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Proteins exist for more than 3 billion years: proof of a sustainable design. They have mechanisms coping with internal perturbations (e.g., amino acid mutations), which tie genetic backgrounds to diseases or drug therapy failure. One difficulty to grasp these mechanisms is the asymmetry of amino acid mutational impact: a mutation at position i in the sequence, which impact a position j does not imply that the mutation at position j impacts the position i. Thus, to distinguish the influence of the mutation of i on j from the influence of the mutation of j on i, position mutational influences must be represented with directions. Using the X ray structure of the third PDZ domain of PDS-95 (Protein Data Bank 1BE9) and in silico mutations, we build a directed network called GCAT that models position mutational influences. In the GCAT, a position is a node with edges that leave the node (out-edges) for the influences of the mutation of the position on other positions and edges that enter the position (in-edges) for the influences of the mutation of other positions on the position. 1BE9 positions split into four influence categories called G, C, A and T going from positions influencing on average less other positions and influenced on average by less other positions (category C) to positions influencing on average more others positions and influenced on average by more other positions (category T). The four categories depict position neighborhoods in the protein structure with different tolerance to mutations.

Summary: The present protocol describes how to measure experimentally the slow protein dynamics that take place upon the thermal unfolding of the B subunit cholera toxin pentamers using broadband dielectric spectroscopy (BDS) in weakly hydrated and nanoconfined conditions. Transient unfolding intermediates, rarely identified otherwise, are revealed thanks to the B subunit's remarkable heat resistance up to 180°C and distinct molecular dynamics. The frequencies detected experimentally are consistent with the spatiotemporal scales of motions of molecular dynamics simulation.For complete details on the use and execution of this protocol, please refer to Bourgeat et al. (2021, 2019). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Chronic inflammation is a hallmark for a variety of disorders and is at least partially responsible for disease progression and poor patient health. In recent years, the microbiota inhabiting the human gut has been associated with not only intestinal inflammatory diseases but also those that affect the brain, liver, lungs, and joints. Despite a strong correlation between specific microbial signatures and inflammation, whether or not these microbes are disease markers or disease drivers is still a matter of debate. In this review, we discuss what is known about the molecular mechanisms by which the gut microbiota can modulate inflammation, both in the intestine and beyond. We identify the current gaps in our knowledge of biological mechanisms, discuss how these gaps have likely contributed to the uncertain outcome of fecal microbiota transplantation and probiotic clinical trials, and suggest how both mechanistic insight and -omics-based approaches can better inform study design and therapeutic intervention.

Saliva is an irritant of the subcutaneous tissue, thus causing the development of a non-epithelial reactive pseudocapsule. Metaplastic ossification of the pseudocapsule is a condition rarely described in the veterinary literature. The main causes of calcification are trauma, tumours, various chronic inflammatory conditions and fibrodysplasia ossificans progressiva. The aim of the present case series was to describe three dogs affected by a calcified salivary mucocele. The medical records of dogs affected by a cervical sialocele were retrospectively evaluated, and three cases met the inclusion criteria. All the dogs in this study were referred to the Veterinary Teaching Hospital (VTH) of the Department of Veterinary Sciences of the University of Turin (Turin, Italy) for a large solid mass in the intermandibular region. The diagnosis of a mucocele was confirmed clinically by centesis and by radiography or CT. Complete excision of both the pseudocyst and the ipsilateral mandibular/monostomatic sublingual salivary gland was performed in all cases. The histological report showed large areas of bone metaplasia within the pseudocapsule and chronic sialadenitis. Based on this limited case series, complete excision of the pseudocyst and a concurrent sialoadenectomy provided an effective treatment for this rare salivary mucocele disorder.

Background: Endocrine therapy (ET) plus cyclin-dependent-kinases 4/6 inhibitors (CDK4/6i) represents the standard treatment for luminal-metastatic breast cancer (MBC). However, prospective head-to-head comparisons are still lacking for 1st line (L) options, and it is still crucial to define the best strategy between 1st and 2nd L. Materials and methods: 717 consecutive luminal-MBC pts treated between 2008 and 2020 were analyzed at the Oncology Department of Aviano and Udine, Italy. Differences about survival outcomes (OS, PFS and PPS) were tested by log-rank test. The attrition rate (AR) between 1st and 2ndL was calculated. Results: At 1stL, pts were treated with ET (49%), chemotherapy (CT) (31%) and ET-CDKi (20%) while, at 2ndL, 33% received ET, 33% CT and 8% ET-CDKi. Overall AR was 10%, 7% for CT, 8% for ET and 17% for ET-CDKi. By multivariate analysis, 1stL ET-CDK4/6i showed a better mPFS1 and OS. Moreover, 2ndL ET-CDK4/6i demonstrated better mPFS2 compared to ET and CT. Notably, 1stL ET-CDKi resulted in higher mPFS than 2ndL ET-CDKi. Intriguingly, 1stL ET-CDK4/6i was associated with worse mPPS compared to CT and ET. Secondarily, 1stL ET-CDK4/6i followed by CT had worse OS compared to 1stL ET-CDK4/6i followed by ET. Notably, none of baseline characteristics at 2ndL influenced 2ndL treatment choice (ET vs. CT) after ET-CDKi. Conclusion: Our real-world data demonstrated that ET-CDKi represents the best option for 1stL luminal-MBC compared to ET and CT. Also, the present study pointed out that 2ndL ET, potentially combined with other molecules, could be a feasible option after CDK4/6i failure, postponing CT on later lines.

A wide inter-individual variability in the therapeutic response to cyclin-dependent kinases 4 and 6 inhibitors (CDKis) has been reported. We herein present a case series of five patients treated with either palbociclib or ribociclib referred to our clinical pharmacological counselling, including therapeutic drug monitoring (TDM), pharmacogenetics, and drug–drug interaction analysis to support clinicians in the management of CDKis treatment for metastatic breast cancer. Patients’ plasma samples for TDM analysis were collected at steady state and analyzed by an LC-MS/MS method for minimum plasma concentration (Cmin) evaluation. Under and overexposure to the drug were defined based on the mean Cmin values observed in population pharmacokinetic studies. Polymorphisms in selected genes encoding for proteins involved in drug absorption, distribution, metabolism, and elimination were analyzed (CYP3A4, CYP3A5, ABCB1, SLCO1B1, and ABCG2). Three of the five reported cases presented a CDKi plasma level above the population mean value and were referred for toxicity. One of them presented a low function ABCB1 haplotype (ABCB1-rs1128503, rs1045642, and rs2032582), possibly causative of both increased drug oral absorption and plasmatic concentration. Two patients showed underexposure to CDKis, and one of them was referred for early progression. In one patient, a CYP3A5*1/*3 genotype was found to be potentially responsible for more efficient drug metabolism and lower drug plasma concentration. This intensified pharmacological approach in clinical practice has been shown to be potentially effective in supporting prescribing oncologists with dose and drug selection and could be ultimately useful for increasing both the safety and efficacy profiles of CDKi treatment.

