bluuebunny/crossref_metadata_2025 huggingface dataset:
Glucocorticoid-Induced Leucine Zipper: A Promising Marker for Monitoring and Treating Sepsis
Authors: He Ya-Jun , Xu Ji-Qian , Sun Miao-Miao , Fang Xiang-Zhi , Peng Zhe-Kang , Pan Shang-Wen , Zhou Ting , Wang Ya-Xin , Shang You
Published: January 2021

Sepsis is a clinical syndrome that resulting from a dysregulated inflammatory response to infection that leads to organ dysfunction. The dysregulated inflammatory response transitions from a hyper-inflammatory phase to a hypo-inflammatory or immunosuppressive phase. Currently, no phase-specific molecular-based therapies are available for monitoring the complex immune response and treating sepsis due to individual variations in the timing and overlap of the dysregulated immune response in most patients. Glucocorticoid-induced leucine zipper (GILZ), is broadly present in multiple tissues and circumvent glucocorticoid resistance (GCR) or unwanted side effects. Recently, the characteristics of GILZ downregulation during acute hyperinflammation and GILZ upregulation during the immunosuppressive phase in various inflammatory diseases have been well documented, and the protective effects of GILZ have gained attention in the field of sepsis. However, whether GILZ could be a promising candidate biomarker for monitoring and treating septic patients remains unknown. Here, we discuss the effect of GILZ in sepsis and sepsis-induced immunosuppression.
Transcriptomic Response of Mussel Gills After a Vibrio splendidus Infection Demonstrates Their Role in the Immune Response
Authors: Saco Amaro , Rey-Campos Magalí , Novoa Beatriz , Figueras Antonio
Published: January 2021

Mussels (Mytilus galloprovincialis) are filter feeder bivalves that are constantly in contact with a wide range of microorganisms, some of which are potentially pathogenic. How mussels recognize and respond to pathogens has not been fully elucidated to date; therefore, we investigated the immune mechanisms that these animals employ in response to a bacterial bath infection from the surrounding water, mimicking the response that mussels mount under natural conditions. After the bath infection, mussels were able to remove the bacteria from their bodies and from the water tank. Accordingly, antibacterial activity was detected in gill extracts, demonstrating that this tissue plays a central role in removing and clearing potential pathogens. A transcriptomic study performed after a bath infection with Vibrio splendidus identified a total of 1,156 differentially expressed genes. The expression levels of genes contributing to a number of biological processes, such as immune response activation pathways and their regulation with cytokines, cell recognition, adhesion and apoptosis, were significantly modulated after infection, suggesting that the gills play important roles in pathogen recognition, as well as being activators and regulators of the mussel innate immune response. In addition to RNA-seq analysis, long non-coding RNAs and their neighboring genes were also analyzed and exhibited modulation after the bacterial challenge. The response of gills against bath infection was compared with the findings of a previous transcriptomic study on hemocytes responding to systemic infection, demonstrating the different and specific functions of gills. The results of this study indicate that recognition processes occur in the gill, thereby activating the effector agents of the immune response to overcome bacterial infection.
Microbiome-Dependent Adaptation of Seaweeds Under Environmental Stresses: A Perspective
Authors: Ghaderiardakani Fatemeh , Quartino Maria Liliana , Wichard Thomas
Published: January 2021

The microbiome of macroalgae facilitates their adaptation to environmental stress. As bacteria release algal growth and morphogenesis promoting factors (AGMPFs), which are necessary for the healthy development of macroalgae, bacteria play a crucial role in stress adaptation of bacterial-algal interactions. To better understand the level of macroalgal dependence on the microbiome under various stress factors such as light, temperature, salt, or micropollutants, we propose a reductionist analysis of a tripartite model system consisting of the axenic green alga Ulva (Chlorophyta) re-infected with two essential bacteria. This analysis will allow us to decipher the stress response of each symbiont within this cross-kingdom interaction. The paper highlights studies on possible survival strategies embedded in cross-kingdom interactions that govern the stress adaptation, including general features of metabolic pathways in the macroalgal host or more specific features such as alterations in the composition and/or diversity of bacterial assemblages within the microbiome community. Additionally, we present some preliminary results regarding the effect of recently isolated bacteria from the Potter Cove, King George Island (Isla 25 de Mayo) in Antarctica, on the model system Ulva mutabilis Føyn purified gametes. The results indicate that cold-adapted bacteria release AGMPFs, inducing cell differentiation, and cell division in purified cultures. We propose that microbiome engineering can be used to increase the adaptability of macroalgae to stressful situations with implications for, e.g., the sustainable management of (land-based) aquaculture systems.
Growth and Age Validation of the Thornback Ray (Raja clavata Linnaeus, 1758) in the South Adriatic Sea (Central Mediterranean)
Authors: Carbonara Pierluigi , Bellodi Andrea , Palmisano Michele , Mulas Antonello , Porcu Cristina , Zupa Walter , Donnaloia Marilena , Carlucci Roberto , Sion Letizia , Follesa Maria Cristina
Published: January 2021

