ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.

SUMMARY: ITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing. AVAILABILITY AND IMPLEMENTATION: ITSoneWB has been deployed on the INFN-Bari ReCaS cloud facility and is freely available on the web at http://itsonewb.cloud.ba.infn.it/galaxy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structural insight into the role of the Ton complex in energy transduction.

In Gram-negative bacteria, outer membrane transporters import nutrients by coupling to an inner membrane protein complex called the Ton complex. The Ton complex consists of TonB, ExbB, and ExbD, and uses the proton motive force at the inner membrane to transduce energy to the outer membrane via TonB. Here, we structurally characterize the Ton complex from Escherichia coli using X-ray crystallography, electron microscopy, double electron-electron resonance (DEER) spectroscopy, and crosslinking. Our results reveal a stoichiometry consisting of a pentamer of ExbB, a dimer of ExbD, and at least one TonB. Electrophysiology studies show that the Ton subcomplex forms pH-sensitive cation-selective channels and provide insight into the mechanism by which it may harness the proton motive force to produce energy.

Graft infusion of adipose-derived mesenchymal stromal cells to prevent rejection in experimental intestinal transplantation: A feasibility study.

BACKGROUND: Mesenchymal stromal cells (MSC) have been proposed as a promising complement to standard immunosuppression in solid organ transplantation because of their immunomodulatory properties. The present work addresses the role of adipose-derived MSC (Ad-MSC) in an experimental model of acute rejection in small bowel transplantation (SBT). MATERIAL/METHODS: Heterotopic allogeneic SBT was performed. A single dose of 1.5x106 Ad-MSC was intra-arterially delivered just before graft reperfusion. Animals were divided into CONTROL (CTRL), CONTROL+Ad-MSC (CTRL_MSC), tacrolimus (TAC), and TAC+Ad-MSC (TAC_MSC) groups. Each Ad-MSC groups was subdivided in autologous and allogeneic third-party groups. RESULTS: Rejection rate and severity were similar in MSC-treated and untreated animals. CTRL_MSC animals showed a decrease in macrophages, T-cell (CD4, CD8, and Foxp3 subsets) and B-cell counts in the graft compared with CTRL, this decrease was attenuated in TAC_MSC animals. Pro- and anti-inflammatory cytokines and some chemokines and growth factors increased in CTRL_MSC animals, especially in the allogeneic group, whereas milder changes were seen in the TAC groups. CONCLUSION: Ad-MSC did not prevent rejection when administered just before reperfusion. However, they showed immunomodulatory effects that could be relevant for a longer-term outcome. Interference between tacrolimus and the MSC effects should be addressed in further studies.

A Generalized Semiempirical Approach to the Modeling of the Optical Band Gap of Ternary Al-(Ga, Nb, Ta, W) Oxides Containing Different Alumina Polymorphs.

A generalization of the modeling equation of optical band gap values for ternary oxides, as a function of cationic ratio composition, is carried out based on the semiempirical correlation between the differences in the electronegativity of oxygen and the average cationic electronegativity proposed some years ago. In this work, a novel approach is suggested to account for the differences in the band gap values of the different polymorphs of binary oxides as well as for ternary oxides existing in different crystalline structures. A preliminary test on the validity of the proposed modeling equations has been carried out by using the numerous experimental data pertaining to alumina and gallia polymorphs as well as the crystalline ternary Ga(1-x)AlxO3 polymorphs (α-Ga(1-x)AlxO3 and ß-Ga(1-x)AlxO3) covering a large range of optical band gap values (4.50-8.50 eV). To make a more rigorous test of the modeling equation, we extended our investigation to amorphous ternary oxides anodically formed on Al-d-metal alloys (Al-Nb, Al-Ta, and Al-W) covering a large range of d-metal composition (xd-metal ≥ 0.2). In the last case, the novel approach allows one to overcome some difficulties experienced in fitting the optical band gap dependence from the Al-d-metal mixed anodic oxide composition as well as to provide a rationale for the departure, at the lowest d-metal content (xd-metal < 0.2), from the behavior observed for anodic films containing higher d-metal content.

Ultrastructural changes in giant cell tumor of bone cultured cells exposed to quercetin.