Social media is increasingly being used to express opinions and attitudes toward vaccines. The vaccine stance of social media posts can be classified in almost real-time using machine learning. We describe the use of a Transformer-based machine learning model for analyzing vaccine stance of Italian tweets, and demonstrate the need to address changes over time in vaccine-related language, through periodic model retraining. Vaccine-related tweets were collected through a platform developed for the European Joint Action on Vaccination. Two datasets were collected, the first between November 2019 and June 2020, the second from April to September 2021. The tweets were manually categorized by three independent annotators. After cleaning, the total dataset consisted of 1,736 tweets with 3 categories (promotional, neutral, and discouraging). The manually classified tweets were used to train and test various machine learning models. The model that classified the data most similarly to humans was XLM-Roberta-large, a multilingual version of the Transformer-based model RoBERTa. The model hyper-parameters were tuned and then the model ran five times. The fine-tuned model with the best F-score over the validation dataset was selected. Running the selected fine-tuned model on just the first test dataset resulted in an accuracy of 72.8% (F-score 0.713). Using this model on the second test dataset resulted in a 10% drop in accuracy to 62.1% (F-score 0.617), indicating that the model recognized a difference in language between the datasets. On the combined test datasets the accuracy was 70.1% (F-score 0.689). Retraining the model using data from the first and second datasets increased the accuracy over the second test dataset to 71.3% (F-score 0.713), a 9% improvement from when using just the first dataset for training. The accuracy over the first test dataset remained the same at 72.8% (F-score 0.721). The accuracy over the combined test datasets was then 72.4% (F-score 0.720), a 2% improvement. Through fine-tuning a machine-learning model on task-specific data, the accuracy achieved in categorizing tweets was close to that expected by a single human annotator. Regular training of machine-learning models with recent data is advisable to maximize accuracy.

Autism spectrum disorders (ASDs) is a multifactorial neurodevelopmental disorder. The communication between the gastrointestinal (GI) tract and the central nervous system seems driven by gut microbiota (GM). Herein, we provide GM profiling, considering GI functional symptoms, neurological impairment, and dietary habits. Forty-one and 35 fecal samples collected from ASD and neurotypical children (CTRLs), respectively, (age range, 3–15 years) were analyzed by 16S targeted-metagenomics (the V3–V4 region) and inflammation and permeability markers (i.e., sIgA, zonulin lysozyme), and then correlated with subjects’ metadata. Our ASD cohort was characterized as follows: 30/41 (73%) with GI functional symptoms; 24/41 (58%) picky eaters (PEs), with one or more dietary needs, including 10/41 (24%) with food selectivity (FS); 36/41 (88%) presenting high and medium autism severity symptoms (HMASSs). Among the cohort with GI symptoms, 28/30 (93%) showed HMASSs, 17/30 (57%) were picky eaters and only 8/30 (27%) with food selectivity. The remaining 11/41 (27%) ASDs without GI symptoms that were characterized by HMASS for 8/11 (72%) and 7/11 (63%) were picky eaters. GM ecology was investigated for the overall ASD cohort versus CTRLs; ASDs with GI and without GI, respectively, versus CTRLs; ASD with GI versus ASD without GI; ASDs with HMASS versus low ASSs; PEs versus no-PEs; and FS versus absence of FS. In particular, the GM of ASDs, compared to CTRLs, was characterized by the increase of Proteobacteria, Bacteroidetes, Rikenellaceae, Pasteurellaceae, Klebsiella, Bacteroides, Roseburia, Lactobacillus, Prevotella, Sutterella, Staphylococcus, and Haemophilus. Moreover, Sutterella, Roseburia and Fusobacterium were associated to ASD with GI symptoms compared to CTRLs. Interestingly, ASD with GI symptoms showed higher value of zonulin and lower levels of lysozyme, which were also characterized by differentially expressed predicted functional pathways. Multiple machine learning models classified correctly 80% overall ASDs, compared with CTRLs, based on Bacteroides, Lactobacillus, Prevotella, Staphylococcus, Sutterella, and Haemophilus features. In conclusion, in our patient cohort, regardless of the evaluation of many factors potentially modulating the GM profile, the major phenotypic determinant affecting the GM was represented by GI hallmarks and patients’ age.

BackgroundA multidisciplinary team meeting (MDM) approach in breast cancer (BC) management is a standard of care. One of the roles of MDMs is to identify the best diagnostic and therapeutic strategies for patients (pts) with new diagnosis of early BC. The purpose of this study was to define whether there was an agreement between the planned program (i.e., MDMs-based decision) and that actually applied. In addition, the study explored factors associated with discordance.MethodsWe conducted a retrospective study of a consecutive series of 291 patients with new diagnosis of early BC, discussed at MDMs at the University Hospital of Udine (Italy), from January 2017 to June 2018. The association between clinico-biological factors and discordance between what was decided during the MDMs and what was consequently applied by the oncologist was explored through uni- and multivariate logistic regression analyses.ResultsThe median age was 62 years (range 27–88 years). Among invasive early BC patients, the most frequent phenotype was luminal A (38%), followed by luminal B (33%), HER2-positive (12%), and triple-negative (5%). In situ carcinoma (DCIS) represented 12% of cases. The median time from MDM discussion to first oncologic examination was 2 weeks. The rate of discordance between MDM-based decision and final choice, during a face-to-face consultation with the oncologist, was 15.8% (46/291). The most frequent reason for changing the MDM-based program was clinical decision (87%). Follow-up was preferred to the chemotherapy (CT) proposed within the MDMs in 15% of cases, and to the endocrine therapy (ET) in 39% of cases (among these, 44.5% had a diagnosis of DCIS). Therapeutic change from sequential CT-ET to ET alone was chosen in 16/46 pts (35%): among these patients, seven had a luminal B disease and six had an HER2-positive disease. On univariate analysis, factors associated with discordance were values of Ki-67 14%–30% (OR 3.91; 95% CI 1.19–12.9), age >70 years (OR 2.44, 95% CI 1.28–4.63), housewife/retired status (OR 2.35, 95% CI 1.14–4.85), polypharmacy (OR 1.95; 95% CI 1.02–3.72), postmenopausal status (OR 4.15; 95% CI 1.58–10.9), and high Charlson Comorbidity Index (OR 1.31; 95% CI 1.09–1.57). The association with marital status, educational level, alcohol and smoke habits, presence of a caregiver, parity, grading, histotype and phenotype, and stage was not statistically significant. On multivariate analysis, only Ki-67 value maintained its statistical significance.ConclusionThe results of our study could be useful for enhancing the role of MDMs in the clinical decision-making process in early BC.

