Giorgio Valle

University of Padua | UNIPD · Department of Biology

We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the i...

Serine-Threonine kinase CK2 supports malignant B-lymphocyte growth but its role in B-cell development and activation is largely unknown. Here, we describe the first B-cell specific knockout (KO) mouse model of the β regulatory subunit of CK2. CK2βKO mice present an increase in marginal zone (MZ) and a reduction in follicular B cells, suggesting a r...

Inflammatory bowel diseases (IBD) are characterised by episodic inflammation of the gastrointestinal tract. Gut microbial dysbiosis characterises the pathoetiology, but its role remains understudied. We report the first use of constraint-based microbial community modelling on a single individual with IBD, covering seven dates over 16 months, enabli...

Background Data on the role of the microbiome in adult patients with eosinophilic oesophagitis (EoE) are limited. Aims To prospectively collect and characterise the salivary, oesophageal and gastric microbiome in patients with EoE, further correlating the findings with disease activity. Methods Adult patients with symptoms of oesophageal dysfunct...

The genetic landscape of melanoma resistance to targeted therapy with small molecules inhibiting BRAF and MEK kinases is still largely undefined. We here portrayed in detail the somatic alterations of resistant melanoma and explored the associated biological processes and their integration with transcriptional profiles. By targeted NGS and WES anal...

MicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for Arundo donax L., one of the most promising bioenergy crops. Here we identified, for the first time, A. donax conserved a...

Ulcerative colitis (UC) is a complex immune-mediated disease in which the gut microbiota plays a central role, and may determine prognosis and disease progression. We aimed to assess whether a specific microbiota profile, as measured by a machine learning approach, can be associated with disease severity in patients with UC. In this prospective pil...

Contacts between organelles create microdomains that play major roles in regulating key intracellular activities and signaling pathways, but whether they also regulate systemic functions remains unknown. Here, we report the ultrastructural organization and dynamics of the inter-organellar contact established by sheets of curved rough endoplasmic re...

Gut microbiome influences athletes' physiology but, due to the complexity of sport performance and the great inter-variability of microbiome features, it is not reasonable to define a single healthy microbiota profile for athletes. We suggest the use of specific meta-omics analysis coupled with innovative computational systems to uncover the hidden...

Brown-Vialetto-Van Laere (BVVL) and Fazio-Londe are disorders with amyotrophic lateral sclerosis–like features, usually with recessive inheritance. We aimed to identify causative mutations in 10 probands. Neurological examinations, genetic analysis, audiometry, magnetic resonance imaging, biochemical and immunological testings, and/or muscle histop...

Anaerobic digestion is a key biological process for renewable energy, yet the mechanistic knowledge on its hidden microbial dynamics is still limited. The present work charted the interaction network in the anaerobic digestion microbiome via the full characterization of pairwise interactions and the associated metabolite exchanges. To this goal, a...

The reproduction of reliable in vitro models of human skeletal muscle is made harder by the intrinsic 3D structural complexity of this tissue. Here we coupled engineered hydrogel with 3D structural cues and specific mechanical properties to derive human 3D muscle constructs (“myobundles”) at the scale of single fibers, by using primary myoblasts or...

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the specie...

Lysosomal storage disorders (LSD) are monogenic diseases, due to accumulation of specific undegraded substrates into lysosomes. LSD diagnosis could take several years, due to both poor knowledge of these diseases and shared clinical features. The diagnostic approach includes clinical evaluations, biochemical tests and genetic analysis of the suspec...

Dent disease (DD), an X-linked renal tubulopathy, is mainly caused by loss-of-function mutations in CLCN5 (DD1) and OCRL genes. CLCN5 encodes the ClC-5 antiporter that in proximal tubules (PT) participates in the receptor-mediated endocytosis of low molecular weight proteins. Few studies have analyzed the PT expression of ClC-5 and of megalin and c...

In mammalian cells, the catabolic activity of the dNTP triphosphohydrolase SAMHD1 sets the balance and concentration of the four dNTPs. Deficiency of SAMHD1 leads to unequally increased pools and marked dNTP imbalance. Imbalanced dNTP pools increase mutation frequency in cancer cells, but it is not known if the SAMHD1‐induced dNTP imbalance favors...

We considered pediatric patients at one year after transplantation with stable renal function. All patients had histological diagnosis and tissue and serum samples stored at -80°C, collected during protocol biopsy. We divided patients into 2 groups: 10 with normal histology (Banff I) and 10 with acute/chronic rejection (Banff II-III-IV). miRNAs wer...

Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder associated to early onset emphysema, mainly imputable to Pi*ZZ genotype. In spite of the serious potential effects, many AATD individuals do not develop emphysema. To identify genes/variants potentially involved in emphysema development we studied 4 AATD families. Each family had at least...

Background “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at sequence level between species, allowing the definition of ortholog and paralog genes. However, the spreading of sequenced genome,...

Background: The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. The resulting hydrogen can then be funneled to anaerobic digesters for biogas upgrading (biomethanation) purposes (power-to-methan...

Background Bacillus licheniformis GL174 is a culturable endophytic strain isolated from Vitis vinifera cultivar Glera, the grapevine mainly cultivated for the Prosecco wine production. This strain was previously demonstrated to possess some specific plant growth promoting traits but its endophytic attitude and its role in biocontrol was only partia...