Raja clavata is the most widespread and landed skate species in the Mediterranean Basin. Despite its diffusion and economic importance, several aspects of its life history, such as age and growth, are poorly understood. This study evaluated the species’ growth in the South Adriatic Sea (Central Mediterranean Sea) and for the first time attempted an age validation through a tagging experiment. Thin sectioning of vertebral centra proved to be a more accurate preparation method in terms of age estimation precision and reproducibility than whole vertebral centrum staining (cobalt nitrate and ammonium sulfide technique). Marginal analysis showed a clear seasonal pattern, confirming the hypothesis of a single annulus deposition per year. A total of 291 vertebral centra were sampled and used for age estimation purposes. The oldest female was estimated to be 12 years old [total length (TL) = 89 cm], while the oldest male was aged 8 years (TL = 79.9 cm). Females were also found to be characterized by a slightly wider longevity range (ωL = 11.5, ωU = 16.8 years) than males (ωL = 7.8, ωU = 11.2 years). The von Bertalanffy growth curve fit the age and length data more accurately than the Gompertz and logistic models. Eighty-three thornback rays were tagged and released, of which two were recaptured. In both recaptured specimens, oxytetracycline marks were clearly visible. The band deposition after oxytetracycline injection and growth during the freedom period (about 1 year) were consistent with the age estimation method and criteria used and with the obtained growth results. Thus, the analysis of the vertebral centra extracted from the two recaptured specimens confirmed the hypothesis of the deposition of a single annulus per year and in general the age estimation criteria used in this study.
Adaptive Behaviors to Marine Ecosystem Shifts: Examining Fishermen’s Strategies in Response to Abundant Juvenile Sablefish (Anoplopoma fimbria) in Alaska
Authors: Szymkowiak Marysia , Rhodes-Reese Melissa
Published: January 2021

Over recent years there have been rapid changes occurring across marine ecosystems worldwide, with high latitude systems seeing ecosystem shifts emerging at unprecedented rates. The Gulf of Alaska and Bering Sea marine ecosystems have experienced substantial fluctuation in fish stocks, with some species experiencing considerable decreases while others thrive. Following the marine heatwave of 2014, sablefish (Anoplopoma fimbria) had a historically unparalleled juvenile recruitment class that is now dominating the stock composition. While this recruitment class bodes well for future fisheries, it is currently undermining the value of the fishery with limited incentives to retain the smaller and less valuable fish, compounding adverse effects on earnings in the fishery due to whale depredation that has been occurring for years. This study examines the well-being implications of fishermen’s adaptive strategies to these ecosystem conditions within the Alaska sablefish fishery using a socio-ecological system framework, operationalized as a qualitative network model (QNMs) and quantitative indicators. We examine the extent to which adaptation strategies, derived from a literature review and stakeholder interviews, are being utilized in the fishery with quantitative indicators. These strategies are then examined with QNMs that explore their impacts across the spectrum of well-being. By coupling quantitative indicators and QNMs, we were able to demonstrate how adaptive strategies can be examined to capture the multi-faceted well-being effects of fisheries participants’ adaptations to changing conditions. This study directly addresses several of the key guiding principles of the U.S. EBFM Road Map, including advancing our understanding of ecosystem processes, exploring trade-offs within an ecosystem, and maintaining resilient ecosystems, inclusive of community well-being. Thus this paper demonstrates how coupled socio-ecological models can elevate the inclusion of human adaptive behaviors, providing a framework for the development of policymaking that can mitigate adverse effects on both the participants and the resource by facilitating the mixture of adaptive strategies that maximizes desired well-being outcomes.
A Closing Window of Opportunity to Save a Unique Marine Ecosystem
Authors: Kleinhaus Karine , Voolstra Christian R. , Meibom Anders , Amitai Yael , Gildor Hezi , Fine Maoz
Published: January 2021

Five years in the making, a massive oil spill of 1 million barrels is imminent in the Red Sea off the coast of Yemen. Emergent action must be taken by the United Nations and its International Maritime Organization (IMO) to remove the oil, despite regional political tensions, as a spill will have disastrous environmental and humanitarian consequences, especially if it occurs during winter. With millions of barrels of oil passing through the Red Sea each day, a regional strategy must be drafted for leak prevention and containment that is specific to the Red Sea’s unique ecosystems, unusual water currents, and political landscape.
Seismic Performance of Recycled Concrete Filled Circular Steel Tube Columns
Authors: Xu Dingyi , Chen Zongping , Zhou Chunheng
Published: January 2021

This study was conducted to experimentally investigate the behavior of recycled concrete-filled circular steel tube (RCFST) columns subjected to cyclic loading. Ten specimens were prepared and tested. Four parameters were used to characterize seismic behavior: the replacement percentage of recycled coarse aggregate, slenderness ratio, axial compression level, and steel ratio. A novel calculation method for the bearing capacity for RCFST columns is established. The failure processes and modes of RCFST columns are found to be similar to normal concrete-filled steel tube columns. Varying the replacement percentage of recycled coarse aggregate has little effect on the hysteresis curves of the RCFST columns. The RCFST columns also show seismic performance similar to that of concrete-filled steel tubes. The displacement ductility of all specimens is larger than 3.0 and the equivalent viscous damping coefficients corresponding to the ultimate load range from 0.305 to 0.460.
Long-Term Outcomes of Retinal Detachment in Phakic Eyes After Implantation of Implantable Collamer Lens V4c for High Myopia Correction
Authors: Xu Weiwei , Song Zhou , Huang Yifei , Tao Ye , Wang Junqing , Wang Liqiang , Li Zhaohui
Published: January 2021

Aim: To estimate whether implantable collamer lens (V4c ICL) implantation increases the risk of retinal detachment in high myopia comparing with myopes with Rigid Gas-Permeable (RGP) correction.

