Colonization Of Surfaces Research Articles

Identification of interaction partners of outer inflammatory protein A: Computational and experimental insights into how Helicobacter pylori infects host cells

Outer membrane proteins (OMPs) play a key role in facilitating the survival of Helicobacter pylori within the gastric tissue by mediating adherence. Among these proteins, Outer inflammatory protein A (OipA) is a critical factor in H. pylori colonization of the host gastric epithelial cell surface. While the role of OipA in H. pylori attachment and its association with clinical outcomes have been established, the structural mechanisms underlying OipA’s action in adherence to gastric epithelial cells remain limited. Our study employed experimental and computational approaches to investigate the interaction partners of OipA on the gastric epithelial cell surface. Initially, we conducted a proteomic analysis using a pull-down assay with recombinant OipA and gastric epithelial cell membrane proteins to identify the OipA interactome. This analysis revealed 704 unique proteins that interacted with OipA. We subsequently analyzed 16 of these OipA partners using molecular modeling tools. Among these 16 partners, we highlight three human proteins, namely Hepatocyte growth factor (HGF), Mesenchymal epithelial transition factor receptor (Met), and Adhesion G Protein-Coupled Receptor B1 (AGRB1) that could play a role in H. pylori adherence to the gastric epithelial cell surface with OipA. Collectively, these findings reveal novel host interactions mediated by OipA, suggesting their potential as therapeutic targets for combating H. pylori infection.

Influence of Enhanced Synthesis of Exopolysaccharides in Rhizobium ruizarguesonis and Overproduction of Plant Receptor to these Compounds on Colonizing Activity of Rhizobia in Legume and Non-Legume Plants and Plant Resistance to Phytopathogenic Fungi.

Rhizobial exopolysaccharides (EPS) may provide stabilization of membranes against external factors, as well as improved surface adhesion, but their role in interaction with legume and non-legume plants is still far from understanding. In this work, the transcriptional regulator RosR of Rhizobium ruizarguesonis, which regulates the synthesis of EPS, was overproduced in a pHC60 plasmid and expressed in the RCAM 1026 strain. This resulted in an improved production of EPS by this recombinant strain. Comparative analysis of the inoculation of pea Pisum sativum plants with R. ruizarguesonis pHC60-rosR and strain carrying the empty plasmid revealed an essential increase in the number of nodules, root length and biomass in plants inoculated with this EPS-overproducing strain. It demonstrates that the enhanced EPS synthesis by rhizobia may stimulate plant root colonization and subsequent nodule formation in pea plants. The influence of enhanced EPS synthesis in rhizobia on colonizing activity was also estimated in non-legume plant tomato Solanum lycopersicum. Our findings shown the increased colonization of the root surface and stimulation of the shoot biomass of inoculated plants. Inoculation of pea and tomato with EPS-overproducing rhizobial strain essentially increased plant resistance to phytopathogenic fungi Fusarium culmorum and F. oxysporum in both legume and non-legume plants, demonstrating a significant biocontrol effect of this recombinant strain. Furthermore, we have identified the PsLYK10 gene that encodes a putative EPS receptor in P. sativum, although no significant effect of PsLYK10 overexpression on nodulation in legume (pea P. sativum) and colonization of roots of non-legume plants by rhizobia was found compared to enhanced production of EPS by rhizobia.

A flagellar accessory protein links chemotaxis to surface sensing.

