bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer
Authors: Zhao Jian , Song Xiaofeng , Xu Tianyi , Yang Qichang , Liu Jingjing , Jiang Bin , Wu Jing
Published: January 2021

Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA–miRNA–mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation analysis is used to cover the problem of weak correlations between miRNA–target pairs, which is mainly due to the difference in the magnitude of the expression level. In addition, besides the miRNA, the impact of lncRNA and mRNA on the interactions in triplets is also considered to improve the identification sensitivity of LncMiM without reducing its accuracy. By using LncMiM, a total of 847 lncRNA-associated competing triplets were found. All the competing triplets form a miRNA–lncRNA pair centered regulatory network, in which ZFAS1, SNHG29, GAS5, AC112491.1, and AC099850.4 are the top five lncRNAs with most connections. The results of biological process and KEGG pathway enrichment analysis indicates that the competing triplets are mainly associated with cell division, cell proliferation, cell cycle, oocyte meiosis, oxidative phosphorylation, ribosome, and p53 signaling pathway. Through survival analysis, 107 potential prognostic biomarkers are found in the competing triplets, including FGD5-AS1, HCP5, HMGN4, TACC3, and so on. LncMiM is available at https://github.com/xiaofengsong/LncMiM.
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq
Authors: Lu Rita Jui-Hsien , Liu Yen-Ting , Huang Chih Wei , Yen Ming-Ren , Lin Chung-Yen , Chen Pao-Yang
Published: January 2021

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph.
Translation of IRF-1 Restricts Hepatic Interleukin-7 Production to Types I and II Interferons: Implications for Hepatic Immunity
Authors: Rueschenbaum Sabrina , Cai Chengcong , Schmidt Matthias , Schwarzkopf Katharina , Dittmer Ulf , Zeuzem Stefan , Welsch Christoph , Lange Christian M.
Published: January 2021

Interleukin-7 (IL-7) is an important cytokine with pivotal pro-survival functions in the adaptive immune system. However, the role of IL-7 in innate immunity is not fully understood. In the present study, the impact of hepatic IL-7 on innate immune cells was assessed by functional experiments as well as in patients with different stages of liver cirrhosis or acute-on-chronic liver failure (ACLF). Human hepatocytes and liver sinusoidal endothelial cells secreted IL-7 in response to stimulation with interferons (IFNs) of type I and II, yet not type III. De novo translation of interferon-response factor-1 (IRF-1) restricted IL-7 production to stimulation with type I and II IFNs. LPS-primed human macrophages were identified as innate immune target cells responding to IL-7 signaling by inactivation of Glycogen synthase kinase-3 (GSK3). IL-7-mediated GSK3 inactivation augmented LPS-induced secretion of pro-inflammatory cytokines and blunted LPS tolerance of macrophages. The IFN-IRF-1-IL-7 axis was present in liver cirrhosis patients. However, liver cirrhosis patients with or without ACLF had significantly lower concentrations of IL-7 in serum compared to healthy controls, which might contribute to LPS-tolerance in these patients. In conclusion, we propose the presence of an inflammatory cascade where IFNs of type I/II induce hepatocellular IL-7 in an IRF-1-restriced way. Beyond its role in adaptive immune responses, IL-7 appears to augment the response of macrophages to LPS and to ameliorate LPS tolerance, which may improve innate immune responses against invading pathogens.
Arginase 1 Insufficiency Precipitates Amyloid-β Deposition and Hastens Behavioral Impairment in a Mouse Model of Amyloidosis
Authors: Ma Chao , Hunt Jerry B. , Selenica Maj-Linda B. , Sanneh Awa , Sandusky-Beltran Leslie A. , Watler Mallory , Daas Rana , Kovalenko Andrii , Liang Huimin , Placides Devon , Cao Chuanhai , Lin Xiaoyang , Orr Michael B. , Zhang Bei , Gensel John C. , Feola David J. , Gordon Marcia N. , Morgan Dave , Bickford Paula C. , Lee Daniel C.
Published: January 2021

