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The use of barley (Hordeum vulgare L.) in Morocco is still limited to food and feed despite the amplified demand by local industries for imported malt. This study aims to evaluate 36 barley elite l...

The activity of frontal motor areas during hand-object interaction is coordinated by dense communication along specific white matter pathways. This architecture allows the continuous shaping of voluntary motor output but, despite extensive investigation in non-human primate studies, remains poorly understood in humans. Disclosure of this system is crucial for predicting and treatment of motor deficits after brain lesions. For this purpose, we investigated the effect of direct electrical stimulation on white matter pathways within the frontal lobe on hand-object manipulation. This was tested in 34 patients (15 left hemisphere, mean age 42 years, 17 male, 15 with tractography) undergoing awake neurosurgery for frontal lobe tumour removal with the aid of the brain mapping technique. The stimulation outcome was quantified based on hand-muscle activity required by task execution. The white matter pathways responsive to stimulation with an interference on muscles were identified by means of probabilistic density estimation of stimulated sites, tract-based lesion-symptom (disconnectome) analysis and diffusion tractography on the single patient level. Finally, we assessed the effect of permanent tract disconnection on motor outcome in the immediate postoperative period using a multivariate lesion-symptom mapping approach. The analysis showed that stimulation disrupted hand-muscle activity during task execution at 66 sites within the white matter below dorsal and ventral premotor regions. Two different EMG interference patterns associated with different structural architectures emerged: (i) an ‘arrest’ pattern, characterized by complete impairment of muscle activity associated with an abrupt task interruption, occurred when stimulating a white matter area below the dorsal premotor region. Local middle U-shaped fibres, superior fronto-striatal, corticospinal and dorsal fronto-parietal fibres intersected with this region. (ii) a ‘clumsy’ pattern, characterized by partial disruption of muscle activity associated with movement slowdown and/or uncoordinated finger movements, occurred when stimulating a white matter area below the ventral premotor region. Ventral fronto-parietal and inferior fronto-striatal tracts intersected with this region. Finally, only resections partially including the dorsal white matter region surrounding the supplementary motor area were associated with transient upper-limb deficit (P = 0.05; 5000 permutations). Overall, the results identify two distinct frontal white matter regions possibly mediating different aspects of hand-object interaction via distinct sets of structural connectivity. We suggest the dorsal region, associated with arrest pattern and postoperative immediate motor deficits, to be functionally proximal to motor output implementation, while the ventral region may be involved in sensorimotor integration required for task execution.

We propose a simple general framework to predict folding, native states, energy barriers, protein unfolding, as well as mutation induced diseases and other protein structural analyses. The model should not be considered as an alternative to classical approaches (Molecular Dynamics or Monte Carlo) because it neglects low scale details and rather focuses on global features of proteins and structural information. We aim at the description of phenomena that are out of the range of classical molecular modeling approaches due to the large computational cost: multimolecular interactions, cyclic behavior under variable external interactions, and similar. To demonstrate the effectiveness of the approach in a real case, we focus on the folding and unfolding behavior of tropoelastin and its mutations. Specifically, we derive a discrete mechanical model whose structure is deduced based on a coarse graining approach that allows us to group the amino acids sequence in a smaller number of `equivalent’ masses. Nearest neighbor energy terms are then introduced to reproduce the interaction of such amino acid groups. Nearest and non-nearest neighbor energy terms, inter and intra functional blocks are phenomenologically added in the form of Morse potentials. As we show, the resulting system reproduces important properties of the folding-unfolding mechanical response, including the monotonic and cyclic force-elongation behavior, representing a physiologically important information for elastin. The comparison with the experimental behavior of mutated tropoelastin confirms the predictivity of the model. Statement of significance Classical approaches to the study of phenomena at the molecular scale such as Molecular Dynamics (MD) represent an incredible tool to unveil mechanical and conformational properties of macromolecules, in particular for biological and medical applications. On the other hand, due to the computational cost, the time and spatial scales are limited. Focusing of the real case of tropoelastin, we propose a new approach based on a careful coarse graining of the system, able to describe the overall properties of the macromolecule and amenable of extension to larger scale effects (protein bundles, protein-protein interactions, cyclic loading). The comparison with tropoelastin behavior, also for mutations, is very promising.

SummaryMany of the current and synonymous names applied to the species of Diospyros L. (Ebenaceae) from Peninsular Malaysia and Singapore lack a type. Here we designate lectotypes and two neotypes and establish the correct combinations for the taxa belonging to the species hitherto known as Diospyros pilosanthera.

In this contribution, new data concerning bryophytes, fungi and lichens of the Italian flora are presented. It includes new records, confirmations or exclusions for the bryophyte genera Acaulon, Campylopus, Entosthodon, Homomallium, Pseudohygrohypnum, and Thuidium, the fungal genera Entoloma, Cortinarius, Mycenella, Oxyporus, and Psathyrella and the lichen genera Anaptychia, Athallia, Baeomyces, Bagliettoa, Calicium, Nephroma, Pectenia, Phaeophyscia, Polyblastia, Protoparmeliopsis, Pyrenula, Ramalina, and Sanguineodiscus.

Objective: The aim of this study is to evaluate the efficacy of a food supplement containing Phyllanthus niruri and Chrysanthellum americanum in association with potassium and magnesium citrates in the treatment and prophylaxis of urinary stones. Materials and methods: Eighty-two patients (mean age 49.7 ± 11.2) with history of urinary stones received this food supplement, one capsule a day for 6 months. Each administration contained a combination of the following ingredients: 244 mg Potassium citrate, 735 mg Magnesium citrate, Phyllanthus (Phyllantus niruri) herb d.e. 15% mg Tannins 220 mg, Chrysanthellum (Chrysanthellum americanum Vatke) plant d.e. ¼ 55 mg. After 6 months, all patients underwent urologic visit, urinalysis, imaging and quality of life (QoL) questionnaires evaluation. Each patient was also evaluated by computed tomography (CT) scan at baseline and at 6 months. Result: From January 2018 to March 2019, 82 patients (mean age 49.7 ± 11.2) completed the follow-up period and were analyzed. Fifty patients showed lower stone dimensions (60.9%). The average stone size was 0.9 mm, with a significant reduction in comparison with the baseline (-6.7 mm ± 3 mm) (p < 0.001). Forty-nine patients (59.7%) did not show any symptomatic episode with an improving in QoL (+0.4 ± 0.1) (p < 0.001) in comparison with the baseline. At the end of the follow-up period, 27 patients out of 82 were stone-free (32.9%). Moreover, we report a significant reduction of patients with asymptomatic bacteriuria (ABU) between the baseline and the end of the follow-up evaluation (p < 0.001). Conclusions: In conclusion, this food supplement is able to improve quality of life in patients with urinary stones, reducing symptomatic episodes and the prevalence of ABU.