Giant cell tumor of bone (GCTB) is a primary bone tumor that affects skeletally mature people and whose main treatment is surgical. Because there are few pharmacological alternatives for the treatment of this tumor to find other molecules or compounds that could be potential therapeutic agents is desirable. Quercetin is a flavonoid with described antitumoral effect in different types of cancer cell lines that could be a possible option in GCTB treatment. However, there is no literature about the effect of quercetin on GCTB. In the present paper, we reported the ultrastructural changes in GCTB cells exposed to quercetin and also determined the expression of RIP1K, Caspase 3 and Caspase 8 on the exposed cells. For this purpose, GCTB sample was obtained from one patient and cultured. Quercetin affected all the histological components of the GCTB. The ultrastructural changes consisted mainly in necroptosis, autophagocytosis and secondary necrosis. This is the first report about quercetin effects on giant cell tumor of bone cultured cells. Further studies in other models could be done to support the use of quercetin as a complementary treatment in giant cell tumor of bone.Abbreviations: Giant cell tumor of bone (GCTB); transmission electron microscopy (TEM); reverse transcription - polymerase chain reaction (RT-PCR); receptor interacting protein kinase 1 (RIP1K); Dulbecco's Modified Eagle's Medium (DMEM).

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive.

A randomized controlled trial to evaluate the effectiveness of a brief motivational intervention to improve exclusive breastfeeding rates: Study protocol.

AIMS: To estimate the effectiveness of a brief motivational intervention (BMI) in increasing the duration of exclusive breastfeeding in the first 6 months postpartum. A complementary aim was to examine a potential mediating role of breastfeeding self-efficacy in the effectiveness of the BMI. BACKGROUND: Breastfeeding is associated with benefits for babies and mothers' health. Among the pool of techniques used to encourage healthy behaviours, BMI is highlighted based on the principles of motivational interviewing. One of the main components of these interventions is the promotion of self-efficacy, which, in fact, is a key factor for breastfeeding success. DESIGN: A multi-centre randomized controlled clinical trial of parallel groups. METHODS: Women who begin to breastfeed in the first hour after birth will be randomly assigned to the intervention group (receiving a BMI at immediate postpartum plus a telephone booster at the 1st and 3rd month postpartum) or the control group (receiving standard breastfeeding education at the same time). Outcome measures include the following: breastfeeding, breastfeeding self-efficacy, general self-efficacy, and postnatal depression. Data will be collected before the intervention and at the 1st, 3rd, and 6th month after birth. The study protocol has been approved by Badajoz Ethics Committee of Clinical Research in October 2017. DISCUSSION: This study will identify the effectiveness of BMI in improving exclusive breastfeeding rates. The findings will give useful evidence to health professionals about how to support breastfeeding. IMPACT: This study will address the low-exclusive breastfeeding rates, that in our country are far lower than World Health Organization's recommendation.

Diagnosis and predictors of sessile serrated adenoma after educational training in a large, community-based, integrated healthcare setting.

BACKGROUND AND AIMS: Sessile serrated adenomas (SSAs) are precursors of 15% to 30% of colorectal cancers but are frequently underdiagnosed. We sought to measure the SSA detection rate (SDR) and predictors of SSA detection after educational training for community gastroenterologists and pathologists. METHODS: Colonoscopy and pathology data (2010-2014) from 3 medical centers at Kaiser Permanente Northern California were accessed electronically. Gastroenterologists and pathologists attended a training session on SSA diagnosis in 2012. Mean SDRs and patient-level predictors of SSA detection post-training (2013-2014) were investigated. RESULTS: Mean SDRs increased from .6% in 2010-2012 to 3.7% in 2013-2014. The increase in the detection of proximal SSAs was accompanied by a decrease in the detection of proximal hyperplastic polyps (HPs). Among 34,161 colonoscopies performed in 2013 to 2014, SDRs for screening, fecal immunochemical test positivity, surveillance, and diagnostic indication were 4.2%, 4.5%, 4.9%, and 3.0%, respectively. SSA detection was lower among Asians (adjusted odds ratio [aOR], .46; 95% confidence interval [CI], .31-.69) and Hispanics (aOR, .59; 95% CI, .36-.95) compared with non-Hispanic whites and higher among patients with synchronous conventional adenoma (aOR, 1.46; 95% CI, 1.15-1.86), HP (aOR, 1.74; 95% CI, 1.30-2.34), and current smokers (aOR, 1.78; 95% CI, 1.17-2.72). SDRs varied widely among experienced gastroenterologists, even after training (1.1%-8.1%). There was a moderately strong correlation between adenoma detection rate (ADR) and SDR for any SSA (r = .64, P = .0003) and for right-sided SSAs (r = .71, P < .0001). CONCLUSIONS: Educational training significantly increased the detection of SSA, but a wide variation in SDR remained across gastroenterologists. SSA detection was inversely associated with Asian and Hispanic race/ethnicity and positively associated with the presence of conventional adenoma, HP, and current smoking. There was a moderately strong correlation between ADR and SDR.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

BACKGROUND: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. RESULTS: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). CONCLUSION: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.

Nuclear α1-antichymotrypsin promotes chromatin condensation and inhibits proliferation of human hepatocellular carcinoma cells.