Bacteria find suitable locations for colonization by sensing and responding to surfaces. Complex signaling repertoires control surface colonization, and surface contact sensing by the flagellum plays a central role in activating colonization programs. Caulobacter crescentus adheres to surfaces using a polysaccharide adhesin called the holdfast. In C. crescentus, disruption of the flagellum through interactions with a surface or mutation of flagellar genes increases holdfast production. Our group previously identified several C. crescentus genes involved in flagellar surface sensing. One of these, fssF, codes for a protein with homology to the flagellar C-ring protein FliN. We show here that a fluorescently tagged FssF protein localizes to the flagellated pole of the cell and requires all components of the flagellar C-ring for proper localization, supporting the model that FssF associates with the C-ring. Deleting fssF results in a severe motility defect, which we show is due to a disruption of chemotaxis. Epistasis experiments demonstrate that fssF promotes adhesion through a stator-dependent pathway when late-stage flagellar mutants are disrupted. Separately, we find that disruption of chemotaxis through deletion of fssF or other chemotaxis genes results in a hyperadhesion phenotype. Key genes in the surface sensing network (pleD, motB, and dgcB) contribute to both ∆flgH-dependent and ∆fssF-dependent hyperadhesion, but these genes affect adhesion differently in the two hyperadhesive backgrounds. Our results support a model in which the stator subunits of the flagella incorporate both mechanical and chemical signals to regulate adhesion.IMPORTANCEBacterial biofilms pose a threat in clinical and industrial settings. Surface sensing is one of the first steps in biofilm formation. Studying surface sensing can improve our understanding of biofilm formation and develop preventative strategies. In this study, we use the freshwater bacterium Caulobacter crescentus to study surface sensing and the regulation of surface attachment. We characterize a previously unstudied gene, fssF, and find that it localizes to the cell pole in the presence of three proteins that make up a component of the flagellum called the C-ring. Additionally, we find that fssF is required for chemotaxis behavior but dispensable for swimming motility. Lastly, our results indicate that deletion of fssF and other genes required for chemotaxis results in a hyperadhesive phenotype. These results support that surface sensing requires chemotaxis for a robust response to a surface.

Clear Cell Carcinoma Arising in Vaginal Endometriosis in a Patient 33 Years after Total Hysterectomy and Bilateral Salpingo-oophorectomy: A Case Report

Abstract Introduction/Objective Endometriosis, a common gynecological disorder characterized by ectopic endometrial tissue, is associated with an increased risk of extraovarian malignancies. Vaginal endometriosis is a rare condition, and the occurrence of vaginal malignancies arising from endometriosis is anticipated to be exceedingly rare. Here, we present a rare case of clear cell carcinoma arising in vaginal endometriosis, occurring three decades post-total hysterectomy and bilateral salpingo-oophorectomy. Methods/Case Report A 71-year-old female presented with abnormal Cologuard results, leading to a colonoscopy revealing a mass in the recto-sigmoid colon. She had undergone total hysterectomy and bilateral salpingo- oophorectomy for leiomyoma and endometriosis 33 years prior. Histopathological examination revealed clear cell carcinoma arising in vaginal endometriosis, with tumor extension through the colon wall to the colonic mucosal surface (Figure 1). Notably, the vaginal mucosal surface was negative for tumor. Immunohistochemistry staining demonstrated positivity for Pax8, CK7, AE1/3, racemase, and p16, while negtive for ER, PR, CDX2, CK20, CAIX, SatB2, RCC, WTI, Napsin, and calretinin (Figure 2). The staining for p53 was patchy (wild type, not mutated). Cancer-type relevant biomarkers reveal BRAF mutation (p.D594G), ARID1A mutation (p.M1564fs), PD-L1 mutation (Positive, CPS:80), and PIK3CA mutation (p.H1047L). The histologic and immunohistochemistry findings are consistent with clear cell carcinoma arising in a long-standing area of endometriosis (previous surgery in 1990). Results (if a Case Study enter NA) NA Conclusion Clear cell adenocarcinoma arising from endometriosis is exceptionally rare. Pathologists must consider the possibility of tumors arising from endometriosis when evaluating bowel or mesenteric neoplasms, even decades post-total hysterectomy and bilateral salpingo-oophorectomy. Immunohistochemistry plays a crucial role in the differential diagnosis between carcinoma arising from endometriosis and primary colonic carcinoma. Additionally, Sampson’s criteria are valuable for diagnosing malignant transformations in endometriosis. The identification of specific cancer-type relevant biomarkers, such as BRAF, ARID1A, PD-L1, and PIK3CA mutations, provides additional insights into the molecular characteristics of the tumor, which may have implications for prognosis and treatment selection.

Benthic litter in fishing grounds of the Northern Adriatic: Role of the trawling fleet as cleaners of the seafloor

This study represents the baseline of estimation of the potential service provided by fishermen as “cleaners of the sea”. The amount, composition and depth distribution of marine litter in fishing grounds of the Northern Adriatic seafloor has been investigated through the fishing for litter (FFL) scheme. Passive FFL campaigns were carried out by trawlers from two of the most important fishing ports in the northern Adriatic, Chioggia and Goro, from May 2020 to May 2021. Over the course of 256 days of fishing, over 6 tons of litter were removed from 265 km2 of seafloor. Abandoned, lost and derelict fishing gears (ALDFG) were the most represented litter category (48 % of the total litter), and of these 67 % were plastic ALDFG (mostly mussel socks and fishing nets). Fouling on plastic waste was analyzed to determine the fraction of collected litter items that could be destinated to recycling. Only a small percentage of the plastic litter analyzed was “clean” from adherent and/or encrusting organisms. Approximately 2.4 tons of plastic were recovered, but, due to the biological colonization of surfaces, they cannot be recycled by using the technologies present in the area.

