Extracellular Processes Research Articles

Nonlinear analysis of cybernetic model for aerobic growth of Saccharomyces cerevisiae in a continuous stirred tank bioreactor. Static bifurcations

This article presents a nonlinear steady-state analysis of a continuous stirred tank bioreactor. The process of bioethanol production under aerobic conditions was analyzed. The kinetics of the growth of Saccharomyces cerevisiae microorganisms was described by the cybernetic model. This model includes metabolic reactions taking place in the biomass cells, which are a response to changes in the extracellular process environment. The dilution rate and the glucose concentration in the feed stream were used as bifurcation parameters. In both cases the performed analysis revealed the existence of multiple steady states areas and Hopf bifurcation points. The continuation of steady states, relative to the concentration of glucose in the feed stream, showed the presence of a rarely detected steady state branch, which was an isola. The numerical investigation was summerized in the form of a map which contains areas with biochemical reactions favoured by biomass cells. The map is made in a coordinate system of bifurcation parameters and illustrates perfectly the complexity of the model. In the opinion of the authors, it can be a very useful tool in planning the implementation of the process. It enables its proper targeting in the direction of activation of a specific metabolic reaction in the cells of microorganisms.

Comprehensive bioinformatics analysis of acquired progesterone resistance in endometrial cancer cell line

BackgroundProgesterone resistance is a problem in endometrial carcinoma, and its underlying molecular mechanisms remain poorly understood. The aim of this study was to elucidate the molecular mechanisms of progesterone resistance and to identify the key genes and pathways mediating progesterone resistance in endometrial cancer using bioinformatics analysis.MethodsWe developed a stable MPA (medroxyprogesterone acetate)-resistant endometrial cancer cell subline named IshikawaPR. Microarray analysis was used to identify differentially expressed genes (DEGs) from triplicate samples of Ishikawa and IshikawaPR cells. PANTHER, DAVID and Metascape were used to perform gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and cBioPortal for progesterone receptor (PGR) coexpression analysis. GEO microarray (GSE17025) was utilized for validation. The protein–protein interaction network (PPI) and modular analyses were performed using Metascape and Cytoscape. Further validation were performed by real-time polymerase chain reaction (RT-PCR).ResultsIn total, 821 DEGs were found and further analyzed by GO, KEGG pathway enrichment and PPI analyses. We found that lipid metabolism, immune system and inflammation, extracellular environment-related processes and pathways accounted for a significant portion of the enriched terms. PGR coexpression analysis revealed 7 PGR coexpressed genes (ANO1, SOX17, CGNL1, DACH1, RUNDC3B, SH3YL1 and CRISPLD1) that were also dramatically changed in IshikawaPR cells. Kaplan–Meier survival statistics revealed clinical significance for 4 out of 7 target genes. Furthermore, 8 hub genes and 4 molecular complex detections (MCODEs) were identified.ConclusionsUsing microarray and bioinformatics analyses, we identified DEGs and determined a comprehensive gene network of progesterone resistance. We offered several possible mechanisms of progesterone resistance and identified therapeutic and prognostic targets of progesterone resistance in endometrial cancer.

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome.

Pathway and network approaches are valuable tools in analysis and interpretation of large complex omics data. Even in the field of rare diseases, like Rett syndrome, omics data are available, and the maximum use of such data requires sophisticated tools for comprehensive analysis and visualization of the results. Pathway analysis with differential gene expression data has proven to be extremely successful in identifying affected processes in disease conditions. In this type of analysis, pathways from different databases like WikiPathways and Reactome are used as separate, independent entities. Here, we show for the first time how these pathway models can be used and integrated into one large network using the WikiPathways RDF containing all human WikiPathways and Reactome pathways, to perform network analysis on transcriptomics data. This network was imported into the network analysis tool Cytoscape to perform active submodule analysis. Using a publicly available Rett syndrome gene expression dataset from frontal and temporal cortex, classical enrichment analysis, including pathway and Gene Ontology analysis, revealed mainly immune response, neuron specific and extracellular matrix processes. Our active module analysis provided a valuable extension of the analysis prominently showing the regulatory mechanism of MECP2, especially on DNA maintenance, cell cycle, transcription, and translation. In conclusion, using pathway models for classical enrichment and more advanced network analysis enables a more comprehensive analysis of gene expression data and provides novel results.