Alzheimer’s disease (AD) includes several hallmarks comprised of amyloid-β (Aβ) deposition, tau neuropathology, inflammation, and memory impairment. Brain metabolism becomes uncoupled due to aging and other AD risk factors, which ultimately lead to impaired protein clearance and aggregation. Increasing evidence indicates a role of arginine metabolism in AD, where arginases are key enzymes in neurons and glia capable of depleting arginine and producing ornithine and polyamines. However, currently, it remains unknown if the reduction of arginase 1 (Arg1) in myeloid cell impacts amyloidosis. Herein, we produced haploinsufficiency of Arg1 by the hemizygous deletion in myeloid cells using Arg1fl/fl and LysMcreTg/+ mice crossed with APP Tg2576 mice. Our data indicated that Arg1 haploinsufficiency promoted Aβ deposition, exacerbated some behavioral impairment, and decreased components of Ragulator-Rag complex involved in mechanistic target of rapamycin complex 1 (mTORC1) signaling and autophagy. Additionally, Arg1 repression and arginine supplementation both impaired microglial phagocytosis in vitro. These data suggest that proper function of Arg1 and arginine metabolism in myeloid cells remains essential to restrict amyloidosis.
Proceedings From the First International Workshop at Sidra Medicine: “Engineered Immune Cells in Cancer Immunotherapy (EICCI): From Discovery to Off-the-Shelf Development”, 15th–16th February 2019, Doha, Qatar
Authors: Guerrouahen Bella , Elnaggar Muhammad , Al-Mohannadi Anjud , Kizhakayil Dhanya , Bonini Chiara , Benjamin Reuben , Brentjens Renier , Buchholz Christian J. , Casorati Giulia , Ferrone Soldano , Locke Frederick L. , Martin Francisco , Schambach Axel , Turtle Cameron , Veys Paul , van der Vliet Hans J. , Maccalli Cristina ,   The EICCI Faculty Group
Published: January 2021

The progress in the isolation and characterization of tumor antigen (TA)-specific T lymphocytes and in the genetic modification of immune cells allowed the clinical development of adoptive cell therapy (ACT). Several clinical studies highlighted the striking clinical activity of T cells engineered to express either Chimeric Antigen (CAR) or T Cell (TCR) Receptors to target molecularly defined antigens expressed on tumor cells. The breakthrough of immunotherapy is represented by the approval of CAR-T cells specific for advanced or refractory CD19+ B cell malignancies by both the Food and Drug Administration (FDA) and the European Medicinal Agency (EMA). Moreover, advances in the manufacturing and gene editing of engineered immune cells contributed to the selection of drug products with desired phenotype, refined specificity and decreased toxicity. An important step toward the optimization of CAR-T cell therapy is the development of “off-the shelf” T cell products that allow to reduce the complexity and the costs of the manufacturing and to render these drugs available for a broad number of cancer patients. The Engineered Immune Cells in Cancer Immunotherapy (EICCI) workshop hosted in Doha, Qatar, renowned experts, from both academia and industry, to present and discuss the progress on both pre-clinical and clinical development of genetically modified immune cells, including advances in the “off-the-shelf” manufacturing. These experts have addressed also organizational needs and hurdles for the clinical grade production and application of these biological drugs.
MicroRNA-30a Modulates Type I Interferon Responses to Facilitate Coxsackievirus B3 Replication Via Targeting Tripartite Motif Protein 25
Authors: Li Jia , Xie Yewei , Li Liwei , Li Xiaobing , Shen Li , Gong Jin , Zhang Rufang
Published: January 2021

Viral myocarditis is caused by a viral infection and characterized by the inflammation of the myocardium. Coxsackievirus B3 (CVB3) infection is one of the most common among the infections caused by this virus. The host’s early innate immune response to CVB3 infection particularly depends on the functions of type I interferons (IFNs). In this study, we report that a host microRNA, miR-30a, was upregulated by CVB3 to facilitate its replication. We demonstrated that miR-30a was a potent negative regulator of IFN-I signaling by targeting tripartite motif protein 25 (TRIM25). In addition, we found that TRIM25 overexpression significantly suppressed CVB3 replication, whereas TRIM25 knockdown increased viral titer and VP1 protein expression. MiR-30a inhibits the expression of TRIM25 and TRIM25-mediated retinoic acid-inducible gene (RIG)-I ubiquitination to suppress IFN-β activation and production, thereby resulting in the enhancement of CVB3 replication. These results indicate the proviral role of miR-30a in modulating CVB3 infection for the first time. This not only provides a new strategy followed by CVB3 in order to modulate IFN-I–mediated antiviral immune responses by engaging host miR-30a but also improves our understanding of its pathogenesis.
Drivers of the Abundance of Tridacna spp. Giant Clams in the Red Sea
Authors: Rossbach Susann , Anton Andrea , Duarte Carlos M.
Published: January 2021

Giant clams (Subfamily Tridacninae), are important members of Indo-Pacific coral reefs, playing multiple roles in the framework of these communities. Although they are prominent species in Red Sea reefs, data on their distribution and densities in the region are scarce. The present study provides the first large-scale survey of Red Sea Tridacna spp. densities, where we examined a large proportion of the Saudi Arabian Red Sea coast (1,300 km; from 18° to 29°N). Overall, Tridacninae were found at densities of 0.19 ± 0.43 individuals m–2 (±SD). Out of the total 4,002 observed clams, the majority (89%) were Tridacna maxima, with 0.17 ± 0.37 individuals m–2, while only 11% were Tridacna squamosa clams with 0.02 ± 0.07 individuals m–2. We also report on a few (total 6) Tridacna squamosina specimens, found at a single reef. We identified different geographical parameters (i.e., latitude and distance to shore) and local environmental factors (i.e., depth and reef zone) as the main drivers for local Tridacna spp. densities. Our results show that the drivers influencing the densities of Red Sea giant clams are complex due to their co-occurrence and that this complexity might explain the high variation in Tridacninae abundances across the Indo-Pacific, but also within a given reef. We also estimate that giant clam calcification likely contributes to an average of 0.7%, but potentially up to 9%, of the overall mean calcium carbonate budget of Red Sea coral reef communities.
Multiple Trophic Markers Trace Dietary Carbon Sources in Barents Sea Zooplankton During Late Summer
Authors: Kohlbach Doreen , Hop Haakon , Wold Anette , Schmidt Katrin , Smik Lukas , Belt Simon T. , Keck Al-Habahbeh Amalia , Woll Matthias , Graeve Martin , Dąbrowska Anna Maria , Tatarek Agnieszka , Atkinson Angus , Assmy Philipp
Published: January 2021