B-357 Siemens CA 72-4: an assay for measurement of Tumor Associated Glycoprotein (TAG) 72

Abstract Background The tumor associated glycoprotein (TAG) 72, also known as CA 72-4 is a mucin protein of high molecular weight. CA 72-4 is found on the surface of many cancer cells, including stomach (gastric), ovary, breast, colon and pancreatic cells. CA 72-4 is currently one of the primary markers for the diagnosis of gastric cancer and monitoring the course and efficacy of gastric cancer. In ovarian cancer, it has a higher sensitivity for mucin- type ovarian cancer, and its combination with CA125 for detection can significantly improve the clinical sensitivity. In colorectal cancer, CA 72-4 combined with CEA detection was also found to significantly improve the sensitivity of the initial diagnosis. An assay for CA 72-4 on Siemens Atellica IM (Siemens CA 72-4) is being developed and analytical performance is being presented. Methods The Siemens CA 72-4 assay (in development) is a one-step chemiluminescent microparticle immunoassay (CMIA) for the quantitative determination of CA 72-4 in human serum and plasma. The specimen is incubated with paramagnetic microparticles coated with the monoclonal antibody (mAb) B72.3 and acridinium-labeled mAb CC49 conjugate on the Siemens Atellica IM® System. After incubation and washing, Acid and Base reagents are added. The resulting relative light units (RLUs) are directly proportional to the amount of CA 72-4 in the sample allowing for the quantitative determination of CA 72-4 in the specimen. Results The following performance were determined using 3 unique lots of reagents and calibrators with the calibration range for the assay being 0.00 to 200.00 U/mL. The limit of blank (LoB), limit of detection (LoD), and limit of quantitation at 20% CV (LoQ) were determined and met the goal of ≤ 1.00 U/mL. Linearity according to CLSI EP06 Ed2 was demonstrated for a range of 1.00 through 200.00 U/mL. A Precision study of 2 controls and 5 panels spanning the range of the assay demonstrated a total %CV ≤ 6% for samples ≥ 5.00 U/mL and ≤ 0.25 SD for samples <5.00 U/mL. In the sample tube type study, a matrix comparison of 23 matched serum and plasma samples were evaluated. Passing-Bablock slopes of < 8% and r > 0.99 were observed when evaluating samples within the measurement range for plasma (LiHep, LiHep separator, K2EDTA and K3EDTA) tubes and serum separator tubes (SST) compared to the Red Top serum samples. Five endogenous substances were evaluated for interference in the CA 72-4 assay. The average percent difference between test and control samples for all endogenous interferents was < 10%. Percent difference in the presence of 28 potentially interfering drugs was ≤ 4.0%. Conclusions The Siemens CA 72-4 assay currently in development is a sensitive and precise assay for the quantitative determination of CA 72-4 in human serum and plasma.

In Vitro Comparison of Titanium Disc Surface Roughness and Bacterial Colonization After Ultrasonic Instrumentation With Three Different Tips.

During implant maintenance, preserving a smooth surface on the machined transmucosal abutment is critical to reduce biofilm attachment and colonization. The present study compared the surface roughness and bacterial colonization of machined titanium surfaces after instrumentation with various materials. Forty-four machined grade 23 titanium discs were instrumented with a round polyether ether ketone (PEEK) tip, a plastic curette tip, or a pure titanium curette tip with piezoelectric devices. Before and after instrumentation, the surface roughness (Ra and Rz) values were analyzed with a profilometer and scanning electron microscopy (SEM). Streptococcus sanguinis was cultured and incubated for 24 hours on the instrumented discs, and colony-forming units per milliliter were obtained for each group. Samples instrumented with the metal ultrasonic tip significantly increased surface roughness compared with the other groups. This resulted in greater colonization by S. sanguinis than surfaces instrumented with PEEK tips or the negative control. Samples instrumented with PEEK and plastic tips did not exhibit any statistically significant increase in surface roughness, and SEM analysis revealed a significantly rougher surface of discs instrumented with metal compared with discs instrumented with plastic or PEEK tips despite the possibility of debris from tip dissolution. Our results suggest that instrumentation with metal ultrasonic tips with piezoelectric devices significantly increased machined titanium's surface roughness and elicited higher biofilm formation in vitro. Meanwhile, instrumentation of machined titanium with PEEK or plastic ultrasonic tips did not affect the surface roughness or bacterial adhesion.