Distinct degenerative phenotype of articular cartilage from knees with meniscus tear compared to knees with osteoarthritis

To compare the transcriptome of articular cartilage from knees with meniscus tears to knees with end-stage osteoarthritis (OA). Articular cartilage was collected from the non-weight bearing medial intercondylar notch of knees undergoing arthroscopic partial meniscectomy (APM; N=10, 49.7±10.8 years, 50% females) for isolated medial meniscus tears and knees undergoing total knee arthroplasty (TKA; N=10, 66.0±7.6 years, 70% females) due to end-stage OA. Ribonucleic acid (RNA) preparation was subjected to SurePrint G3 human 8×60K RNA microarrays to probe differentially expressed transcripts followed by computational exploration of underlying biological processes. Real-time polymerase chain reaction amplification was performed on selected transcripts to validate microarray data. We observed that 81 transcripts were significantly differentially expressed (45 elevated, 36 repressed) between APM and TKA samples (≥ 2 fold) at a false discovery rate of ≤ 0.05. Among these, CFD, CSN1S1, TSPAN11, CSF1R and CD14 were elevated in the TKA group, while CHI3L2, HILPDA, COL3A1, COL27A1 and FGF2 were highly expressed in APM group. A few long intergenic non-coding RNAs (lincRNAs), small nuclear RNAs (snoRNAs) and antisense RNAs were also differentially expressed between the two groups. Transcripts up-regulated in TKA cartilage were enriched for protein localization and activation, chemical stimulus, immune response, and toll-like receptor signaling pathway. Transcripts up-regulated in APM cartilage were enriched for mesenchymal cell apoptosis, epithelial morphogenesis, canonical glycolysis, extracellular matrix organization, cartilage development, and glucose catabolic process. This study suggests that APM and TKA cartilage express distinct sets of OA transcripts. The gene profile in cartilage from TKA knees represents an end-stage OA whereas in APM knees it is clearly earlier in the degenerative process.

Mechanical Strength, Biodegradation, and in Vitro and in Vivo Biocompatibility of Zn Biomaterials.

Zn-based biomaterials have emerged as promising new types of bioresorbable metallics applicable to orthopedic devices, cardiovascular stents, and other medical applications recently. Compared to other degradable metallic biomaterials (i.e., Mg- or Fe-based), Zn biomaterials have a more appropriate corrosion rate without hydrogen gas evolution. Here, we evaluated the potential of Zn-based metallics as medical implants, both in vitro and in vivo, alongside a standard benchmark Mg alloy, AZ31. The mechanical properties of the pure Zn were not strong enough but were significantly enhanced (microhardness > 70 kg/mm2, strength > 220 MPa, elongation > 15%) after alloying with Sr or Mg (1.5 at. %), surpassing the minimal design criteria for load-bearing device applications. The corrosion rate of Zn-based biomaterials was about 0.4 mm/year, significantly slower than that of AZ31. The measured cell viability and proliferation of three different human primary cells fared better for Zn-based biomaterials than AZ31 using both direct and indirect culture methods. Platelet adhesion and activation on Zn-based materials were minimal, significantly less than on AZ31. The hemolysis ratio of red cells (<0.5%) after incubation with Zn-based materials was also well below the ISO standard of 5%. Moreover, Zn-based biomaterials promoted stem cell differentiation to induce the extracellular matrix mineralization process. In addition, in vivo animal testing using subcutaneous, bone, and vascular implantations revealed that the acute toxicity and immune response of Zn-based biomaterials were minimal/moderate, comparable to that of AZ31. No extensive cell death and foreign body reactions were observed. Taken together, Zn-based biomaterials may have a great potential as promising candidates for medical implants.

Overexpression of oncostatin M receptor regulates local immune response in glioblastoma.