We investigated diets of 24 Barents Sea zooplankton taxa to understand pelagic food-web processes during late summer, including the importance of sea ice algae-produced carbon. This was achieved by combining insights derived from multiple and complementary trophic marker approaches to construct individual aspects of feeding. Specifically, we determined proportions of algal-produced fatty acids (FAs) to reflect the reliance on diatom- versus dinoflagellate-derived carbon, highly branched isoprenoid (HBI) lipids that distinguish between ice-associated and pelagic carbon sources, and sterols to indicate the degree of carnivory. Copepods had the strongest diatom signal based on FAs, while a lack of sea ice algae-associated HBIs (IP25, IPSO25) suggested that they fed on pelagic rather than ice-associated diatoms. The amphipodThemisto libellulaand the ctenophoresBeroë cucumisandMertensia ovumhad a higher contribution of dinoflagellate-produced FAs. There was a high degree of carnivory in this food web, as indicated by the FA carnivory index 18:1(n−9)/18:1(n−7) (mean value < 1 only in the pteropodClione limacina), the presence of copepod-associated FAs in most of the taxa, and the absence of algal-produced HBIs in small copepod taxa, such asOithona similisandPseudocalanusspp. The coherence between concentrations of HBIs and phytosterols within individuals suggested that phytosterols provide a good additional indication for algal ingestion. Sea ice algae-associated HBIs were detected in six zooplankton species (occurring in krill, amphipods, pteropods, and appendicularians), indicating an overall low to moderate contribution of ice-associated carbon from late-summer sea ice to pelagic consumption. The unexpected occurrence of ice-derived HBIs in pteropods and appendicularians, however, suggests an importance of sedimenting ice-derived material at least for filter feeders within the water column at this time of year.
Stable Isotope Mixing Models Are Biased by the Choice of Sample Preservation and Pre-treatment: Implications for Studies of Aquatic Food Webs
Authors: Silberberger Marc J. , Koziorowska-Makuch Katarzyna , Kuliński Karol , Kędra Monika
Published: January 2021

Stable isotope analysis has become one of the most widely used techniques in ecological studies. However, there are still uncertainties about the effects of sample preservation and pre-treatment on the ecological interpretation of stable isotope data and especially on Bayesian stable isotope mixing models. Here, Bayesian mixing models were used to study how three different preservation methods (drying, freezing, formalin) and two pre-treatments (acidification, lipid removal) affect the estimation of the utilized organic matter sources for two benthic invertebrate species (Limecola balthica, Crangon crangon) collected in the Baltic Sea. Furthermore, commonly used mathematical lipid normalization and formalin correction were applied to check if they were able to adjust the model results correctly. Preservation effects were strong on model outcomes for frozen as well as formalin preserved L. balthica samples, but not for C. crangon. Pre-treatment effects varied with species and preservation method and neither lipid normalization nor mathematical formalin correction consistently resulted in the desired model outcomes. Our analysis highlights that particularly small, not significant changes in stable isotope ratios introduced by different preservation and pre-treatments display a so far unrecognized source of error in stable isotope mixing models. We conclude that mathematical correction of benthic invertebrate stable isotopes data should be avoided for Bayesian mixing models and that previously unaddressed effects of sample preservation (especially those arising from preservation by freezing) have potentially biased our understanding of the utilization of organic matter in aquatic food webs.
Quantifying the High-Temperature Separation Behavior of Lamellar Interfaces in γ-Titanium Aluminide Under Tensile Loading by Molecular Dynamics
Authors: Ganesan Hariprasath , Scheider Ingo , Cyron Christian J.
Published: January 2021