Oral delivery of solid lipid nanoparticles surface decorated with hyaluronic acid and bovine serum albumin: A novel approach to treat colon cancer through active targeting

The present study aims to prepare and evaluate solid lipid nanoparticles (SLNs) loaded with irinotecan (IRN) drug and daidzein (DZN) isoflavonoid and surface coated with ligand materials such as hyaluronic acid (HA) and bovine serum albumin (BSA) with additional coating of chitosan for active targeting to receptors present on colon surface epithelium for oral targeted delivery. The optimized batch was evaluated for particle size, zeta potential exhibiting nanometric size with good entrapment efficiency. Nanoparticles were found to be spherical. FTIR and DSC revealed that all the excipients and formulation were compatabile to each other and showed better encapsulation exhibiting amorphous and crystallinity forms. In vitro drug release of SLNs confirmed that initially a burst release, followed by sustained release pattern was exhibited. Cell lines studied performed on HT-29 cells showed demonstrated that conjugated SLNs inhibited cytotoxicity at 75 μg/ml, indicating that cells were taken up through a receptor-mediated endocytosis process. Cell cycle analysis showed that cell arrest was done at 67.8 % (G0/G1 phase) and inhibited apoptosis by 56 %. Further during In vivo studies, RT-PCR study revealed downregulation of Carcinoembryonic antigen (CEA), a non-specific serum biomarker overexpressed in tumor cells and upregulation of pro-inflammatory cytokine TNF-α. Histopathological study revealed that conjugated (HA-BSA) coated with chitosan SLNs restored normal mucosa and colon architecture, depicting all mucosal layers. Hence, these conjugated SLNs may serve as a novel combination for the treatment of colon cancer.

Reactive oxygen species-inducing itraconazole and its anti-biofilm activity against resistant Candida parapsilosis sensu lato biofilm cells isolated from patients with recalcitrant onychomycosis.

Candida parapsilosis was introduced as the second most responsible for nail involvement. The colonization of biotic and abiotic surfaces by Candida spp.can result in the formation of biofilms, which possess a high level of resistance to typical antifungal agents. Since Candida spp. can produce biofilm mass on the surface of the nails, dermatologists should consider appropriate antifungals to eliminate both the planktonic and biofilm cells. The aim of this research was to determine the antifungal efficacy of itraconazole against C. parapsilosis sensu lato biofilm formations, in addition to its static effects. Ten C. parapsilosis sensu lato isolates were enrolled in this study. The use of itraconazole results in the accumulation of reactive oxygen species (ROS) during treatment. In order to verify the correlation between ROS and itraconazole-induced cell death, the viability of cells was analyzed by administering the ROS scavenger Ascorbic acid. The apoptotic features of itraconazole were analyzed using the Annexin V-FITC method. Based on current data, it was found that the generation of intracellular stresses by itraconazole is not observed in cells upon ROS inhibition, emphasizing the importance of intracellular ROS in the apoptotic mechanism of itraconazole. Targeting the oxidative defense system is a powerful point to use ROS-inducing antifungals as a superior choice for more effective therapies in case of recalcitrant onychomycosis.

A membrane-associated conveyor belt controls the rotational direction of the bacterial type 9 secretion system.