In the context of the European Joint Action on Vaccination, we analyzed, through quantitative and qualitative methods, a random sample of vaccine-related tweets published in Italy between November 2019 and June 2020, with the aim of understanding how the Twitter conversation on vaccines changed during the first phase of the pandemic, compared to the pre-pandemic months. Tweets were analyzed by a multidisciplinary team in terms of kind of vaccine, vaccine stance, tone of voice, population target, mentioned source of information. Multiple correspondence analysis was used to identify variables associated with vaccine stance. We analyzed 2,473 tweets. 58.2% mentioned the COVID-19 vaccine. Most had a discouraging stance (38.1%), followed by promotional (32.5%), neutral (22%) and ambiguous (2.5%). The discouraging stance was the most represented before the pandemic (69.6%). In February and March 2020, discouraging tweets decreased intensely and promotional and neutral tweets dominated the conversation. Between April and June 2020, promotional tweets remained more represented (36.5%), followed by discouraging (30%) and neutral (24.3%). The tweets' tone of voice was mainly polemical/complaining, both for promotional and for discouraging tweets. The multiple correspondence analysis identified a definite profile for discouraging and neutral tweets, compared to promotional and ambiguous tweets. In conclusion, the emergence of SARS-CoV-2 caused a deep change in the vaccination discourse on Twitter in Italy, with an increase of promotional and ambiguous tweets. Systematic monitoring of Twitter and other social media, ideally combined with traditional surveys, would enable us to better understand Italian vaccine hesitancy and plan tailored, data-based communication strategies.

Abstract Background The denial of death in Western society deprives young people of the tools to derive meaning from experiences of death and dying. Literature shows that death education may allow them to become familiar with this topic without causing negative effects. This article describes the effects of a death education course with adolescents, wherein participants were given the opportunity to meet palliative doctors and palliative psychologists at school and in a hospice, where they were able to converse with the families of the dying. Methods This study used mixed methods and included an evaluation of a death education intervention with longitudinal follow-up of outcomes. The course involved 87 secondary school students (experimental group) aged between 16 and 20 years. We also recruited a control group of 76 similarly-aged students to observe differences. The variables we examined were: alexithymia, representation of death, value attributed to life and spirituality. These were measured with the following instruments: the Toronto Alexithymia Scale-20, the Testoni Death Representation Scale, the Personal Meaning Profile and the Spiritual Orientation Inventory, respectively. To better understand how the students perceived the experience, we asked the experimental group to answer some open-ended questions. Their answers were analysed through thematic analysis. Results The study showed that death education and the hospice experience did not produce negative effects, but rather allowed students to decrease alexithymia, improving their ability to recognise and express emotions. Thematic analysis revealed that all participants perceived the experience as very positive. Conclusions Our findings affirm that death education programs can be successfully implemented in high schools, and that they can usefully involve local hospices and palliative care professionals, especially physicians and psychologists.

The ability to identify the broadest range of targetable gene fusions is crucial to facilitate personalized therapy selection for advanced lung adenocarcinoma (LuADs) patients harboring targetable receptor tyrosine kinase (RTK) genomic alterations. In order to evaluate the most effective testing approach for LuAD targetable gene fusion detection, we analyzed 210 NSCLC selected clinical samples, comparing in situ (Fluorescence In Situ Hybridization, FISH, and ImmunoHistoChemistry, IHC) and molecular (targeted RNA Next-Generation Sequencing, NGS, and RealTime-PCR, RT-PCR) approaches. The overall concordance among these methods was high (>90%), and targeted RNA NGS was confirmed to be the most efficient technique for gene fusion identification in clinical practice, allowing the simultaneous analysis of a large set of genomic rearrangements at the RNA level. However, we observed that FISH was useful to detect targetable fusions in those samples with inadequate tissue material for molecular testing as well as in those few cases whose fusions were not identified by the RNA NGS panel. We conclude that the targeted RNA NGS analysis of LuADs allows accurate RTK fusion detection; nevertheless, standard methods such as FISH should not be dismissed, as they can crucially contribute to the completion of the molecular characterization of LuADs and, most importantly, the identification of patients as candidates for targeted therapies.

Ni-Ti alloys are widely used for biomedical applications due to their superelastic properties, which are especially convenient for endovascular devices that require minimally invasive insertion and durable effects, such as peripheral/carotid stents and valve frames. After crimping and deployment, stents undergo millions of cyclic loads imposed by heart/neck/leg movements, causing fatigue failure and device fracture that can lead to possibly severe consequences for the patient. Standard regulations require experimental testing for the preclinical assessment of such devices, which can be coupled with numerical modeling to reduce the time and costs of such campaigns and to obtain more information regarding the local state of stress and strain in the device. In this frame, this review aimed to enlighten the relevant choices that can affect the outcome of the fatigue analysis of Ni-Ti devices, both from experimental and numerical perspectives.

Gut microbiota (GM) modulation can be investigated as possible solution to enhance recovery after COVID-19. An open-label, single-center, single-arm, pilot, interventional study was performed by enrolling twenty patients recently recovered from COVID-19 to investigate the role of a mixed probiotic, containing Lactobacilli, Bifidobacteria and Streptococcus thermophilus, on gastrointestinal symptoms, local and systemic inflammation, intestinal barrier integrity and GM profile. Gastrointestinal Symptom Rating Scale, cytokines, inflammatory, gut permeability, and integrity markers were evaluated before (T0) and after 8 weeks (T1) of probiotic supplementation. GM profiling was based on 16S-rRNA targeted-metagenomics and QIIME 2.0, LEfSe and PICRUSt computational algorithms. Multiple machine learning (ML) models were trained to classify GM at T0 and T1. A statistically significant reduction of IL-6 (p < 0.001), TNF-α (p < 0.001) and IL-12RA (p < 0.02), citrulline (p value < 0.001) was reported at T1. GM global distribution and microbial biomarkers strictly reflected probiotic composition, with a general increase in Bifidobacteria at T1. Twelve unique KEGG orthologs were associated only to T0, including tetracycline resistance cassettes. ML classified the GM at T1 with 100% score at phylum level. Bifidobacteriaceae and Bifidobacterium spp. inversely correlated to reduction of citrulline and inflammatory cytokines. Probiotic supplementation during post-COVID-19 may trigger anti-inflammatory effects though Bifidobacteria and related-metabolism enhancement.

Towards a carbon-neutral society, the building sector has a pivotal role with still a great potential for improvement. A new generation of buildings is rising but, to set a more ambitious shift in the paradigm and to fully justify the additional efforts (technological and economic) needed to fill the gap between net zero and plus energy performances, it is essential to consider not only the direct effects, but also all the indirect impacts. However, research conducted in the last decade solely focuses on the direct effects, mainly energy savings, while the indirect impacts neither have a clear identity nor terminology and a defined list of the impacts and methodologies for their quantification is still missing. With these premises, a systematic literature review on the current state of the art was performed in this work, with the aim of (i) investigating the heterogeneous terminology used for such indirect effects, (ii) identifying a final potential list of impacts both at the household and at the community level and (iii) their macro-categorizations, and (iv) exploring the current implemented methodologies and indicators for an economic quantification. As a final result of the analysis, the authors propose a unique terminology for addressing the indirect effects of high-performance buildings. This paper sets the needed basis and common ground for future research in this field, meant to economically quantify the indirect effects in the building sector.