γ-titanium aluminide (TiAl) alloys with fully lamellar microstructure possess excellent properties for high-temperature applications. Such fully lamellar microstructure has interfaces at different length scales. The separation behavior of the lamellae at these interfaces is crucial for the mechanical properties of the whole material. Unfortunately, quantifying it by experiments is difficult. Therefore, we use molecular dynamics (MD) simulations to this end. Specifically, we study the high-temperature separation behavior under tensile loading of the four different kinds of lamellar interfaces appearing in TiAl, namely, the γ/α2, γ/γPT, γ/γTT, and γ/γRB interfaces. In our simulations, we use two different atomistic interface models, a defect-free (Type-1) model and a model with preexisting voids (Type-2). Clearly, the latter is more physical but studying the former also helps to understand the role of defects. Our simulation results show that among the four interfaces studied, the γ/α2 interface possesses the highest yield strength, followed by the γ/γPT, γ/γTT, and γ/γRB interfaces. For Type-1 models, our simulations reveal failure at the interface for all γ/γ interfaces but not for the γ/α2 interface. By contrast, for Type-2 models, we observe for all the four interfaces failure at the interface. Our atomistic simulations provide important data to define the parameters of traction–separation laws and cohesive zone models, which can be used in the framework of continuum mechanical modeling of TiAl. Temperature-dependent model parameters were identified, and the complete traction–separation behavior was established, in which interface elasticity, interface plasticity, and interface damage could be distinguished. By carefully eliminating the contribution of bulk deformation from the interface behavior, we were able to quantify the contribution of interface plasticity and interface damage, which can also be related to the dislocation evolution and void nucleation in the atomistic simulations.
Role of Vanadium Carbide in Hydrogen Embrittlement of Press-Hardened Steels: Strategy From 1500 to 2000 MPa
Authors: Lin Yi-Ting , Yi Hong Liang , Chang Zhi Yuan , Lin Hsin-Chih , Yen Hung-Wei
Published: January 2021

This work investigated hydrogen trapping and hydrogen embrittlement (HE) in two press-hardened steels, 22MnB5 for 1,500 MPa grade and 34MnB5V for 2000 MPa grade, respectively. Superior to the 22MnB5 steel, the newly developed 34MnB5V steel has an ultimate tensile strength of over 2000 MPa without sacrificing ductility due to the formation of vanadium carbides (VCs). Simulated press hardening was applied to two steels, and hydrogen was induced by cathodic charging. Susceptibility to HE was validated by slow strain-rate tensile test. When hydrogen content was high, the 34MnB5V steel fractured in elastic regime. However, when hydrogen content was 0.8–1.0 ppmw, the 34MnB5V steel bore much higher stress than the 22MnB5 steel before fracture. The behavior of hydrogen trapping was investigated by thermal desorption analyses. Although the two steels trapped similar amounts of hydrogen after cathodic charging, their trapping mechanisms and effective trapping sites were different. In summary, a finer prior austenite grain size due to the pinning effect of VCs can also improve the toughness of 34MnB5V steel. Moreover, trapping hydrogen by grain boundary suppresses the occurrence of hydrogen-enhanced local plasticity. Microstructural refinement enhanced by VCs improves the resistance to HE in 34MnB5V steel. Importantly, the correlation between hydrogen trapping by VCs and improvement of HE is not significant. Hence, this work presents the challenge in designing irreversible trapping sites in future press-hardened steels.
Susceptibility Factors of Stomach for SARS-CoV-2 and Treatment Implication of Mucosal Protective Agent in COVID-19
Authors: Zhang Min , Feng Chao , Zhang Xingchen , Hu Shuofeng , Zhang Yuan , Min Min , Liu Bing , Ying Xiaomin , Liu Yan
Published: January 2021

Objectives: This work aims to study the gastrointestinal (GI) symptoms in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients and the susceptibility factors of the stomach for SARS-CoV-2.

Materials and Methods: We investigated the SARS-CoV-2 susceptibility by analyzing the expression distribution of viral entry-associated genes, ACE2 and TMPRSS2, in single-cell RNA sequencing data derived from 12 gastric mucosa samples. We also analyzed the epidemiological, demographic, clinical, and laboratory data of 420 cases with SARS-CoV-2-caused coronavirus disease 2019 (COVID-19).

Results:ACE2 and TMPRSS2 are specifically expressed in enterocytes which are mainly from gastric mucosa samples with Helicobacter pylori (H. pylori) infection history and intestinal metaplasia (IM). A total of 420 patients were surveyed, of which 62 were with and 358 were without GI symptoms. There is a significant difference in average hospital stay (p < 0.001) and cost (p < 0.001) between the two groups. Among 23 hospitalized patients including seven with upper GI symptoms and 16 with lower GI symptoms, six (85.7%) and five (31.3%) had H. pylori infection history, respectively (p = 0.03). Of 18 hospitalized patients with initial upper GI symptoms, none of the eight patients with mucosal protective agent therapy (e.g., sucralfate suspension gel, hydrotalcite tablets) had diarrhea subsequently, whereas six out of 10 patients without mucosal protective agent therapy had diarrhea subsequently (p = 0.01).