BACKGROUND & AIMS: α1-Antichymotrypsin (α1-ACT), a member of the serpin family (SERPINA3), is an acute-phase protein secreted by hepatocytes in response to cytokines such as oncostatin M. α1-ACT is a protease inhibitor thought to limit tissue damage produced by excessive inflammation-associated proteolysis. However, α1-ACT also is detected in the nuclei of cells, where its activities are unknown. Expression of α1-ACT is down-regulated in human hepatocellular carcinoma (HCC) tissues and cells; we examined its roles in liver regeneration and HCC proliferation. METHODS: We measured levels of α1-ACT messenger RNA in human HCC samples and healthy liver tissue. We reduced levels of α1-ACT using targeted RNA interference in human HCC (HepG2) and mouse hepatocyte (AML12) cell lines, and overexpressed α1-ACT from lentiviral vectors in Huh7 (HCC) cells and adeno-associated viral vectors in livers of mice. We assessed proliferation, differentiation, and chromatin compaction in cultured cells, and liver regeneration and tumor formation in mice. RESULTS: Reducing levels of α1-ACT promoted proliferation of HCC cells in vitro. Oncostatin M up-regulated α1-ACT expression and nuclear translocation, which inhibited HCC cell proliferation and activated differentiation of mouse hepatocytes. We identified amino acids required for α1-ACT nuclear localization, and found that α1-ACT inhibits cell-cycle progression and anchorage-independent proliferation of HCC cells. HCC cells that overexpressed α1-ACT formed smaller tumors in mice than HCC cells that did not express the protein. α1-ACT was observed to self-associate and polymerize in the nuclei of cells; nuclear α1-ACT strongly bound chromatin to promote a condensed state that could prevent cell proliferation. CONCLUSIONS: α1-ACT localizes to the nuclei of hepatic cells to control chromatin condensation and proliferation. Overexpression of α1-ACT slows the growth of HCC xenograft tumors in nude mice.

Reference databases for taxonomic assignment in metagenomics.

Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.

Enhancing nutritional and sensory properties of plant-based beverages: a study on chickpea and Kamut® flours fermentation using Lactococcus lactis.

The study aimed to set up a protocol for the production of a clean-label plant-based beverage (PBB), obtained by mixing chickpeas and Kamut® flours and using a commercial Lactococcus lactis (LL) as fermentation starter, and to characterize it, from nutritional, microbiological, textural, shelf-life, and sensory points of view. The effect of using the starter was evaluated comparing the LL-PBB with a spontaneously fermented beverage (CTRL-PBB). Both PBBs were high in proteins (3.89/100 g) and could be considered as sources of fiber (2.06/100 g). Notably, L. lactis fermentation enhanced the phosphorus (478 vs. 331 mg/kg) and calcium (165 vs. 117 mg/kg) concentrations while lowering the raffinose content (5.51 vs. 5.08 g/100 g) compared to spontaneous fermentation. Cell density of lactic acid bacteria increased by ca. two log cycle during fermentation of LL-PBB, whereas undesirable microbial groups were not detected. Furthermore, L. lactis significantly improved the beverage's viscosity (0.473 vs. 0.231 Pa s), at least for 10 days, and lightness. To assess market potential, we conducted a consumer test, presenting the LL-PBB in "plain" and "sweet" (chocolate paste-added) variants. The "sweet" LL-PBB demonstrated a higher acceptability score than its "plain" counterpart, with 88 and 78% of participants expressing acceptability and a strong purchase intent, respectively. This positive consumer response positions the sweet LL-PBB as a valuable, appealing alternative to traditional flavored yogurts, highlighting its potential in the growing plant-based food market.

Ni,Fe,Co-LDH Coated Porous Transport Layers for Zero-Gap Alkaline Water Electrolyzers.

Next-generation alkaline water electrolyzers will be based on zero-gap configuration to further reduce costs related to technology and to improve performance. Here, anodic porous transport layers (PTLs) for zero-gap alkaline electrolysis are prepared through a facile one-step electrodeposition of Ni,Fe,Co-based layered double hydroxides (LDH) on 304 stainless steel (SS) meshes. Electrodeposited LDH structures are characterized using Scanning Electron Microscopy (SEM) confirming the formation of high surface area catalytic layers. Finally, bi and trimetallic LDH-based PTLs are tested as electrodes for oxygen evolution reaction (OER) in 1 M KOH solution. The best electrodes are based on FeCo LDH, reaching 10 mA cm-2 with an overpotential value of 300 mV. These PTLs are also tested with a chronopotentiometric measurement carried out for 100 h at 50 mA cm-2, showing outstanding durability without signs of electrocatalytic activity degradation.

Modeling of Optical Band-Gap Values of Mixed Oxides Having Spinel Structure AB2O4 (A = Mg, Zn and B = Al, Ga) by a Semiempirical Approach.