Glioblastoma (GBM) is the most lethal cancer in central nervous system. It is urgently needed to look for novel therapeutics for GBM. Oncostatin M receptor (OSMR) is a cytokine receptor gene of IL-6 family and has been reported to be involved in regulating GBM tumorigenesis. However, the role of OSMR regulating the disrupted immune response in GBM need to be further investigated. Three gene expression profiles, Chinese Glioma Genome Atlas (CGGA), The Cancer Genome Atlas (TCGA), and Gene Expression Omnibus (GEO) data set (GSE16011), were enrolled in our study and used for OSMR expression and survival analysis. The expression of OSMR was further verified with immunohistochemistry and western blot analysis in glioma tissues. Microenvironment cell populations-counter (MCP-counter) was applied for analyzing the relationship between OSMR expression and nontumor cells. The functions of OSMR in GBM was investigated by Gene Ontology, Gene set enrichment analysis (GSEA), gene set variation analysis and so on. The analysis of cytokine receptor activity-related genes in glioma identifies OSMR as a gene with an independent predictive factor for progressive malignancy in GBM. Furthermore, OSMR expression is a prognostic marker in the response prediction to radiotherapy and chemotherapy. OSMR contributes to the regulation of local immune response and extracellular matrix process in GBM. Our findings define an important role of OSMR in the regulation of local immune response in GBM, which may suggest OSMR as a possible biomarker in developing new therapeutic immune strategies in GBM.

Study on optogenetics technology and the design of its script for virtual simulation experiment

Optogenetics is one of the biggest breakthroughs in neurobiology in recent decades, which is a revolutionary approach to precise intervention of specific cell functions through the combination of optical and genetic engineering techniques. However, this technique involves the interdisciplinary theoretical knowledge and methods, and it requires expensive equipments and long experimental period. Thus, it is not convenient to carry out widely in experiment teaching for undergraduates except the virtual simulation teaching. In present virtual simulation experiment, we aim to learn the basic principle, operation and application of optogenetics and achieve the desired teaching effects by simulating the process of the virus package, simulating the process of the animal selection, surgery and virus stereotactic microinjection, simulating the expression process of photosensitive channel, the extracellular verification process of photosensitive channel function in vivo, and simulating the observation process that optogenetic inhibition of glutamate neurons in the amygdala affect animal fear behavior. In this paper, the content design of the script making of the virtual experiment has been discussed in the above ways. Key words: Virtual simulation experiment; Experimental teaching; Optogenetics; Script

Amyloid burden accelerates white matter degradation in cognitively normal elderly individuals.

Alterations in parietal and temporal white matter microstructure derived from diffusion tensor imaging occur in preclinical and clinical Alzheimer's disease. Amyloid beta (Aβ) deposition and such white matter alterations are two pathological hallmarks of Alzheimer's disease. However, the relationship between these pathologies is not yet understood, partly since conventional diffusion MRI methods cannot distinguish between cellular and extracellular processes. Thus, we studied Aβ-associated longitudinal diffusion MRI changes in Aβ-positive (N = 21) and Aβ-negative (N = 51) cognitively normal elderly obtained from the Alzheimer's Disease Neuroimaging Initiative dataset using linear mixed models. Aβ-positivity was based on Alzheimer's Disease Neuroimaging Initiative amyloid-PET recommendations using a standardized uptake value ratio cut-off of 1.11. We used free-water imaging to distinguish cellular and extracellular changes. We found that Aβ-positive subjects had increased baseline right uncinate fasciculus free-water fraction (FW), associated with worse baseline Alzheimer's disease assessment scale scores. Furthermore, Aβ-positive subjects showed faster decrease in fractional anisotropy (FW-corrected) in the right uncinate fasciculus and faster age-dependent right inferior longitudinal fasciculus FW increases over time. Right inferior longitudinal fasciculus FW increases were associated with greater memory decline. Importantly, these results remained significant after controlling for gray and white matter volume and hippocampal volume. This is the first study to illustrate the influence of Aβ burden on early longitudinal (in addition to baseline) white matter changes in cognitively normal elderly individuals at-risk of Alzheimer's disease, thus underscoring the importance of longitudinal studies in assessing microstructural alterations in individuals at risk of Alzheimer's disease prior to symptoms onset.

