Search

Abstract Background With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Description Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. Conclusions The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

Abstract Background Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for identifying continuous epitopes in the protein regions protruding from the protein's globular surface. The aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes. Results Here we present ElliPro, a web-tool that implements Thornton's method and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. ElliPro has been tested on a benchmark dataset of discontinuous epitopes inferred from 3D structures of antibody-protein complexes. In comparison with six other structure-based methods that can be used for epitope prediction, ElliPro performed the best and gave an AUC value of 0.732, when the most significant prediction was considered for each protein. Since the rank of the best prediction was at most in the top three for more than 70% of proteins and never exceeded five, ElliPro is considered a useful research tool for identifying antibody epitopes in protein antigens. ElliPro is available at http://tools.immuneepitope.org/tools/ElliPro. Conclusion The results from ElliPro suggest that further research on antibody epitopes considering more features that discriminate epitopes from non-epitopes may further improve predictions. As ElliPro is based on the geometrical properties of protein structure and does not require training, it might be more generally applied for predicting different types of protein-protein interactions.

Abstract Background The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org. Description To identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation. Conclusion Formalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise.

The biological relevance and dynamics of mRNA modifications have been extensively studied; however, whether rRNA modifications are dynamically regulated, and under which conditions, remains unclear. Here, we systematically characterize bacterial rRNA modifications upon exposure to diverse antibiotics using native RNA nanopore sequencing. To identify significant rRNA modification changes, we develop NanoConsensus, a novel pipeline that is robust across RNA modification types, stoichiometries and coverage, with very low false positive rates, outperforming all individual algorithms tested. We then apply NanoConsensus to characterize the rRNA modification landscape upon antibiotic exposure, finding that rRNA modification profiles are altered in the vicinity of A and P-sites of the ribosome, in an antibiotic-specific manner, possibly contributing to antibiotic resistance. Our work demonstrates that rRNA modification profiles can be rapidly altered in response to environmental exposures, and provides a robust workflow to study rRNA modification dynamics in any species, in a scalable and reproducible manner., Competing Interests: Competing interests: E.M.N. is a member of the Scientific Advisory Board of IMMAGINA Biotech. E.M.N. has received travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences. A.D.-T. and O.B. have received travel bursaries from ONT to present their work in conferences. The remaining authors declare no competing interests., (© 2024. The Author(s).)

Background: Patients with severe acute respiratory distress syndrome (ARDS) show a high mortality rate of up to 60 %. In such cases, extracorporeal membrane oxygenation (ECMO) support is often required, which would necessitate anticoagulation therapy, predominantly with heparin. Some bleeding events occurred more frequently in patients during the COVID-19 pandemic who were on venovenous (V-V) ECMO, so it is necessary to investigate whether anticoagulation management should be adjusted., Methods: We collected data on 90 patients with severe ARDS who underwent ECMO support at the University Hospital Magdeburg between 2014 and 2022. In order to estimate the role of anticoagulation therapy as a cause of bleeding, patients were divided into two groups based on their mean activated partial thromboplastin time (aPTT): one group with a mean aPTT of more than 58 s (45 patients) and another with a mean aPTT of less than 58 s (45 patients). Demographic data, data before, during ECMO support, and bleeding complications were retrospectively recorded. We compared laboratory parameters before ECMO, essential coagulation parameters on days 3, 7, 10 of ECMO support, before the bleeding event occurred, and analyzed hospital survival in both groups., Results: The incidence of major bleeding complications was significantly higher in the group of patients with higher aPTT (68.9 % vs 33.3 %, p < 0.001), the differences in the occurrence of hemothorax were especially significant (28.9 % vs 2.2 %, p < 0.001). We observed better hospital patients' survival in the group with lower aPTT (40.0 % vs 68.9 %, p = 0.006). The results of the bivariate analysis indicate that the independent predictors of hospital mortality in adult patients receiving V-V ECMO support due to severe ARDS were COVID-19 (OR: 3.504; 95 % confidence interval [CI]: 1.415-8.681, p = 0.007) acute liver failure (OR: 8.0000; 95 % CI: 1.692-37.822; p = 0.009), high antithrombin level (%) (OR: 1.036; 95 % CI: 1.003-1.071, p = 0.035). A high mean aPTT level increased the risk of major bleeding (OR: 1.080; 95 % CI: 1.016-1.148, p = 0.014) without a significant increase in mortality., Conclusion: Prolonged aPTT during V-V ECMO support in patients with ARDS significantly impacts the risk of major bleeding, especially hemothorax, without significant increase in hospital mortality., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Subcellular compartmentalization of metabolic enzymes establishes a unique metabolic environment that elicits specific cellular functions. Indeed, the nuclear translocation of certain metabolic enzymes is required for epigenetic regulation and gene expression control. Here, we show that the nuclear localization of the mitochondrial enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) ensures mitosis progression. Nuclear MTHFD2 interacts with proteins involved in mitosis regulation and centromere stability, including the methyltransferases KMT5A and DNMT3B. Loss of MTHFD2 induces severe methylation defects and impedes correct mitosis completion. MTHFD2 deficient cells display chromosome congression and segregation defects and accumulate chromosomal aberrations. Blocking the catalytic nuclear function of MTHFD2 recapitulates the phenotype observed in MTHFD2 deficient cells, whereas restricting MTHFD2 to the nucleus is sufficient to ensure correct mitotic progression. Our discovery uncovers a nuclear role for MTHFD2, supporting the notion that translocation of metabolic enzymes to the nucleus is required to meet precise chromatin needs., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