Many bacteria utilize the type 9 secretion system (T9SS) for gliding motility, surface colonization, and pathogenesis. This dual-function motor supports both gliding motility and protein secretion, where rotation of the T9SS plays a central role. Fueled by the energy of the stored proton motive force and transmitted through the torque of membrane-anchored stator units, the rotary T9SS propels an adhesin-coated conveyor belt along the bacterial outer membrane like a molecular snowmobile, thereby enabling gliding motion. However, the mechanisms controlling the rotational direction and gliding motility of T9SS remain elusive. Shedding light on this mechanism, we find that in the gliding bacterium Flavobacterium johnsoniae , deletion of the C-terminus of a conveyor belt protein controls, and in fact, reverses the rotational direction of T9SS from counterclockwise (CCW) to clockwise (CW). Largescale conformational changes at the interface of the T9SS ring with the C-terminus of the conveyer belt, as well as those of the ring protein themselves, in concert with a CW bias of the stators general rotation brings forth a 'tri-component gearset' model: the conveyor belt controls the conformation of the T9SS ring, and thereby its rotational direction. Consequently, the CW rotating stator either push the outer edge of the T9SS rings, causing its CCW rotation or press against the inner surface of the rings, resulting in CW rotation. This regulatory mechanism exemplifies how an outer membrane associated conveyor belt adjusts the rotational direction of its driver, the T9SS, thus providing adaptive sensory feedback to control the motility of a molecular snowmobile.

Effect of a Beneficial Flora Colonization of Pen Surfaces on Health of Weanling Piglets

Introduction: Undesirable bacterial colonization of farm surfaces affects animal health after weaning. The objective of the study was to test the preventive effects of a positive biofilm formation on the surfaces of piglet facilities on beneficial flora colonization and animal health. Methods: 494 piglets from two weaning batches (Exp.1 and Exp.2) were allocated in 2 identical rooms. The rooms were sprayed either with water (Control) or a mix of selected bacteria strains (LFP) 48 h before the entrance, and again on day 15 in Exp.1, and on days 5, 12, 19, 26, and 33 in Exp.2. The microbiological status of the surfaces was assessed on days 0, 5, and 14 and on days -2, 0, 5, 7, and 35 in Exp.1 and 2, using peptone water swabs. Fecal consistency was scored on days 5, 8, 14, 21, and 28 on 16 randomly selected piglets per treatment. Statistical analysis was performed in SAS 9.4. Non-parametric tests were used to analyze the microbiological data, fecal scores, and death distributions. Results: There was a significant (P<0.05) higher load of aerobic bacteria (Lactobacillus spp., Bacillus spp.) in LFP pen surfaces in both experiments. Fecal scores were significantly improved on day 8 in Exp.1 (P<0.01) and on days 9 (P=0.01) and 28 (P<0.01) in Exp.2. Digestive disease outbreaks occurred 2 days later in Exp.1 and 7 days later in Exp.2 in LFP rooms. Conclusion: spraying a beneficial flora on surfaces may result in a protective positive biofilm that would help piglets to better deal with the weaning challenges.

Evaluation of the long-term protection conferred by an organosilicon-based disinfectant formulation against bacterial contamination of surfaces.

The aim of this work was to evaluate the efficacy of an organosilicon-based, commercially available antimicrobial formulation in the My-shield® product line against bacterial surface contamination. The antimicrobial product was tested in vitro for its long-term persistence on surfaces and effectiveness against Staphylococcus aureus biofilms in comparison to 70% ethanol and 0.1% or 0.6% sodium hypochlorite. Field testing was also conducted over 6 weeks at a university athletic facility. In vitro studies demonstrated the log reductions achieved by the test product, 70% ethanol, and 0.1% sodium hypochlorite were 3.6, 3.1, and 3.2, respectively. The test product persisted on surfaces after washing and scrubbing, and pre-treatment with this product prevented S. aureus surface colonization for up to 30 days. In comparison, pre-treatment with 70% ethanol or 0.6% sodium hypochlorite was not protective against S. aureus biofilm formation after seven days. The field test demonstrated that weekly applications of the test product were more effective at reducing surface bacterial load than daily applications of a control product. The test product conferred greater long-term protection against bacterial growth and biofilm formation by S. aureus than ethanol and sodium hypochlorite. Even with less frequent applications, the test product maintained a high level of antimicrobial activity.