Conclusion: IM and H. pylori infection history may be susceptibility factors of SARS-CoV-2, and the mucosal protective agent may be useful for the blockade of SARS-CoV-2 transmission from the stomach to the intestine.
Renal Expression of Light Chain Binding Proteins
Authors: Reiter Thomas , Pajenda Sahra , O'Connell David , Lynch Ciara , Kapps Sebastian , Agis Hermine , Schmidt Alice , Wagner Ludwig , Leung Nelson , Winnicki Wolfgang
Published: January 2021

Overproduction of human light chains (LCs) and immunoglobulins can result in various forms of renal disease such as cast nephropathy, monoclonal immunoglobulin deposition disease, LC proximal tubulopathy, AL amyloidosis, and crystal storing histiocytosis. This is caused by cellular uptake of LCs and overwhelmed intracellular transport and degradation in patients with high urine LC concentrations. LC kappa and lambda purification was evaluated by sodium dodecyl sulfate gel electrophoresis. LC and myeloma protein binding to immobilized renal proteins was measured by enzyme-linked immunosorbent assay (ELISA). The human protein microarray (HuProt™) was screened with purified kappa and lambda LC. Identified LC partners were subsequently analyzed in silico for renal expression sites using protein databases, Human Protein Atlas, UniProt, and Bgee. Binding of urinary LCs and immunoglobulins to immobilized whole renal proteins from 22 patients with myeloma or plasma cell dyscrasia was shown by ELISA. Forty lambda and 23 kappa interaction partners were identified from HuProt™ array screens, of which 21 were shared interactors. Among the total of 42 interactors, 12 represented cell surface proteins. Lambda binding signals were approximately 40% higher than kappa signals. LC interaction with renal cells and disease-causing pathologies are more complex than previously thought. It involves an extended spectrum of proteins expressed throughout the nephron, and their identification has been enabled by recently developed methods of protein analysis such as protein microarray screening. Further biochemical studies on interacting proteins are warranted to elucidate their clinical relevance.
Exploring the Pattern Associated With Longitudinal Changes of β-Amyloid Deposition During Cognitively Normal Healthy Aging
Authors: Xie Yunyan , Yang Qin , Liu Chunhua , Zhang Qi , Jiang Jiehui , Han Ying ,   The Alzheimer's Disease Neuroimaging Initiative
Published: January 2021

The aim of this study was to determine a pattern associated with longitudinal changes of β-amyloid (Aβ) deposition during cognitively normal(CN) healthy aging. We used 18F-florbetapir (AV-45) PET images of the brains of 207 cognitively normal subjects (CN1), obtained through the Alzheimer's Disease Neuroimaging Initiative (ADNI), to identify the healthy aging pattern and 76 cognitively normal healthy subjects (CN2), obtained through the Xuanwu Hospital of Capital Medical University, Beijing, China, to verify it. A voxel-based correlation analysis of standardized uptake value ratio (SUVR) map image and age was conducted using the DPABI (Data Processing & Analysis of Brain Imaging) software to identify the pattern. The sum of squares due to errors (SSE), R-square (R2) and the root-mean-square error (RMSE) were calculated to assess the quality of curve fitting. Among them, R2 was proposed as the coherence coefficient, which was as an index to assess the correlation between SUVR value of the pattern and subjects' age. The pattern characterized by age-associated longitudinal changes of Aβ deposition was mainly distributed in the right middle and inferior temporal gyrus, the right temporal pole: middle temporal gyrus, the right inferior occipital gyrus, the right inferior frontal gyrus (triangular portion), and the right precentral gyrus. There were a significant positive correlation between the SUVR value of the pattern and age for each CN group (CN1: R2 = 0.120, p < 0.001 for quadratic model; CN2: R2 = 0.152, p = 0.002 for quadratic model). These findings suggest a pattern of changes in Aβ deposition that can be used to distinguish physiological changes from pathophysiological changes, constituting a new method for elucidating the neuropathological mechanism of Alzheimer's disease.
Inhibitory Effects of Lipopeptides and Glycolipids on C. albicans–Staphylococcus spp. Dual-Species Biofilms
Authors: Ceresa Chiara , Rinaldi Maurizio , Tessarolo Francesco , Maniglio Devid , Fedeli Emanuele , Tambone Erica , Caciagli Patrizio , Banat Ibrahim M. , Diaz De Rienzo Mayri Alessandra , Fracchia Letizia
Published: January 2021

