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The effort of the Humane Microbiome Project has led to the awareness that many districts of the human organism, like the skin, gastrointestinal tract, and genitals harbor their normal resident microbes. For this reason, the scientific community overcame the dogma that urines are sterile. Instead, the urinary tract hosts many bacteria, the so-called urobiome, that contribute to its homeostasis and pathology. Urobiome seems to be involved in the pathogenesis of the urinary tract infections (UTIs) and its relationship with the gut microbiome is still far from being understood. We describe a case of an emergent urinary condition, the “purple urine bag syndrome” (PUBS) that displayed with a peculiar combination of pathogens: Corynebacterium urealitycum and Enterococcus faecium. Both bacteria have been described as components of the urobiome and the latter is a well-known member of the gut microbiome but also a possible uropathogen. This case report is the starting point to analyze what we know about urobiome, its role in UTIs, and its interactions with the gut microbiome in the socalled “gut-UTIs axis”.

Volatile organic compounds (VOCs) produced by yeasts can positively affect crops, acting as antifungals or biostimulants. In this study, Aureobasidium pullulans and Metschnikowia pulcherrima were evaluated as potential antagonists of Trichoderma spp., common fungal pathogen in mushroom cultivation. To assess the biocontrol ability and biostimulant properties of the selected yeast species, in vitro co-culture and VOCs exposure assays were conducted. In both assays, VOCs produced by Aureobasidium spp. showed the stronger antifungal activity with a growth inhibition up to 30 %. This result was further confirmed by the higher volatilome alcohol content revealed by solid phase microextraction-gas chromatography mass spectrometry (SPME/GC-MS). Overall, Aureobasidium strains can be potentially used as biocontrol agent in Pleorotus ostreatus and Cyclocybe cylindracea mycelial growth, without affecting their development as demonstrated by VOCs exposure assay and Fourier-transform infrared spectroscopy (FT-IR). Conversely, M. pulcherrima was characterized by a lower or absent antifungal properties and by a volatilome composition rich in isobutyl acetate, an ester often recognized as plant growth promoter. As confirmed by FT-IR, Lentinula mycelia exposed to M. pulcherrima VOCs showed a higher content of proteins and lipids, suggesting an improvement of some biochemical properties. Our study emphasizes that VOCs produced by specific yeast strains are potentially powerful alternative to synthetic fungicide in the vegetative growth of mushroom-forming fungi and also able to modify their biochemical composition., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 British Mycological Society. All rights reserved.)

Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto 'raw sequence' exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a 'guide schematic' resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

Foods contaminated by pathogens are responsible for foodborne diseases which have socioeconomic impacts. Many approaches have been extensively investigated to obtain specific and sensitive methods to detect pathogens in food, but they are often not easy to perform and require trained personnel. This work aims to propose a textile organic electrochemical transistor-based (OECT) biosensor to detect L. monocytogenes in food samples. The analyses were performed with culture-based methods, Listeria Precis™ method, PCR, and our textile OECT biosensor which used poly(3,4-ethylenedioxythiophene) (PEDOT):polystyrene sulfonate (PSS) (PEDOT:PSS) for doping the organic channel. Atomic force microscopy (AFM) was used to obtain topographic maps of the gold gate. The electrochemical activity on gate electrodes was measured and related to the concentration of DNA extracted from samples and hybridized to the specific capture probe immobilized onto the gold surface of the gate. This assay reached a limit of detection of 1.05 ng/μL, corresponding to 0.56 pM of L. monocytogenes ATCC 7644, and allowed the specific and rapid detection of L. monocytogenes in the analyzed samples. KEYPOINTS: • Textile organic electrochemical transistors functionalized with a specific DNA probe • AFM topographic and surface potential maps of a functionalized gold gate surface • Comparison between the Listeria monocytogenes Precis™ method and an OECT biosensor., (© 2023. The Author(s).)

Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system is assembled in an E. coli -based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a 'bio-orthogonal' hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect the femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include the real-time monitoring of the self-assembly of nucleic-acid-based devices in vivo and of the intracellular delivery of therapeutic nanostructures, as well as the in vitro and in vivo detection of different DNA/RNA targets.

Background and Objectives : The COVID-19 pandemic has been shaking lives around the world for nearly two years. The discovery of highly effective vaccines has not been able to stop the transmission of the virus. SARS-CoV-2 shows completely different clinical manifestations. A large percentage (about 40%) of admitted patients require treatment in an intensive care unit (ICU). This study investigates the factors associated with admission of COVID-19 patients to the ICU and whether it is possible to obtain a score that can help the emergency physician to select the hospital ward. Materials and Methods : We retrospectively recorded 313 consecutive patients who were presented to the emergency department (ED) of our hospital and had a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR) on an oropharyngeal swab. We used multiple logistic regression to evaluate demographic, clinical, and laboratory data statistically associated with ICU admission. These variables were used to create a prognostic score for ICU admission. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and receiver-operating characteristic curve (ROC) of the score for predicting ICU admission during hospitalization were calculated. Results : Of the variables evaluated, only blood type A ( p = 0.003), PaO2/FiO2 ( p = 0.002), LDH ( p = 0.004), lactate ( p = 0.03), dyspnea ( p = 0.03) and SpO2 ( p = 0.0228) were significantly associated with ICU admission after adjusting for sex, age and comorbidity using multiple logistic regression analysis. We used these variables to create a prognostic score called GOL2DS (group A, PaO2/FiO2, LDH, lactate and dyspnea, and SpO2), which had high accuracy in predicting ICU admission (AUROC 0.830 [95% CI, 0.791-0.892). Conclusions : In our single-center experience, the GOL2DS score could be useful in identifying patients at high risk for ICU admission.

It has been proposed that vaccines may exert an unspecific protective effect against infectious agents, different than expected. Coronavirus disease 2019 (COVID-19) is a pandemic infection with high mortality in older patients due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The high number of vaccinations may be one of the reasons why children show a lower susceptibility to SARS-CoV-2 infection and milder severity when compared to adults. We have designed a study aimed at investigating whether the influenza vaccine may reduce the susceptibility and severity of SARS-CoV-2 infection. We retrospectively enrolled 635 patients who accessed our Emergency Department from March 1st to June 30th, 2020, and were diagnosed with COVID-19 infection confirmed by an RT-PCR on an oropharyngeal swab. Clinical data, outcomes, and influenza vaccination status were collected from the electronic medical records of our Hospital. We also used data from the Italian Health Ministry to compare the prevalence of flu vaccination among the general population of the Lazio Region and our enrolled patients. We then compared clinical outcomes between vaccinated and non-vaccinated patients, by univariate and multivariate analysis. COVID-19-positive patients older than 65 years reported a lower prevalence of flu vaccination when compared to the general population residing in the Lazio (p = 0.004). After correction for gender, age, and comorbidities, we found a lower risk of death at 60 days in patients with flu vaccination than in not vaccinated patients (p = 0.001). Our study shows that flu vaccination could reduce the mortality of COVID-19. Prospective studies are needed to confirm this result., (© 2021. Società Italiana di Medicina Interna (SIMI).)

DNA-based memory systems are being reported with increasing frequency. However, dynamic DNA data structures able to store and recall information in an ordered way, and able to be interfaced with external nucleic acid computing circuits, have so far received little attention. Here we present an in vitro implementation of a stack data structure using DNA polymers. The stack is able to record combinations of two different DNA signals, release the signals into solution in reverse order, and then re-record. We explore the accuracy limits of the stack data structure through a stochastic rule-based model of the underlying polymerisation chemistry. We derive how the performance of the stack increases with the efficiency of washing steps between successive reaction stages, and report how stack performance depends on the history of stack operations under inefficient washing. Finally, we discuss refinements to improve molecular synchronisation and future open problems in implementing an autonomous chemical data structure., (© 2021. The Author(s).)