Methods: This prospective study was comprised of an ICL group (704 eyes) and an RGP group (628 eyes). Patients were enrolled according to the inclusion criteria and exclusion criteria, then divided into the ICL group and RGP group. Patients in the ICL and RGP groups received V4c ICL implantation and RGP fitting respectively. Retinal details, spherical equivalent refraction (SE), uncorrected distance visual acuity (UDVA), corrected distance vision acutivity (CDVA), axis length (AL), anterior chamber depth (ACD) and other relevant parameters were recorded at different time points. Rhegmatogenous retinal detachment (RRD) morbidity and incidence, RRD morphology and relevant parameters were analyzed.

Results: All enrolled patients were followed for 3–6 years. Patients characteristics before the refractive procedure did not show a statistical difference. At the end of the follow up, all the RD cases were RRD. The RRD morbidity of the ICL group and RGP group was 1.99% (14 eyes) and 0.96% (6 eyes) respectively, which did not show statistical difference (P = 0.12). During the first year after refractive procedure, the RRD incidence of the ICL group was 0.85% (6/704), while this number of the RGP group was 0.16% (1/628). It did not show statistical difference (P = 0.08).

Conclusion: Compared with RGP fitting, V4c ICL implantation for high myopia correction does not add RRD risk in the long term. V4c ICL implantation is a safe method for high myopia correction.
Risk Factors for the Occurrence and Progression of Posttraumatic Elbow Stiffness: A Case-Control Study of 688 Cases
Authors: Qian Yun , Yu Shiyang , Shi Yue , Huang Hengye , Fan Cunyi
Published: January 2021

Background: Elbow stiffness is a severe complication after trauma. Surgical or conservative treatments may be ineffective for restoring functional elbow motion. We aim to evaluate intrinsic and extrinsic factors for the occurrence and severity of elbow stiffness.

Methods: This retrospective case–control study included mild/moderate stiffness, severe stiffness, and non-stiffness groups between January 2011 and December 2017 at a single orthopedic center. Multivariable logistic regression analysis and subgroup analysis were used to evaluate age, gender, body mass index, muscle strength, fracture type and site, injury mechanism, immobilization time, elbow dysfunction time, multiple surgeries, nerve symptoms, physical therapy, smoking and alcohol abuse, and dominant hand of stiff elbow as potential risk factors for the occurrence and severity of elbow stiffness.

Results: There were 461 patients in the stiffness group and 227 patients in the non-stiffness group. The odds ratios (ORs) of the age, muscle strength, and injury mechanism were 0.960, 0.333, and 0.216 for the occurrence of elbow stiffness. In subgroup evaluation, increased cast immobilization time might be a risk factor for patients receiving conservative therapies (OR = 2.02; p = 0.014). In the evaluation on factors for progression of elbow stiffness, “multiple surgeries” might be a risk factor in surgical treatment by subgroup analysis (OR = 1.943; p = 0.026). Nevertheless, alcohol abuse might increase severity of elbow stiffness in conservatively treated patients (OR = 3.082; p = 0.025).

Conclusion: Increased cast immobilization time in the conservative therapy might be a risk factor for stiffness occurrence. Multiple surgeries might be risk factors for stiffness progression. Alcohol abuse potentially increased stiffness severity after conservative treatment.
10-Year Molecular Surveillance of Listeria monocytogenes Using Whole-Genome Sequencing in Shanghai, China, 2009–2019
Authors: Zhang Hongzhi , Chen Weijie , Wang Jing , Xu Biyao , Liu Hong , Dong Qingli , Zhang Xi
Published: January 2021