KMT2A-rearranged (KMT2A-R) is an aggressive and chemo-refractory acute leukemia which mostly affects children. Transcriptomics-based characterization and chemical interrogation identified kinases as key drivers of survival and drug resistance in KMT2A-R leukemia. In contrast, the contribution and regulation of phosphatases is unknown. In this study we uncover the essential role and underlying mechanisms of SET, the endogenous inhibitor of Ser/Thr phosphatase PP2A, in KMT2A-R-leukemia. Investigation of SET expression in acute myeloid leukemia (AML) samples demonstrated that SET is overexpressed, and elevated expression of SET is correlated with poor prognosis and with the expression of MEIS and HOXA genes in AML patients. Silencing SET specifically abolished the clonogenic ability of KMT2A-R leukemic cells and the transcription of KMT2A targets genes HOXA9 and HOXA10. Subsequent mechanistic investigations showed that SET interacts with both KMT2A wild type and fusion proteins, and it is recruited to the HOXA10 promoter. Pharmacological inhibition of SET by FTY720 disrupted SET-PP2A interaction leading to cell cycle arrest and increased sensitivity to chemotherapy in KMT2A-R-leukemic models. Phospho-proteomic analyses revealed that FTY720 reduced the activity of kinases regulated by PP2A, including ERK1, GSK3β, AURB and PLK1 and led to suppression of MYC, supporting the hypothesis of a feedback loop among PP2A, AURB, PLK1, MYC, and SET. Our findings illustrate that SET is a novel player in KMT2A-R leukemia and they provide evidence that SET antagonism could serve as a novel strategy to treat this aggressive leukemia., (© 2023. The Author(s).)

The hydrophilic extractives isolated from black alder ( Alnus glutinosa ) bark through hot water extraction were characterized as novel renewable macromonomers capable of forming polyurethane (PU) networks based on a commercial polyisocyanate, with partial or complete replacement of petroleum-derived polyol polyether. The bark-sourced bio-polyol mainly consists of the xyloside form of the diarylheptanoid oregonin, along with oligomeric flavonoids and carbohydrates, resulting in a total OH group content of 15.1 mmol·g -1 and a molecular weight (M n ) of approximately 750 g∙mol -1 . The 31 P NMR data confirmed a similar proportion of aliphatic OH and phenolic groups. Three-component PU compositions were prepared using polyethylene glycol (M n = 400 g∙mol -1 ), bio-polyol (up to 50%), and polymeric diphenylmethane diisocyanate, which were pre-polymerized in tetrahydrofuran (THF) solution with tin organic and tertiary amine catalysts. The resulting mixture was cast and subjected to thermal post-curing. Calculation and experimental data confirmed the crosslinking activity of the bark-sourced bio-polyol in PU, leading to an increase in glass transition temperature (Tg), a decrease in sol fraction yield upon leaching of cured PU networks in THF, a significant increase in Young's modulus and tensile strength. The macromonomers derived from bark promoted char formation under high temperature and oxidative stress conditions, limiting heat release during macromolecular network degradation compared to bio-polyol-free PU. It was observed that amine catalysts, which are active in urethane formation with phenolic groups, promoted the formation of PU with higher Tg and modulus at tensile but with less limitation of heat liberation during PU macromolecular structure degradation. The high functionality of the bark-derived bio-polyol, along with the equal proportion of phenolic and aliphatic OH groups, allows for further optimization of PU characteristics using three variables: increasing the substitution extent of commercial polyethers, decreasing the NCO/OH ratio, and selecting the type of catalyst used.

