FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms.

MOTIVATION: Defining the full domain of protein functions belonging to an organism is a complex challenge that is due to the huge heterogeneity of the taxonomy, where single or small groups of species can bear unique functional characteristics. FunTaxIS-lite provides a solution to this challenge by determining taxon-based constraints on Gene Ontology (GO) terms, which specify the functions that an organism can or cannot perform. The tool employs a set of rules to generate and spread the constraints across both the taxon hierarchy and the GO graph. RESULTS: The taxon-based constraints produced by FunTaxIS-lite extend those provided by the Gene Ontology Consortium by an average of 300%. The implementation of these rules significantly reduces errors in function predictions made by automatic algorithms and can assist in correcting inconsistent protein annotations in databases. AVAILABILITY AND IMPLEMENTATION: FunTaxIS-lite is available on https://www.medcomp.medicina.unipd.it/funtaxis-lite and from https://github.com/MedCompUnipd/FunTaxIS-lite.

Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature.

PURPOSE: Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS: Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature. RESULTS: We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism. CONCLUSION: Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood.

Clinical heterogeneity of Kabuki syndrome in a cohort of Italian patients and review of the literature.

Kabuki syndrome (KS) is a well-recognized disorder characterized by postnatal growth deficiency, dysmorphic facial features, skeletal anomalies, and intellectual disability. The syndrome is caused by KMT2D gene mutations or less frequently KDM6A gene mutations or deletions. We report a systematic evaluation of KS patients from Campania region of Italy; data were also compared with literature ones. We collected data of 15 subjects (8 males and 7 females with age range 10-26 years; mean age 16.9 years) with confirmed diagnosis of KS, representing the entire cohort of patients from Campania Region. Each patient performed biochemical testing and instrumental investigation. Neuro-intellectual development, cranio-facial dysmorphisms, and multisystem involvement data were collected retrospectively. For each category, type of defects and frequency of the anomalies were analyzed. Our observation shows that KS patients from Campania region have some particular and previously underscored, neurological and immunological findings. We found high prevalence of EEG's abnormalities (43%) and MRI brain abnormalities (60%). Microcephaly resulted more common in our series (33%), if compared with major cohorts described in literature. Biochemical features of immunodeficiency and autoimmune diseases including thyroid autoimmunity, polyserositis, and vitiligo were observed with high prevalence (54.5%). Low immunoglobulins levels were a frequent finding. Lymphocyte class investigation showed significantly reduced CD8 levels in one patient.Conclusions: These data confirm great heterogeneity of clinical manifestations in KS and suggest to introduce further clinical diagnostic criteria in order to perform a correct and precocious diagnosis. What is Known • Kabuki syndrome is characterized by growth deficiency, dysmorphic facial features, skeletal anomalies, and intellectual disability • Immune dysfunction is a common finding but autoimmune diseases are rarely seen • Neurological features are common What is New • Some particular facial features could help gestalt diagnosis (hypertelorism, broad nasal bridge, micrognathia, tooth agenesis, cutaneous haemangiomas and strabismus) • Higher prevalence of autoimmune disorders than previously reported • Particular neurological features are present in this cohort (EEG and MRI brain abnormalities).

Clinical and molecular characterizations of 11 new patients with type 1 Feingold syndrome: Proposal for selecting diagnostic criteria and further genetic testing in patients with severe phenotype.

Feingold Syndrome type 1 (FS1) is an autosomal dominant disorder due to a loss of function mutations in the MYCN gene. FS1 is generally clinically characterized by mild learning disability, microcephaly, short palpebral fissures, short stature, brachymesophalangy, hypoplastic thumbs, as well as syndactyly of toes, variably associated with organ abnormalities, the most common being gastrointestinal atresia. In current literature, more than 120 FS1 patients have been described, but diagnostic criteria are not well agreed upon, likewise the genotype-phenotype correlations are not well understood. Here, we describe 11 FS1 patients, belonging to six distinct families, where we have identified three novel MYCN mutations along with three pathogenetic variants, the latter which have already been reported. Several patients presented a mild phenotype of the condition and they have been diagnosed as being affected only after segregation analyses of the MYCN mutation identified in the propositus. We also describe here the first ever FS1 patient with severe intellectual disability having a maternally inherited MYCN variant together with an additional GNAO1 mutation inherited paternally. Mutations in the GNAO1 gene are associated with a specific form of intellectual disability and epilepsy, thus the finding of two different rare diseases in the same patient could explain his severe phenotype. Therein, a thorough investigation is merited into the possibility that additional variants in patients with a MYCN mutation and severe phenotype do exist. Finally, in order to guarantee a more reliable diagnosis of FS1, we suggest using both major and minor clinical-molecular diagnostic criteria.