Listeria monocytogenes is an etiologic agent of listeriosis, and has emerged as an important foodborne pathogen worldwide. In this study, the molecular characteristics of 155 L. monocytogenes isolates from seven food groups in Shanghai, the biggest city in China, were identified using whole-genome sequencing (WGS). Most L. monocytogenes isolates (79.3%) were obtained between May and October from 2009 to 2019. The serogroups and clonal complexes (CCs) of L. monocytogenes were found useful for identifying potential health risks linked to foods. Differences in distributions of serogroups and CCs among different food groups were analyzed using t-test. The results showed that the IIa and IVb serogroups were identified among most of food groups. However, the prevalence of serogroup IIb was significantly higher in ready-to-eat (RTE) food and raw seafood than in other food groups, similar to group IIc in raw meat and raw poultry than others. Meanwhile, the prevalence of CC9 in raw meat and raw poultry, CC8 in raw poultry, and CC87 in raw seafood significantly exceeded that of in other food groups. Specially, CC87 was the predominant CC in foodborne and clinical isolates in China, indicating that raw seafood may induce a high-risk to food safety. Also, hypervirulence pathogenicity islands LIPI-3 and LIPI-4 were found in CC3, CC1, and CC87, respectively. The clonal group CC619 carried LIPI-3 and LIPI-4, as previously reported in China. Core genome multilocus sequence typing (cgMLST) analysis suggested that CC87 isolates from the same food groups in different years had no allelic differences, indicating that L. monocytogenes could persist over years. These 10-year results in Shanghai underscore the significance of molecular epidemiological surveillance of L. monocytogenes in foodborne products in assessing the potential risk of this pathogen, and further address food safety issues in China.
Proteomic Analysis of Vesicle-Producing Pseudomonas aeruginosa PAO1 Exposed to X-Ray Irradiation
Authors: Zhang Li , Zhao Shi-qiao , Zhang Jie , Sun Ying , Xie Ya-liu , Liu Yan-bin , Ma Cui-cui , Jiang Bo-guang , Liao Xue-yuan , Li Wen-fang , Cheng Xing-jun , Wang Zhen-ling
Published: January 2021

Ionizing irradiation kills pathogens by destroying nucleic acids without protein structure destruction. However, how pathogens respond to irradiation stress has not yet been fully elucidated. Here, we observed that Pseudomonas aeruginosa PAO1 could release nucleic acids into the extracellular environment under X-ray irradiation. Using scanning electron microscopy (SEM) and transmission electron microscopy (TEM), X-ray irradiation was observed to induce outer membrane vesicle (OMV) formation in P. aeruginosa PAO1. The size distribution of the OMVs of the irradiated PAO1 was similar to that of the OMVs of the non-irradiated PAO1 according to nanoparticle tracking analysis (NTA). The pyocin-related proteins are involved in OMV production in P. aeruginosa PAO1 under X-ray irradiation conditions, and that this is regulated by the key SOS gene recA. The OMV production was significantly impaired in the irradiated PAO1 Δlys mutant, suggesting that Lys endolysin is associated with OMV production in P. aeruginosa PAO1 upon irradiation stress. Meanwhile, no significant difference in OMV production was observed between PAO1 lacking the pqsR, lasR, or rhlR genes and the parent strain, demonstrating that the irradiation-induced OMV biosynthesis of P. aeruginosa was independent of the Pseudomonas quinolone signal (PQS).
A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria
Authors: Hook John C. , Blagotinsek Vitan , Pané-Farré Jan , Mrusek Devid , Altegoer Florian , Dornes Anita , Schwan Meike , Schier Lukas , Thormann Kai M. , Bange Gert
Published: January 2021

Flagella are bacterial organelles of locomotion. Their biogenesis is highly coordinated in time and space and relies on a specialized flagellar type III secretion system (fT3SS) required for the assembly of the extracellular hook, rod, and filament parts of this complex motor device. The fT3SS protein FlhB switches secretion substrate specificity once the growing hook reaches its determined length. Here we present the crystal structure of the cytoplasmic domain of the transmembrane protein FlhB. The structure visualizes a so-far unseen proline-rich region (PRR) at the very C-terminus of the protein. Strains lacking the PRR show a decrease in flagellation as determined by hook- and filament staining, indicating a role of the PRR during assembly of the hook and filament structures. Phylogenetic analysis shows that the PRR is a primary feature of FlhB proteins of flagellated beta- and gamma-proteobacteria. Taken together, our study adds another layer of complexity and organismic diversity to the process of flagella biogenesis.
A Klebsiella variicola Plasmid Confers Hypermucoviscosity-Like Phenotype and Alters Capsule Production and Virulence
Authors: Rodríguez-Medina Nadia , Martínez-Romero Esperanza , De la Cruz Miguel Angel , Ares Miguel Angel , Valdovinos-Torres Humberto , Silva-Sánchez Jesús , Lozano-Aguirre Luis , Martínez-Barnetche Jesús , Andrade Veronica , Garza-Ramos Ulises
Published: January 2021