SU53 - GENOME-WIDE DNA METHYLATION ANALYSIS IN THE SALIVA OF CRACK COCAINE DEPENDENTS

Background DNA methylation has been increasingly recognized in the etiology of drug dependence. Due to the difficulties in assessing brain tissue in living humans, peripheral cells such as blood and saliva have been explored as alternatives to explore the involvement of DNA methylation in drug dependency. Here, we characterized DNA methylation changes in the saliva from crack cocaine users compared to health controls. Methods DNA was extracted from saliva of 128 crack cocaine dependents and 109 health controls (males, age 34.8 +/- 9.9 years). Bisulfite converted DNA was hybridized in the Illumina Infinium MethylationEPIC BeadChip arrays. Cellular composition heterogeneity was corrected using RefFreeEwas followed identification of differentially CpG sites using limma (DMSs). Using DMSs with pvalue Results Comparison between crack cocaine dependents and controls revealed 3,857 DMRs which were involved with metabolic processes related to nucleic acid, ncRNA and rRNA processing, gene expression and protein-DNA complex assembly. The gene-gene interaction analysis revealed three networks: one containing 11 genes, which were enriched for biological processes related to mitochondrial function; a second network composed by 36 genes which was enriched mainly for glycosylphosphatidylinositol (GPI) activity and extracellular membrane interaction biological processes; and a third network with 22 genes that was enriched for synapse related processes (GABaergic, serotononergic and cholinergic synapses) and, interestingly, biological processes related to visual perception. Discussion These results suggest that the use of saliva may help to understand the mechanisms underlying the pathology of drug abuse. Changes in DNA methylation found in the saliva revealed perturbation in pathways related to the reward system, often found affected in drug dependents. Moreover, the enrichment analysis of the networks replicated our previous study performed in peripheral blood where molecular functions related to protein activity were associated with cocaine and crack dependency.

Identification of a laccase gene involved in shell periostracal tanning of the clam Meretrix petechialis

Tanning is a complex extracellular process that is a mechanism for stabilizing proteinaceous extracellular structures. Phenoloxidases play important roles in cross-linking during tanning, and laccase (EC 1.10.3.2) is a member of the phenoloxidase enzyme class. In this study, we identified a laccase gene (MpLac) from the clam Meretrix petechialis and found that MpLac might be involved in shell periostracal tanning of clams. Using whole-mount in situ hybridization, we found that MpLac mRNA in the larval clam was mainly expressed in the mantle edge. In the adult clam, our quantitative real-time PCR results showed that the mantle was also a tissue with a high MpLac expression level; in addition, by combining the results of fluorescence in situ hybridization, H&E staining and transmission electron microscopy, we found that the inner epithelium of the outer fold of the mantle edge, which is involved in periostracum formation, was the exact region in which MpLac mRNA was expressed. Furthermore, knocking down the expression of MpLac by RNA interference (RNAi) bleached the new shell periostracum. All of our results suggest the involvement of MpLac in shell periostracal tanning of M. petechialis.

Imatinib Protects Against Hypoxia/Reoxygenation Induced Lung and Kidney Injury in a Humanized Mouse Model for SCD