Microbial biofilms strongly resist host immune responses and antimicrobial treatments and are frequently responsible for chronic infections in peri-implant tissues. Biosurfactants (BSs) have recently gained prominence as a new generation of anti-adhesive and antimicrobial agents with great biocompatibility and were recently suggested for coating implantable materials in order to improve their anti-biofilm properties. In this study, the anti-biofilm activity of lipopeptide AC7BS, rhamnolipid R89BS, and sophorolipid SL18 was evaluated against clinically relevant fungal/bacterial dual-species biofilms (Candida albicans, Staphylococcus aureus, Staphylococcus epidermidis) through quantitative and qualitative in vitro tests. C. albicans–S. aureus and C. albicans–S. epidermidis cultures were able to produce a dense biofilm on the surface of the polystyrene plates and on medical-grade silicone discs. All tested BSs demonstrated an effective inhibitory activity against dual-species biofilms formation in terms of total biomass, cell metabolic activity, microstructural architecture, and cell viability, up to 72 h on both these surfaces. In co-incubation conditions, in which BSs were tested in soluble form, rhamnolipid R89BS (0.05 mg/ml) was the most effective among the tested BSs against the formation of both dual-species biofilms, reducing on average 94 and 95% of biofilm biomass and metabolic activity at 72 h of incubation, respectively. Similarly, rhamnolipid R89BS silicone surface coating proved to be the most effective in inhibiting the formation of both dual-species biofilms, with average reductions of 93 and 90%, respectively. Scanning electron microscopy observations showed areas of treated surfaces that were free of microbial cells or in which thinner and less structured biofilms were present, compared to controls. The obtained results endorse the idea that coating of implant surfaces with BSs may be a promising strategy for the prevention of C. albicans–Staphylococcus spp. colonization on medical devices, and can potentially contribute to the reduction of the high economic efforts undertaken by healthcare systems for the treatment of these complex fungal–bacterial infections.
Evaluation of a Loop-Mediated Isothermal Amplification Assay to Detect Carbapenemases Directly From Bronchoalveolar Lavage Fluid Spiked With Acinetobacter spp.
Authors: Moreno-Morales Javier , Vergara Andrea , Kostyanev Tomislav , Rodriguez-Baño Jesús , Goossens Herman , Vila Jordi
Published: January 2021

Carbapenem-resistant Acinetobacter spp. mainly Acinetobacter baumannii are frequently causing nosocomial infections with high mortality. In this study, the efficacy of the Eazyplex® SuperBug Complete A system, based on loop-mediated isothermal amplification (LAMP), to detect the presence of carbapenemases in Acinetobacter spp. directly from bronchoalveolar lavage (BAL) samples was assessed. A total of 22 Acinetobacter spp. strains producing OXA-23, OXA-40, OXA-58, NDM, and IMP were selected. Eazyplex SuperBug Complete A kit, used with the Genie II device, is a molecular diagnostics kit that detects a selection of genes that express carbapenemases (blaKPC, blaNDM, blaVIM, blaOXA–48, blaOXA–23, blaOXA–40, and blaOXA–58). Negative BAL samples were identified, McFarland solutions were prepared from each of the 22 Acinetobacter strains and serial dilutions in saline solution were made to finally spike BAL samples to a concentration of 102 and 103 CFU/ml. Fifteen concentrations out of the 44 tested out did not provide detection of the carbapenemase-producing gene, all but one being at the lowest concentration tested at 102 CFU/ml; therefore, the limit of sensitivity is 103 CFU/ml. This assay represents the kind of advantages that investing in molecular diagnostics brings to the clinical practice, allowing the identification of carbapenemases in less than 30 min with a sensitivity of 103 CFU/ml.
Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation
Authors: Massot Francisco , Gkorezis Panagiotis , Van Hamme Jonathan , Marino Damian , Trifunovic Bojana Spirovic , Vukovic Gorica , d’Haen Jan , Pintelon Isabel , Giulietti Ana María , Merini Luciano , Vangronsveld Jaco , Thijs Sofie
Published: January 2021

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.
Forensic Applications of Microbiomics: A Review
Authors: Robinson Jake M. , Pasternak Zohar , Mason Christopher E. , Elhaik Eran
Published: January 2021

The rise of microbiomics and metagenomics has been driven by advances in genomic sequencing technology, improved microbial sampling methods, and fast-evolving approaches in bioinformatics. Humans are a host to diverse microbial communities in and on their bodies, which continuously interact with and alter the surrounding environments. Since information relating to these interactions can be extracted by analyzing human and environmental microbial profiles, they have the potential to be relevant to forensics. In this review, we analyzed over 100 papers describing forensic microbiome applications with emphasis on geolocation, personal identification, trace evidence, manner and cause of death, and inference of the postmortem interval (PMI). We found that although the field is in its infancy, utilizing microbiome and metagenome signatures has the potential to enhance the forensic toolkit. However, many of the studies suffer from limited sample sizes and model accuracies, and unrealistic environmental settings, leaving the full potential of microbiomics to forensics unexplored. It is unlikely that the information that can currently be elucidated from microbiomics can be used by law enforcement. Nonetheless, the research to overcome these challenges is ongoing, and it is foreseeable that microbiome-based evidence could contribute to forensic investigations in the future.
Relative Influence of Plastic Debris Size and Shape, Chemical Composition and Phytoplankton-Bacteria Interactions in Driving Seawater Plastisphere Abundance, Diversity and Activity
Authors: Cheng Jingguang , Jacquin Justine , Conan Pascal , Pujo-Pay Mireille , Barbe Valérie , George Matthieu , Fabre Pascale , Bruzaud Stéphane , Ter Halle Alexandra , Meistertzheim Anne-Leila , Ghiglione Jean-François
Published: January 2021