The hypothalamus and Locus Coeruleus (LC) share a variety of functions, as both of them take part in the regulation of the sleep/wake cycle and in the modulation of autonomic and homeostatic activities. Such a functional interplay takes place due to the dense and complex anatomical connections linking the two brain structures. In Alzheimer’s disease (AD), the occurrence of endocrine, autonomic and sleep disturbances have been associated with the disruption of the hypothalamic network; at the same time, in this disease, the occurrence of LC degeneration is receiving growing attention for the potential roles it may have both from a pathophysiological and pathogenetic point of view. In this review, we summarize the current knowledge on the anatomical and functional connections between the LC and hypothalamus, to better understand whether the impairment of the former may be responsible for the pathological involvement of the latter, and whether the disruption of their interplay may concur to the pathophysiology of AD. Although only a few papers specifically explored this topic, intriguingly, some pre-clinical and post-mortem human studies showed that aberrant protein spreading and neuroinflammation may cause hypothalamus degeneration and that these pathological features may be linked to LC impairment. Moreover, experimental studies in rodents showed that LC plays a relevant role in modulating the hypothalamic sleep/wake cycle regulation or neuroendocrine and systemic hormones; in line with this, the degeneration of LC itself may partly explain the occurrence of hypothalamic-related symptoms in AD.

The catecholamine-containing brainstem nuclei locus coeruleus (LC) and ventral tegmental area (VTA) are critically involved in stress responses. Alterations of catecholamine systems during chronic stress may contribute to neurodegeneration, including cognitive decline. Stress-related catecholamine alterations, while contributing to anxiety and depression, might accelerate neuronal degeneration by increasing the formation of toxic dopamine and norepinephrine by-products. These, in turn, may impair proteostasis within a variety of cortical and subcortical areas. In particular, the molecular events governing neurotransmission, neuroplasticity, and proteostasis within LC and VTA affect a variety of brain areas. Therefore, we focus on alterations of autophagy machinery in these nuclei as a relevant trigger in this chain of events. In fact, these catecholamine-containing areas are mostly prone to autophagy-dependent neurodegeneration. Thus, we propose a dynamic hypothesis according to which stress-induced autophagy alterations within the LC-VTA network foster a cascade towards early neurodegeneration within these nuclei.

In this contribution, new data concerning bryophytes, fungi, and lichens of the Italian flora are presented. It includes new records and confirmations for the bryophyte generaAneura,Aulacomnium,Dumortiera,Fossombronia,Hennediella,Hygrohypnella,Pohlia,Porella,Riccardia,Tortella, andTortula, the fungal generaCortinarius,Mycena,Naucoria,Trichoglossum, andTubariaand the lichen generaAgonimia,Blastenia,Chaenotheca,Cladonia,Endocarpon,Gyalecta,Lecanographa,Parmeliella,Porpidia,Stenhammarella, andThelidium.

Background: Inflammatory breast cancer (IBC) has a distinctive and aggressive clinical behavior but its underlying biological characteristics have not been fully elucidated. The extended analysis of somatic alterations in The Cancer Genome Atlas (TCGA) highlighted canonical oncogenic pathways that were consistently represented across different tumor subtypes. The aim of this study was to translate such pathway-based characterization to the clinical setting through ctDNA NGS to dissect IBC’s biology and prognosis. Methods: The study retrospectively analyzed 255 metastatic breast cancer (MBC) patients (pts) treated and characterized for ctDNA at Northwestern University (Chicago, IL). ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health). Only non-synonymous alterations were analyzed. Pathway classification was defined based on prior work (Sanchez-Vega F et al, Cell. 2018). Associations among clinical characteristics, pathway classification, and IBC were explored through uni- and multivariate logistic regression; survival was tested though uni- and multivariate Cox regression both for progression-free survival (PFS) and overall survival (OS). Results: Of 255 enrolled pts, 124 (48%) were diagnosed with hormone receptor positive (HR pos) MBC, 75 (30%) with HER2-positive (HER2_pos) MBC and 56 (22%) with triple negative (TNBC) MBC. IBC was diagnosed in 74 pts (30%). Receptor-tyrosine kinase, RTK (130 pts, 51%), p53 (130 pts, 51%), PI3K/Akt (116 pts, 46%), and cell cycle (91 pts, 36%) were the most often altered pathways. The multivariate model highlighted the association of IBC with HER2_pos (OR: 2.19; 95%CI: 1.09 - 4.38; P=0.0276), an increased number of alterations in the p53 pathway (OR: 2.05; 95%CI: 1.12 - 3.75; P=0.0197) and a decreased number of alterations in the RAS pathway (OR: 0.34; 95%CI: 0.14 - 0.80; P=0.0137). Decreased alterations in the ER pathway were borderline significant (OR: 0.48; 95%CI: 0.22 - 1.03; P=0.0584). Only cell cycle alterations had an impact on PFS for IBC (HR: 2.20; 95%CI: 1.18 - 4.08; P=0.0127), while p53 and Wnt had an impact on nonIBC (respectively HR: 2.00; 95%CI: 1.23 - 3.25; P=0.0052 and HR: 3.40; 95%CI: 1.20 - 9.64; P=0.0212). The univariate model showed a significant impact on OS RAF, ER, and cell cycle pathways alterations for IBC, the role of ER and cell cycle pathways alterations was confirmed in the multivariate model (respectively HR: 6.19; 95%CI: 1.63 - 23.48; P=0.0073 and HR: 3.79; 95%CI: 1.04 - 13.75; P=0.0431). The multivariate model showed a prognostic impact only for p53 in the nonIBC subgroup (HR: 2.20; 95%CI: 1.11 - 4.36; P=0.0237) Conclusion: The ctDNA-based oncogenic signaling pathway characterization showed different biological and prognostic features across IBC and nonIBC MBC patients. Alterations of the p53 pathway were more likely to be present in IBC pts, while alterations in the RAS pathway were less represented in this cohort. ER and cell cycle pathways’ alterations impacted the OS of IBC MBC patients. Although preliminary, these results suggest a more comprehensive biological characterization based on ctDNA for treatment selection and clinical decision-making. Main alterations and pathwayGeneNumber of alterations%PathwayTP5318815.58p53PIK3CA14111.68PI3K/AktERBB2725.97RTKESR1705.8ERMYC574.72MycFGFR1463.81RTKEGFR453.73RTKCCNE1383.15Cell cycleMET322.65RTKNF1322.65RAS Citation Format: Lorenzo Gerratana, Andrew A Davis, Marco Mina, Saya L Jacob, Qiang Zhang, Ami N Shah, Paolo D’Amico, Neelima Katam, Firas Wehbe, Elena Vagia, Lisa Flaum, Leonidas Platanias, Amir Behdad, Fabio Puglisi, William J Gradishar, Giovanni Ciriello, Massimo Cristofanilli. Investigating oncogenic signaling pathways in inflammatory metastatic breast cancer (MBC) though circulating tumor DNA (ctDNA) next-generation sequencing (NGS) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS2-33.

In this contribution, new data concerning bryophytes, fungi, and lichens of the Italian flora are presented. It includes new records and confirmations for the bryophyte genera Encalypta, Grimmia, and Riccia, for the fungal genera Hericium, Inocybe, Inocutis, Pluteus, and Russula, and for the lichen genera Bryoria, Farnoldia, Hypocenomyce, Lecania, Paracollema, Peltigera, Sarcogyne, and Teloschistes.