Sickle cell disease (SCD) is a worldwide distributed hereditary red cell disorder characterized by chronic hemolytic anemia in association with acute and chronic life-threatening complications mainly related to acute vaso-occlusive events (VOCs) due to amplified inflammatory response and defective pro-resolving events.Imatinib is an oral Tyrosine (Tyr)-kinase inhibitor, developed for the treatment of chronic myeloid leukemia (CML). Few case reports on SCD patients with CML undergoing imatinib treatment highlight the beneficial impact of imatinib on severity and recurrence of acute VOCs in SCD. In red blood cells (RBCs), Imatinib has been shown to interfere with Tyr-phosphorylation state of the integral membrane protein band 3, affecting RBC microparticle formation. Here, we study the actions of Imatinib on a model of acute VOCs using humanized SCD mice (Hbatm1(HBA)TowHbbtm2(HBG1,HBB*)Tow). We treated SCD and control healthy mice (AA, Hbatm1(HBA)Tow Hbbtm3(HBG1,HBB)Tow) (n=6-7 animals in each group) with Imatinib 50 mg/Kg/d for 2 weeks before hypoxia/Reoxygenation (H/R) stress used to mimic acute VOCs. Under normoxia, we found that in SCD mice Imatinib significantly reduced (i) Tyr-phosphorylation state of sickle red cell membrane proteins; (ii) the amount of phosphatidyl-serine (PS)+ sickle RBCs; and (iii) the release of erythroid microparticles, which was associated with accumulation of hemichromes and a more efficient erythrophagocytosis compared to vehicle treated animals. In SCD mice exposed to H/R stress, imatinib significantly decreased the H/R-induced (i) increase in peripheral neutrophil count; (ii) lung inflammatory cell infiltrate; (iii) kidney inflammatory cell infiltrate. In the lung of H/R SCD mice, Imatinib inhibited the H/R induced NF-kB activation and prevented the up-regulation of (i) pro-inflammatory cytokines such as ET-1; (ii) vascular endothelial activation markers (VCAM-1, ICAM-1); (iii) pro-fibrotic markers such as PDGF-B and (iv) the activation of UPR system. In the kidney of H/R SCD mice, Imatinib significantly reduced H/R induced expression of ET-1, VCAM-1 and E-selectin, which were again associated with inhibition of NF-kB. In addition, Imatinib significantly upregulated the expression of the microRNAs miR200a/b, which has been described to reduce renal fibrosis. Finally, in isolated aorta from Imatinib treated SCD exposed to H/R stress, a significant reduction in vascular activation markers was observed compared to vehicle treated animals. Collectively, our data indicate that Imatinib acts on multiple targets, modulating signal transduction and reducing inflammatory vasculopathy and extracellular matrix remodeling process related to VOC in SCD. Thus, Imatinib might represent a new therapeutic tool in clinical management of SCD patients. DisclosuresEl Nemer:Imara: Research Funding.

Physiological function of myocilin and its role in the pathogenesis of glaucoma in the trabecular meshwork (Review).

Myocilin is highly expressed in the trabecular meshwork (TM), which plays an important role in the regulation of intraocular pressure (IOP). Myocilin abnormalities may cause dysfunction of the TM, potentially leading to increased IOP. High IOP is a well-known primary risk factor for glaucoma. Myocilin mutations are common among glaucoma patients, and they are implicated in juvenile-onset open-angle glaucoma (JOAG) and adult-onset primary open-angle glaucoma (POAG). Aggregation of aberrant mutant myocilins is closely associated with glaucoma pathogenesis. The aim of the present review was to discuss the recent findings regarding the major physiological functions of myocilin, such as intra- and extracellular proteolytic processes. We also aimed to discuss the risk factors associated with myocilin and the development of glaucoma, such as misfolded/mutant myocilin, imbalance of myocilin and extracellular proteins, and instability of mutant myocilin associated with temperature. Finally, we further outlined certain issues that are yet to be resolved, which may represent the basis for future studies on the role of myocilin in glaucoma.

Electrode Potential Dependency of Single-Cell Activity Identifies the Energetics of Slow Microbial Electron Uptake Process.

