Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival Strategies of Streptococcus pyogenes in Response to Phage Infection

Bacteriophages exert strong evolutionary pressure on their microbial hosts. In their lytic lifecycle, complete bacterial subpopulations are utilized as hosts for bacteriophage replication. However, during their lysogenic lifecycle, bacteriophages can integrate into the host chromosome and alter the host’s genomic make-up, possibly resulting in evolutionary important adjustments. Not surprisingly, bacteria have evolved sophisticated immune systems to protect against phage infection. Streptococcus pyogenes isolates are frequently lysogenic and their prophages have been shown to be major contributors to the virulence of this pathogen. Most S. pyogenes phage research has focused on genomic prophages in relation to virulence, but little is known about the defensive arsenal of S. pyogenes against lytic phage infection. Here, we characterized Phage A1, an S. pyogenes bacteriophage, and investigated several mechanisms that S. pyogenes utilizes to protect itself against phage predation. We show that Phage A1 belongs to the Siphoviridae family and contains a circular double-stranded DNA genome that follows a modular organization described for other streptococcal phages. After infection, the Phage A1 genome can be detected in isolated S. pyogenes survivor strains, which enables the survival of the bacterial host and Phage A1 resistance. Furthermore, we demonstrate that the type II-A CRISPR-Cas system of S. pyogenes acquires new spacers upon phage infection, which are increasingly detectable in the absence of a capsule. Lastly, we show that S. pyogenes produces membrane vesicles that bind to phages, thereby limiting the pool of phages available for infection. Altogether, this work provides novel insight into survival strategies employed by S. pyogenes to combat phage predation.
Pinus pinaster Early Hormonal Defence Responses to Pinewood Nematode (Bursaphelenchus xylophilus) Infection

The pinewood nematode (PWN) is the causal agent of pine wilt disease, a pathology that affects conifer forests, mainly Pinus spp. PWN infection can induce the expression of phytohormone-related genes; however, changes at the early phytohormone level have not yet been explored. Phytohormones are low-abundance metabolites, and thus, difficult to quantify. Moreover, most methodologies focus mainly on Arabidopsis or crop species. This work aimed to validate a fast (run time 6.6 min) liquid chromatography-triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS) analytical method to quantify 14 phytohormones in Pinus pinaster stem tissues. This method was further applied to evaluate, for the first time, early phytohormone changes in susceptible and resistant phenotypes of P. pinaster 24, 48 and 72 h after inoculation (HAI) with PWN. A significant increase in salicylic acid (SA, 48 and 72 HAI) and jasmonic acid methyl ester (JA-ME, 72 HAI) was observed in susceptible phenotypes. Results indicate that the higher susceptibility of P. pinaster to PWN infection might result from an inefficient trigger of hypersensitive responses, with the involvement of JA and SA pathways. This work provides an important update in forest research, and adds to the current knowledge of Pinus spp. defence responses to PWN infection.
Pectin Dependent Cell Adhesion Restored by a Mutant Microtubule Organizing Membrane Protein

The cellulose- and pectin-rich plant cell wall defines cell structure, mediates defense against pathogens, and facilitates plant cell adhesion. An adhesion mutant screen of Arabidopsis hypocotyls identified a new allele of QUASIMODO2 (QUA2), a gene required for pectin accumulation and whose mutants have reduced pectin content and adhesion defects. A suppressor of qua2 was also isolated and describes a null allele of SABRE (SAB), which encodes a previously described plasma membrane protein required for longitudinal cellular expansion that organizes the tubulin cytoskeleton. sab mutants have increased pectin content, increased levels of expression of pectin methylesterases and extensins, and reduced cell surface area relative to qua2 and Wild Type, contributing to a restoration of cell adhesion.
A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA

Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding—equilibrium and kinetics—by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4–DNA interactions. We found a strong enthalpy–entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.
Synchrotron Radiation Spectroscopy and Transmission Electron Microscopy Techniques to Evaluate TiO2 NPs Incorporation, Speciation, and Impact on Root Cells Ultrastructure of Pisum sativum L. Plants