Introduction: To date, mainly due to age-related vulnerability and to coexisting comorbidities, older patients often face a more severe COVID-19. This study aimed to identify at Emergency Department (ED) admission the predictors of in-hospital mortality and suitable scores for death risk stratification among COVID-19 patients ≥ 80 years old., Methods: Single-centre prospective study conducted in the ED of an university hospital, referral center for COVID-19 in central Italy. We included 239 consecutive patients ≥ 80 years old with laboratory-confirmed COVID-19. The primary study endpoint was all-cause in-hospital mortality. Multivariable Cox regression analysis was performed on significant variables at univariate analysis to identify independent risk factor for death. Overall performance in predicting mortality of WHO severity scale, APACHE II score, NEWS score, and CURB-65 was calculated., Results: Median age was 85 [82-89] and 112 were males (46.9%). Globally, 77 patients (32.2%) deceased. The presence of consolidations at chest x-ray and the hypoxemic respiratory failure were significant predictors of poor prognosis. Moreover, age ≥ 85 years, dependency in activities of daily living (ADL), and dementia were risk factors for death, even after adjusting for clinical covariates and disease severity. All the evaluated scores showed a fairly good predictive value in identifying patients who could experience a worse outcome., Conclusions: Among patients ≥ 80 years old hospitalized with COVID-19, not only a worse clinical and radiological presentation of the disease, but also the increasing age, dementia, and impairment in ADL were strong risk factors for in-hospital death, regardless of disease severity., (Copyright © 2021 Elsevier B.V. All rights reserved.)

How can the knowledge of probiotics and their mechanisms of action be translated into clinical practice when treating patients with diverticular disease and acute diverticulitis? Changes in microbiota composition have been observed in patients who were developing acute diverticulitis, with a reduction of taxa with anti-inflammatory activity, such as Clostridium cluster IV, Lactobacilli and Bacteroides. Recent observations supported that a dysbiosis characterised by decreased presence of anti-inflammatory bacterial species might be linked to mucosal inflammation, and a vicious cycle results from a mucosal inflammation driving dysbiosis at the same time. An alteration in gut microbiota can lead to an altered activation of nerve fibres, and subsequent neuronal and muscular dysfunction, thus favoring abdominal symptoms' development. The possible role of dysbiosis and mucosal inflammation in leading to dysmotility is linked, in turn, to bacterial translocation from the lumen of the diverticulum to perivisceral area. There, a possible activation of Toll-like receptors has been described, with a subsequent inflammatory reaction at the level of the perivisceral tissues. Being aware that bacterial colonisation of diverticula is involved in the pathogenesis of acute diverticulitis, the rationale for the potential role of probiotics in the treatment of this disease becomes clearer. For this review, articles were identified using the electronic PubMed database through a comprehensive search conducted by combining key terms such as "gut microbiota", "probiotics and gut disease", "probiotics and acute diverticulitis", "probiotics and diverticular disease", "probiotics mechanism of action". However, the amount of data present on this matter is not sufficient to draw robust conclusions on the efficacy of probiotics for symptoms' management in diverticular disease.