Electrochemical measurements have been widely applied to study microbial extracellular electron transport processes. However, because electrochemistry detects not only microbial electron transport but also other reactions, background signals comparable to or larger than microbial ones hamper the identification of microbial electrochemical properties. This problem is crucial especially for the detection of electron uptake processes by slow-growing microbes in low-energy subsurface sediments, as the environmental samples contain electrochemically active humus and mineral particles. In this study, we report a cell-specific stable isotope analysis to quantify the electrode potential dependency of anabolic activity in individual cells for identifying the electron uptake energetics of slow-growing bacteria. Followed by the incubation of Desulfovibrio ferrophilus IS5 cells with isotopic 15N-ammonium as the sole N source on electrodes poised at potentials of -0.2, -0.3, -0.4, and -0.5 V [vs. standard hydrogen electrode (SHE)], we conducted nanoscale secondary ion mass spectroscopy (NanoSIMS) to quantify 15N assimilation in more than 100 individual cells on the electrodes. We observed significant 15N assimilation at potentials of -0.4 and more 15N assimilation at -0.5 V, which is consistent with the onset potential for electron uptake via outer-membrane cytochromes (OMCs). The activation of cell energy metabolism was further examined by transcriptome analysis. Our results showed a novel methodology to study microbial electron uptake energetics. The results also serve as the first direct evidence that energy acquisition is coupled to the electron uptake process in sulfate-reducing bacteria that are ubiquitous in the subsurface environments, with implications on the electron-fueled subsurface biosphere hypothesis and other microbial processes, such as anaerobic iron corrosion and anaerobic methane oxidation.

Emerging roles of noncoding RNAs in multiple myeloma: A review.

Multiple myeloma (MM) is a hematologic malignancy characterized by unrestricted secretion of monoclonal immunoglobulin and uncontrolled plasma cell proliferation. Extra-medullary infiltration and drug resistance are two major obstacles in the treatment of MM. To solve these problems, it is necessary to elucidate the underlying pathological mechanisms and findnew therapeutic targets. Noncoding RNAs (ncRNAs), which were once considered "transcriptional noise," have been recognized as crucial regulators in the process of tumorigenesis including MM. Increasing evidence has shown that ncRNAs participate in MM pathogenesis via a series of complex cellular or extracellular processes. This review article summarizes examples of ncRNAs involved in myelosis and discusses their potential as biomarkers and therapeutic targets in the diagnosis and treatment of myelosis.

Monitoring the energy of the metal ion-content plasma-assisted deposition and its implication for bacterial inactivation

Cu-polyester (Cu-PES) was sputtered by high power impulse magnetron sputtering (HIPIMS) and by low energy direct current magnetron sputtering (DCMS). The total amount and distribution of the Ar+, Cu+ and Cu2+ ions were determined as well as the bacterial inactivation kinetics mediated by DCMS and HIPIMS samples. The separation of extracellular and intracellular processes leading to bacterial inactivation was assessed on normal and genetically modified E. coli.

Antiviral activity of metal chelates of caffeic acid and similar compounds towards herpes simplex, VSV-Ebola pseudotyped and vaccinia viruses

Organic compounds with a caffeoyl moiety (e.g. caffeic acid, rosmarinic acid, chicoric acid, etc.) have antiviral properties towards herpes simplex (HSV), influenza and immunodeficiency viruses (HIV). This study evaluated the HSV antiviral properties of caffeic acid when paired with a variety of metal and other inorganic ions. The results demonstrated that the antiviral activity of caffeic acid increased upwards of 100-fold by the addition of cations, such as Fe3+, and anionic molecules, such as molybdate and phosphate. Cellular toxicity tests of the caffeic acid chelates showed that they have low toxicities with selectivity indices (TD50/EC50) for Fe3+, MoO42−, and PO43− chelates being 1700, >540, and >30, respectively. Caffeic acid paired with Fe3+ was tested against eight strains of viruses, including those from different families. The caffeic acid chelates were mostly effective against HSV1 and HSV2, but they also had moderate activity against vaccinia virus and a VSV-Ebola pseudotyped virus. All the viruses that were strongly impacted by the caffeic chelates require heparan sulfate proteoglycans for cellular attachment, so it is likely that caffeic chelates target and interfere with this mechanism. Since the caffeic acid chelates target an extra-cellular process, they might be able to be combined with existing medications, such as acyclovir, that target an intracellular process to achieve greater viral control.

A Novel Shewanella Isolate Enhances Corrosion by Using Metallic Iron as the Electron Donor with Fumarate as the Electron Acceptor.