Supplementing kindergarten children during a cold season with a prebiotic inulin-type fructans product with shorter and longer fructan chains has been shown to reduce febrile episodes requiring medical attention and to lower the incidence of sinusitis. These beneficial effects may be connected to the specific modulation of children’s gut microbiota. By applying quantitative and qualitative microbiota analysis this study aimed at characterising the gut microbiota composition and at exploring effects of prebiotic intervention on the gut microbiota during a 24-weeks intervention and during antibiotic treatment in healthy children. The study was a randomised, placebo-controlled trial with 258 healthy children aged 3 to 6 years consuming 6 g/day prebiotic inulin-type fructans or maltodextrin. During the course of the study, faecal samples were collected and subject to targeted qPCR analysis and phylogenetic profiling by multiplexed high throughput sequencing of the prokaryotic 16S rRNA gene PCR amplicons. The microbiota composition of the cohort could be clustered into three distinct constellations (enterotypes). Prebiotic intake resulted in a selective modulation of the gut microbiota composition. Relative abundance of Bifidobacterium was significantly higher in the prebiotic group (n=104) compared to control group (n=105) and this effect was found for all three enterotypes. Antibiotic administration decreased the relative abundance of Bifidobacterium in both groups. Nonetheless, children of the prebiotic group receiving antibiotic treatment displayed significantly higher levels of Bifidobacterium than children receiving the placebo control. Prebiotic supplementation induced specific changes in the gut microbiota composition of children aged 3 to 6 years. Moreover, it attenuated antibiotic-induced disturbances in the gut microbiota composition as shown by higher relative abundance of bifidobacteria at the end of the antibiotic treatment in the prebiotic group. With the previously reported benefits on immune function, the study contributes to the evidence on the immune-modulating effects of prebiotics through gut microbiota modifications. The study was registered as NCT03241355 (https://clinicaltrials.gov/show/NCT03241355). Refereed/Peer-reviewed

We analysed the Horizon 2020 project database, currently the European Union’s (EU) largest framework programme for research and innovation—nearly 80 billion euros available over 7 years (2014–2020), to estimate the amount and type of EU-supported biomedical and health research and funding distribution among EU member states and non-European countries. Out of 20,877 projects as of 14th January 2019, a total of 4865 projects were classified as human health related. Ninety-four countries/territories worldwide participated in at least one biomedical project. The EU-15 original member states showed the highest participation as project leaders/partners and for acquired funding. Strong unequal funding distribution and participation between EU-15 and the 13 newest members—with EU-15 receiving about 87% of funding and EU-13 only 3%—have been evidenced. For both EU-15 and EU-13 we detected about 20% of projects involving the public and private sectors, according to Horizon 2020 guidelines. The largest percentage of projects was in the areas of biotechnological research (28.28%) and “basic research” (26.95%); these two sectors together accounted for 46.99% of the total funding assigned (7.9 billion euros). Research in neurosciences and neurological diseases appeared to be an increasing study area. Neurological and mental diseases covered about 21% of projects. Epidemiological studies accounted for about 5% of the total projects and for 14% of funding. Strong correlations were shown by indicators of financial and scientific capacity to identify success rates in obtaining EU funding, making the gap between countries with strong and weak research infrastructures difficult to overcome. Electronic supplementary material The online version of this article (10.1007/s10654-020-00690-9) contains supplementary material, which is available to authorized users.

Single- and group-housed pregnant sows were assessed during 8 weeks (4th and 8th to 14th) with regard to physiological, reproductive, welfare indicators and gene expression profiling. Compared to single-housed sows, group-housed sows had decreased non-return to estrus at 56 days after artificial insemination (AI) (83% vs 92%) and farrowing rate (78% vs 88%), respectively. Furthermore, group-housed sows showed a higher degree (

The blood red color of pigmented orange fruit varieties [Citrus sinensis L. (Osbeck)] is due to the presence of anthocyanin pigments that largely contribute to determine the high organoleptic qualities and the nutritional properties of the fruits. The content of pigments in sweet orange depends primarily on genetic factors and on environmental conditions. In particular, it has been extensively shown that cold temperature induces an increase of anthocyanin content that is achieved by the induction of the related gene expression. The purpose of our work is to understand the mechanism underlying the color variegation occurring inside the blood oranges during the cold induction of anthocyanin biosynthesis, despite the fact that the entire fruit is genotypically programmed to produce pigments. Therefore, the amount of anthocyanin and the expression of both structural and regulatory genes have been monitored in either high-pigmented (HP) or not/low pigmented (NP) segments of the same fruit during the storage at 4 °C for a total experimental period of 25 days. Our results clearly indicate that the anthocyanin content is directly correlated with the levels of gene transcription, with higher pigmented areas showing higher enhancement of gene expression. Furthermore, we analyzed the reshaping of the DNA methylation status at the promoter regions of genes related to anthocyanin biosynthetic pathway, such as DFR and Ruby. Our results unequivocally demonstrate that in the promoter regions of both DFR and Ruby, the amount of cytosine methylation strongly decreases along the cold storage in the HP areas, whereas it increases in the NP areas of the same fruit, probably causing a partial block of the gene transcription. Finally, by measuring the changes in the expression levels of the Citrus DNA demethylases, we found that DML1 might play a crucial role in determining the observed demethylation of DFR and Ruby promoters, with its expression induced by cold in the HP areas of the fruits. This is the first report in which different levels of gene expression implicated in anthocyanin production in blood orange fruit is correlated with an epigenetic control mechanism such as promoter methylation.

New Fe[Formula: see text] complexes of formula [Py8TPyzPzFe] · xH2O, its bis-pyridine adduct [Py8TPyzPzFe(py)2] · xH2O, the pentanuclear species [(MCl[Formula: see text]Py8TPyzPzFe] · xH2O (M [Formula: see text] Pd[Formula: see text], Pt[Formula: see text] and the bis-DABCO adducts [Py8TPyzPzFe(DABCO)2] · 11H2O and [(PdCl[Formula: see text]Py8TPyzPzFe(DABCO)2] · H2O (Py8TPyzPz [Formula: see text] octapyridino-tetrapyrazinoporphyrazinato dianion; DABCO [Formula: see text] 1,4-diazabiciclo[2.2.2]octane) were synthesized and characterized by elemental and thermogravimetric analysis, IR and UV-vis spectroscopy, with added studies on the starting complex [Py8TPyzPzFe] · xH2O regarding magnetic and electrochemical behavior. Clathrated water molecules are present in all compounds and have little to no effect on their physicochemical behavior as was observed for all previously reported analogs. UV-vis spectra of the mononuclear [Py8PyzPzFe] · xH2O complex in DMSO and pyridine are indicative of aggregation immediately after dissolving the compound. However, the spectra change slowly over time leading to formation of a porphyrazine species having spectral features typical of a monomer. UV-vis spectra of the parent pentanuclear [(MCl[Formula: see text]Py8TPyzPzFe] · xH2O (M [Formula: see text] Pd[Formula: see text], Pt[Formula: see text] complexes show a smaller degree of aggregation upon dissolution in DMSO or pyridine and the spectra of these solutions also change over time to those of a monomer. The presence of aggregation, spectral evolution with time and final species formed from the N-base adducts [Py8TPyzPzFe(DABCO)2] · 11H2O and [(PdCl[Formula: see text]Py8TPyzPzFe(DABCO)2] · H2O are reported and discussed.