Introduction: This study was aimed to assess if combining the evaluation of blood glucose level (BGL) and the Triage Revised Trauma Score (T-RTS) may result in a more accurate prediction of the actual clinical outcome, both in general adult population and in elderly patients with trauma., Methods: This is a retrospective cohort study, conducted in the emergency department (ED) of an urban teaching hospital, with an average ED admission rate of 75,000 patients per year. Those excluded: known diagnosis of diabetes, age <18 years old, pregnancy, and mild trauma (classified as isolate trauma of upper or lower limb, in absence of exposed fractures). A combined Revised Trauma Score Glucose (RTS-G) score was obtained adding to T-RTS: two for BGL <160mg/dL (8.9mmol/L); one for BGL ≥160mg/dL and < 200mg/dL (11.1mmol/L); and zero for BGL ≥ 200mg/dL. The primary outcome was a composite of patient's death in ED or admission to intensive care unit (ICU). Receiver Operating Characteristic (ROC) curve analysis was used to evaluate the overall performance of T-RTS and of the combined RTS-G score., Results: Among a total of 68,933 traumas, 9,436 patients (4,407 females) were enrolled, aged from 18 to 103 years; 4,288 were aged ≥65 years. A total of 577 (6.1%) met the primary endpoint: 38 patients died in ED (0.4%) and 539 patients were admitted to ICU. The T-RTS and BGL were independently associated to primary endpoint at multivariate analysis. The cumulative RTS-G score was significantly more accurate than T-RTS and reached the best accuracy in elderly patients. In general population, ROC area under curve (AUC) for T-RTS was 0.671 (95% CI, 0.661 - 0.680) compared to RTS-G ROC AUC 0.743 (95% CI, 0.734 - 0.752); P <.001. In patients ≥65 years, T-RTS ROC AUC was 0.671 (95% CI, 0.657 - 0.685) compared to RTS-G ROC AUC 0.780 (95% CI, 0.768 - 0.793); P <.001., Conclusions: Results showed RTS-G could be used effectively at ED triage for the risk stratification for death in ED and ICU admission of trauma patients, and it could reduce under-triage of approximately 20% compared to T-RTS. Comparing ROC AUCs, the combined RTS-G score performs significantly better than T-RTS and gives best results in patients ≥65 years.

Objective: Mild Traumatic Brain Injury (MTBI) in anticoagulated patients is a common challenge for Emergency Department (ED) Physicians. Anticoagulation is considered a risk factor for developing delayed intracranial hemorrhage (ICH) after MTBI. The occurrence of this event in patients on Vitamin K Antagonists (VKA) or Direct Oral Anticoagulants (DOACs) remains unclear. Primary endpoint: to analyze the role of anticoagulants as risk factors for developing delayed ICH after MTBI and evaluate the indications to repeat a cranial computed tomography (CT) after a period of observation. Secondary endpoint: to assess the difference in the prevalence rate of delayed ICH in patients on VKA versus those on DOACs., Patients and Methods: We evaluated all consecutive patients admitted to our ED for MTBI, which had a control CT for late ICH after a negative CT at admission. We used a propensity score match (PSM) on factors affecting the need for oral anticoagulation to adjust the comparison between anticoagulated vs. non-anticoagulated patients for the baseline clinical characteristics., Results: Among 685 patients enrolled, 15 (2.2%) developed ICH at control CT. After PSM, the incidence of ICH, although slightly higher, was not statistically different in anticoagulated patients vs. non-anticoagulated (2.3% vs. 0.6%, p=0.371). Among the 111 patients on VKA, 5 (4.5%) had a late ICH, compared to 4 out of 99 (4.0%) on DOACs; the difference was not statistically significant (p=0.868)., Conclusions: The risk of developing delayed ICH after MTBI in patients on anticoagulation therapy is low. After correction for baseline covariates, the risk does not appear higher compared to non-anticoagulated patients. Thus, a routine control CT scan seems advisable only for patients presenting a clinical deterioration. Larger, prospective trials are required to clarify the safety profile of DOACs vs. VKA in MTBI.