The involvement of Shewanella spp. in biocorrosion is often attributed to their Fe(III)-reducing properties, but they could also affect corrosion by using metallic iron as an electron donor. Previously, we isolated Shewanella strain 4t3-1-2LB from an acetogenic community enriched with Fe(0) as the sole electron donor. Here, we investigated its use of Fe(0) as an electron donor with fumarate as an electron acceptor and explored its corrosion-enhancing mechanism. Without Fe(0), strain 4t3-1-2LB fermented fumarate to succinate and CO2, as was shown by the reaction stoichiometry and pH. With Fe(0), strain 4t3-1-2LB completely reduced fumarate to succinate and increased the Fe(0) corrosion rate (7.0 ± 0.6)-fold in comparison to that of abiotic controls (based on the succinate-versus-abiotic hydrogen formation rate). Fumarate reduction by strain 4t3-1-2LB was, at least in part, supported by chemical hydrogen formation on Fe(0). Filter-sterilized spent medium increased the hydrogen generation rate only 1.5-fold, and thus extracellular hydrogenase enzymes appear to be insufficient to explain the enhanced corrosion rate. Electrochemical measurements suggested that strain 4t3-1-2LB did not excrete dissolved redox mediators. Exchanging the medium and scanning electron microscopy (SEM) imaging indicated that cells were attached to Fe(0). It is possible that strain 4t3-1-2LB used a direct mechanism to withdraw electrons from Fe(0) or favored chemical hydrogen formation on Fe(0) through maintaining low hydrogen concentrations. In coculture with an Acetobacterium strain, strain 4t3-1-2LB did not enhance acetogenesis from Fe(0). This work describes a strong corrosion enhancement by a Shewanella strain through its use of Fe(0) as an electron donor and provides insights into its corrosion-enhancing mechanism.IMPORTANCEShewanella spp. are frequently found on corroded metal structures. Their role in microbial influenced corrosion has been attributed mainly to their Fe(III)-reducing properties and, therefore, has been studied with the addition of an electron donor (lactate). Shewanella spp., however, can also use solid electron donors, such as cathodes and potentially Fe(0). In this work, we show that the electron acceptor fumarate supported the use of Fe(0) as the electron donor by Shewanella strain 4t3-1-2LB, which caused a (7.0 ± 0.6)-fold increase of the corrosion rate. The corrosion-enhancing mechanism likely involved cell surface-associated components in direct contact with the Fe(0) surface or maintenance of low hydrogen levels by attached cells, thereby favoring chemical hydrogen formation by Fe(0). This work sheds new light on the role of Shewanella spp. in biocorrosion, while the insights into the corrosion-enhancing mechanism contribute to the understanding of extracellular electron uptake processes.

Co-expression network analysis identified CDH11 in association with progression and prognosis in gastric cancer.

Background and aimsGastric cancer (GC) is one of the most common cancers worldwide, and its pathogenesis is related to a complex network of gene interactions. The aims of our study were to find hub genes associated with the progression and prognosis of GC and illustrate the underlying mechanisms.MethodsWeighted gene co-expression network analysis (WGCNA) was conducted using the microarray dataset and clinical data of GC patients from Gene Expression Omnibus (GEO) database to identify significant gene modules and hub genes associated with TNM stage in GC. Functional enrichment analysis and protein–protein interaction network analysis were performed using the significant module genes. We regarded the common hub genes in the co-expression network and protein–protein interaction (PPI) network as “real” hub genes for further analysis. Hub gene was validated in another independent dataset and The Cancer Genome Atlas (TCGA) dataset.ResultsIn the significant purple module (R2=0.35), a total of 12 network hub genes were identified, among which six were also hub nodes in the PPI network of the module genes. Functional annotation revealed that the genes in the purple module focused on the biological processes of system development, biological adhesion, extracellular structure organization and metabolic process. In terms of validation, CDH11 had a higher correlation with the TNM stage than other hub genes and was strongly correlated with biological adhesion based on GO functional enrichment analysis. Data obtained from the Gene Expression Profiling Interactive Analysis (GEPIA) showed that CDH11 expression had a strong positive correlation with GC stages (P<0.0001). In the testing set and Oncomine dataset, CDH11 was highly expressed in GC tissues (P<0.0001). Survival analysis indicated that samples with a high CDH11 expression showed a poor prognosis. Cox regression analysis demonstrated an independent predictor of CDH11 expression in GC prognosis (HR=1.482, 95% CI: 1.015–2.164). Furthermore, gene set enrichment analysis (GSEA) demonstrated that multiple tumor-related pathways, especially focal adhesion, were enriched in CDH11 highly expressed samples.ConclusionCDH11 was identified and validated in association with progression and prognosis in GC, probably by regulating biological adhesion and focal adhesion-related pathways.