Purpose: Patients with HER2+ breast cancer benefit from trastuzumab-containing regimens with improved survival. Adaptive immunity, including cytotoxic T-cell and antibody immunity, is critical to clinical efficacy of trastuzumab. Because Th cells are central to the activation of these antitumor effectors, we reason that HER2 patients treated with trastuzumab may benefit by administering vaccines that are designed to stimulate Th-cell immunity. Patients and Methods: We developed a degenerate HER2 epitope–based vaccine consisting of four HLA class II–restricted epitopes mixed with GM-CSF that should immunize most (≥84%) patients. The vaccine was tested in a phase I trial. Eligible women had resectable HER2+ breast cancer and had completed standard treatment prior to enrollment and were disease free. Patients were vaccinated monthly for six doses and monitored for safety and immunogenicity. Results: Twenty-two subjects were enrolled and 20 completed all six vaccines. The vaccine was well tolerated. All patients were alive at analysis with a median follow-up of 2.3 years and only two experienced disease recurrence. The percent of patients that responded with augmented T-cell immunity was high for each peptide ranging from 68% to 88%, which led to 90% of the patients generating T cells that recognized naturally processed HER2 antigen. The vaccine also augmented HER2-specific antibody. Immunity was sustained in patients with little sign of diminishing at 2 years following the vaccination. Conclusions: Degenerate HLA-DR–based HER2 vaccines induce sustainable HER2-specific T cells and antibodies. Future studies, could evaluate whether vaccination during adjuvant treatment with trastuzumab-containing regimens improves patient outcomes.

Combining no-till and cover crops (NT + CC) as an alternative to conventional tillage (CT) is generating interest to build-up farming systems&rsquo, resilience while promoting climate change adaptation in agriculture. Our field study aimed to assess the impact of long-term NT + CC management and short-term water stress on soil microbial communities, enzymatic activities, and the distribution of C and N within soil aggregates. High-throughput sequencing (HTS) revealed the positive impact of NT + CC on microbial biodiversity, especially under water stress conditions, with the presence of important rhizobacteria (e.g., Bradyrhizobium spp.). An alteration index based on soil enzymes confirmed soil depletion under CT. C and N pools within aggregates showed an enrichment under NT + CC mostly due to C and N-rich large macroaggregates (LM), accounting for 44% and 33% of the total soil C and N. Within LM, C and N pools were associated to microaggregates within macroaggregates (mM), which are beneficial for long-term C and N stabilization in soils. Water stress had detrimental effects on aggregate formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a promising alternative to CT, due to the contribution to soil C and N stabilization while enhancing the biodiversity and enzymes.

Complementary and alternative medicines represent an interesting field of research on which worldwide academics are focusing many efforts. In particular, the possibility to exploit pharmaceutical technology strategies, such as the nanoencapsulation, for the delivery of essential oils is emerging as a promising strategy not only in Italy but also all over the world. The aim of this work was the development of nanostructured lipid carriers (NLC) for the delivery of essential oils (Lavandula, Mentha, and Rosmarinus) by intranasal administration, an interesting topic in which Italian contributions have recently increased. Essential oil-loaded NLC, projected as a possible add-on strategy in the treatment of neurodegenerative diseases, were characterized in comparison to control formulations prepared with Tegosoft CT and Neem oil. Homogeneous (polydispersity index, PDI &lt, 0.2) nanoparticles with a small size (&lt, 200 nm) and good stability were obtained. Morphological and physical-chemical studies showed the formation of different structures depending on the nature of the liquid oil component. In particular, NLC prepared with Lavandula or Rosmarinus showed the formation of a more ordered structure with higher cytocompatibility on two cell lines, murine and human fibroblasts. Taken together, our preliminary results show that optimized positively charged NLC containing Lavandula or Rosmarinus can be proposed as a potential add-on strategy in the treatment of neurodegenerative diseases through intranasal administration, due to the well-known beneficial effects of essential oils and the mucoadhesive properties of NLC.

During the cell cycle, DNA suffers several lesions that need to be repaired prior to entry into mitosis to preserve genome integrity in daughter cells. Toward this aim, cells have developed complex enzymatic machinery, the so-called DNA damage response (DDR), which is able to repair DNA, temporarily stopping the cell cycle to provide more time to repair, or if the damage is too severe, inducing apoptosis. This DDR mechanism is considered the main source of resistance to DNA-damaging therapeutic treatments in oncology. Recently, cancer stem cells (CSCs), which are a small subset of tumor cells, were identified as tumor-initiating cells. CSCs possess self-renewal potential and persistent tumorigenic capacity, allowing for tumor re-growth and relapse. Compared with cancer cells, CSCs are more resistant to therapeutic treatments. Wee1 is the principal gatekeeper for both G2/M and S-phase checkpoints, where it plays a key role in cell cycle regulation and DNA damage repair. From this perspective, Wee1 inhibition might increase the effectiveness of DNA-damaging treatments, such as radiotherapy, forcing tumor cells and CSCs to enter into mitosis, even with damaged DNA, leading to mitotic catastrophe and subsequent cell death.

Background: Dietary strategies, including the use of probiotics as preventive agents that modulate the gut microbiota and regulate the function of adipose tissue, are suitable tools for the prevention or amelioration of obesity and its comorbidities. We aimed to evaluate the effect of lactic acid bacteria (LAB) with different adipo- and immuno-modulatory capacities on metabolic and immunological parameters and intestinal composition microbiota in high-fat-diet-induced in mice fed a high-fat dietMethods: Balb/c weaning male mice were fed a standard (SD) or high-fat diet (HFD) with or without supplementation with Limosilactobacillus fermentum CRL1446 (CRL1446), Lactococcus lactis CRL1434 (CRL1434), or Lacticaseibacillus casei CRL431 (CRL431) for 45 days. Biochemical and immunological parameters, white-adipose tissue histology, gut microbiota composition, and ex vivo cellular functionality (adipocytes and macrophages) were evaluated in SD and HFD mice.Results: CRL1446 and CRL1434 administration, unlike CRL431, induced significant changes in the body and adipose tissue weights and the size of adipocytes. Also, these strains caused a decrease in plasmatic glucose, cholesterol, triglycerides, leptin, TNF-α, IL-6 levels, and an increase of IL-10. The CRL1446 and CRL1434 obese adipocyte in ex vivo functionality assays showed, after LPS stimulus, a reduction in leptin secretion compared to obese control, while with CRL431, no change was observed. In macrophages from obese mice fed with CRL1446 and CRL1434, after LPS stimulus, lower levels of MCP-1, TNF-α, IL-6 compared to obese control were observed. In contrast, CRL431 did not induce modification of cytokine values. Regarding gut microbiota, all strain administration caused a decrease in Firmicutes/Bacteroidetes index and diversity. As well as, related to genus results, all strains increased, mainly the genera Alistipes, Dorea, Barnesiella, and Clostridium XIVa. CRL1446 induced a higher increase in the Lactobacillus genus during the study period.Conclusions: The tested probiotic strains differentially modulated the intestinal microbiota and metabolic/immunological parameters in high-fat-diet-induced obese mice. These results suggest that CRL1446 and CRL1434 strains could be used as adjuvant probiotics strains for nutritional treatment to obesity and overweight. At the same time, the CRL431 strain could be more beneficial in pathologies that require regulation of the immune system.