Carbohydrate determination in honey samples by ion chromatography-mass spectrometry (HPAEC-MS).

Honey is a complex mixture of carbohydrates, in which the monosaccharides glucose and fructose are the most abundant compounds. Currently, more than 20 oligosaccharides have been identified in different varieties of honey normally at quite low concentration. A method was developed and validated using high-performance anion-exchange chromatography coupled to a mass spectrometry detector to investigate the composition of carbohydrates in honey samples. The method was tested for linearity range, trueness, instrumental and method detection and quantification limits, repeatability, and reproducibility. It was applied to determine seven monosaccharides, eight disaccharides, four trisaccharides, and one tetrasaccharide in various honey samples. The present work describes the composition of sugars in unifloral, multifloral, and some honeydew honey, which were produced and collected by beekeepers in the Trentino Alto-Adige region. Statistical techniques have been used to establish a relationship based on levels of carbohydrates among different Italian honey. The results emphasize that mono- and oligosaccharide profiles can be useful to discriminate different honeys according to their floral characteristics and inter-annual variability.

Delineation of MidXq28-duplication syndrome distal to MECP2 and proximal to RAB39B genes.

Two distinct genomic disorders have been linked to Xq28-gains, namely Xq28-duplications including MECP2 and Int22h1/Int22h2-mediated duplications involving RAB39B. Here, we describe six unrelated patients, five males and one female, with Xq28-gains distal to MECP2 and proximal to the Int22h1/Int22h2 low copy repeats. Comparison with patients carrying overlapping duplications in the literature defined the MidXq28-duplication syndrome featuring intellectual disability, language impairment, structural brain malformations, microcephaly, seizures and minor craniofacial features. The duplications overlapped for 108 kb including FLNA, RPL10 and GDI1 genes, highly expressed in brain and candidates for the neurologic phenotype.

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.

SUMMARY: Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. AVAILABILITY AND IMPLEMENTATION: Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. CONTACT: Contact:paolo.fontana@fmach.it

Alterations in metabolic patterns have a key role in diagnosis and progression of primrose syndrome.

Primrose syndrome is characterized by unusual facial features, macrocephaly, intellectual disability, enlarged, and calcified external ears, sparse body hair, and distal muscle wasting. Nine patients have been described in the literature. The disorder is due to missense mutations in ZBTB20. Here we describe one newly diagnosed 18-month-old patient and provide 10 year follow-up of an earlier reported patient, highlighting the progression and complexity of the disorder. Metabolic studies showed reduced glucose tolerance with prevalence of amino acids and fatty acids catabolism, ketogenesis, and gluconeogenesis, resulting in a Krebs cycle reversion.

First evidence of Smith-Magenis syndrome in mother and daughter due to a novel RAI mutation.

Smith-Magenis syndrome (SMS) is a complex genetic disorder caused by interstitial 17p11.2 deletions encompassing multiple genes, including the retinoic acid induced 1 gene-RAI1-or mutations in RAI1 itself. The clinical spectrum includes developmental delay, cognitive impairment, and behavioral abnormalities, with distinctive physical features that become more evident with age. No patients have been reported to have had offspring. We here describe a girl with developmental delay, mainly compromising the speech area, and her mother with mild intellectual disabilities and minor dysmorphic features. Both had sleep disturbance and attention deficit disorder, but no other atypical behaviors have been reported. In both, CGH-array analysis detected a 15q13.3 interstitial duplication, encompassing CHRNA7. However, the same duplication has been observed in several, apparently healthy, maternal relatives. We, thus, performed a whole exome sequencing analysis, which detected a frameshift mutation in RAI1, de novo in the mother, and transmitted to her daughter. No other family members carried this mutation. This is the first report of an SMS patient having offspring. Our experience confirms the importance of searching for alternative causative genetic mechanisms in case of confounding/inconclusive findings such as a CGH-array result of uncertain significance. © 2016 Wiley Periodicals, Inc.

Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.unipd.it/Argot2-5/.

A novel 5q11.2 microdeletion in a child with mild developmental delay and dysmorphic features.

5q11.2 Deletion is a very rare genomic disorder, and its clinical phenotype has not yet been characterized. This report describes a patient with an 8.6 Mb deletion, showing hypotonia, mild developmental delay, short stature, and distinctive dysmorphic features (frontal bossing, square face, deep-set eyes, prominent columella, long philtrum, thin lips). © 2016 Wiley Periodicals, Inc.

keeSeek: searching distant non-existing words in genomes for PCR-based applications.