This chapter describes MasterOfPores v.2 (MoP2), an open-source suite of pipelines for processing and analyzing direct RNA Oxford Nanopore sequencing data. The MoP2 relies on the Nextflow DSL2 framework and Linux containers, thus enabling reproducible data analysis in transcriptomic and epitranscriptomic studies. We introduce the key concepts of MoP2 and provide a step-by-step fully reproducible and complete example of how to use the workflow for the analysis of S. cerevisiae total RNA samples sequenced using MinION flowcells. The workflow starts with the pre-processing of raw FAST5 files, which includes basecalling, read quality control, demultiplexing, filtering, mapping, estimation of per-gene/transcript abundances, and transcriptome assembly, with support of the GPU computing for the basecalling and read demultiplexing steps. The secondary analyses of the workflow focus on the estimation of RNA poly(A) tail lengths and the identification of RNA modifications. The MoP2 code is available at https://github.com/biocorecrg/MOP2 and is distributed under the MIT license., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The present study examined the influence of inulin on fecal microbiota, cardiometabolic risk factors, eicosanoids, and oxidative stress in rats on a high-fat (HF) diet. Thirty-six male Wistar-Kyoto rats were divided into three dietary groups: standard diet, HF diet, and HF diet + Inulin diet. After 10 weeks, the HF + Inulin diet promoted high dominance of a few bacterial genera including Blautia and Olsenella in feces while reducing richness, diversity, and rarity compared to the HF diet. These changes in fecal microbiota were accompanied by an increased amount of propionic acid in feces. The HF + Inulin diet decreased cardiometabolic risk factors, decreased the amount of the eicosanoids 11(12)-EET and 15-HETrE in the liver, and decreased oxidative stress in blood compared to the HF diet. In conclusion, increasing consumption of inulin may be a useful nutritional strategy to protect against the onset of obesity and its associated metabolic abnormalities by means of modulation of gut microbiota.

The goal of this work is to explore if the changes induced by d-fagomine in the gut microbiota are compatible with its effect on body weight and inflammation markers in rats. Methods: Sprague Dawley rats were fed a standard diet supplemented with d-fagomine (or not, for comparison) for 6 months. The variables measured were body weight, plasma mediators of inflammation (hydroxyeicosatetraenoic acids, leukotriene B4, and IL-6), and the concentration of acetic acid in feces and plasma. The composition and diversities of microbiota in cecal content and feces were estimated using 16S rRNA metabarcoding and high-throughput sequencing. We found that after just 6 weeks of intake d-fagomine significantly reduced body weight gain, increased the plasma acetate concentration, and reduced the plasma concentration of the pro-inflammatory biomarkers' leukotriene B4, interleukin 6 and 12 hydroxyeicosatetraenoic acids. These changes were associated with a significantly increased prevalence of Bacteroides and Prevotella feces and increased Bacteroides , Prevotella , Clostridium, and Dysgonomonas while reducing Anaerofilum , Blautia, and Oribacterium in cecal content. In conclusion, d-fagomine induced changes in the composition and diversity of gut microbiota similar to those elicited by dietary fiber and compatible with its anti-inflammatory and body-weight-reducing effects.