The peri-infarct region, which surrounds the irreversible ischemic stroke area is named ischemic penumbra. This term emphasizes the borderline conditions for neurons placed within such a critical region. Area penumbra separates the ischemic core, where frank cell loss occurs, from the surrounding healthy brain tissue. Within such a brain region, nervous matter, and mostly neurons are impaired concerning metabolic conditions. The classic biochemical marker, which reliably marks area penumbra is the over-expression of the heat shock protein 70 (HSP70). However, other proteins related to cell clearing pathways are modified within area penumbra. Among these, autophagy proteins like LC3 increase in a way, which recapitulates Hsp70. In contrast, components, such as P20S, markedly decrease. Despite apparent discrepancies, the present study indicates remarkable overlapping between LC3 and P20S redistribution within area penumbra. In fact, the amount of both proteins is markedly reduced within vacuoles. Specifically, a massive loss of LC3 + P20S immuno-positive vacuoles (autophagoproteasomes) is reported here. This represents the most relevant sub-cellular alteration here described in cell clearing pathways within area penumbra. The functional significance of these findings remains to be determined and it will take a novel experimental stream to decipher the fine-tuning of such a phenomenon.

Background: Bruton&rsquo, s tyrosine kinase (BTK) is involved in the immune response and its deficiency impairs B cell maturation. We evaluated the expression of a novel BTK isoform, p65BTK, in colorectal cancer (CRC), to identify its impact on survival. Materials and Methods: This retrospective study evaluated 87 consecutive stage III CRC patients treated at the National Cancer Institute of Aviano (1999&ndash, 2017). Multiple specimens were collected and analyzed for staining intensity and percentage of tumor cells positive for p65BTK. Prognostic impact was tested by univariate Cox regression analysis. Results: After a median follow-up of 82.59 months, median disease-free survival (DFS) and overall survival (OS) were 11.67 months and 31.33 months, respectively. Interestingly, 10% of patients did not express p65BTK. For the immunohistochemistry IHC intensity 1, the best cutoff point was 1% of p65BTK positivity, for IHC intensity 2, it was 50%, and for IHC intensity 3, it was 80%. Through univariate analysis, patients with highly expressed p65BTK (IHC intensity 3 and &ge, 80%) were shown to have the worst prognosis in terms of DFS (HR: 6.23, p = 0.005, 95% C.I. 1.75&ndash, 22.79) and OS (HR: 2.54, p = 0.025, 95% C.I. 1.12&ndash, 5.76). Conclusions: p65BTK is frequently expressed in CRC and, if highly expressed, is an unfavourable prognostic factor. However, further confirmation is needed and its potential targeting needs to be studied.

In this contribution, new data concerning algae, bryophytes, fungi, and lichens of the Italian flora are presented. It includes new records and confirmations for the algae genusChara, the bryophyte generaHomalia,Mannia, andTortella, the fungal generaCortinarius,Russula, andStereum, and the lichen generaCetrelia,Cladonia,Enterographa,Graphis,Lecanora,Lepraria,Multiclavula,Mycomicrothelia,Parmelia,Peltigera,Pleopsidium,Psora,Scytinium,Umbilicaria, andRhizocarpon.

Human frataxin is an iron-binding protein involved in the mitochondrial iron-sulfur (Fe-S) clusters assembly, a process fundamental for the functional activity of mitochondrial proteins. Decreased level of frataxin expression is associated with the neurodegenerative disease Friedreich ataxia. Defective function of frataxin may cause defects in mitochondria, leading to increased tumorigenesis. Tumor-initiating cells show higher iron uptake, a decrease in iron storage and a reduced Fe-S clusters synthesis and utilization. In this study, we selected, from COSMIC database, the somatic human frataxin missense variants found in cancer tissues p.D104G, p.A107V, p.F109L, p.Y123S, p.S161I, p.W173C, p.S181F, and p.S202F to analyze the effect of the single amino acid substitutions on frataxin structure, function, and stability. The spectral properties, the thermodynamic and the kinetic stability, as well as the molecular dynamics of the frataxin missense variants found in cancer tissues point to local changes confined to the environment of the mutated residues. The global fold of the variants is not altered by the amino acid substitutions; however, some of the variants show a decreased stability and a decreased functional activity in comparison with that of the wild-type protein.

In this contribution, new data concerning algae, bryophytes, fungi, and lichens of the Italian flora are presented. It includes new records and confirmations for the algae genusChara, the bryophyte generaCephalozia,Conardia,Conocephalum,Didymodon,Sphagnum,Tetraplodon, andTortula, the fungal generaEndophyllum,Gymnosporangium,Microbotryum,Phragmidium, andPluteus, and the lichen generaCandelariella,Cladonia,Flavoplaca,Lichenothelia,Peltigera,Placolecis,Rinodina,Scytinium, andSolenopsora.

In this contribution, new data concerning red algae, bryophytes, fungi and lichens of the Italian flora are presented. It includes new records and confirmations for the algal genus Thorea, for the bryophyte genera Ephemerum, Hedwigia, Pogonatum, Riccia, Sphagnum, and Tortella, the fungal genera Pileolaria and Sporisorium, and the lichen genera Bacidia, Cerothallia, Chaenotheca, Cladonia, Halecania, Lecanora, Phylloblastia, Physcia, Protoparmelia, Pycnora, Segestria, and Sphaerophorus.

Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in viral infection1 and a common target of antiretroviral drugs2. The reaction is catalysed by viral reverse transcriptase (RT)3,4 that is packaged in an infectious virion with two copies of viral genomic RNA5 each bound to host lysine 3 transfer RNA (tRNALys3), which acts as a primer for initiation of reverse transcription6,7. Upon viral entry into cells, initiation is slow and non-processive compared to elongation8,9. Despite extensive efforts, the structural basis of RT function during initiation has remained a mystery. Here we use cryo-electron microscopy to determine a three-dimensional structure of an HIV-1 RT initiation complex. In our structure, RT is in an inactive polymerase conformation with open fingers and thumb and with the nucleic acid primer–template complex shifted away from the active site. The primer binding site (PBS) helix formed between tRNALys3 and HIV-1 RNA lies in the cleft of RT and is extended by additional pairing interactions. The 5′ end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site, with a linker that connects these helices to the RNase H region of the PBS. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action. A cryo-EM structure of an initiation complex of HIV-1 reverse transcriptase sheds light on the initiation of reverse transcription of viral RNA.