Lung ultrasound (LUS) has recently been advocated as an accurate tool to diagnose coronavirus disease 2019 (COVID-19) pneumonia. However, reports on its use are based mainly on hypothesis studies, case reports or small retrospective case series, while the prognostic role of LUS in COVID-19 patients has not yet been established. We conducted a prospective study aimed at assessing the ability of LUS to predict mortality and intensive care unit admission of COVID-19 patients evaluated in a tertiary level emergency department. Patients in our sample had a median of 6 lung areas with pathologic findings (inter-quartile range [IQR]: 6, range: 0-14), defined as a score different from 0. The median rate of lung areas involved was 71% (IQR: 64%, range: 0-100), while the median average score was 1.14 (IQR: 0.93, range: 0-3). A higher rate of pathologic lung areas and a higher average score were significantly associated with death, with an estimated difference of 40.5% (95% confidence interval [CI]: 4%-68%, p = 0.01) and of 0.47 (95% CI: 0.06-0.93, p = 0.02), respectively. Similarly, the same parameters were associated with a significantly higher risk of intensive care unit admission with estimated differences of 29% (95% CI: 8%-50%, p = 0.008) and 0.47 (95% CI: 0.05-0.93, p = 0.02), respectively. Our study indicates that LUS is able to detect COVID-19 pneumonia and to predict, during the first evaluation in the emergency department, patients at risk for intensive care unit admission and death., (Copyright © 2020 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)

Systemic or localized lympho-adenomegaly is a common cause of access to the emergency department (ED), and differential diagnosis is often complicated. The combination of anamnesis, physical examination, laboratory tests, and instrumental diagnosis are extremely important to orientate toward a rapid and correct therapy, even if a prompt discrimination of the etiology of this lymphadenomegaly is not often possible. Our aim with this review is to improve the management of a differential diagnosis between hematological and infective diseases as leishmaniasis in ED and suggest quick diagnostic techniques that might be useful for early identification. Together in the review, we describe a case report of a young man affected from visceral leishmaniasis who presented to our ED and was incorrectly addressed to the wrong ward for the study of his condition. Subsequently, we focus on the clinical presentation of visceral leishmaniasis and compare it to the most common differential diagnoses that are usually taken into account in the management of such patients.

The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which, for the first time, all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in a high synthesis yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy, and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time. Our work suggests that the scaffolded origami technique is a viable, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications.

Some studies have highlighted benefits for Lobesia botrana by adding Botrytis cinerea mycelium to an artificial larval diet and have suggested a mutualistic relationship between the two organisms on grapevine, hypothesizing that fungal sterols were the nutritional factor involved. Because the nutritional quality of an artificial diet should be similar to grapes to allow extrapolation of the results to the field conditions, in the current study L. botrana larval performance was compared when larvae were fed on grapes (berries) or two artificial diets either with or without enrichment with B. cinerea. Based on sterol analysis, the two artificial diets had high cholesterol content, but relative to berries showed comparable and low phytosterol contents, respectively (high- and low-phytosterol, HPh, and LPh). While larval fitness on the HPh diet was similar to berries, the LPh diet led to higher mortality and worse larval performance. The addition of the fungus compensated for the shortage in the LPh diet but did not improve the HPh diet. Supplementing the LPh diet with linoleic acid, which is supplied also from B. cinerea, partially improved larval performance. In a field experiment, females did not show any egg-laying preferences towards naturally botrytized bunches. The positive effect of B. cinerea on the moth's next generation that is reported in the literature could be a consequence of fungus developed inside berry tunnels bored by larvae. Therefore, based on our data and previous reports the existence of a mutualistic relationship between L. botrana and B. cinerea is not well-founded., (© 2020 Wiley Periodicals, Inc.)

Objective: Acute pancreatitis (AP) may present an aspecific clinical picture without abdominal symptoms (atypical AP). We compared clinical outcomes between typical and atypical AP., Patients and Methods: Thirty out of 1163 patients (2.6%) presented an atypical AP. Demographic, clinical data, laboratory and radiological findings, management type, length of hospital stay (LOS) and mortality rate were retrospectively reviewed. A case match analysis 2:1 was performed. The final groups comprised 50 typical APs (TAP group) and 25 atypical APs (AAP group)., Results: The AAP patients presented fever (36%), syncope (32%) and dyspnea (16%) as the most frequent symptoms. Laboratory values showed similarity between the two groups. We noted a comparable edematous AP rate in both groups (p=0.36). Ten (20%) TAP and 3 (12%) AAP patients needed ERCP, respectively (p=0.38). Cholecystectomy was similarly performed in both cohorts (p=0.81). One TAP patient underwent a percutaneous drainage and subsequent surgical necrosectomy compared to none in the AAP cohort (p=0.47). LOS and mortality rate were comparable (p=0.76 and 0.3, respectively)., Conclusions: Similar outcomes have been reached in the two groups. Routine evaluation of the serum amylase values fundamentally contributed to early diagnosis and appropriate treatment.