Spinel oxides with the general formula AB2O4 comprise a large family of compounds covering a very wide range of band-gap values (1 eV < Eg < 8 eV) as a function of the nature of the metallic cations A and B. Owing to this, the physical properties of these materials have been largely exploited both from a fundamental point of view, for their variable electronic properties, and for their possible use in numerous engineering applications. Herein, the modeling of ZnAl2O4, ZnGa2O4, MgAl2O4, and MgGa2O4 cubic spinel oxides has been carried out by using the semiempirical approach based on the difference of electronegativity between oxygen and the average electronegativity of cations present in the oxides. The results of recent theoretical extensions of our semiempirical approach to ternary and quaternary oxides have been tested for spinel oxides with metallic ions occupying both octahedrally and tetrahedrally coordinated sites in different ratios. A detailed analysis of the experimental band-gap values and comparison with the theoretically estimated values has been carried out for ternary ZnAl2O4, ZnGa2O4, MgAl2O4, and MgGa2O4 spinels as well as for double spinels Mg(Al2xGa2-x)O4 and Zn(Al2xGa2-x)O4, and quaternary mixed oxides (ZnxMg(1-x))Al2O4 and (ZnxMg(1-x))Ga2O4. The wide range of band-gap values reported in the literature for simple or double spinels has been related to the different preparation methods affecting the grain dimension of crystalline spinel samples as well as to the presence of crystallographic defects and/or impurities in the spinel matrix. The good agreement between experimental band-gap values and the theoretical ones strongly supports the use of our semiempirical approach in the area of band-gap engineering of new materials.

Efficient Photocatalytic Partial Oxidation of Aromatic Alcohols by Using ZnIn2S4 under Green Conditions.

The ternary chalcogenide ZnIn2S4 (ZIS) has been synthesized by a simple hydrothermal method in which the carcinogen thiacetamide, universally used as a precursor, has been, for the first time, replaced successfully with the harmless thiourea. ZIS has been used as photocatalyst for the partial oxidation of different aromatic alcohols to their corresponding aldehyde in water solution, under ambient conditions and simulated solar light irradiation. The photocatalytic performance of ZnIn2S4 was better than TiO2 P25. In the presence of ZIS for 4-methoxybenzyl alcohol, piperonyl alcohol, and benzyl alcohol, a selectivity towards the corresponding aldehyde of 99% for a conversion of 46%, 75% for a conversion of 81%, and 87% for a conversion of 25%, respectively, was obtained. For the same alcohols a selectivity of 19% for a conversion of 41%, 19% for a conversion of 13%, and 16% for a conversion of 26%, was observed in the presence of TiO2 P25.

Pt-TiO2 catalysts for glycerol photoreforming: comparison of anatase, brookite and rutile polymorphs.

We compared the H2 production from glycerol photoreforming for different TiO2 polymorphs, highlighting an increase of activity in the order Pt-rutile < Pt-P25 ≈ Pt-anatase < Pt-brookite with a different distribution of the reaction intermediates. We show that the highest ability to adsorb water and the different distribution of Pt active sites in brookite can positively influence its photoactivity.

Mono-, bi- and tri-metallic Fe-based platinum group metal-free electrocatalysts derived from phthalocyanine for oxygen reduction reaction in alkaline media.

In this manuscript, a comprehensive study is presented on Fe-based electrocatalysts with mono, bi, and tri-metallic compositions, emphasizing the influence of processing-structure correlations on the electrocatalytic activity for the oxygen reduction reaction (ORR) in the alkaline medium. These electrocatalysts were synthesized through the mixing of transition metal phthalocyanines (TM-Pc) with conductive carbon support, followed by controlled thermal treatment at specific temperatures (600 °C and 900 °C). An extensive analysis was conducted, employing various techniques, including X-ray Absorption Spectroscopy (XAS), Transmission Electron Microscopy (TEM), and X-ray Diffraction (XRD), providing valuable insights into the structural characteristics of the synthesized nanoparticles. Importantly, an increase in the Fe-Pc weight percentage from 10% to 30% enhanced the ORR activity, although not proportionally. Furthermore, a comparative analysis between mono, bi, and tri-metallic samples subjected to different functionalization temperatures highlighted the superior electrocatalytic activity of electrocatalysts functionalized at 600 °C, particularly Fe 600 and Fe-Ni-Cu 600. These electrocatalysts featured Eon values of 0.96 V vs. RHE and E1/2 values of 0.9 V vs. RHE, with the added benefit of reduced anionic peroxide production. The potential of these Fe-based electrocatalysts to enhance ORR efficiency is underscored by this research, contributing to the development of more effective and sustainable electrocatalysts for energy conversion technologies.