Although several studies have explored the molecular landscape of metastatic melanoma, the genetic determinants of therapy resistance are still largely unknown. Here, we aimed to determine the contribution of whole-exome sequencing and circulating free DNA (cfDNA) analysis in predicting response to therapy in a consecutive real-world cohort of 36 patients, undergoing fresh tissue biopsy and followed during treatment. Although the underpowered sample size limited statistical analysis, samples from non-responders had higher copy number variations and mutations in melanoma driver genes compared to responders in the BRAF V600+ subset. In the BRAF V600− subset, Tumor Mutational Burden (TMB) was twice that in responders vs. non-responders. Genomic layout revealed commonly known and novel potential intrinsic/acquired resistance driver gene variants. Among these, RAC1, FBXW7, GNAQ mutations, and BRAF/PTEN amplification/deletion were present in 42% and 67% of patients, respectively. Both Loss of Heterozygosity (LOH) load and tumor ploidy were inversely associated with TMB. In immunotherapy-treated patients, samples from responders showed higher TMB and lower LOH and were more frequently diploid compared to non-responders. Secondary germline testing and cfDNA analysis proved their efficacy in finding germline predisposing variants carriers (8.3%) and following dynamic changes during treatment as a surrogate of tissue biopsy, respectively.

Abstract Purpose This study was a quality-control study of resting and exercise Doppler echocardiography (EDE) variables measured by 19 echocardiography laboratories with proven experience participating in the RIGHT Heart International NETwork. Methods All participating investigators reported the requested variables from ten randomly selected exercise stress tests. Intraclass correlation coefficients (ICC) were calculated to evaluate the inter-observer agreement with the core laboratory. Inter-observer variability of resting and peak exercise tricuspid regurgitation velocity (TRV), right ventricular outflow tract acceleration time (RVOT Act), tricuspid annular plane systolic excursion (TAPSE), tissue Doppler tricuspid lateral annular systolic velocity (S’), right ventricular fractional area change (RV FAC), left ventricular outflow tract velocity time integral (LVOT VTI), mitral inflow pulsed wave Doppler velocity (E), diastolic mitral annular velocity by TDI (e’) and left ventricular ejection fraction (LVEF) were measured. Results The accuracy of 19 investigators for all variables ranged from 99.7 to 100%. ICC was > 0.90 for all observers. Inter-observer variability for resting and exercise variables was for TRV = 3.8 to 2.4%, E = 5.7 to 8.3%, e’ = 6 to 6.5%, RVOT Act = 9.7 to 12, LVOT VTI = 7.4 to 9.6%, S’ = 2.9 to 2.9% and TAPSE = 5.3 to 8%. Moderate inter-observer variability was found for resting and peak exercise RV FAC (15 to 16%). LVEF revealed lower resting and peak exercise variability of 7.6 and 9%. Conclusions When performed in expert centers EDE is a reproducible tool for the assessment of the right heart and the pulmonary circulation.

Natural disasters can cause widespread damage to buildings and infrastructures and kill thousands of living beings. These events are difficult to be overcome both by the populations and by government authorities. Two challenging issues require in particular to be addressed: find an effective way to evacuate people first, and later to rebuild houses and other infrastructures. An adequate recovery strategy to evacuate people and start reconstructing damaged areas on a priority basis can then be a game changer allowing to overcome effectively those terrible circumstances. In this perspective, we here present DiReCT, an approach based on i) a dynamic optimization model designed to timely formulate an evacuation plan of an area struck by an earthquake, and ii) a decision support system, based on double deep Q Network, able to guide efficiently the reconstruction the affected areas. The latter works by considering both the resources available and the needs of the various stakeholders involved (e.g., residents social benefits and political priorities). The ground on which both the above solutions stand was a dedicated geographical data extraction algorithm, called “GisToGraph”, especially developed for this purpose. To check applicability of the whole approach, we dovetailed it on the real use-case of the historical city center of L’Aquila (Italy) using detailed GIS data and information on urban land structure and buildings vulnerability. Several simulations were run on the underlining network generated. First, we ran experiments to safely evacuate in the shortest possible time as many people as possible from an endangered area towards a set of safe places. Then, using DDQN, we generated different reconstruction plans and selected the best ones considering both social benefits and political priorities of the building units. The described approaches are comprised in a more general data science framework delved to produce an effective response to natural disasters.

Abstract Background Identification of somatic mutations in key oncogenes in melanoma is important to lead the effective and efficient use of personalized anticancer treatment. Conventional methods focus on few genes per run and, therefore, are unable to screen for multiple genes simultaneously. The use of Next-Generation Sequencing (NGS) technologies enables sequencing of multiple cancer-driving genes in a single assay, with reduced costs and DNA quantity needed and increased mutation detection sensitivity. Methods We designed a customized IMI somatic gene panel for targeted sequencing of actionable melanoma mutations; this panel was tested on three different NGS platforms using 11 metastatic melanoma tissue samples in blinded manner between two EMQN quality certificated laboratory. Results The detection limit of our assay was set-up to a Variant Allele Frequency (VAF) of 10% with a coverage of at least 200x. All somatic variants detected by all NGS platforms with a VAF ≥ 10%, were also validated by an independent method. The IMI panel achieved a very good concordance among the three NGS platforms. Conclusion This study demonstrated that, using the main sequencing platforms currently available in the diagnostic setting, the IMI panel can be adopted among different centers providing comparable results.

In the late 2020s, less than 1 year into the coronavirus disease 2019 (COVID-19) pandemic, several anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines were introduced on a worldwide scale, with a significant positive impact on the consequences of the disease for several high-risk population groups. In the case of most bacterial or viral respiratory infections, pregnant women are at increased risk of complications, however, neither pregnant nor breastfeeding women were included in the first round of randomized clinical trials evaluating the safety and effectiveness of COVID-19 vaccines, because of safety and ethical concerns. Nevertheless, most anti-SARS-CoV-2 vaccines have not been expressly contraindicated during pregnancy or breastfeeding, and observational data on immune response, adverse effects, and clinical efficacy in pregnant and breastfeeding women have been progressively gathered during 2021. The vast majority of these data is reassuring for what concerns side effects for women and infants and points out the efficacy of vaccines in protecting women against COVID-19-related complications. Despite this, the hesitancy of pregnant and breastfeeding women at being vaccinated is still real. In this mini-review, we resume the available data on the clinical consequences of COVID-19 in pregnant women, as well as adverse effects, systemic and mucosal immune response, and clinical effectiveness of COVID-19 vaccines in pregnant and breastfeeding women. Moreover, we offer an updated overview of European, North American, and Australasian recommendations concerning COVID-19 vaccination in pregnant and breastfeeding women, in order to safely ensure the highest protection of women and their infants.