With our study, we searched the medical literature to find magnesium (Mg) correlation with Emergency situations or its use in Emergency Medicine. Our aim is to fill the gap that we find in our daily routine between Mg studies on its role in Emergency and the real conception that doctors have of it in medical practice. We searched the literature for terms as magnesium or magnesium sulphate, magnesium in emergency, eclampsia, arrhythmias, acute asthma exacerbation, magnesium, and pediatric population. After a thorough research, we divided our discoveries into chapters to sort out a large amount often discordant articles.

RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.

Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37). While no phenotype change associated with Tn6212 mobilization could be detected, strains CRAFRU 12.29 and CRAFRU 12.50 did not elicit the hypersensitivity response (HR) on tobacco and eggplant leaves and were limited in their growth in kiwifruit leaves due to insertion of ISPsy31 and ISPsy36 in the hrpS and hrpR genes, respectively, interrupting the hrp cluster. Both strains had been isolated from symptomatic plants, suggesting coexistence of variant strains with reduced virulence together with virulent strains in mixed populations. The structural differences caused by rearrangements of self-genetic elements within European and New Zealand strains were comparable in number and type to those occurring among the European strains, in contrast with the significant difference in terms of nucleotide polymorphisms. We hypothesize a relaxation, during clonal expansion, of the selection limiting the accumulation of deleterious mutations associated with genome structural variation due to transposition of mobile elements. This consideration may be relevant when evaluating strategies to be adopted for epidemics management.

In the quest of greater sensitivity and specificity of diagnostic systems, one continually searches for alternative DNA hybridization methods, enabling greater versatility and where possible field-enabled detection of target analytes. We present, herein, a hybrid molecular self-assembled scaffolded DNA origami entity, intimately immobilized via capture probes linked to aminopropyltriethoxysilane, onto a glass optical fiber end-face transducer, thus producing a novel biosensor. Immobilized DNA nanorobots with a switchable flap can then be actuated by a specific target DNA present in a sample, by exposing a hemin/G-quadruplex DNAzyme, which then catalyzes the generation of chemiluminescence, once the specific fiber probes are immersed in a luminol-based solution. Integrating organic nanorobots to inorganic fiber optics creates a hybrid system that we demonstrate as a proof-of-principle can be utilized in specific DNA sequence detection. This system has potential applications in a wide range of fields, including point-of-care diagnostics or cellular in vivo biosensing when using ultrathin fiber optic probes for research purposes., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding. We demonstrate our fully synthetic scaffold design with both DNA and RNA origamis and describe a protocol to produce these bio-orthogonal and uniquely addressable origami scaffolds.

A strategy for an innovative, continuous and reversible LSPR tuning using DNA origami actuation to modulate the nanometric separation of two gold nanoparticles has been developed. The actuation mechanism is based on DNA hybridization, in particular three different DNA sequences were shown to induce resonance shift of up to 6 nm.

Xanthomonas perforans causes bacterial spot of tomato and pepper. A genome draft of an unusual isolate (strain 4P1S2), differing in that it was associated with stem pith necrosis, was assembled from Illumina MiSeq sequencing data using the draft of X. perforans strain 91-118 as a reference. The resulting draft (accession number JRWW00000000) largely overlapped with the reference draft. In addition, the reads not mapping on the reference assembly were selected and used for a further assembly, that revealed a large putative plasmid. The analysis of the predicted proteins showed only few gene features that could be potentially implicated in the switch of a phytopathological behavior., (© FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Pantoea agglomerans strains inducing a hypersensitive reaction in tobacco leaves are frequently isolated inside olive knots caused by Pseudomonas savastanoi pv. savastanoi. Here, we report the draft genome sequence of the Italian P. agglomerans strain, which is able to increase olive knot disease severity when coinoculated with P. savastanoi pv. savastanoi., (Copyright © 2014 Moretti et al.)