Grassland restoration on linear landscape elements – comparing the effects of topsoil removal and topsoil transfer

Artificial linear landscape elements, including roads, pipelines, and drainage channels, are main sources of global habitat fragmentation. Restoration of natural habitats on unused linear landscape elements can increase habitat quality and connectivity without interfering with agricultural or industrial development. Despite that topsoil removal and transfer are widely applied methods in restoration projects, up to our knowledge these were previously not compared in the same study system. To address this knowledge gap, we compared spontaneous vegetation recovery after the elimination of positive (embankments) and negative landscape scars (drainage channels) in lowland alkaline landscapes in South Hungary. The novelty of our study is that we compared the fine-scale and landscape-scale results of both methods. At the fine scale, we monitored the spontaneous vegetation development on the created open surfaces in the first, second and fourth year after restoration in 160 permanent plots per year. For characterizing the habitat changes on the landscape scale, we prepared habitat maps and assigned naturalness scores to each patch before and after the restoration activities. Both restoration methods resulted in a rapid vegetation recovery at the fine scale, progressing toward the reference state. In the topsoil removal treatment, a large part of the soil seed bank was removed; therefore, the colonization of the bare surface was a slower process. Seeds of halophytes, including the endemic and protected Suaeda pannonica, were probably present in the deeper soil layers, and these species became established in the restored surfaces, despite being absent in the surrounding vegetation. For restoring vegetation cover, topsoil transfer was a more rapid option; however, vegetation closure and competition by generalist species and weeds hampered the establishment of target species. The removal of the landscape scars by both methods made the sites accessible for grazing. At the landscape scale, the two methods had different effects: there was a slight increase in the habitat naturalness in the topsoil removal site, and a slight decrease in the topsoil transfer site because of weed encroachment. Spreading an upper layer of nutrient-poor soil with low amounts of weed seeds, direct propagule transfer, and targeted grazing regimes could enhance restoration success.

Depth estimation from monocular endoscopy using simulation and image transfer approach

Obtaining accurate distance or depth information in endoscopy is crucial for the effective utilization of navigation systems. However, due to space constraints, incorporating depth cameras into endoscopic systems is often impractical. Our goal is to estimate depth images directly from endoscopic images using deep learning. This study presents a three-step methodology for training a depth-estimation network model. Initially, simulated endoscopy images and corresponding depth maps are generated using Unity based on a colon surface model obtained from segmented computed tomography colonography data. Subsequently, a cycle generative adversarial network model is employed to enhance the realism of the simulated endoscopy images. Finally, a deep learning model is trained using the synthesized endoscopy images and depth maps to estimate depths accurately. The performance of the proposed approach is evaluated and compared against prior studies utilizing unsupervised training methods. The results demonstrate the superior precision of the proposed technique in estimating depth images within endoscopy. The proposed depth estimation method holds promise for advancing the field by enabling enhanced navigation, improved lesion marking capabilities, and ultimately leading to better clinical outcomes.

Enhancing the Antimicrobial Properties of Experimental Resin-Based Dental Composites through the Addition of Quaternary Ammonium Salts.

Secondary caries is one of the main reasons for dental filling replacement. There is a need to obtain dental restorative material that is able to act against caries-inducing microorganisms. This study explores the antimicrobial properties of cetyltrimethylammonium bromide (CTAB) or dimethyldioctadecylammonium bromide (DODAB)-modified photo-cured experimental dental composites against Escherichia coli, Streptococcus mutans, and Candida albicans. The antimicrobial activity against Escherichia coli, Streptococcus mutans, and Candida albicans was assessed by using an Accuri C6 flow cytofluorimeter, and then analyzed using BD CSampler software (1.0.264). Bacterial/yeast surface colonization was carried out by using an GX71 inverted-optics fluorescence microscope equipped with a DP 73 digital camera. For bactericidal surface analysis of each sample type, simultaneous standardization was performed using a positive control (live cells) and a negative control (dead cells). A positive correlation between the increasing concentration of CTAB or DODAB and the dead cell ratio of Escherichia coli, Streptococcus mutans, and Candida albicans was revealed. In particular, CTAB at a 2.0 wt% concentration exhibits superior efficiency against pathogens (65.0% dead cells of Escherichia coli, 73.9% dead cells of Streptococcus mutans, and 23.9% dead cells of Candida albicans after 60 min). However, Candida albicans is more resistant to used salts than bacteria. A CTAB- or DODAB-modified experimental dental composite exhibits antimicrobial potential against Escherichia coli, Streptococcus mutans, and Candida albicans after 10 and 60 min of incubation, and the antimicrobial efficiency increases with the wt% of QAS in the tested material.