The human gut microbiome (GM) is a complex ecosystem that includes numerous prokaryotic and eukaryotic inhabitants. The composition of GM can influence an array of host physiological functions including immune development. Accumulating evidence suggest that several members of non-bacterial microbiota, including protozoa and helminths, that were earlier considered as pathogens, could have a commensal or beneficial relationship with the host. Here we examine the most recent data from omics studies on prokaryota-meiofauna-host interaction as well as the impact of gut parasitome on gut bacterial ecology and its role as ‘immunological driver’ in health and disease to glimpse new therapeutic perspectives.

Cystic fibrosis (CF) is the most common rare disease caused by a mutation of the CF transmembrane conductance regulator gene encoding a channel protein of the apical membrane of epithelial cells leading to alteration of Na+ and K+ transport, hence inducing accumulation of dense and sticky mucus and promoting recurrent airway infections. The most detected bacterium in CF patients is Pseudomonas aeruginosa (PA) which causes chronic colonization, requiring stringent antibiotic therapies that, in turn induces multi-drug resistance. Despite eradication attempts at the first infection, the bacterium is able to utilize several adaptation mechanisms to survive in hostile environments such as the CF lung. Its adaptive machinery includes modulation of surface molecules such as efflux pumps, flagellum, pili and other virulence factors. In the present study we compared surface protein expression of PA multi- and pan-drug resistant strains to wild-type antibiotic-sensitive strains, isolated from the airways of CF patients with chronic colonization and recent infection, respectively. After shaving with trypsin, microbial peptides were analyzed by tandem-mass spectrometry on a high-resolution platform that allowed the identification of 174 differentially modulated proteins localized in the region from extracellular space to cytoplasmic membrane. Biofilm assay was performed to characterize all 26 PA strains in term of biofilm production. Among the differentially expressed proteins, 17 were associated to the virulome (e.g., Tse2, Tse5, Tsi1, PilF, FliY, B-type flagellin, FliM, PyoS5), six to the resistome (e.g., OprJ, LptD) and five to the biofilm reservoir (e.g., AlgF, PlsD). The biofilm assay characterized chronic antibiotic-resistant isolates as weaker biofilm producers than wild-type strains. Our results suggest the loss of PA early virulence factors (e.g., pili and flagella) and later expression of virulence traits (e.g., secretion systems proteins) as an indicator of PA adaptation and persistence in the CF lung environment. To our knowledge, this is the first study that, applying a shaving proteomic approach, describes adaptation processes of a large collection of PA clinical strains isolated from CF patients in early and chronic infection phases.

Birt–Hogg–Dubé syndrome (BHDS) is a rare autosomal dominant inherited disorder caused by a mutation in folliculin (FLCN) gene transmitted via germline autosomal dominant pattern. Patients with this syndrome have an increased susceptibility to renal cell carcinoma, lung cysts, spontaneous pneumothorax, and benign skin hamartomas, and its diagnosis is not easy and consequently underestimated. Several mutations have been identified in FLCN gene, among which the majority of alterations are frameshift (insertion/deletion), nonsense, or splice-site mutations that generally produce unfunctional truncated FLCN proteins. Our aim is to present a case of a BHDS family whose proband is a 56-year-old patient who has been experiencing multiple disorders, has an FLCN genetic mutation, and has also been identified to have a pathogenic variant in BRCA2 gene. Our further purpose is to emphasize the importance of the next-generation sequencing (NGS) approach to identify potential multiple germline mutations in complex and rare oncologic disorders, allowing strict and more targeted cancer screening programs.

The aim of the paper is to provide a theoretical insight into the feminist concept of cuerpo-territorio and the strict interrelation between the two terms – body and territory –, both object of predatory capitalist exploitation and protagonists of resistance against patriarchal extractivism in Latin America. The research intends to shed light on how capitalism, through the exploitation of territories and natural resources, is able to exploit also the reproductive role of women, strengthening their subordinated position and their confinement within the patriarchal society in the name of the profit. In this scenario, the study adopts a gender-sensitive perspective to reveal to what extent men and women are differently affected by extractivism and, as a matter of fact, it supports the evidence that this dominant model of accumulation cannot be considered gender-neutral, as impacts on women are definitely more severe than on the male counterpart. Consequently, through some cases in Colombia, greater attention has been put on women’s status, roles and capacities of challenging the system, in order to highlight the gendered implications of capitalist extractivism and to stress the capabilities of women in creating an alternative conception of development, aware of women’s needs and pointing at a more fair and inclusive society.

Hard ticks (Acari: Ixodidae) have been historically identified by morphological methods which require highly specialized expertise and more recently by DNA-based molecular assays that involve high costs. Although both approaches provide complementary data for tick identification, each method has limitations which restrict their use on large-scale settings such as regional or national tick surveillance programs. To overcome those obstacles, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced as a cost-efficient method for the identification of various organisms, as it balances performance, speed, and high data output. Here we describe the use of this technology to validate the distinction of two closely related Dermacentor tick species based on the development of the first nationwide MALDI-TOF MS reference database described to date. The dataset obtained from this protein-based approach confirms that tick specimens collected from United States regions west of the Rocky Mountains and identified previously as Dermacentor variabilis are the recently described species, Dermacentor similis. Therefore, we propose that this integrative taxonomic tool can facilitate vector and vector-borne pathogen surveillance programs in the United States and elsewhere.

Abstract Background Despite the efficacy of immune checkpoint inhibitors (ICIs) only the 20–30% of treated patients present long term benefits. The metabolic changes occurring in the gut microbiota metabolome are herein proposed as a factor potentially influencing the response to immunotherapy. Methods The metabolomic profiling of gut microbiota was characterized in 11 patients affected by non-small cell lung cancer (NSCLC) treated with nivolumab in second-line treatment with anti-PD-1 nivolumab. The metabolomics analyses were performed by GC–MS/SPME and 1H-NMR in order to detect volatile and non-volatile metabolites. Metabolomic data were processed by statistical profiling and chemometric analyses. Results Four out of 11 patients (36%) presented early progression, while the remaining 7 out of 11 (64%) presented disease progression after 12 months. 2-Pentanone (ketone) and tridecane (alkane) were significantly associated with early progression, and on the contrary short chain fatty acids (SCFAs) (i.e., propionate, butyrate), lysine and nicotinic acid were significantly associated with long-term beneficial effects. Conclusions Our preliminary data suggest a significant role of gut microbiota metabolic pathways in affecting response to immunotherapy. The metabolic approach could be a promising strategy to contribute to the personalized management of cancer patients by the identification of microbiota-linked “indicators” of early progressor and long responder patients.