Expression pattern of galectin-1 and galectin-3 in rat testes and epididymis during postnatal development

Galectins are a family of lectins-binding beta-galactosides involved in a variety of extracellular and intracellular processes, thereby contributing to homeostasis, cell adhesion, cellular turnover, and immunity. This study aimed to determine the localization and expression of galectin-1 (Gal-1) and galectin-3 (Gal-3) in the testis and epididymis of rats at postnatal [(prepubertal (day 5), pubertal (day 20), postpubertal (day 50) and mature (day 70)] periods by using immunohistochemistry and Western blotting. Gal-1 and Gal-3 were differentially expressed in different types of cells in the testis and epididymis during postnatal development. While we detected Gal-1 expression in some spermatogenic cells and Leydig cells in the testis, not in the epididymal epithelium, Gal-3 was expressed in Sertoli cells, peritubular myoid cells, Leydig cells, smooth muscles and interstitial CD68-positive macrophages. Epithelial cells of the corpus and cauda epididymis showed an intense Gal-3 expression. Gal-1 expression was higher in the testis than in the epididymis on days 50 and 70. The expression of Gal-3 in the testis increased from the prepubertal to mature period. While the expression difference of Gal-3 was not statistically significant in the testis and epididymis until puberty, Gal-3 expression in the postpubertal and mature periods was higher in the epididymis. The expression of Gal-3 in the corpus and cauda epididymis was higher than that in the caput epididymis. In conclusion, our findings suggest that puberty has potential regulatory effect on the expression of galectins in testis and epididymis of rats. Gal-1 and 3 may play a role in the development of the reproductive system and the preservation of the immune-privileged environment in the testis, due to their pro-apoptotic and anti-apoptotic functions. The presence of intense expression of Gal-3 in the corpus and cauda epididymis may contribute to the maturation and storage of spermatozoa.

Integrin Beta 1 Is Crucial for Urinary Concentrating Ability and Renal Medulla Architecture in Adult Mice

Integrins are heterodimers anchoring cells to the surrounding extracellular matrix (ECM), an active and complex process mediating a series of inside-out and outside-in stimuli regulating cellular turn-over, tissue growth and architecture. Itgb1 is the main subunit of the renal integrins and it is critical for renal development. This study aims to investigate the role of Itgb1 in the adult renal epithelial cells by knocking down Itgb1 in PAX8 expressing cells. Itgb1-Pax8 cKO mice develop a progressively worsening proteinuria and renal abnormalities leading to severe renal failure and hypertension. This phenotype is also associated with severe dysfunction of distal nephron and polyuria. To further investigate whether distal nephron involvement was primarily related to Itgb1 suppression or secondary to renal failure, an Itgb1-AQP2 cKO mouse model was generated. These mice lack Itgb1 expression in AQP2 expressing cells. They do not show any developmental alteration, but 1 month old mice are resistant to dDAVP administration and finally, at 2 months of age, they develop overt polyuria. This phenotype is due to primary collecting duct (CD) cells anoikis. The entire architecture of the outer medulla is altered, with loss of the typical organization pattern of vascular and tubular bundles alternation. Indeed, even though not primarily affected by genetic ablation, the TAL is secondarily affected in this model. It is sufficient to suppress Itgb1 expression in the CD in order to stimulate proliferation and then disappearance of neighboring TAL cells. This study shows that cell to cell interaction through the ECM is critical for architecture and function maintenance of the outer medulla and that Itgb1 is crucial for this process.