Hypermucoviscosity (hmv) is a capsule-associated phenotype usually linked with hypervirulent Klebsiella pneumoniae strains. The key components of this phenotype are the RmpADC proteins contained in non-transmissible plasmids identified and studied in K. pneumoniae. Klebsiella variicola is closely related to K. pneumoniae and recently has been identified as an emergent human pathogen. K. variicola normally contains plasmids, some of them carrying antibiotic resistance and virulence genes. Previously, we described a K. variicola clinical isolate showing an hmv-like phenotype that harbors a 343-kb pKV8917 plasmid. Here, we investigated whether pKV8917 plasmid carried by K. variicola 8917 is linked with the hmv-like phenotype and its contribution to virulence. We found that curing the 343-kb pKV8917 plasmid caused the loss of hmv, a reduction in capsular polysaccharide (P < 0.001) and virulence. In addition, pKV8917 was successfully transferred to Escherichia coli and K. variicola strains via conjugation. Notably, when pKV8917 was transferred to K. variicola, the transconjugants displayed an hmv-like phenotype, and capsule production and virulence increased; these phenotypes were not observed in the E. coli transconjugants. These data suggest that the pKV8917 plasmid carries novel hmv and capsule determinants. Whole-plasmid sequencing and analysis revealed that pKV8917 does not contain rmpADC/rmpA2 genes; thus, an alternative mechanism was searched. The 343-kb plasmid contains an IncFIB backbone and shares a region of ∼150 kb with a 99% identity and 49% coverage with a virulence plasmid from hypervirulent K. variicola and multidrug-resistant K. pneumoniae. The pKV8917-unique region harbors a cellulose biosynthesis cluster (bcs), fructose- and sucrose-specific (fru/scr) phosphotransferase systems, and the transcriptional regulators araC and iclR, respectively, involved in membrane permeability. The hmv-like phenotype has been identified more frequently, and recent evidence supports the existence of rmpADC/rmpA2-independent hmv-like pathways in this bacterial genus.
Antimicrobial Resistance as a Hidden Menace Lurking Behind the COVID-19 Outbreak: The Global Impacts of Too Much Hygiene on AMR
Authors: Rezasoltani Sama , Yadegar Abbas , Hatami Behzad , Asadzadeh Aghdaei Hamid , Zali Mohammad Reza
Published: January 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus that was recently discovered in 2019. While the world is working hard to overcome and control the coronavirus disease 2019 (COVID-19) pandemic, it is also crucial to be prepared for the great impacts of this outbreak on the development of antimicrobial resistance (AMR). It is predicted that inappropriate and too much use of antibiotics, biocides, and disinfectants during this pandemic may raise disastrous effects on antibiotic stewardship programs and AMR control all around the world. Furthermore, the use of certain antibiotics alone or in combination with antiviral agents or other medications for the treatment of secondary bacterial infections among COVID-19 patients may be regarded as a major factor that negatively affects host immune response by disrupting mitochondrial function and activity. Herein, we suggest that the current management strategies to control AMR and prioritize antibiotic stewardship schemes should be extremely highlighted in relation to the COVID-19 outbreak. The rising concerns about excessive use of antimicrobials and biocides and taking too much hygiene also need to be addressed during this pandemic due to their impacts on AMR, public health, and the environment.
A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration
Authors: Gallardo-Carreño Ignacio , Moreno-Paz Mercedes , Aguirre Jacobo , Blanco Yolanda , Alonso-Pintado Eduardo , Raymond-Bouchard Isabelle , Maggiori Catherine , Rivas Luis A. , Engelbrektson Anna , Whyte Lyle , Parro Víctor
Published: January 2021

Perchlorate anions are produced by chemical industries and are important contaminants in certain natural ecosystems. Perchlorate also occurs in some natural and uncontaminated environments such as the Atacama Desert, the high Arctic or the Antarctic Dry Valleys, and is especially abundant on the surface of Mars. As some bacterial strains are capable of using perchlorate as an electron acceptor under anaerobic conditions, their detection is relevant for environmental monitoring on Earth as well as for the search for life on Mars. We have developed an antibody microarray with 20 polyclonal antibodies to detect perchlorate-reducing bacteria (PRB) strains and two crucial and highly conserved enzymes involved in perchlorate respiration: perchlorate reductase and chlorite dismutase. We determined the cross-reactivity, the working concentration, and the limit of detection of each antibody individually and in a multiplex format by Fluorescent Sandwich Microarray Immunoassay. Although most of them exhibited relatively high sensitivity and specificity, we applied a deconvolution method based on graph theory to discriminate between specific signals and cross-reactions from related microorganisms. We validated the system by analyzing multiple bacterial isolates, crude extracts from contaminated reactors and salt-rich natural samples from the high Arctic. The PRB detecting chip (PRBCHIP) allowed us to detect and classify environmental isolates as well as to detect similar strains by using crude extracts obtained from 0.5 g even from soils with low organic-matter levels (<103cells/g of soil). Our results demonstrated that PRBCHIP is a valuable tool for sensitive and reliable detection of perchlorate-reducing bacteria for research purposes, environmental monitoring and planetary exploration.
Biological Management of Banana Fusarium Wilt Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 Using Antagonistic Fungal Isolate CSR-T-3 (Trichoderma reesei)
Authors: Damodaran Thukkaram , Rajan Shailendra , Muthukumar Manoharan , Ram Gopal  , Yadav Kavita , Kumar Sandeep , Ahmad Israr , Kumari Nidhi , Mishra Vinay K. , Jha Sunil K.
Published: January 2021