A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The phytoplasmas are currently named using the Candidatus category, as the inability to grow them in vitro prevented (i) the performance of tests, such as DNA-DNA hybridization, that are regarded as necessary to establish species boundaries, and (ii) the deposition of type strains in culture collections. The recent accession to complete or nearly complete genome sequence information disclosed the opportunity to apply to the uncultivable phytoplasmas the same taxonomic approaches used for other bacteria. In this work, the genomes of 14 strains, belonging to the 16SrI, 16SrIII, 16SrV and 16SrX groups, including the species "Ca. P. asteris", "Ca. P. mali", "Ca. P. pyri", "Ca. P. pruni", and "Ca. P. australiense" were analyzed along with Acholeplasma laidlawi, to determine their taxonomic relatedness. Average nucleotide index (ANIm), tetranucleotide signature frequency correlation index (Tetra), and multilocus sequence analysis of 107 shared genes using both phylogenetic inference of concatenated (DNA and amino acid) sequences and consensus networks, were carried out. The results were in large agreement with the previously established 16S rDNA based classification schemes. Moreover, the taxonomic relationships within the 16SrI, 16SrIII and 16SrX groups, that represent clusters of strains whose relatedness could not be determined by 16SrDNA analysis, could be comparatively evaluated with non-subjective criteria. "Ca. P. mali" and "Ca. P. pyri" were found to meet the genome characteristics for the retention into two different, yet strictly related species; representatives of subgroups 16SrI-A and 16SrI-B were also found to meet the standards used in other bacteria to distinguish separate species; the genomes of the strains belonging to 16SrIII were found more closely related, suggesting that their subdivision into Candidatus species should be approached with caution., (Copyright © 2013 Elsevier GmbH. All rights reserved.)

Fourier transform near infrared (FT-NIR) spectroscopy is an analytical procedure generally used to detect organic compounds in food. In this work the ability to predict fumonisin B(1)+B(2) contents in corn meal using an FT-NIR spectrophotometer, equipped with an integration sphere, was assessed. A total of 143 corn meal samples were collected in Friuli Venezia Giulia Region (Italy) and used to define a 15 principal components regression model, applying partial least square regression algorithm with full cross validation as internal validation. External validation was performed to 25 unknown samples. Coefficients of correlation, root mean square error and standard error of calibration were 0.964, 0.630 and 0.632, respectively and the external validation confirmed a fair potential of the model in predicting FB(1)+FB(2) concentration. Results suggest that FT-NIR analysis is a suitable method to detect FB(1)+FB(2) in corn meal and to discriminate safe meals from those contaminated., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Background: Contamination by mycotoxins is a major concern to the maize industry in north-east Italy where maize grain is often spoiled by Fusarium spp. In this work, fumonisins, deoxynivalenol and zearalenone were determined and an artificial neural network (ANN) model suitable for predicting mycotoxin contamination of maize at harvest time was developed., Results: The occurrence of deoxynivalenol and zearalenone was very limited, while fumonisins concentration ranged from 163 and to 3663 µg kg(-1) in 2007, and from 333 to 11473 µg kg(-1) in 2008. Statistical data analysis of factors affecting fumonisins concentration revealed that irrigation, chemical treatment against the European corn borer and harvest date significantly affected the level of contamination (P < 0.05), although the relevance of the factors was different in 2007 and 2008. The neural network approach showed a significant correlation between ascertained values and predictions based on agronomic data., Conclusion: This is the first time that an artificial neural network has been used to predict fumonisin accumulation in maize: the prediction has been shown to have the potential for the development of a new approach for the rapid cataloging of grain lots., (Copyright © 2012 Society of Chemical Industry.)