Biosolids (Bs) for use in agriculture are an important way for introducing and transferring TiO2 nanoparticles (NPs) to plants and food chain. Roots of Pisum sativum L. plants grown in Bs-amended soils spiked with TiO2 800 mg/kg as rutile NPs, anatase NPs, mixture of both NPs and submicron particles (SMPs) were investigated by Transmission Electron Microscopy (TEM), synchrotron radiation based micro X-ray Fluorescence and micro X-ray Absorption Near-Edge Structure (µXRF/µXANES) and Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES). TEM analysis showed damages in cells ultrastructure of all treated samples, although a more evident effect was observed with single anatase or rutile NPs treatments. Micro-XRF and TEM evidenced the presence of nano and SMPs mainly in the cortex cells near the rhizodermis. Micro-XRF/micro-XANES analysis revealed anatase, rutile, and ilmenite as the main TiO2 polymorphs in the original soil and Bs, and the preferential anatase uptake by the roots. For all treatments Ti concentration in the roots increased by 38–56%, however plants translocation factor (TF) increased mostly with NPs treatment (261–315%) and less with SMPs (about 85%), with respect to control. In addition, all samples showed a limited transfer of TiO2 to the shoots (very low TF value). These findings evidenced a potential toxicity of TiO2 NPs present in Bs and accumulating in soil, suggesting the necessity of appropriate regulations for the occurrence of NPs in Bs used in agriculture.
Gut Dysbiosis and Western Diet in the Pathogenesis of Essential Arterial Hypertension: A Narrative Review

Metabolic syndrome is a cluster of the most dangerous cardiovascular (CV) risk factors including visceral obesity, insulin resistance, hyperglycemia, alterations in lipid metabolism and arterial hypertension (AH). In particular, AH plays a key role in the complications associated with metabolic syndrome. High salt intake is a well-known risk factor for AH and CV diseases. Vasoconstriction, impaired vasodilation, extracellular volume expansion, inflammation, and an increased sympathetic nervous system (SNS) activity are the mechanisms involved in the pathogenesis of AH, induced by Western diet. Gut dysbiosis in AH is associated with reduction of short chain fatty acid-producing bacteria: acetate, butyrate and propionate, which activate different pathways, causing vasoconstriction, impaired vasodilation, salt and water retention and a consequent high blood pressure. Moreover, increased trimethylamine N-oxide and lipopolysaccharides trigger chronic inflammation, which contributes to endothelial dysfunction and target organs damage. Additionally, a high salt-intake diet impacts negatively on gut microbiota composition. A bidirectional neuronal pathway determines the “brain–gut” axis, which, in turn, influences blood pressure levels. Then, we discuss the possible adjuvant novel treatments related to gut microbiota modulation for AH control.
Assessment of the Hyperspectral Data Analysis as a Tool to Diagnose Xylella fastidiosa in the Asymptomatic Leaves of Olive Plants

Xylella fastidiosa is a bacterial pathogen affecting many plant species worldwide. Recently, the subspecies pauca (Xfp) has been reported as the causal agent of a devastating disease on olive trees in the Salento area (Apulia region, southeastern Italy), where centenarian and millenarian plants constitute a great agronomic, economic, and landscape trait, as well as an important cultural heritage. It is, therefore, important to develop diagnostic tools able to detect the disease early, even when infected plants are still asymptomatic, to reduce the infection risk for the surrounding plants. The reference analysis is the quantitative real time-Polymerase-Chain-Reaction (qPCR) of the bacterial DNA. The aim of this work was to assess whether the analysis of hyperspectral data, using different statistical methods, was able to select with sufficient accuracy, which plants to analyze with PCR, to save time and economic resources. The study area was selected in the Municipality of Oria (Brindisi). Partial Least Square Regression (PLSR) and Canonical Discriminant Analysis (CDA) indicated that the most important bands were those related to the chlorophyll function, water, lignin content, as can also be seen from the wilting symptoms in Xfp-infected plants. The confusion matrix of CDA showed an overall accuracy of 0.67, but with a better capability to discriminate the infected plants. Finally, an unsupervised classification, using only spectral data, was able to discriminate the infected plants at a very early stage of infection. Then, in phase of testing qPCR should be performed only on the plants predicted as infected from hyperspectral data, thus, saving time and financial resources.
Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.
Frontal Transcranial Direct Current Stimulation as a Potential Treatment of Parkinson’s Disease-Related Fatigue