Fusarium wilt in bananas is one of the most devastating diseases that poses a serious threat to the banana industry globally. With no effective control measures available to date, biological control has been explored to restrict the spread and manage the outbreak. We studied the effective biological control potential of different Trichoderma spp. in the management of Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Expression of the defense related genes and metabolites in banana plants inoculated with Foc TR4 and treated with effective Trichoderma sp interactions were also studied. The in vitro growth inhibition of Foc TR4 by Trichoderma reesei isolate CSR-T-3 was 85.19% indicating a higher antagonistic potential than other Trichoderma isolates used in the study. Further, in in vivo assays, the banana plants treated with the isolate CSR-T-3 T. reesei had a significant reduction in the disease severity index (0.75) and also had increased phenological indices with respect to Foc TR4 treated plants. Enhanced activity of defense enzymes, such as β-1, 3-glucanase, peroxidase, chitinase, polyphenol oxidase, and phenylalanine ammonia lyase with higher phenol contents were found in the Trichoderma isolate CSR-T-3 treated banana plants challenge-inoculated with Foc TR4. Fusarium toxins, such as fusaristatin A, fusarin C, chlamydosporal, and beauveric acid were identified by LC-MS in Foc TR4-infected banana plants while high intensity production of antifungal compounds, such as ß-caryophyllene, catechin-o-gallate, soyasapogenol rhamnosyl glucoronide, peptaibols, fenigycin, iturin C19, anthocyanin, and gallocatechin-o-gallate were detected in T. reesei isolate CSR-T-3 treated plants previously inoculated with Foc TR4. Gene expression analysis indicated the upregulation of TrCBH1/TrCBH2, TrXYL1, TrEGL1, TrTMK1, TrTGA1, and TrVEL1 genes in CSR-T-3 treatment. LC-MS and gene expression analysis could ascertain the upregulation of genes involved in mycoparasitism and the signal transduction pathway leading to secondary metabolite production under CSR-T-3 treatment. The plants in the field study showed a reduced disease severity index (1.14) with high phenological growth and yield indices when treated with T. reesei isolate CSR-T-3 formulation. We report here an effective biocontrol-based management technological transformation from lab to the field for successful control of Fusarium wilt disease caused by Foc TR4 in bananas.
Single Amino Acids G196 and R198 in hr1 of Subgroup K Avian Leukosis Virus Glycoprotein Are Critical for Tva Receptor Binding
Authors: Chen Jian , Li Jinqun , Li Lizhen , Liu Peng , Xiang Yong , Cao Weisheng
Published: January 2021

Avian leukosis viruses (ALVs), a type of retrovirus responsible for various tumor diseases in chickens, are divided into 11 subgroups: ALV-A to ALV-K. After the envelope glycoproteins of ALV interact with the cellular receptor to initiate viral invasion, alterations in a few amino acids of the viral glycoproteins or cell receptors may trigger changes in their conformation and binding affinity. To identify the functional determinants of the ALV-K envelope protein that binds to Tva (a recently identified cellular receptor of ALV-K), using the strategy of continuous, segment-by-segment substitution of the gp85-encoded surface glycoprotein (SU) of ALV-K GDFX0602 with ALV-E ev-1 (using Tvb as the receptor), a series of chimeric soluble gp85 proteins were expressed for co-immunoprecipitation (co-IP) analysis and a series of recombinant viruses with replication-competent avian retrovirus vectors containing Bryan polymerase (RCASBP) as their skeleton were created for transfecting to DF-1 cells and titer determination. The co-IP analysis, fluorescence-activated cell sorting, and virus titer measurements revealed that the substitution of residues 194–198, 206–216 of hr1, residues 251–256 between hr1 and hr2, and residues 269–280 of hr2 were identified to reduce the binding of gp85 to Tva. The substitution of residues 194–221 in hr1 nullified the infectiveness of these viruses, similar to the effect of single amino acid mutations in K251E and L252I located between hr1 and hr2; continuous amino acid mutations in hr2 could not produce the same effect despite reducing their infectiveness. Finally, single amino acid mutations G196A and R198H nearly abolished the binding of gp85 to Tva and nullified the infectiveness of these viruses to DF-1. This study paves the way for exploring the molecular mechanisms of the binding of Tva to ALV-K SU.
Streptococcus thermophilus Attenuates Inflammation in Septic Mice Mediated by Gut Microbiota
Authors: Han Fu , Wu Gaofeng , Zhang Yijie , Zheng Haotian , Han Shichao , Li Xiaoqiang , Cai Weixia , Liu Jiaqi , Zhang Wanfu , Zhang Xiaowei , Hu Dahai
Published: January 2021

Sepsis is a life-threatening organ dysfunction condition caused by a dysregulated host response to infection and lack of effective treatment method. Supplementation of probiotics has emerged as a potential biotherapy for inflammatory diseases in recent years, but its role in protecting viscera against the damage caused by sepsis and the underlying mechanism is poorly understood. Streptococcus thermophilus 19 is one of the most well-studied probiotics, which is selected in this study among seven strains isolated from homemade yogurt due to its optimal ability of suppressing the inflammation response in vitro. It showed significant decrease in the expression of TNF-α, IL-1β, and IL-6 in the co-culture of S. thermophilus 19 and LPS-treated mouse macrophage. The effect of S. thermophilus 19 in mice and the response of mice gut microbiota were subsequently investigated. In LPS-induced septic mouse model, S. thermophilus 19 was highly resistant to LPS and exhibited significantly decreased expressions of inflammatory factors compared to LPS-treated mice. A MiSeq-based 16S rDNA sequence analysis revealed that the decrease of gut microbial diversity in mice intraperitoneally injected with 1 mg/ml LPS were mitigated by the administration of S. thermophilus 19. Fusobacterium significantly decreased during the development of sepsis and rose again after supplement strain 19, while Flavonifractor showed the opposite trend, which demonstrated these two genera were the key bacteria that may function in the mice gut microbiota for alleviation of LPS-induced inflammation reaction. To conclude, S. thermophilus 19 may be a potential candidate for novel biotherapeutic interventions against inflammation caused by sepsis.
Proteomic Analysis of Stationary Growth Stage Adaptation and Nutritional Deficiency Response of Brucella abortus
Authors: Yang Jianghua , Liu Mengzhi , Liu Jinling , Liu Baoshan , He Chuanyu , Chen Zeliang
Published: January 2021