Schizophrenia (SCZ) and bipolar disorder (BPD) are highly heritable disorders with an estimated co-heritability of 68%. Hundreds of common alleles have been implicated, but recently a role for rare, high-penetrant variants has been also suggested in both disorders. This study investigated a familial cohort of SCZ and BPD patients from a closed popu...

Background Identification of heart transplant rejection currently rely on immunohistologic and immunohistochemistry. We aimed to identify specific sets of microRNAs (miRNAs) to characterize acute cellular (ACR), antibody-mediated (pAMR) and mixed (MR) rejections in monitoring formalinfixed paraffin-embedded (FFPE) endomyocardial biopsies (EMBs) in...

The aim of this research was the identification of novel pharmacogenomic biomarkers for better understanding the complex gene regulation mechanisms underpinning glucocorticoid (GC) action in paediatric inflammatory bowel disease (IBD). This goal was achieved by evaluating high-throughput microRNA (miRNA) profiles during GC treatment, integrated wit...

Whole exome sequencing detected novel likely pathogenic variants in LRP2 gene in 2 patients presenting with hearing and vision loss, and the Dent disease (DD) classical renal phenotype, that is, low molecular weight proteinuria (LMWP), hypercalciuria and nephrocalcinosis/nephrolithiasis. We propose that a subset of patients presenting as DD may rep...

Background The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can help to cope with these problem...

The success of therapeutic proteins such as insulin has led to the massive recognition of biological medical products as highly effective clinical drugs. As the use of biologics gains popularity, in industrial biotechnology there is a push to maximise their production. The ovary cells of the Chinese hamster (CHO cells) are the most common productio...

Amputated tails of lizards regenerate while limbs form scars which histological structure is very different from the original organs. Lizards provide useful information for regenerative medicine and some hypotheses on the loss of regeneration in terrestrial vertebrates. Analysis of tail and limb transcriptomes shows strong downregulation in the tai...

α-1 antitrypsin deficiency (AATD) is a Mendelian genetic disorder predisposing to the development of severe emphysema. However, many individuals with AATD might not develop lung disease, suggesting that other unidentified genetic modifiers are required for manifestation of the disease. Aim To identify variants discriminating between affected and no...

Lysosomal storage disorders (LSDs) are a group of about 50 genetic metabolic disorders, mainly affecting children, sharing the inability to degrade specific endolysosomal substrates. This results in failure of cellular functions in many organs, including brain that in most patients may go through progressive neurodegeneration. In this study, we ana...

Background Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. ResultsHere we describe QueryOR, a web platform suitable for searching among known candidate genes as wel...

Grapevine (Vitis vinifera L.) is routinely grafted and rootstocks inducing drought tolerance represent a source for adapting vineyards to climate change in temperate areas. Our goal was to investigate drought stress effects on miRNA abundance in a drought-resistant grapevine rootstock, M4 (Vitis vinifera X Vitis berlandieri), compared with a commer...

64Background: At present, the clinical management of resected GC is only based on risk stratification according to the AJCC staging. This project evaluates molecular factors on formalin-fixed, paraffin-embedded (FFEP) specimens of the primary tumor radically resected in an omogeneous group patients considered at poor prognosis according by nodal in...

Whole-genome comparisons of Vitis vinifera subsp. sativa and V. vinifera subsp. sylvestris are expected to provide a better estimate of the valuable genetic diversity still present in grapevine, and help to reconstruct the evolutionary history of a major crop worldwide. To this aim, the increase of molecular marker density across the grapevine geno...

Scripts used for alignment and variant calling. (PDF)

RADseq genetic profiles of the validation panel at the 148 SNPs confirmed with Sanger sequencing. Unfitted genotypes between RAD and Sanger assays are marked in red, with the Sanger genetic profile indicated in brackets. Missing genotypes are represented as “0 0”. (XLSX)

List of the grapevine accessions included in the SNP discovery panel. 'True-to-type' variaties are marked in bold. Samples excluded from the analyses of genetic diversity and LD are marked with an asterisk. (XLSX)

Number of restriction sites recovered with RAD-Seq on PN40024 genomic DNA using three different restiction enzymes. (XLSX)

List of primers used for the SNP validation with Sanger sequencing. The SNPs included in the PCR-products are indicated between squared brackets. (XLSX)

Iron chlorosis is a serious deficiency that affects orchards and vineyards reducing quality and yield production. Chlorotic plants show abnormal photosynthesis and yellowing shoots. In grapevine iron uptake and homeostasis are most likely controlled by a mechanism known as “Strategy I,” characteristic of non-graminaceous plants and based on a syste...

PCA plot of mRNA-Seq unique reads.

List of Differentially Expressed Genes identified in root apices of 101.14 rootstock genotype upon −Fe growing conditions.

List of Differentially Expressed Genes identified in root apices of 101.14 rootstock genotype upon FeBic growing conditions.

List of common (−Fe + FeBic), Fe-specific and FeBic-specific Differentially Expressed Genes identified in root apices of 101.14 rootstock genotype upon −Fe and FeBic growing conditions.