The thin film of life that inhabits all plastics in the oceans, so-called “plastisphere,” has multiple effects on the fate and impacts of plastic in the marine environment. Here, we aimed to evaluate the relative influence of the plastic size, shape, chemical composition, and environmental changes such as a phytoplankton bloom in shaping the plastisphere abundance, diversity and activity. Polyethylene (PE) and polylactide acid (PLA) together with glass controls in the forms of meso-debris (18 mm diameter) and large-microplastics (LMP; 3 mm diameter), as well as small-microplastics (SMP) of 100 μm diameter with spherical or irregular shapes were immerged in seawater during 2 months. Results of bacterial abundance (confocal microscopy) and diversity (16S rRNA Illumina sequencing) indicated that the three classical biofilm colonization phases (primo-colonization after 3 days; growing phase after 10 days; maturation phase after 30 days) were not influenced by the size and the shape of the materials, even when a diatom bloom (Pseudo-nitzschiasp.) occurred after the first month of incubation. However, plastic size and shape had an effect on bacterial activity (3H leucine incorporation). Bacterial communities associated with the material of 100 μm size fraction showed the highest activity compared to all other material sizes. A mature biofilm developed within 30 days on all material types, with higher bacterial abundance on the plastics compared to glass, and distinct bacterial assemblages were detected on each material type. The diatom bloom event had a great impact on the plastisphere of all materials, resulting in a drastic change in diversity and activity. Our results showed that the plastic size and shape had relatively low influence on the plastisphere abundance, diversity, and activity, as compared to the plastic composition or the presence of a phytoplankton bloom.
Analysis of Cell–Cell Bridges in Haloferax volcanii Using Electron Cryo-Tomography Reveal a Continuous Cytoplasm and S-Layer
Authors: Sivabalasarma Shamphavi , Wetzel Hanna , Nußbaum Phillip , van der Does Chris , Beeby Morgan , Albers Sonja-Verena
Published: January 2021

Halophilic archaea have been proposed to exchange DNA and proteins using a fusion-based mating mechanism. Scanning electron microscopy previously suggested that mating involves an intermediate state, where cells are connected by an intercellular bridge. To better understand this process, we used electron cryo-tomography (cryoET) and fluorescence microscopy to visualize cells forming these intercellular bridges. CryoET showed that the observed bridges were enveloped by an surface layer (S-layer) and connected mating cells via a continuous cytoplasm. Macromolecular complexes like ribosomes and unknown thin filamentous helical structures were visualized in the cytoplasm inside the bridges, demonstrating that these bridges can facilitate exchange of cellular components. We followed formation of a cell–cell bridge by fluorescence time-lapse microscopy between cells at a distance of 1.5 μm. These results shed light on the process of haloarchaeal mating and highlight further mechanistic questions.
Targeting Autophagy as a Strategy for Developing New Vaccines and Host-Directed Therapeutics Against Mycobacteria
Authors: Strong Emily J. , Lee Sunhee
Published: January 2021

Mycobacterial disease is an immense burden worldwide. This disease group includes tuberculosis, leprosy (Hansen’s disease), Buruli Ulcer, and non-tuberculous mycobacterial (NTM) disease. The burden of NTM disease, both pulmonary and ulcerative, is drastically escalating globally, especially in developed countries such as America and Australia. Mycobacteria’s ability to inhibit or evade the host immune system has contributed significantly to its continued prevalence. Pre-clinical studies have highlighted promising candidates that enhance endogenous pathways and/or limit destructive host responses. Autophagy is a cell-autonomous host defense mechanism by which intracytoplasmic cargos can be delivered and then destroyed in lysosomes. Previous studies have reported that autophagy-activating agents, small molecules, and autophagy-activating vaccines may be beneficial in restricting intracellular mycobacterial infection, even with multidrug-resistant strains. This review will examine how mycobacteria evade autophagy and discusses how autophagy could be exploited to design novel TB treatment strategies, such as host-directed therapeutics and vaccines, againstMycobacterium tuberculosisand NTMs.
Exploring Marine Planktonic Archaea: Then and Now
Authors: DeLong Edward F.
Published: January 2021

In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities
Authors: Parizadeh Mona , Mimee Benjamin , Kembel Steven W.
Published: January 2021

The phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices. Widespread pesticide application may have had non-target impacts on these beneficial microorganisms. Neonicotinoids are a family of systemic insecticides being vastly used to control soil and foliar pests in recent decades. A few studies have demonstrated the long-term and non-target effects of neonicotinoids on agroecosystem microbiota, but the generality of these findings remains unclear. In this study, we used 16S rRNA gene amplicon sequencing to characterize the effects of neonicotinoid seed treatment on soil and phyllosphere bacterial community diversity, composition and temporal dynamics in a 3-year soybean/corn rotation in Quebec, Canada. We found that habitat, host species and time are stronger drivers of variation in bacterial composition than neonicotinoid application. They, respectively, explained 37.3, 3.2, and 2.9% of the community variation. However, neonicotinoids did have an impact on bacterial community structure, especially on the taxonomic composition of soil communities (2.6%) and over time (2.4%). They also caused a decrease in soil alpha diversity in the middle of the growing season. While the neonicotinoid treatment favored some bacterial genera known as neonicotinoid biodegraders, there was a decline in the relative abundance of some potentially beneficial soil bacteria in response to the pesticide application. Some of these bacteria, such as the plant growth-promoting rhizobacteria and the bacteria involved in the nitrogen cycle, are vital for plant growth and improve soil fertility. Overall, our results indicate that neonicotinoids have non-target effects on phyllosphere and soil bacterial communities in a soybean-corn agroecosystem. Exploring the interactions among bacteria and other organisms, as well as the bacterial functional responses to the pesticide treatment, may enhance our understanding of these non-target effects and help us adapt agricultural practices to control these impacts.
Evaluation of Live Bacterial Prophylactics to Decrease IncF Plasmid Transfer and Association With Intestinal Small RNAs
Authors: Redweik Graham A. J. , Horak Mary Kate , Hoven Ryley , Ott Logan , Mellata Melha
Published: January 2021

Chicken intestinalEscherichia coliare a reservoir for virulence and antimicrobial resistance (AMR) genes that are often carried on incompatibility group F (IncF) plasmids. The rapid transfer of these plasmids between bacteria in the gut contributes to the emergence of new multidrug-resistant and virulent bacteria that threaten animal agriculture and human health. Thus, the aim of the present study was to determine whether live bacterial prophylactics could affect the distribution of large virulence plasmids and AMR in the intestinal tract and the potential role of smRNA in this process. In this study, we tested ∼100 randomly selectedE. colifrom pullet feces (n= 3 per group) given no treatment (CON), probiotics (PRO), a liveSalmonellavaccine (VAX), or both (P + V).E. coliisolates were evaluated via plasmid profiles and several phenotypic (siderophore production and AMR), and genotypic (PCR for virulence genes and plasmid typing) screens. P + V isolates exhibited markedly attenuated siderophore production, lack of AMR and virulence genes, which are all related to the loss of IncF and ColV plasmids (P< 0.0001). To identify a causal mechanism, we evaluated smRNA levels in the ceca mucus and found a positive association between smRNA concentrations and plasmid content, with both being significantly reduced in P + V birds compared to other groups (P< 0.01). To test this positive association between IncF plasmid transfer and host smRNA concentration, we evenly pooled smRNA per group and treatedE. colimating pairs with serial concentrations of smRNAin vitro. Higher smRNA concentrations resulted in greater rates of IncF plasmid transfer betweenE. colidonors (APEC O2 or VAX isolate IA-EC-001) and recipient (HS-4) (all groups;P< 0.05). Finally, RNAHybrid predictive analyses detected several chicken miRNAs that hybridize with pilus assembly and plasmid transfer genes on the IncF plasmid pAPEC-O2-R. Overall, we demonstrated P + V treatment reduced smRNA levels in the chicken ceca, which was associated with a reduction in potentially virulentE. coli. Furthermore, we propose a novel mechanism in which intestinal smRNAs signal plasmid exchange betweenE. coli. Investigations to understand the changes in bacterial gene expression as well as smRNAs responsible for this phenomenon are currently underway.
Horizontal Transmission of the Heritable Protective Endosymbiont Hamiltonella defensa Depends on Titre and Haplotype
Authors: Kaech Heidi , Vorburger Christoph
Published: January 2021

Secondary endosymbionts of aphids have an important ecological and evolutionary impact on their host, as they provide resistance to natural enemies but also reduce the host’s lifespan and reproduction. While secondary symbionts of aphids are faithfully transmitted from mother to offspring, they also have some capacity to be transmitted horizontally between aphids. Here we explore whether 11 isolates from 3 haplotypes of the secondary endosymbiont Hamiltonella defensa differ in their capacity for horizontal transmission. These isolates vary in the protection they provide against parasitoid wasps as well as the costs they inflict on their host, Aphis fabae. We simulated natural horizontal transmission through parasitoid wasps by stabbing aphids with a thin needle and assessed horizontal transmission success of the isolates from one shared donor clone into three different recipient clones. Specifically, we asked whether potentially costly isolates reaching high cell densities in aphid hosts are more readily transmitted through this route. This hypothesis was only partially supported. While transmissibility increased with titre for isolates from two haplotypes, isolates of the H. defensa haplotype 1 were transmitted with greater frequency than isolates of other haplotypes with comparable titres. Thus, it is not sufficient to be merely frequent—endosymbionts might have to evolve specific adaptations to transmit effectively between hosts.