Brucellosis, an important bacterial zoonosis caused by Brucella species, has drawn increasing attention worldwide. As an intracellular pathogen, the ability of Brucella to deal with stress within the host cell is closely related to its virulence. Due to the similarity between the survival pressure on Brucella within host cells and that during the stationary phase, a label-free proteomics approach was used to study the adaptive response of Brucella abortus in the stationary stage to reveal the possible intracellular adaptation mechanism in this study. A total of 182 downregulated and 140 upregulated proteins were found in the stationary-phase B. abortus. B. abortus adapted to adverse environmental changes by regulating virulence, reproduction, transcription, translation, stress response, and energy production. In addition, both exponential- and stationary-phase B. abortus were treated with short-term starvation. The exponential B. abortus restricted cell reproduction and energy utilization and enhanced material transport in response to nutritional stress. Compared with the exponential phase, stationary Brucella adjusted their protein expression to a lesser extent under starvation. Therefore, B. abortus in the two growth stages significantly differed in the regulation of protein expression in response to the same stress. Overall, we outlined the adaptive mechanisms that B. abortus may employ during growth and compared the differences between exponential- and stationary-phase B. abortus in response to starvation.
Influence of High Intensity Focused Ultrasound on the Microstructure and c-di-GMP Signaling of Pseudomonas aeruginosa Biofilms
Authors: Bharatula Lakshmi Deepika , Marsili Enrico , Rice Scott A. , Kwan James J.
Published: January 2021

Bacterial biofilms are typically more tolerant to antimicrobials compared to bacteria in the planktonic phase and therefore require alternative treatment approaches. Mechanical biofilm disruption from ultrasound may be such an alternative by circumventing rapid biofilm adaptation to antimicrobial agents. Although ultrasound facilitates biofilm dispersal and may enhance the effectiveness of antimicrobial agents, the resulting biological response of bacteria within the biofilms remains poorly understood. To address this question, we investigated the microstructural effects of Pseudomonas aeruginosa biofilms exposed to high intensity focused ultrasound (HIFU) at different acoustic pressures and the subsequent biological response. Confocal microscopy images indicated a clear microstructural response at peak negative pressures equal to or greater than 3.5 MPa. In this pressure amplitude range, HIFU partially reduced the biomass of cells and eroded exopolysaccharides from the biofilm. These pressures also elicited a biological response; we observed an increase in a biomarker for biofilm development (cyclic-di-GMP) proportional to ultrasound induced biofilm removal. Cyclic-di-GMP overproducing mutant strains were also more resilient to disruption from HIFU at these pressures. The biological response was further evidenced by an increase in the relative abundance of cyclic-di-GMP overproducing variants present in the biofilm after exposure to HIFU. Our results, therefore, suggest that both physical and biological effects of ultrasound on bacterial biofilms must be considered in future studies.
Bovine Teat Cistern Microbiota Composition and Richness Are Associated With the Immune and Microbial Responses During Transition to Once-Daily Milking
Authors: Rault Lucie , Lévêque Pierre-Alexandre , Barbey Sarah , Launay Frederic , Larroque Hélène , Le Loir Yves , Germon Pierre , Guinard-Flament Jocelyne , Even Sergine
Published: January 2021

The relationship between microbiota and health has been widely reported in humans and animals. We established a link between teat cistern microbiota composition and bovine mastitis, an inflammatory disease often due to bacterial infections. To further decipher the relationships between teat cistern microbiota and immune and microbial responses, a switch from twice- to once-daily milking (ODM) in 31 initially healthy quarters of dairy cows was used to trigger an udder perturbation. In this study, a temporal relationship was reported between initial teat cistern microbiota composition and richness, the immune response to ODM, and mastitis development. Quarters with a low initial microbiota richness and taxonomic markers such as Bacteroidetes and Proteobacteria were associated with a higher rate of mastitis during ODM. Quarters with a higher richness and taxonomic markers such as Firmicutes, including the Lachnospiraceae family, and genera such as Bifidobacterium and Corynebacterium displayed early inflammation following transition to ODM but without developing mastitis (no infection). Short-term compositional shifts of microbiota indicates that microbiotas with a higher initial richness were more strongly altered by transition to ODM, with notably the disappearance of rare OTUs. Microbiota modifications were associated with an early innate immune system stimulation, which, in turn, may have contributed to the prevention of mastitis development.
Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding
Authors: Alibrandi Pasquale , Schnell Sylvia , Perotto Silvia , Cardinale Massimiliano
Published: January 2021