In contrast to motor symptoms, non-motor symptoms in Parkinson’s disease (PD) are often poorly recognized and inadequately treated. Fatigue is one of the most common non-motor symptoms in PD and affects a broad range of everyday activities, causes disability, and substantially reduces the quality of life. It occurs at every stage of PD, and once present, it often persists and worsens over time. PD patients attending the 2013 World Parkinson Congress voted fatigue as the leading symptom in need of further research. However, despite its clinical significance, little progress has been made in understanding the causes of Parkinson’s disease-related fatigue (PDRF) and developing effective treatment options, which argues strongly for a greater effort. Transcranial direct current stimulation (tDCS) is a technique to non-invasively modulate cortical excitability by delivering low electrical currents to the cerebral cortex. In the past, it has been consistently evidenced that tDCS has the ability to induce neuromodulatory changes in the motor, sensory, and cognitive domains. Importantly, recent data present tDCS over the frontal cortex as an effective therapeutic option to treat fatigue in patients suffering from multiple sclerosis (MS). The current opinion paper reviews recent data on PDRF and the application of tDCS for the treatment of fatigue in neuropsychiatric disorders to further develop an idea of using frontal anodal tDCS as a potential therapeutic strategy to alleviate one of the most common and severe non-motor symptoms of PD.
Factors That Affect Symptoms of Injection Site Infection among Japanese Patients Who Self-Inject Insulin for Diabetes

In Japan, skin disinfection is typically considered necessary before an insulin injection to prevent infection at the injection site. This cross-sectional study evaluated factors that influenced symptoms of injection site infection among 238 Japanese patients who self-injected insulin for diabetes between October 2015 and January 2016. A structured questionnaire was used to collect data regarding skin disinfection practices, infection symptoms at the injection site, frequency of injections, environment at the time of injection, and hygiene habits. The majority of patients (83.2%) performed skin disinfection before the self-injection. Logistic regression analysis revealed that infection at the injection site was positively associated with skin disinfection before injection, age, and performing injections outside home. It was speculated that omitting skin disinfection before administering subcutaneous insulin injection was not the factor that affected the symptoms of injection site infection. The greatest contributor to infection symptoms was injections performed outside the home. Future studies focusing on the environment, in which patients administer insulin injections, to assess its influence on symptoms of injection site infections are warranted.
Social Modeling and Eating Behavior—A Narrative Review

Social modeling of eating is the adjustment of the amount of food eaten to the intake of the accompanying person. In this paper we provide a narrative review of literature on social modeling of eating with a particular focus on recent studies. Firstly, we describe the structure of a typical modeling experiment. Secondly, we present a variety of research in this field: experiments with various types of confederates, experiments aimed at the evaluation of the influence of gender, partner’s body weight, type of food, hunger, personal characteristics, etc. Thirdly, we present practical implications of this knowledge. The common conclusion is that social modeling of eating occurs in different situations and consumption is adapted to the standards established by the eating partner, but is not their direct reflection. Social influence of eating is not restricted to "artificial" laboratory situations; social modeling and social norms manipulations may be used to change people’s dietary practices, especially in children and young adults. Within the home environment parental modeling has been shown to promote children’s snacking and fruit and vegetable consumption. Social modeling may be used in nutrition interventions aimed at the improvement of children’s diet and in obesity prevention programs.
“The Good, The Bad, and the Minimum Tolerable”: Exploring Expectations of Institutional Food

There is a tendency towards greater expectations of consumer goods and services in society—what was once judged as ideal may now be a bare minimum. This presents a challenge for food providers in the upcoming decades. As the more demanding baby boomer cohort ages, health institutions of the future will face challenges meeting their food expectations. The purpose of this study was to explore expectation type dynamics and function with updated empirical material on aging consumers expectations of institutional food and advance our current understanding of how consumers evaluate their expectations. This qualitative study employed in-depth semi structured interviews with 14 informants between the age of 58–79. Content analysis was performed to capture the informants’ food expectations based on the expectation hierarchy proposed by Santos and Boote. Analyzing the content and relationship between different expectation types led to three main findings: expectation functions and content, interconnectedness, and the role of affect. Based on the findings, this study contributes by making several propositions for future research and proposes an updated expectancy–disconfirmation model. Importantly, this study provides novel knowledge that can help health institutions understand and meet aging consumers expectations of institutional food.
A Novel Combination Therapy Using Rosuvastatin and Lactobacillus Combats Dextran Sodium Sulfate-Induced Colitis in High-Fat Diet-Fed Rats by Targeting the TXNIP/NLRP3 Interaction and Influencing Gut Microbiome Composition