The barks of aspen ( Populus tremula ) and pine ( Pinus sylvestris) are byproducts of wood processing, characterized by their low economic value. In the present study, microwave-assisted one-cycle water extraction was explored as a tool for the valorization of this biomass as a source of biologically active compounds. The microwave extractor of the original construction equipped with a pressurized extraction chamber and a condenser section was used. The microwave-assisted extraction (MAE), specially including dynamic dielectric heating up to 70 °C followed by 30 min of isothermal heating, promoted the isolation of salicin from aspen bark, allowing for the obtention of a two-times-higher free salicin concentration in water extracts (-14% vs. 7%) reached by multi-cycle accelerated solvent extraction (ASE), which is an advanced technique used as a reference. The MAE of pine bark with dynamic heating up to 90-130 °C, avoiding the isothermal heating step, allowed for the obtention of a 1.7-times-higher concentration of proantocyanidin dimers-tetramers, a 1.3-times-higher concentration of catechin and a 1.2-times-higher concentration of quinic acid in water extracts in comparison to a more time- and solvent-consuming ASE performed at the same temperature. The biological activity of the obtained extracts was characterized in terms of their ability to inhibit xahntine oxidase enzyme, which is a validated target for the therapeutic treatment of hyperuricemia.

Signaling via the T cell receptor (TCR) is critical during the development, maintenance, and activation of T cells. Quantitative aspects of TCR signaling have an important role during positive and negative selection, lineage choice, and ability to respond to small amounts of antigen. By using a mutant mouse line expressing a hypomorphic allele of the CD3ζ chain, we show here that the strength of pre-TCR–mediated signaling during T cell development determines the diversity of the TCRβ repertoire available for positive and negative selection, and hence of the final αβTCR repertoire. This finding uncovers an unexpected, pre-TCR signaling–dependent and repertoire–shaping role for β-selection beyond selection of in-frame rearranged TCRβ chains. Our data furthermore support a model of pre-TCR signaling in which the arrangement of this receptor in stable nanoclusters determines its quantitative signaling capacity.

An experimentally proven novel analytical approach for chromatographic analysis of diarylheptanoids in grey alder (Alnus incana) and black alder (Alnus glutinosa) bark matrices was established. A method for qualitative and quantitative determination of oregonin (dominant diarylheptanoid) and semiquantitative analysis of related diarylheptanoids from alder bark using a photodiode array (PDA) detector coupled to a high-resolution mass spectrometer (QTOF-MS) was developed. A comparison of different liquid chromatography detectors (UV, MS and ELS) showed that only a combination of them is applicable for comprehensive analysis of multicomponent extracts. A total of sixteen different diarylheptanoids were simultaneously identified and semi-quantified in alder bark extracts. This is the first report of the method for individual and total diarylheptanoid determination in alder bark extracts, discussed in detail. The liquid chromatography complex is suggested as a tool for the reliable identification and quality control of the diarylheptanoids containing extracts isolated from the Alnus species and their dominant component - oregonin. The semiquantitative methodology established, and the dominant compound quantification provided means for assessing comparative sample complexities., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and circulatory systems, the composition of the oral microbiome is relevant beyond just oral health, impacting systemic processes across the body. However, we still have a very limited understanding about intrinsic and extrinsic factors that shape the composition of the healthy oral microbiome. Here, we followed a citizen-science approach to assess the relative impact on the oral microbiome of selected biological, social, and lifestyle factors in 1648 Spanish individuals. We found that the oral microbiome changes across age, with middle ages showing a more homogeneous composition, and older ages showing more diverse microbiomes with increased representation of typically low abundance taxa. By measuring differences within and between groups of individuals sharing a given parameter, we were able to assess the relative impact of different factors in driving specific microbial compositions. Chronic health disorders present in the analyzed population were the most impactful factors, followed by smoking and the presence of yeasts in the oral cavity. Finally, we corroborate findings in the literature that relatives tend to have more similar oral microbiomes, and show for the first time a similar effect for classmates. Multiple intrinsic and extrinsic factors jointly shape the oral microbiome. Comparative analysis of metabarcoding data from a large sample set allows us to disentangle the individual effects., (© 2022. The Author(s).)