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.
Trans-Acting Effectors Versus RNA Cis-Elements: A Tightly Knit Regulatory Mesh
Authors: Carrier Marie-Claude , Ng Kwan Lim Evelyne , Jeannotte Gabriel , Massé Eric
Published: January 2021

Prokaryotic organisms often react instantly to environmental variations to ensure their survival. They can achieve this by rapidly and specifically modulating translation, the critical step of protein synthesis. The translation machinery responds to an array of cis-acting elements, located on the RNA transcript, which dictate the fate of mRNAs. These cis-encoded elements, such as RNA structures or sequence motifs, interact with a variety of regulators, among them small regulatory RNAs. These small regulatory RNAs (sRNAs) are especially effective at modulating translation initiation through their interaction with cis-encoded mRNA elements. Here, through selected examples of canonical and non-canonical regulatory events, we demonstrate the intimate connection between mRNA cis-encoded features and sRNA-dependent translation regulation. We also address how sRNA-based mechanistic studies can drive the discovery of new roles for cis-elements. Finally, we briefly overview the challenges of using translation regulation by synthetic regulators as a tool.
Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads
Authors: Amacker Nathalie , Gao Zhilei , Agaras Betina C. , Latz Ellen , Kowalchuk George A. , Valverde Claudio F. , Jousset Alexandre , Weidner Simone
Published: January 2021

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.
Algal Oil Rich in n-3 PUFA Alleviates DSS-Induced Colitis via Regulation of Gut Microbiota and Restoration of Intestinal Barrier
Authors: Xu Zhenxia , Tang Hu , Huang Fenghong , Qiao Zhixian , Wang Xu , Yang Chen , Deng Qianchun
Published: January 2021

Algal oil is rich in docosahexaenoic acid (DHA) and has various health benefits against human metabolic disorders and disease. This study aimed to investigate the effects of DHA algal oil on colonic inflammation and intestinal microbiota in dextran sulfate sodium (DSS)-induced colitis mice model. Male C57BL/6 mice was induced colitis by 2.5% DSS and followed by 2 weeks of treatment with algal oil (250 or 500 mg/kg/day). The colonic inflammation was assessed by colon macroscopic damage scores, and the degree of neutrophil infiltration was evaluated by measuring tissue-associated myeloperoxidase (MPO) activity in colonic mucosa. Tight junction proteins in the colonic tissue were measured by real-time PCR and western blot. Moreover, the intestinal microbiota and shot chain fatty acids (SCFAs) were estimated by bioinformatic analysis and GC, respectively. Colonic damage due to DSS treatment was significantly ameliorated by algal oil supplementation. In addition, algal oil significantly inhibited the increases of malondialdehyde (MDA) content, MPO activity, pro-inflammatory cytokines level and tight junction proteins expression in DSS-treated mice. Furthermore, supplementation of algal oil modulated the intestinal microbiota structure in DSS induced colitis mice by increasing the proportion of the unidentified_S24_7 and decreasing the relative abundance of unidentified_Ruminococcaceae, Clostridium and Roseburia. On the analysis of SCFAs, the caecal content of acetic acid, propionic acid, isobutyric acid, buturic, and the total SCFAs showed a significant increase in algal oil-administered mice. Together, these results suggested that algal oil rich in DHA inhibited the progress of DSS-induced colitis in mice by modulating the intestinal microbiota and metabolites and repairing the intestinal barrier, which may be applied in the development of therapeutics for intestinal inflammation.
A Novel OmpR-Type Response Regulator Controls Multiple Stages of the Rhizobium etli – Phaseolus vulgaris N2-Fixing Symbiosis
Authors: Rodríguez Susana , Correa-Galeote David , Sánchez-Pérez Mishael , Ramírez Mario , Isidra-Arellano Mariel C. , Reyero-Saavedra María del Rocío , Zamorano-Sánchez David , Hernández Georgina , Valdés-López Oswaldo , Girard Lourdes
Published: January 2021

OmpR, is one of the best characterized response regulators families, which includes transcriptional regulators with a variety of physiological roles including the control of symbiotic nitrogen fixation (SNF). TheRhizobium etliCE3 genome encodes 18 OmpR-type regulators; the function of the majority of these regulators during the SNF in common bean, remains elusive. In this work, we demonstrated that aR. etlimutant strain lacking the OmpR-type regulator RetPC57 (ΔRetPC57), formed less nodules when used as inoculum for common bean. Furthermore, we observed reduced expression level of bacterial genes involved in Nod Factors production (nodAandnodB) and of plant early-nodulation genes (NSP2,NIN,NF-YAandENOD40), in plants inoculated with ΔRetPC57. RetPC57 also contributes to the appropriate expression of genes which products are part of the multidrug efflux pumps family (MDR). Interestingly, nodules elicited by ΔRetPC57 showed increased expression of genes relevant for Carbon/Nitrogen nodule metabolism (PEPCandGOGAT) and ΔRetPC57 bacteroids showed higher nitrogen fixation activity as well as increased expression of key genes directly involved in SNF (hfixL, fixKf, fnrN, fixN, nifAandnifH). Taken together, our data show that the previously uncharacterized regulator RetPC57 is a key player in the development of theR. etli-P. vulgarissymbiosis.