Abstract Background The p.E318K variant of the Melanocyte Inducing Transcription Factor (MITF) has been implicated in genetic predisposition to melanoma as an intermediate penetrance allele. However, the impact of this variant on clinico-phenotypic, as well as on dermoscopic patterns features of affected patients is not entirely defined. The purpose of our study was to assess the association between the p.E318K germline variant and clinic-phenotypical features of MITF+ compared to non-carriers (MITF−), including dermoscopic findings of melanomas and dysplastic nevi. Methods we retrospectively analyzed a consecutive series of 1386 patients recruited between 2000 and 2017 who underwent genetic testing for CDKN2A, CDK4, MC1R and MITF germline variants in our laboratory for diagnostic/research purposes. The patients were probands of melanoma-prone families and apparently sporadic single or multiple primary melanoma patients. For all, we collected clinical, pathological information and dermoscopic images of the histopathologically diagnosed melanomas and dysplastic nevi, when available. Results After excluding patients positive for CDKN2A/CDK4 pathogenic variants and those affected by non-cutaneous melanomas, our study cohort comprised 984 cutaneous melanoma patients, 22 MITF+ and 962 MITF−. MITF+ were more likely to develop dysplastic nevi and multiple primary melanomas. Nodular melanoma was more common in MITF+ patients (32% compared to 19% in MITF−). MITF+ patients showed more frequently dysplastic nevi and melanomas with uncommon dermoscopic patterns (unspecific), as opposed to MITF− patients, whose most prevalent pattern was the multicomponent. Conclusions MITF+ patients tend to develop melanomas and dysplastic nevi with histopathological features, frequency and dermoscopic patterns often different from those prevalent in MITF− patients. Our results emphasize the importance of melanoma prevention programs for MITF+ patients, including dermatologic surveillance with digital follow-up.

Interferon-α (IFN-α) comprises a family of 13 cytokines involved in the modulation of antiviral, immune, and anticancer responses by orchestrating a complex transcriptional network. The activation of IFN-α signaling pathway in endothelial cells results in decreased proliferation and migration, ultimately leading to suppression of angiogenesis. In this study, we knocked-down the expression of seven established or candidate modulators of IFN-α response in endothelial cells to reconstruct a gene regulatory network and to investigate the antiangiogenic activity of IFN-α. This genetic perturbation approach, along with the analysis of interferon-induced gene expression dynamics, highlighted a complex and highly interconnected network, in which the angiostatic chemokine C-X-C Motif Chemokine Ligand 10 (CXCL10) was a central node targeted by multiple modulators. IFN-α-induced secretion of CXCL10 protein by endothelial cells was blunted by the silencing of Signal Transducer and Activator of Transcription 1 (STAT1) and of Interferon Regulatory Factor 1 (IRF1) and it was exacerbated by the silencing of Ubiquitin Specific Peptidase 18 (USP18). In vitro sprouting assay, which mimics in vivo angiogenesis, confirmed STAT1 as a positive modulator and USP18 as a negative modulator of IFN-α-mediated sprouting suppression. Our data reveal an unprecedented physiological regulation of angiogenesis in endothelial cells through a tonic IFN-α signaling, whose enhancement could represent a viable strategy to suppress tumor neoangiogenesis.

IntroductionA potential complication of term prelabor rupture of membranes (term PROM) is chorioamnionitis with an increased burden on neonatal outcomes of chronic lung disease and cerebral palsy. The purpose of the study was to analyze the efficacy of a standing clinical protocol designed to identify women with term PROM at low risk for chorioamnionitis, who may benefit from expectant management, and those at a higher risk for chorioamnionitis, who may benefit from early induction.Material and methodsThis retrospective study enrolled all consecutive singleton pregnant women with term PROM. Subjects included women with at least one of the following factors: white blood cell count ≥ 15×100/μL, C-reactive protein ≥ 1.5 mg/dL, or positive vaginal swab for beta-hemolytic streptococcus. These women comprised the high risk (HR) group and underwent immediate induction of labor by the administration of intravaginal dinoprostone. Women with none of the above factors and those with a low risk for chorioamnionitis waited for up to 24 hours for spontaneous onset of labor and comprised the low-risk (LR) group.ResultsOf the 884 consecutive patients recruited, 65 fulfilled the criteria for HR chorioamnionitis and underwent immediate induction, while 819 were admitted for expectant management. Chorioamnionitis and Cesarean section rates were not significantly different between the HR and LR groups. However, the prevalence of maternal fever (7.7% vs. 2.9%; p = 0.04) and meconium-stained amniotic fluid was significantly higher in the HR group than in LR group (6.1% vs. 2.2%; p = 0.04). This study found an overall incidence of 4.2% for chorioamnionitis, 10.9% for Cesarean section, 0.5% for umbilical artery blood pH < 7.10, and 1.9% for admission to the neonatal intensive care unit. Furthermore, no confirmed cases of neonatal sepsis were encountered.ConclusionsA clinical protocol designed to manage, by immediate induction, only those women with term PROM who presented with High Risk factors for infection/inflammation achieved similar maternal and perinatal outcomes between such women and women without any risks who received expectant management. This reduced the need for universal induction of term PROM patients, thereby reducing the incidence of maternal and fetal complications without increasing the rate of Cesarean sections.

In the present work, nineteen analogues of 1-[(2,2-Diphenyl-1,3-dioxolan-4-yl)methyl]-4-(2-methoxyphenyl)piperazine 5 and N-[2-(2-Methoxyphenoxy)ethyl]-2,2-diphenyl-1,3-dioxolane-4-methanamine 18 were synthesized. The compounds were tested for binding affinity at 5-HT1AR and α1-AR subtypes. They were also tested using functional assays as α1-AR antagonists and the most promising were tested for functional activity at 5-HT1AR, where they were shown to behave as agonists. The results highlight that the replacement of the 1,3-dioxolane ring with a 1,3-oxathiolane or a 1,3-dithiolane moiety leads to an overall reduction in in-vitro affinity at the α1-AR, while affinity, potency and efficacy were strongly enhanced at the 5-HT1A receptor. Overall, the nitrogen-containing aromatic moieties scarcely affect the affinity at the 5-HT1A receptor, while reducing potency and increasing efficacy. The oxidation of the sulphur atom in the 1,3-oxathiolane to give sulfoxides and solfones has a negative effect on affinity and potency at both receptor systems. Regardless of the effect on the other parameters, selectivity toward 5-HT1AR with respect to the α1-AR is often favoured, but never the contrary. The most striking result is the inversion of selectivity. In fact, while the lead 5 is 100-fold selective for α1-AR, the new derivatives, although to differing degrees, are selective for 5-HT1AR.

Research on minors who have a close family member with amyotrophic lateral sclerosis (ALS) is scarce. This study aims to analyze the relationships between reflective function and wellbeing among such children, considering their reflective function, representations of death, and behavioral problems with the following instruments: Reflective Functioning Questionnaire, Testoni Death Representation Scale for Children, Positive and Negative Affect Schedule for Children, and Strengths and Difficulties Questionnaire. Participants were 248 minors divided into the target group (38 children–16 females, 22 males–7–18 years old (M = 11.61, SD = 2.97)) and the control group (210 students–120 females, 90 males 9–14 years old (M = 11.17, SD = 1.33)). Results showed that the target group exhibited more negative affect and hyperactivity. However, they also showed less uncertainty in their mental states. The opportunity to support these minors is discussed.