Objectives This study is aimed to report a case of SV-related gastritis and the results of a systematic review of SV infections in the literature. Methods Following a case presentation, we systematically searched different databases (MEDLINE, PubMed, Scopus, Web of Science, EMBASE) for the items “sarcina,” “ventriculi,” “clostridium” with AND/OR. Results A total of 55 articles reporting 65 cases of Sarcina Ventriculi were found. Thus, 66 patients, including our case, were reviewed. Median age was 51 years (IQR: 0-87 years). Females accounted for 51% of cases. 68% of patients had one or more comorbidities. SV was isolated in the gastrointestinal tract (88%), respiratory (5%), urine (4%), and bloodstream (3%) systems. Upper endoscopy was performed in 52 patients (79%). Biopsies were obtained in all 52 cases, and resulted normal in 23%. Surgery was warranted in 15 patients (23%), and specific antimicrobial therapy was delivered in 34 (52%) patients. Mortality was 14%. At follow-up, 88% of patients showed complete eradication of the SV infection. Conclusions Upper gastrointestinal biopsy positive for SV should prompt an evaluation of the clinical conditions, being the risk of gastric perforation not negligible. Antibiotic therapy may eradicate the infection and prevent complications. Emergency surgery is required in case of source control.

Primary-Motor-Cortex (M1) hosts two functional components, at its posterior and anterior borders, being the first faster and more excitable. We developed a mapping-technique for M1 components identification and determined their functional cortical-subcortical architecture in M1 gliomas and the impact of their identification on tumor resection and motor performance. A novel advanced mapping technique was used in 102 tumors within M1 or CorticoSpinal-Tract to identify M1-two components. High-Frequency-stimulation (2–5 pulses) with an on-line qualitative and quantitative analysis of motor responses was used, the two components’ cortical/subcortical spatial distribution correlated to clinical, tumor-related factor and patients’ motor outcome, a cohort treated with standard-mapping was used for comparison. The two functional components were always identified on-line, in tumors not affecting M1, its functional segregation was preserved. In M1 tumors, two architectures, both preserving the two components, were disclosed: in 50%, a normal cortical/subcortical architecture emerged, while 50% revealed a distorted architecture with loss of anatomical reference and somatotopy, not associated with tumor histo-molecular features or volume, but with a previous treatment. Motor performance was maintained, suggesting functional compensation. By preserving the highest and resecting the lowest excitability component, the complete-resection increased with low morbidity. The real-time identification of two M1 functional components and the preservation of the highest excitability one increases safe resection, revealing M1 plasticity potentials.

Genomic stability in proliferating cells critically depends on telomere maintenance by telomerase reverse transcriptase. Here we developed a real-time single-molecule RNA sequencing approach that visualizes telomerase catalysis and structural dynamics at single-nucleotide resolution using FRET and zero-mode waveguides. The method permits direct detection of dynamic steps and structural states throughout the telomerase catalytic cycle and can be generalized to other nucleic acid polymerase systems.

The interplay between autophagy (ATG) and ubiquitin proteasome (UP) cell-clearing systems was recently evidenced at biochemical and morphological levels, where subunits belonging to both pathways co-localize within a novel organelle named autophagoproteasome (APP). We previously documented that APP occurs at baseline conditions, while it is hindered by neurotoxicant administration. This is bound to the activity of the mechanistic target of rapamycin (mTOR), since APP is stimulated by mTOR inhibition, which in turn, is correlated with cell protection. In this brief report, we provide novel, morphological and biochemical evidence on APP, suggesting the presence of active UP subunits within ATG vacuoles. Although a stream of interpretation considers such a merging as a catabolic pathway to clear inactive UP subunits, our data further indicate that UP-ATG merging may rather provide an empowered catalytic organelle.

Synthetic pesticides may have non-target effects on soil microorganisms which have been identified as a specific protection goal in pesticide environmental risk assessment. Most studies to date have focused on the effects of synthetic pesticides on soil microorganisms, whereas little is known about the response of the soil microbial community to the so-called low-risk pesticide classes. The main objective of this study was to assess the impact of a botanical (azadirachtin) and a low-dose pesticide (trifloxystrobin), applied as commercial formulations, on soil microbial functions. In a microcosm study, pesticides were applied in soil at increasing dose rates (up to ×100 the recommended dose rate). Their dissipation and the formation of the major transformation product (TP) of trifloxystrobin were determined. Enzymatic activities and the abundance of key functional microbial groups were measured via fluorometric assays, potential nitrification (PNT) and q-PCR. Trifloxystrobin and azadirachtin did not persist in soil at all dose rates with DT50s of 1.1–1.4 and 1.3 days respectively. No pesticide dose-dependent inhibitory effects on the activity of soil enzymes, the abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), sulfur-oxidizing bacteria (SOB) and on PNT were seen. Instead the application of both pesticides at all dose rates stimulated PNT. Trifloxystrobin was transformed to trifloxystrobin acid (TFSA), which persisted in soil. However its formation did not correlate with adverse effects on soil microbial functions. We provide first evidence that trifloxystrobin and azadirachtin do not impose unacceptable effects on soil microbial functions even at high dose rates.

Receptor for activated C kinase 1 (RACK1) is a eukaryote-specific ribosomal protein implicated in diverse biological functions. To engineer ribosomes for specific fluorescent labeling, we selected RACK1 as an target given its location on the small ribosomal subunit and other properties. However, prior results suggested that RACK1 has roles both on and off the ribosome, and such an exchange might be related to its various cellular functions and hinder our ability to use RACK1 as a stable fluorescent tag for the ribosome. In addition, the kinetics of spontaneous exchange of RACK1 or any ribosomal protein from a mature ribosomein vitroremain unclear. To address these issues, we engineered fluorescently-labeled human ribosomes via RACK1, and applied bulk and single-molecule biochemical analyses to track RACK1 on and off the human ribosome. Our results demonstrate that, despite its cellular non-essentiality from yeast to humans, RACK1 readily re-associates with the ribosome, displays limited conformational dynamics, and remains stably bound to the ribosome for hoursin vitro. This work sheds insight onto the biochemical basis of ribosomal protein exchange on and off a mature ribosome and provides tools for single-molecule analysis of human translation.

Amaranth (Amaranthus sp.) is a promising indigenous leafy vegetable plant capable of contributing to food security in sub-Saharan Africa, thanks to its adaptability to diverse soils and its drought tolerance. Its edible parts such as leaves are characterized by high nutrient content. Food losses along the supply chain due to spoilage, however, especially of fresh produce is a challenge facing most of the sub-Saharan African countries in tackling food insecurity in the region. This calls for innovative yet inexpensive solutions such as natural fermentation to preserve the quality and safety of the commodity. To demonstrate the feasibility of natural fermentation in the preservation of vegetable amaranth, leaves were submerged (1:0.5 w/v) in distilled water with 3% sucrose and 3% NaCl dissolved. Control batches were prepared using only distilled water (1:0.5 w/v) with amaranth leaves. Samplings of both treated leaves and controls occurred at 0, 24, 48, 72, and 168 h to measure the pH and determine microbial population changes using culture and molecular-based techniques. Furthermore, the effects of treatment on nutritional content were assayed at the end of the process to determine the levels of B-group vitamins, β-carotene, lutein, and anti-nutrient phytic acid from unfermented fresh air-dried and 3% sucrose and 3% NaCl treated amaranth leaves. Finally, a visive and olfactive analysis was carried out to evaluate the acceptability of the final product. The significant drop of pH and the correct growth of Lactobacillaceae occurred only in treated batches, although Lactococcus was found in both treated and control samples. Furthermore, mean counts observed on selective media for controls and molecular high-throughput sequencing (HTS) analyses confirmed that in control samples, the undesired bacteria represented more than 60% of the microbial population. In treated amaranth leaves the amount of thiamin, riboflavin, vitamin B6, β-carotene and lutein content were higher compared to the fresh unfermented air-dried leaves, and phytic acid content diminished after 7-days treatment. These findings suggest that treatment of amaranth leaves using 3% sucrose and 3% NaCl does not only preserve the commodity by arresting the growth of undesired microorganisms involved in spoilage and fosters the lactic acid bacteria but also improves the nutritional content of the fermented end product that has been warmly welcomed by panelists.