Potentially pathogenic culturable bacteria in hemodialysis waters

BackgroundHemodialysis patients are at risk of acquiring healthcare-related infections due to using non-sterile water to prepare hemodialysis fluid. Therefore, microbiological control and monitoring of used water are of crucial importance.Materials and methodsIn this work, we identified bacterial populations occupying a hemodialysis water distribution system for almost a 6-month period in Ahvaz city, southwest of Iran. A total of 18 samples from three points were collected. We found high colony counts of bacteria on R2A agar. 31 bacteria with different morphological and biochemical characteristics were identified by molecular-genetic methods based on 16 S rRNA gene sequencing. Endotoxin concentrations were measured, using Endosafe® Rapid LAL Single-Test Vials.ResultsA diverse bacterial community was identified, containing predominantly Gram-negative bacilli. The most frequently isolated genus was Sphingomonas. Five species including M. fortuitum, M. lentiflavum, M.szulgai, M. barrassiae, and M. gordonae was identified .Despite the presence of Gram-negative bacteria the endotoxin analysis of all samples revealed that their endotoxin values were below the detection limit.ConclusionThe members of Sphingomonas genus along with Bosea and mycobacteria could be regarded as pioneers in surface colonization and biofilm creation. These bacteria with others like Pelomonas, Bradyrhizobium, staphylococcus, and Microbacterium may represent a potential health risk to patients under hemodialysis treatment.

Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.

In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Development of systemic and mucosal immune responses against gut microbiota in early life and implications for the onset of allergies.

The early microbial colonization of human mucosal surfaces is essential for the development of the host immune system. Already during pregnancy, the unborn child is prepared for the postnatal influx of commensals and pathogens via maternal antibodies, and after birth this protection is continued with antibodies in breast milk. During this critical window of time, which extends from pregnancy to the first year of life, each encounter with a microorganism can influence children's immune response and can have a lifelong impact on their life. For example, there are numerous links between the development of allergies and an altered gut microbiome. However, the exact mechanisms behind microbial influences, also extending to how viruses influence host-microbe interactions, are incompletely understood. In this review, we address the impact of infants' first microbial encounters, how the immune system develops to interact with gut microbiota, and summarize how an altered immune response could be implied in allergies.

Optimising the hygiene of a liquid feeding system to improve the quality of liquid feed for pigs

Poor feeding system hygiene may contribute to uncontrolled spontaneous fermentation in liquid pig feed and its associated undesirable effects. This study aimed to determine the effects of an intensive sanitisation programme in a grow-finisher liquid feeding system by monitoring microbiological and physico-chemical parameters of liquid feed and microbial colonisation of the feeding system surfaces. The sanitisation programme involved a combination of physical and chemical cleaning between batches of grow-finisher pigs, combined with nightly rinsing of the system with an organic acid blend. Improved hygiene of the internal surfaces of the mixing tank and feed pipeline, particularly until week 5 post-cleaning, was evidenced by reduced counts of lactic acid bacteria, total aerobes, Enterobacteriaceae, yeasts and moulds and decreased adenosine triphosphate concentrations. Enterobacteriaceae and moulds remained undetectable on pipeline surfaces for 10 weeks. Scanning electron microscopy of the feed pipelines confirmed these findings. Conversely, the impact on liquid feed microbiology was minimal and short-lived. However, acetic acid, ethanol and biogenic amine concentrations decreased in the feed post-cleaning and no gross energy losses were observed. Therefore, by controlling surface microbial communities on liquid feeding systems via implementation of the sanitisation programme developed in the current study, on-farm liquid feed quality should be improved.

An experimental assessment of active and passive dispersal of red snow algae on the Harding Icefield, southcentral Alaska

ABSTRACT Red snow algae seasonally color glacier and alpine snow surfaces with characteristic red blooms. These blooms significantly reduce the albedo of the snow surface resulting in increased snow ablation. The global cryosphere is sensitive to the melt effect of expansive reoccurring blooms; however, the primary dispersal path by which snow algae seasonally recolonize snow surfaces is currently unresolved. Using an experimental field approach that inhibited resurfacing populations with a physical barrier, then sampled algal surface abundance the following growing season, we assessed two pathways of algal surface colonization on the Harding Icefield, Alaska. Our results provide the first experimental depiction of active resurfacing as the primary pathway of seasonal snow surface colonization by red snow algae above the equilibrium line elevation on an Alaskan glacier. Results suggest that, at the peak of the growing season, 65 percent of surface abundance was derived from actively resurfacing cells and 35 percent from passively dispersing cells.