Colonization by multidrug-resistant (MDR) organisms in liver transplant (LT) candidates significantly affects the LT outcome. To date, consensus about patient management is lacking, including microbiological screening indications. This pilot study aimed to evaluate the impact of carbapenem-resistant Klebsiella pneumoniae (CR-KP) colonization in LT paediatric candidates to enable optimal prevention and therapeutic strategies that exploit both clinical and microbiological approaches. Seven paediatric patients colonized by CR-KP were evaluated before and until one-year post LT. At the time of the transplant, patients were stratified based on antibiotic (ATB) prophylaxis into two groups: ‘standard ATB’ (standard ATB prophylaxis), and ‘targeted ATB’ (MDR antibiogram-based ATB prophylaxis). Twenty-eight faecal samples were collected during follow-up and used for MDR screening and gut microbiota 16S rRNA-based profiling. Post-transplant hospitalization duration was comparable for both groups. With the exception of one patient, no serious infections and/or complications, nor deaths were recorded. A progressive MDR decontamination was registered. In the ‘standard ATB’ group, overall bacterial richness increased. Moreover, 6 months after LT, Lactobacillus and Bulleidia were increased and Enterobacteriaceae and Klebsiella spp. were reduced. In the ‘targeted ATB’ group Klebsiella spp., Ruminococcus gnavus, Erysipelotrichaceae, and Bifidobacterium spp. were increased 12 months after LT. In conclusion, both antibiotics prophylaxis do not affect nor LT outcomes or the risk of intestinal bacterial translocation. However, in the ‘standard ATB’ group, gut microbiota richness after LT was increased, with an increase of beneficial lactic acid- and short-chain fatty acids (SCFA)-producing bacteria and the reduction of harmful Enterobacteriaceae and Klebsiella spp. It could therefore be appropriate to administer standard prophylaxis, reserving the use of ATB-based molecules only in case of complications.

Italiano, tedesco e inglese sono lingue che si comportano diversamente per quanto riguarda l’uso di forme femminilizzate. Se per il tedesco esiste un modello grammaticale affermato, per l’italiano l’uso di forme marcate non è “automatico” ed è spesso oggetto di discussione. Date queste premesse, ci siamo chiesti come si comporti google translate rispetto alla traduzione in italiano di agentivi riferiti a donne. Grazie a tre corpora basati sui profili wikipedia di 200 donne (il primo corpus con testi in italiano, gli altri due con le traduzioni in italiano dal tedesco e dall’inglese) abbiamo osservato quali sono gli elementi che facilitano o ostacolano il riconoscimento del genere, alla luce del nuovo sistema con reti neurali.

Type 1 diabetes (T1D) is a chronic autoimmune metabolic disorder with onset in pediatric/adolescent age, characterized by insufficient insulin production, due to a progressive destruction of pancreatic β-cells. Evidence on the correlation between the human gut microbiota (GM) composition and T1D insurgence has been recently reported. In particular, 16S rRNA-based metagenomics has been intensively employed in the last decade in a number of investigations focused on GM representation in relation to a pre-disease state or to a response to clinical treatments. On the other hand, few works have been published using alternative functional omics, which is more suitable to provide a different interpretation of such a relationship. In this work, we pursued a comprehensive metaproteomic investigation on T1D children compared with a group of siblings (SIBL) and a reference control group (CTRL) composed of aged matched healthy subjects, with the aim of finding features in the T1D patients’ GM to be related with the onset of the disease. Modulated metaproteins were found either by comparing T1D with CTRL and SIBL or by stratifying T1D by insulin need (IN), as a proxy of β-cells damage, showing some functional and taxonomic traits of the GM, possibly related to the disease onset at different stages of severity.

ATM germline pathogenic variants were recently found enriched in high-risk melanoma patients. However, ATM loss of heterozygosity (LOH) has never been investigated in melanoma and, therefore, a causal association with melanoma development has not been established yet. The purpose of this study was to functionally characterize 13 germline ATM variants found in high-risk melanoma patients—and classified by in silico tools as pathogenic, uncertain significance, or benign—using multiple assays evaluating ATM/pATM expression and/or LOH in melanoma tissues and cell lines. We assessed ATM status by Immunohistochemistry (IHC), Western Blot, Whole-Exome Sequencing/Copy Number Variation analysis, and RNA sequencing, supported by Sanger sequencing and microsatellite analyses. For most variants, IHC results matched those obtained with in silico classification and LOH analysis. Two pathogenic variants (p.Ser1135_Lys1192del and p.Ser1993ArgfsTer23) showed LOH and complete loss of ATM activation in melanoma. Two variants of unknown significance (p.Asn358Ile and p.Asn796His) showed reduced expression and LOH, suggestive of a deleterious effect. This study, showing a classic two-hit scenario in a well-known tumor suppressor gene, supports the inclusion of melanoma in the ATM-related cancer spectrum.

The human body contains a very complex and dynamic ecosystem of bacteria. The bacteriome interacts with the host bi-directionally, and changes in either factor impact the entire system. It has long been known that chronic airway diseases are associated with disturbances in the lung bacteriome. However, less is known about the role of gut bacteriome in the most common respiratory diseases. Here, we aim to summarise the evidence concerning the role of the intestinal bacteriome in the pathogenesis and disease course of bronchial asthma, chronic obstructive pulmonary disease, and obstructive sleep apnea. Furthermore, we discuss the consequences of an altered gut bacteriome on the most common comorbidities of these lung diseases. Lastly, we also reflect on the therapeutic potential of influencing the gut microbiome to improve disease outcomes.

Purpose: This meta-analysis summarizes the incidence of treatment-related adverse events (AE) of BRAFi and MEKi. Methods: A systematic search of Medline/PubMed was conducted to identify suitable articles published in English up to 31 December 2021. The primary outcomes were profiles for all-grade and grade 3 or higher treatment-related AEs, and the analysis of single side effects belonging to both categories. Results: The overall incidence of treatment-related all-grade Aes was 99% for Encorafenib (95% CI: 0.97–1.00) and 97% for Trametinib (95% CI: 0.92–0.99; I2 = 66%) and Binimetinib (95% CI: 0.94–0.99; I2 = 0%). In combined therapies, the rate was 98% for both Vemurafenib + Cobimetinib (95% CI: 0.96–0.99; I2 = 77%) and Encorafenib + Binimetinib (95% CI: 0.96–1.00). Grade 3 or higher adverse events were reported in 69% of cases for Binimetinib (95% CI: 0.50–0.84; I2 = 71%), 68% for Encorafenib (95% CI: 0.61–0.74), and 72% for Vemurafenib + Cobimetinib (95% CI: 0.65–0.79; I2 = 84%). The most common grade 1–2 AEs were pyrexia (43%) and fatigue (28%) for Dabrafenib + Trametinib and diarrhea for both Vemurafenib + Cobimetinib (52%) and Encorafenib + Binimetinib (34%). The most common AEs of grade 3 or higher were pyrexia, rash, and hypertension for Dabrafenib + Trametinib (6%), rash and hypertension for Encorafenib + Binimetinib (6%), and increased AST and ALT for Vemurafenib + Cobimetinib (10%). Conclusions: Our study provides comprehensive data on treatment-related adverse events of BRAFi and MEKi combination therapies, showing related toxicity profiles to offer a helpful tool for clinicians in the choice of therapy.