The exploitation of a plant-based sensor, able to measure ultraviolet radiation intensity with wavelength of UV-A band (315–400 nm) is here proposed. The approach presented arouses interest in the context of the realization of sensing devices and novel measurement systems green, non-toxic, environmentally friendly, low-cost and disseminable. The working principle is based on the use of natural sensing properties to UV-A radiation of the plant and its metabolic process in order to respond to the received UV intensity. The device is composed of Dimorphotheca ecklonis, which is a particularly sensitive plant to the physical quantity of interest and two implanted electrical contacts to convert, through a chemo-electrical process, the measurand into an output voltage across the electrodes. A suitable experimental setup has been developed and a LabVIEW™ routine has been used for the acquisition of the signal. Experimental results and the characterization of the plant-based sensor show the suitability of the proposed method which is able to work in absence of batteries making the system interesting for several intriguing applications.

We assessed the effects of EDTA and selected plant growth-promoting rhizobacteria (PGPR) on the phytoremediation of soils and sediments historically contaminated by Cr, Ni, and Cu. A total of 42 bacterial strains resistant to these heavy metals (HMs) were isolated and screened for PGP traits and metal bioaccumulation, and two Enterobacter spp. strains were finally selected. Phytoremediation pot experiments of 2 months duration were carried out with hemp (Cannabis sativa L.) and giant reed (Arundo donax L.) grown on soils and sediments respectively, comparing in both cases the effects of bioaugmentation with a single PGPR and EDTA addition on plant and root growth, plant HM uptake, HM leaching, as well as the changes that occurred in soil microbial communities (structure, biomass, and activity). Good removal percentages on a dry mass basis of Cr (0.4%), Ni (0.6%), and Cu (0.9%) were observed in giant reed while negligible values ( > roots > leaves > stems) with largest quantities in rhizomes (Cr 0.6, Ni 3.7, and Cu 2.2 g plant–1). EDTA increased Ni and Cu translocation to aerial parts in both crops, despite that in sediments high HM concentrations in leachates were measured. PGPR did not impact fine root diameter distribution of both crops compared with control while EDTA negatively affected root diameter class length (DCL) distribution. Under HM contamination, giant reed roots become shorter (from 5.2 to 2.3 mm cm–3) while hemp roots become shorter and thickened from 0.13 to 0.26 mm. A consistent indirect effect of HM levels on the soil microbiome (diversity and activity) mediated by plant response (root DCL distribution) was observed. Multivariate analysis of bacterial diversity and activity revealed not only significant effects of plant and soil type (rhizosphere vs. bulk) but also a clear and similar differentiation of communities between control, EDTA, and PGPR treatments. We propose root DCL distribution as a key plant trait to understand detrimental effect of HMs on microbial communities. Positive evidence of the soil-microbe-plant interactions occurring when bioaugmentation with PGPR is associated with deep-rooting perennial crops makes this combination preferable over the one with chelating agents. Such knowledge might help to yield better bioaugmented bioremediation results in contaminated sites.

How translation stops Protein synthesis concludes when a ribosome encounters a stop codon in a transcript, which triggers the recruitment of highly conserved release factors to liberate the protein product. Lawson et al . used traditional biochemical methods and single-molecule fluorescence assays to track the interplay of release factors with ribosomes and reveal the molecular choreography of termination. They identified two distinct classes of effectors, small molecules and mRNA sequences, that directly inhibited the release factors and promoted stop codon readthrough. These findings may buttress ongoing efforts to treat diseases caused by premature stop codons, which cause 11% of all heritable human diseases. —DJ

Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bind together to recognize stop codons rapidly and elicit termination via a tightly regulated, multi-step process that resembles tRNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis.One Sentence SummaryDirect visualization of eukaryotic translation reveals the dynamics of termination at stop codons.

Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) is a severe multisystemic disease characterized by immunological abnormalities and dysfunction of energy metabolism. Recent evidences suggest strong correlations between dysbiosis and pathological condition. The present research explored the composition of the intestinal and oral microbiota in CFS/ME patients as compared to healthy controls. The fecal metabolomic profile of a subgroup of CFS/ME patients was also compared with the one of healthy controls. The fecal and salivary bacterial composition in CFS/ME patients was investigated by Illumina sequencing of 16S rRNA gene amplicons. The metabolomic analysis was performed by an UHPLC-MS. The fecal microbiota of CFS/ME patients showed a reduction of Lachnospiraceae, particularly Anaerostipes, and an increased abundance of genera Bacteroides and Phascolarctobacterium compared to the non-CFS/ME groups. The oral microbiota of CFS/ME patients showed an increase of Rothia dentocariosa. The fecal metabolomic profile of CFS/ME patients revealed high levels of glutamic acid and argininosuccinic acid, together with a decrease of alpha-tocopherol. Our results reveal microbial signatures of dysbiosis in the intestinal microbiota of CFS/ME patients. Further studies are needed to better understand if the microbial composition changes are cause or consequence of the onset of CFS/ME and if they are related to any of the several secondary symptoms.

The strawberry is a low-growing, herbaceous perennial plant, sensitive to iron deficiency. The iron deficiency represents a nutritional disorder, leading to a decreased content of photosynthetic pigments, which determines the yellow color characteristic of chlorotic leaves. Therefore, in calcareous soils, the use of synthetic iron chelate is often mandatory in strawberry cultivation. The employment of novel microorganism-based formulations as alternatives to the use of iron chelates, was evaluated during strawberry cultivation by monitoring the morpho-biometric parameters, chlorophylls, the iron content in leaves and roots, and the Fe chelate reductase activity involved in absorption of iron during the chlorosis event in plants using the strategy I. The experimental design envisaged growing strawberry seedlings on an inert substrate (pumice), irrigated with Hoagland solution iron-free, with a 12 h photoperiod. After 42 days, at the first appearance of chlorosis symptoms, plants were transplanted into a calcareous soil, and after seven days, they were treated, by a single application, with a microorganism-based formulations (MBF), an inoculum (In) of Trichoderma spp. and Streptomyces spp., or Sequestrene (Sq). Strawberry plants were sampled and analyzed at 5, 10, 15, and 20 days from the treatments. The results showed that microorganism-based formulations positively affected the strawberry seedlings, by reducing the chlorosis symptoms, producing comparable effects to the Sequestrene treatment.