UNLABELLED: The search for short words that are absent in the genome of one or more organisms (neverwords, also known as nullomers) is attracting growing interest because of the impact they may have in recent molecular biology applications. keeSeek is able to find absent sequences with primer-like features, which can be used as unique labels for exogenously inserted DNA fragments to recover their exact position into the genome using PCR techniques. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers. KeeSeek has been implemented in C++ and CUDA (Compute Unified Device Architecture) to work in a General-Purpose Computing on Graphics Processing Units (GPGPU) environment. AVAILABILITY AND IMPLEMENTATION: Freely available under the Q Public License at http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek.

Reducing bias in RNA sequencing data: a novel approach to compute counts.

BACKGROUND: In the last decade, Next-Generation Sequencing technologies have been extensively applied to quantitative transcriptomics, making RNA sequencing a valuable alternative to microarrays for measuring and comparing gene transcription levels. Although several methods have been proposed to provide an unbiased estimate of transcript abundances through data normalization, all of them are based on an initial count of the total number of reads mapping on each transcript. This procedure, in principle robust to random noise, is actually error-prone if reads are not uniformly distributed along sequences, as happens indeed due to sequencing errors and ambiguity in read mapping. Here we propose a new approach, called maxcounts, to quantify the expression assigned to an exon as the maximum of its per-base counts, and we assess its performance in comparison with the standard approach described above, which considers the total number of reads aligned to an exon. The two measures are compared using multiple data sets and considering several evaluation criteria: independence from gene-specific covariates, such as exon length and GC-content, accuracy and precision in the quantification of true concentrations and robustness of measurements to variations of alignments quality. RESULTS: Both measures show high accuracy and low dependency on GC-content. However, maxcounts expression quantification is less biased towards long exons with respect to the standard approach. Moreover, it shows lower technical variability at low expressions and is more robust to variations in the quality of alignments. CONCLUSIONS: In summary, we confirm that counts computed with the standard approach depend on the length of the feature they are summarized on, and are sensitive to the non-uniform distribution of reads along transcripts. On the opposite, maxcounts are robust to biases due to the non-uniformity distribution of reads and are characterized by a lower technical variability. Hence, we propose maxcounts as an alternative approach for quantitative RNA-sequencing applications.

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data.

Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. The development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins. Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism, one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires a clear picture of the potentialities of existing tools and development of new tools to characterize, reconstruct and model biochemical and regulatory pathways as the result of integration of function in complex symbiotic interactions of ontologically and evolutionary distinct cell types.

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.

Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we assess assemblers' performance, quantifying and characterizing assembly gaps and errors, and evaluating their ability to solve complex genomic regions containing repeats. The final goal of this analysis is to highlight pros and cons of each method, in order to provide the final user with general criteria for the right choice of the appropriate assembly strategy, depending on the specific needs. A further aspect we have explored is the relationship between coverage of a sequencing project and quality of the obtained results. The final outcome suggests that, for a good tradeoff between costs and results, the planned genome coverage of an experiment should not exceed 20-30 ×.

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.

SUMMARY: Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher's test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway expression, leading to the identification of differentially regulated pathways in a dataset of choice. AVAILABILITY AND IMPLEMENTATION: Pathway Processor 2.0 is available as a web service at http://compbiotoolbox.fmach.it/pathwayProcessor/. Sample datasets to test the functionality can be used directly from the application. CONTACT: duccio.cavalieri@fmach.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bronchial isomerism in a Kabuki syndrome patient with a novel mutation in MLL2 gene.