Assessment of HRD status is now essential for ovarian cancer patient management. A relevant percentage of high-grade serous carcinoma (HGSC) is characterized by HRD, which is caused by genetic alterations in the homologous recombination repair (HRR) pathway. Recent trials have shown that not only patients with pathogenic/likely pathogenic BRCA variants, but also BRCAwt/HRD patients, are sensitive to PARPis and platinum therapy. The most common HRD test is Myriad MyChoice CDx, but there is a pressing need to offer an alternative to outsourcing analysis, which typically requires high costs and lengthy turnaround times. In order to set up a complete in-house workflow for HRD testing, we analyzed a small cohort of HGSC patients using the CE-IVD AmoyDx HRD Focus Panel and compared our results with Myriad’s. In addition, to further deepen the mechanisms behind HRD, we analyzed the study cohort by using both a custom NGS panel that analyzed 21 HRR-related genes and FISH analysis to determine the copy numbers of PTEN and EMSY. We found complete concordance in HRD status detected by the Amoy and the Myriad assays, supporting the feasibility of internal HRD testing.

Type 1 diabetes (T1D) is a multifactorial autoimmune disease driven by T-cells against the insulin-producing islet β-cells, resulting in a marked loss of β-cell mass and function. Although a genetic predisposal increases susceptibility, the role of epigenetic and environmental factors seems to be much more significant. A dysbiotic gut microbial profile has been associated with T1D patients. Moreover, new evidence propose that perturbation in gut microbiota may influence the T1D onset and progression. One of the prominent features in clinically silent phase before the onset of T1D is the presence of a microbiota characterized by low numbers of commensals butyrate producers, thus negatively influencing the gut permeability. The loss of gut permeability leads to the translocation of microbes and microbial metabolites and could lead to the activation of immune cells. Moreover, microbiota-based therapies to slow down disease progression or reverse T1D have shown promising results. Starting from this evidence, the correction of dysbiosis in early life of genetically susceptible individuals could help in promoting immune tolerance and thus in reducing the autoantibodies production. This review summarizes the associations between gut microbiota and T1D for future therapeutic perspectives and other exciting areas of research.

Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.

The development of the human gut microbiota is characterized by a dynamic sequence of events from birth to adulthood, which make the gut microbiota unique for everyone. Its composition and metabolism may play a critical role in the intestinal homeostasis and health. We propose a study on a single mother-infant dyad to follow the dynamics of an infant fecal microbiota and metabolome changes in relation to breast milk composition during the lactation period and evaluate the changes induced by introduction of complementary food during the weaning period. Nuclear Magnetic Resonance (NMR)-based metabolomics was performed on breast milk and, together with 16S RNA targeted-metagenomics analysis, also on infant stool samples of a mother-infant dyad collected over a period running from the exclusive breastfeeding diet to weaning. Breast milk samples and neonatal stool samples were collected from the 4th to the 10th month of life. Both specimens were collected from day 103 to day 175, while from day 219–268 only stool samples were examined. An exploratory and a predictive analysis were carried out by means of Common component and specific weight analysis and multi-block partial least squares discriminant analysis, respectively. Stools collected during breastfeeding and during a mixed fruit/breastfeeding diet were characterized by high levels of fucosyl-oligosaccharides and glycolysis intermediates, including succinate and formate. The transition to a semi-solid food diet was characterized by several changes in fecal parameters: increase in short-chain fatty acids (SCFAs) levels, including acetate, propionate and butyrate, dissapearance of HMOs and the shift in the community composition, mainly occurring within the Firmicutes phylum. The variations in the fecal metabolome reflected the infant’s diet transition, while the composition of the microbiota followed a more complex and still unstable behavior.

Proteins fulfill complex and diverse biological functions through the controlled atomic motions of their structures (functional dynamics). The protein composition is given by its amino-acid sequence, which was assumed to encode the function. However, the discovery of functional sequence variants proved that the functional encoding does not come down to the sequence, otherwise a change in the sequence would mean a change of function. Likewise, the discovery that function is fulfilled by a set of structures and not by a unique structure showed that the functional encoding does not come down to the structure either. That leaves us with the possibility that a set of atomic motions, achievable by different sequences and different structures, encodes a specific function. Thanks to the exponential growth in annual depositions in the Protein Data Bank of protein tridimensional structures at atomic resolutions, network models using the Cartesian coordinates of atoms of a protein structure as input have been used over 20 years to investigate protein features. Combining networks with experimental measures or with Molecular Dynamics (MD) simulations and using typical or ad-hoc network measures is well suited to decipher the link between protein dynamics and function. One perspective is to consider static structures alone as alternatives to address the question and find network measures relevant to dynamics that can be subsequently used for mining and classification of dynamic sequence changes functionally robust, adaptable or faulty. This way the set of dynamics that fulfill a function over a diversity of sequences and structures will be determined.

Inborn errors of metabolism (IEMs) represent a complex system model, in need of a shift of approach exploring the main factors mediating the regulation of the system, internal or external and overcoming the traditional concept of biochemical and genetic defects. In this context, among the established factors influencing the metabolic flux, i.e., diet, lifestyle, antibiotics, xenobiotics, infectious agents, also the individual gut microbiota should be considered. A healthy gut microbiota contributes in maintaining human health by providing unique metabolic functions to the human host. Many patients with IEMs are on special diets, the main treatment for these diseases. Hence, IEMs represent a good model to evaluate how specific dietary patterns, in terms of macronutrients composition and quality of nutrients, can be related to a characteristic microbiota associated with a specific clinical phenotype (“enterophenotype”). In the present review, we aim at reporting the possible links existing between dysbiosis, a condition reported in IEMs patients, and a pro-inflammatory status, through an altered “gut-liver” cross-talk network and a major oxidative stress, with a repercussion on the health status of the patient, increasing the risk of non-communicable diseases (NCDs). On this basis, more attention should be paid to the nutritional status assessment and the clinical and biochemical signs of possible onset of comorbidities, with the goal of improving the long-term wellbeing in IEMs. A balanced intestinal ecosystem has been shown to positively contribute to patient health and its perturbation may influence the clinical spectrum of individuals with IEMs. For this, reaching eubiosis through the improvement of the quality of dietary products and mixtures, the use of pre-, pro- and postbiotics, could represent both a preventive and therapeutic strategy in these complex diseases.