Plant growth promoting rhizobacteria (PGPR) can display several plant-beneficial properties, including support to plant nutrition, regulation of plant growth, and biocontrol of pests. Mechanisms behind these effects are directly related to the presence and expression of specific genes, and different PGPR strains can be differentiated by the presence of different genes. In this study we reported a comprehensive evaluation of a novel PGPR Klebsiella variicola UC4115 from the field to the lab, and from the lab to the plant. The isolate from tomato field was screened in-vitro for different activities related to plant nutrition and growth regulation as well as for antifungal traits. We performed a functional annotation of genes contributing to plant-beneficial functions previously tested in-vitro. Furthermore, the in-vitro characterization, the whole genome sequencing and annotation of K. variicola UC4115, were compared with the well-known PGPR Azospirillum brasilense strain Sp7. This novel comparative analysis revealed different accumulation of plant-beneficial functions contributing genes, and the presence of different genes that accomplished the same functions. Greenhouse assays on tomato seedlings from BBCH 11–12 to BBCH > 14 were performed under either organic or conventional management. In each of them, three PGPR inoculations (control, K. variicola UC4115, A. brasilense Sp7) were applied at either seed-, root-, and seed plus root level. Results confirmed the PGP potential of K. variicola UC4115; in particular, its high value potential as indole-3-acetic acid producer was observed in increasing of root length density and diameter class length parameters. While, in general, A. brasilense Sp7 had a greater effect on biomass, probably due to its high ability as nitrogen-fixing bacteria. For K. variicola UC4115, the most consistent data were noticed under organic management, with application at seed level. While, A. brasilense Sp7 showed the greatest performance under conventional management. Our data highlight the necessity to tailor the selected PGPR, with the mode of inoculation and the crop-soil combination.

Apis mellifera is an important provider of ecosystem services, and during flight and foraging behaviour is exposed to environmental pollutants including airborne particulate matter (PM). While exposure to insecticides, antibiotics, and herbicides may compromise bee health through alterations of the gut microbial community, no data are available on the impacts of PM on the bee microbiota. Here we tested the effects of ultrapure Titanium dioxide (TiO2) submicrometric PM (i.e., PM1, less than 1 µm in diameter) on the gut microbiota of adult bees. TiO2 PM1 is widely used as a filler and whitening agent in a range of manufactured objects, and ultrapure TiO2 PM1 is also a common food additive, even if it has been classified by the International Agency for Research on Cancer (IARC) as a possible human carcinogen in Group 2B. Due to its ubiquitous use, honey bees may be severely exposed to TiO2 ingestion through contaminated honey and pollen. Here, we demonstrated that acute and chronic oral administration of ultrapure TiO2 PM1 to adult bees alters the bee microbial community; therefore, airborne PM may represent a further risk factor for the honey bee health, promoting sublethal effects against the gut microbiota.

Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different size-aggregates, and the persistence and turnover of eDNA are thus uneven. Uneven persistence and distribution of eDNA could lead to heterogeneity in community analysis biases that arise due to eDNA sequences at micro-scale distribution. Here, we investigated the diversity and structure of eDNA and iDNA bacterial communities in bulk soil and different size-aggregates. Significant differences were observed between eDNA and iDNA bacterial diversity and composition. Changes in community composition are more important than the amount of eDNA to assess the biases caused by eDNA in community analysis. Furthermore, variations were also observed in aggregates-levels for eDNA and iDNA community which indicates that colonization pattern of iDNA community and protection of eDNA through absorbance on particle surface within soil-matrix is heterogeneous. Our work provides empirical evidence that eDNA presence could mask the detection of aggregates-level spatial dynamics in soil microbial community and have potential to qualitatively baffle observed live effects of given treatment by adequately muting the actual response dynamics of the soil microbiome.

High-throughput sequencing data sets are usually deposited in public repositories (e.g., the European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached petabyte scale, repositories do not allow one to perform online sequence searches, yet, such a feature would be highly useful to investigators. Toward this goal, in the last few years several computational approaches have been introduced to index and query large collections of data sets. Here, we propose an accessible survey of these approaches, which are generally based on representing data sets as sets of k-mers. We review their properties, introduce a classification, and present their general intuition. We summarize their performance and highlight their current strengths and limitations.

A 3-m thick sediment was found in a limestone mine located in the southern part of the Gargano Promontory, Apulia region (south of Italy), at a depth of ca. 25-30 m from the current ground level.Samples from 5 layers were analysed by X-ray diffraction (XRD), elementar analysis (CHNS), and Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Microbial DNA was also extracted and bacterial diversity analysed by PCR amplification and Illumina High-Throughput Sequencing (HTS) of the V3-V4 hypervariable regions of 16S rRNA.Preliminary data showed that these sediments formed by subsequent weathering of carbonates and silicates, either by in situ oxidation or by dissolution followed by migration and reprecipitation, rather than during the accumulation of shallow marine sediments occurring between the middle Pliocene and the lower Pleistocene, when the extreme western sectors of the Apulian foreland underwent strong subsidence.The main mineral compounds occurring in the 5 layers, from the top to the bottom, were the following: calcite (80%) and clay minerals in sample #1, goethite (75%) and hematite in sample #2, manganese (66%) and iron oxides in sample #3, almost exclusively goethite in sample #4, and calcite (71%) and clay minerals in sample #5.From the microbiological point of view, drawn from a 16S metabarcoding amplicons sequencing analysis, these 5 layers appear to cluster in three groups: a) the uppermost layer (sample #1), dominated by a single and abundant taxon of Arthrobacter sp., which includes species known for the capability of calcite precipitation; b) a middle layer (including samples #2 and #3), without prevailing abundances and less consistent occurrences across replicates, which featured members of the Oxalobacteraceae family and of the Methylophilus genus. Their closest matches in Genbank subjects included isolates from habitats such as calcium carbonate (moonmilk) muds in percolating waters within caves, mine tailings and other groundwater microcosms; c) a bottom layer (samples #4 and #5), showing an oligarchic situation and high abundances of bacteria but different from the ones that prevailed in the top layer and including members of the Nocardioidacaeae family. Also for these sequence queries, the closest GenBank subjects include cases with calcium carbonate-precipitating capabilities isolated from cave and groundwater sediments or former mining sites in studies on iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations.Overall, such a distribution suggests that, both in the top and bottom layer, different communities would have undergone in situ-reproduction and colonization exploiting metabolically the substrate, whereas the mid layers would have received bacterial convection by passive transport of percolating waters.

Simple Summary Smallholder farmers in Sub-Saharan Africa (SSA) are food insecure. Underexploited African indigenous vegetables (AIVs) are consumed locally without being considered a primary source of food and income. However, AIVs hold great potential for the future challenges of food security and climate change. We investigated the effects of different cropping systems and inclusion of AIVs in farming on the soil biodiversity and fertility status of smallholder farmers in Naivasha, Kenya. Compared to mainstream farming approaches, soil microorganisms under AIV cultivations differed significantly. Tillage, fertilization, soil amendments, and traditional homemade plant protection were singled out as the most important factors. The soil alteration index based on enzyme activity offered a reliable way to determine the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future and may contribute to the mitigation of food insecurity. Abstract Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.