urgently needed since current therapy targeting the pro-angiogenic receptor VEGFR2 has significant side effects. We show that a metabolite of arachidonic acid, formed in a biosynthetic cross-over of the enzymes that generate the pro-inflammatory leukotriene and prostaglandin mediators, respectively, promotes VEGFR2 activation to induce angiogenesis. This finding suggests that common drugs targeting the arachidonic acid pathway may be viewed as valid anti-angiogenic candidates.

pharmacology and toxicology↗

bioRxiv2020

Sex estimation in cranial remains: A comparison of machine learning and discriminant analysis in Italian populations

ObjectivesUsing cranial measurements in two Italian populations, we compare machine learning methods to the more traditional method of linear discriminant analysis in estimating sex. We use crania in sex estimation because it is useful especially when remains are fragmented or displaced, and the cranium may be the only remains found. Materials and MethodsUsing the machine learning methods of decision tree learning, support-vector machines, k-nearest neighbor algorithm, and ensemble methods we estimate the sex of two populations: Samples from Bologna and samples from the island of Sardinia. We used two datasets, one containing 17 cranial measurements, and one measuring the foramen magnum. Results and DiscussionOur results indicate that machine learning models produce similar results to linear discriminant analysis, but in some cases machine learning produces more consistent accuracy between the sexes. Our study shows that sex can be accurately predicted (> 80%) in Italian populations using the cranial measurements we gathered, except for the foramen magnum, which shows a level of accuracy of [~]70% accurate which is on par with previous geometric morphometrics studies using crania in sex estimation. We also find that our trained machine learning models produce population-specific results; we see that Italian crania are sexually dimorphic, but the features that are important to this dimorphism differ between the populations.

bioinformatics↗

bioRxiv2020

A new member in the Argonaute crew: the mt-miRNAs

Mutations within the mitochondrial genome have been linked to many diverse phenotypes. Moreover, the effects of these mutations have been shown to differ across sexes and environments. The mechanisms that explain the manifold array of mitochondrial genotypic effects on organismal function, and their context-dependency, have however remained a mystery. Here, we present evidence that mitochondria are involved in nuclear gene regulation via RNA interference; transcribing mitochondrial (mt-)miRNAs that may repress the transcription of nuclear genes that previously had no known involvement in mitochondrial function. Our findings uncover a new mechanism by which mitochondria may shape the expression of animal life-histories and health components; implying that the influence of the mitochondria in regulating organismal function extends well beyond the process of energy production.

molecular biology↗

bioRxiv2019

Family saga: reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty

Gene duplication is associated with the evolution of many novel biological functions at the molecular level. The dominant view, often referred to as "neofunctionalization", states that duplications precede many novel gene functions by creating functionally redundant copies which are less constrained than singletons. However, numerous alternative models have been formulated, including some in which novel functions emerge prior to duplication. Unfortunately, few studies have reconstructed the evolutionary history of a functionally diverse gene family sufficiently well to differentiate between these models. Here we examined the evolution of the g2 family of phospholipase A2 (EC 3.1.1.4) in the genomes of 93 species from all major lineages of Vertebrata. This family is evolutionarily important and has been co-opted for a diverse range of functions, including innate immunity and venom. The genomic region in which this family is located is remarkably syntenic. This allowed us to reconstruct all duplication events over hundreds of millions of years of evolutionary history using manual annotation of gene clusters, which enabled the discovery of a large number of previously un-annotated genes. Intriguingly, we found that the same ancestral gene in the phospholipase gene cluster independently acquired novel molecular functions in birds, mammals and snake, and all subsequent expansion of the cluster originates from this locus. This suggests that the locus has a deep ancestral propensity for multiplication, likely conferred by a structural arrangement of genomic material (i.e. the "genomic context" of the locus) that dates back at least the amniote MRCA. These results highlight the underlying complexity of gene family evolution, as well as the historical- and context-dependence of gene family evolution. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/583344v3_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1c3228forg.highwire.dtl.DTLVardef@12053forg.highwire.dtl.DTLVardef@11683c0org.highwire.dtl.DTLVardef@123eb3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