Inflammasome targeting and controlling dysbiosis are promising therapeutic approaches to control ulcerative colitis. This report is the first to investigate the mechanisms underlying the coloprotective effects of rosuvastatin and Lactobacillus and their combined therapy on dextran sodium sulfate (DSS)-induced colitis in high-fat diet (HFD)-fed rats. Our results demonstrate the aggravation of intestinal inflammation as a consequence of an HFD following DSS administration. An association between dyslipidemia, LDL oxidation, CD36 expression, ROS generation, thioredoxin-interacting protein (TXNIP) upregulation, and NLRP3 inflammasome activation was demonstrated by DSS exposure in HFD-fed rats. We demonstrated that rosuvastatin/Lactobacillus significantly suppressed the DSS/HFD-induced increase in colon weight/length ratio, DAI, MDI, and myeloperoxidase, as well as corrected dysbiosis and improved histological characteristics. Additionally, caspase-1 activity and IL-1β-driven pyroptotic activity was significantly reduced. Rosuvastatin/Lactobacillus showed prominent anti-inflammatory effects as revealed by the IL-10/IL-12 ratio and the levels of TNF-α and IL-6. These latter effects may be attributed to the inhibition of phosphorylation-induced activation of NF-κB and a concomitant reduction in the expression of NLRP3, pro-IL-1β, and pro-IL-18. Furthermore, rosuvastatin/Lactobacillus reduced Ox-LDL-induced TXNIP and attenuated the inflammatory response by inhibiting NLRP3 inflammasome assembly. To conclude, rosuvastatin/Lactobacillus offers a safe and effective strategy for the management of ulcerative colitis.
Testing a Benchtop Wet-Milling Method for Preparing Nanoparticles and Suspensions as Hospital Formulations

In clinical practice, for elderly or pediatric patients who have difficulty swallowing, solid dosage forms such as tablets or capsules are crushed or unsealed, prepared as powder forms, and often administered as suspensions. However, because their dispersibility is poor, aggregation or precipitation occurs readily. Once precipitation and deposition happen, redispersion is difficult, which can limit patient and caretaker drug adherence. In this study, we attempted to prepare nanoparticles as a hospital formulation by a benchtop wet-milling method to obtain a suspension with high dispersibility. This is the first study to apply the wet-milling method to prepare the hospital formulation. We chose cefditoren pivoxil (CDTR-PI) as an experimental active pharmaceutical ingredient. CDTR-PI crystals were physically mixed with various water-soluble polymers such as polyvinylpyrrolidone, polyethylene oxide, hydroxypropyl cellulose, or hypromellose and wet-milled with a surface-active agent (sodium lauryl sulfate) under different conditions. The mean particle diameter of most of the samples was less than 200 nm. In FTIR spectra of ground samples, peak shifts suggesting inter- or intramolecular interactions between CDTR-PI and the other additive agents were not observed. Besides, the nanoparticle suspension had favorable dispersibility, as determined using a dispersion stability analyzer. Providing a suspension with high dispersibility makes dispense with the resuspension, the patient’s medication adherence would improve. These results show that suspended liquid formulations of active pharmaceutical ingredients could be obtained by the simple wet-milling method as hospital formulations.
Correlation of CD47 Expression with Adverse Clinicopathologic Features and an Unfavorable Prognosis in Colorectal Adenocarcinoma

CD47, a transmembrane protein, is widely overexpressed on the tumor cell surface. However, the prognostic significance of CD47 expression in colorectal adenocarcinoma (CRA) has not yet been clarified. Here, we investigated the clinicopathologic significance of CD47 expression in CRA. CD47 expression was evaluated via immunohistochemical analysis of microarray sections of 328 CRA tissues. CD47 expression was observed in 53 (16.2%) of the 328 CRA tissues, and positive expression was associated with lymphatic invasion (p = 0.018), perineural invasion (p = 0.024), tumor budding (p = 0.009), the pathologic N stage (p = 0.022), and the American Joint Committee on Cancer (AJCC) stage (p = 0.027). In survival analyses of 329 patients, a positive CD47 expression was associated with a poor recurrence-free survival (RFS) (p = 0.032). In multivariate analysis, however, it was not an independent prognostic factor. In patients who underwent surgical resection without adjuvant treatment, a positive CD47 expression was associated with a shorter RFS (p = 0.001) but not with cancer-specific survival (CSS). In patients who received postoperative adjuvant treatment, no significant differences were found in both RFS and CSS. In conclusion, we investigated CD47 expression in 328 CRA tissues. A positive CD47 expression was observed in a minority (16.2%) of the tissues and was significantly associated with adverse clinicopathologic features and a poor patient outcome.