Background: In maize-growing areas where fumonisin contamination is endemic, there is an urgent need for novel methods to assess the quality of grain lots before their delivery to common drying and storage collection centres. Aerobiological samples of fungal spores released during harvest were analysed to establish a relationship between fumonisin contamination and the abundance of pathogen propagules collected in the combine harvester using a cyclone and membrane filters. Filter-captured propagules were analysed by direct plating, immunoenzymatic assay of specific Fusarium extracellular polysaccharides and real time polymerase chain reaction of the extracted DNA using fum1, a gene involved in the biosynthesis of fumonisin, as a target., Results: The results showed that time of harvest and environmental conditions strongly influenced the efficiency and performance of the collection system. The data obtained were informative in comparing individual samples collected under similar conditions. The immunoenzymatic assay provided the most reliable data, which improved the ability of a neural network to predict the fumonisin content of lots, when added to agronomic, environmental and phytosanitary data., Conclusion: This is the first attempt to evaluate the Fusarium propagules dispersed during harvesting as a predictive means to assess maize quality. A method based on cyclone/filter capture and immunological detection has been shown to be feasible and to have the potential for the development of a continuous monitoring system, but the prediction capabilities in the present implementation were limited.

The post-harvest mycobiota of dried grapes, used in Friuli Venezia Giulia (Northern-East Italy) for the production of "passito" dessert wines, was investigated in order to detect potential ochratoxin A (OTA)-producers. Five grape cultivars were analysed and only isolates belonging to the genera Aspergillus and Penicillium were evaluated. No Aspergillus spp. was found while 379 strains of Penicillium spp. were isolated. Four strains produced UV fluorescent metabolites on grape juice agar and synthetic liquid media as observed by thin-layer chromatography (TLC). Three of these resulted OTA producers when analyzed by high pressure liquid chromatography (HPLC), following immunoaffinity column purification. According to the results of morphological examinations and ribosomal DNA sequencing, the OTA producer strains did not belong to the species P. verrucosum or P. nordicum. The corresponding passito wines did not contain OTA.

Objective: To compare the efficacy of two protocols for the eradication of Helicobacter pylori infection and the healing of active duodenal ulcer: (i) ranitidine bismuth citrate (RBC) plus two antibiotics for 7 days, and (ii) the same triple therapy followed by 3 weeks of anti-secretory drug treatment., Methods: The study comprised 102 patients with active duodenal ulcer and H. pylori infection; the patients were randomized to open treatment with either RBC 400 mg b.d. plus amoxycillin 1 g b.d. and clarithromycin 500 mg b.d. for 7 days, or the same treatment followed by 3 weeks of RBC 400 mg b.d. alone. Ulcer healing was confirmed by endoscopy. H. pylori eradication was assessed by endoscopy, rapid urease test and histology., Results: The ulcer healed in 48/50 patients on RBC-based triple therapy alone (96.0%) and in 51/52 patients on triple therapy plus further anti-secretory treatment (98.1%). On an intention-to-treat basis, H. pylori had been successfully eradicated in 42/50 patients on triple therapy (84.0%) and in 44/52 patients on triple therapy plus anti-secretory treatment (84.6%), while by per protocol analysis the H. pylori eradication rates were 91.3% (42/46) and 89.8% (44/49), respectively., Conclusions: One-week triple therapy with RBC, amoxycillin and clarithromycin is highly effective in eradicating H. pylori and healing duodenal ulcers, even if not followed by anti-secretory drug treatment.

We report a 62-year-old man who presented with Schönlein-Henoch purpura (SHP) associated with duodenal ulcer and gastric Helicobacter pylori (HP) infection. The recurrent purpuric rash faded after HP eradication with amoxycillin, clarythromycin, and omeprazole treatment. These findings suggest a causative role for HP in the occurrence of SHP.