BACKGROUND: Kabuki syndrome (KS) is a rare, multiple congenital anomalies/intellectual disability syndrome caused by mutations of MLL2 gene, which codifies for a histone methyltrasferase that regulates the embryogenesis and the tissue development. Left-bronchial isomerism is a rare congenital abnormality that can be defined as the absence of the normal lateralizing features which distinguish right and left-sides in the lungs. To date, this is the first report of left-bronchial isomerism in association with KS. CASE PRESENTATION: A one-month-old Caucasian male patient underwent our attention for microcephaly, dysmorphic features (long palpebral fissures, eyebrows with sparse lateral third, everted lower eyelids, blue sclerae, large dysplastic ears, lower lip pits), persistent fetal fingertip pads, short stature, heart defects (interventricular defect and aortic coarctation), unilateral cryptorchidism, hypotonia and delay in gross motor skills. These features suggested a diagnosis of KS and a molecular analysis confirmed a novel frame-shift mutation in the exon 11 of MLL2 gene. Subsequently, given recurrent respiratory infections with a normal immunological status, he underwent a chest CT scan that showed a left bronchial isomerism. CONCLUSION: We report a patient affected by KS, with a novel MLL2 mutation and an atypical phenotype characterized by left-side bronchial isomerism. Interestingly, genes involved in the heterotaxia/isomerism such as ROCK2 and SHROOM3 are known to interact with MLL2 gene. In order to achieve a correct diagnosis and an appropriate therapy, the presence of pulmonary anatomical variations should be investigated in KS patients with respiratory signs not associated to immunological deficiency. Finally, our findings support the hypothesis that the mutations leading to a complete loss of function of MLL2 gene is often associated with complex visceral malformations.

Studies in Mexican Grasshoppers: Liladownsia fraile, a new genus and species of Dactylotini (Acrididae: Melanoplinae) and an updated molecular phylogeny of Melanoplinae.

Liladownsia fraile gen. nov. sp. nov. Fontana, Mariño-Pérez, Woller & Song (Lila Downs' friar grasshopper) of the tribe Dactylotini (Orthoptera: Acrididae: Melanoplinae) is described from the pine-oak forest of the Sierra Madre del Sur Mountain Range in Oaxaca, Mexico. Taxonomic placement of this new genus is justified based on morphological characters as well as a molecular phylogeny. Information about the probable host plant, phenology, and known localities is also presented. We also present an updated molecular phylogeny of Melanoplinae, which includes representatives of five of the seven recognized tribes. The monophyly of the subfamily and the included tribes is tested and we find Dactylotini to be paraphyletic because of the placement of Hesperotettix Scudder, 1876. We also recover strong close relationships between the new genus and Perixerus Gerstaecker, 1873 and Dactylotum Charpentier, 1845.  

A new species of the genus Embia Latreille, 1825 (Insecta, Embioptera) from the Madonie Regional Natural Park (Sicily, Italy).

Embia minapalumboi n. sp., a new species of the genus Embia Latreille, 1925, was collected during an excursion in the Madonie Regional Natural Park that took place at the conclusion of the XXVII Italian National Congress of Entomology celebrated in Palermo from 12 to 16 June 2023. In the location of discovery, at an elevation of just under 1400 m and therefore unusual for European Embioptera, the new species was found to be very rare and for this reason most of the few juvenile specimens found were kept in breeding by the author. The new species was compared with all 36 species known to date for the genus and in particular with the 21 species from the Mediterranean area and the 8 known from Europe. The author also presents the general distribution of all species of the genus. Embia tyrrhenica, Stefani, 1953 is also reported for the Madonie and reconfirmed for Sicily.

Impact of landscape composition on honey bee pollen contamination by pesticides: A multi-residue analysis.

The honey bee is the most common and important managed pollinator of crops. In recent years, honey bee colonies faced high mortality for multiple causes, including land-use change and the use of plant protection products (hereafter pesticides). This work aimed to explore how contamination by pesticides of pollen collected by honey bees was modulated by landscape composition and seasonality. We placed two honey bee colonies in 13 locations in Northern Italy in contrasting landscapes, from which we collected pollen samples monthly during the whole flowering season in 2019 and 2020. We searched for almost 400 compounds, including fungicides, herbicides, insecticides, and acaricides. We then calculated for each pollen sample the Pollen Hazard Quotient (PHQ), an index that provides a measure of multi-residue toxicity of contaminated pollen. Almost all pollen samples were contaminated by at least one compound. We detected 97 compounds, mainly fungicides, but insecticides and acaricides showed the highest toxicity. Fifteen % of the pollen samples had medium-high or high levels of PHQ, which could pose serious threats to honey bees. Fungicides showed a nearly constant PHQ throughout the season, while herbicides and insecticides and acaricides showed higher PHQ values in spring and early summer. Also, PHQ increased with increasing cover of agricultural and urban areas from April to July, while it was low and independent of landscape composition at the end of the season. The cover of perennial crops, i.e., fruit trees and vineyards, but not of annual crops, increased PHQ of pollen samples. Our work highlighted that the potential toxicity of pollen collected by honey bees was modulated by complex interactions among pesticide category, seasonality, and landscape composition. Due to the large number of compounds detected, our study should be complemented with additional experimental research on the potential interactive effects of multiple compounds on honey bee health.