Functional Multivariable Logistic Regression With an Application to HIV Viral Suppression Prediction.

Motivated by improving the prediction of the human immunodeficiency virus (HIV) suppression status using electronic health records (EHR) data, we propose a functional multivariable logistic regression model, which accounts for the longitudinal binary process and continuous process simultaneously. Specifically, the longitudinal measurements for either binary or continuous variables are modeled by functional principal components analysis, and their corresponding functional principal component scores are used to build a logistic regression model for prediction. The longitudinal binary data are linked to underlying Gaussian processes. The estimation is done using penalized spline for the longitudinal continuous and binary data. Group-lasso is used to select longitudinal processes, and the multivariate functional principal components analysis is proposed to revise functional principal component scores with the correlation. The method is evaluated via comprehensive simulation studies and then applied to predict viral suppression using EHR data for people living with HIV in South Carolina.

Gene co-expression modules behind the three-pistil formation in wheat.

Multi-pistil trait in wheat is of great potential value in plant development research and crop breeding. Our previous studies identified the Pis1 locus that causes three pistils in wheat by genetic mapping using multiple DNA marker systems. However, there are still 26 candidate genes on the locus, and the causal gene remains to be found. In this study, we aimed to approach the molecular mechanism of multi-pistil formation. Comparative RNA sequencing (RNA-Seq) during the pistil formation was undertaken in four wheat lines: a three-pistil mutant TP, a single-pistil TILLING mutant of TP (SP), a three-pistil near-isogenic line CM28TP with the background of cultivar Chunmai 28 (CM28), and CM28. Electron microscopic analysis specified probable developmental stages of young spikes for the three-pistil formation. mRNA sequencing in the young spikes of the four lines represented 253 down-regulated genes and 98 up-regulated genes in both three-pistil lines, which included six potential genes for ovary development. Weighted gene co-expression analysis represented three-pistil trait-associated transcription factor-like genes, among which one hub gene, ARF5, was the most highlighted. ARF5 is on the Pis1 locus and an orthologue of MONOPTEROS which mediates tissue development in Arabidopsis. qRT-PCR validation implies that the deficiency of ARF5 underlies the three-pistil formation in wheat.

Insulin-induced gene 2 protects against hepatic ischemia-reperfusion injury via metabolic remodeling.

BACKGROUND: Hepatic ischemia-reperfusion (IR) injury is the primary reason for complications following hepatectomy and liver transplantation (LT). Insulin-induced gene 2 (Insig2) is one of several proteins that anchor the reticulum in the cytoplasm and is essential for metabolism and inflammatory responses. However, its function in IR injury remains ambiguous. METHODS: Insig2 global knock-out (KO) mice and mice with adeno-associated-virus8 (AAV8)-delivered Insig2 hepatocyte-specific overexpression were subjected to a 70% hepatic IR model. Liver injury was assessed by monitoring hepatic histology, inflammatory responses, and apoptosis. Hypoxia/reoxygenation stimulation (H/R) of primary hepatocytes and hypoxia model induced by cobalt chloride (CoCl2) were used for in vitro experiments. Multi-omics analysis of transcriptomics, proteomics, and metabolomics was used to investigate the molecular mechanisms underlying Insig2. RESULTS: Hepatic Insig2 expression was significantly reduced in clinical samples undergoing LT and the mouse IR model. Our findings showed that Insig2 depletion significantly aggravated IR-induced hepatic inflammation, cell death and injury, whereas Insig2 overexpression caused the opposite phenotypes. The results of in vitro H/R experiments were consistent with those in vivo. Mechanistically, multi-omics analysis revealed that Insig2 is associated with increased antioxidant pentose phosphate pathway (PPP) activity. The inhibition of glucose-6-phosphate-dehydrogenase (G6PD), a rate-limiting enzyme of PPP, rescued the protective effect of Insig2 overexpression, exacerbating liver injury. Finally, our findings indicated that mouse IR injury could be attenuated by developing a nanoparticle delivery system that enables liver-targeted delivery of substrate of PPP (glucose 6-phosphate). CONCLUSIONS: Insig2 has a protective function in liver IR by upregulating the PPP activity and remodeling glucose metabolism. The supplementary glucose 6-phosphate (G6P) salt may serve as a viable therapeutic target for alleviating hepatic IR.

Cholesterol-conjugated siRNAs silence gene expression in mucosal dendritic cells in cervicovaginal tissue in mice.

BACKGROUND: RNA interference (RNAi) provides a powerful way to investigate the role of genes in disease pathogenesis and modulate gene expression to treat disease. In 2018, the FDA approved patisiran, the first RNAi-based drug, hence paving the way for a novel class of RNAi therapeutics. Harnessing RNAi to inhibit vaginal HIV transmission requires effective gene silencing in immune cells, which remains difficult. Knockdown in accessible mucosal tissues may be easier than systemic gene silencing. Vaginally applied cholesterol-conjugated small interfering RNAs (chol-siRNAs) blocked herpes simplex virus transmission in mice without tissue damage or immunostimulation. OBJECTIVES AND METHODS: To investigate using flow cytometry, confocal microscopy, and quantitative imaging if chol-siRNAs silence gene expression in vaginal immune cells in mice. RESULTS: Although chol-siRNAs and lipoplexed-siRNAs silence gene expression in dendritic cells (DCs) in vitro, most internalized siRNAs concentrate within multivesicular bodies, where they are inaccessible to the cellular RNAi machinery. When applied intravaginally in vivo, chol-siRNAs penetrate the vaginal mucosa, including the lamina propria, and are efficiently internalized by intraepithelial (IE) and lamina propria (LP) DCs, and CD11b+ CD45+ cells, but not by T cells. Chol-siRNAs induce partial gene silencing in IE and LP DCs throughout the genital mucosa in vivo but are inactive in F4/80+ CD11b+ macrophages and T cells. CONCLUSION: As mucosal DCs play an essential role for mucosal viral entry and dissemination, chol-siRNAs could be harnessed to target various host factors that are critical for viral uptake, DC migration and trans-infection of virions to T cells, hence allowing the development of a preventive vaginal HIV microbicide. Furthermore, chol-siRNAs could help elucidate the pathways of HIV transmission and understand the immunologic function of DCs in the genital tract.

Targeted metabolomics analysis for serum Helicobacter pylori-positive based on liquid chromatography-tandem mass spectrometry.

Helicobacter pylori (H. pylori), as a harmful bacteria associated with gastric cancer, can have adverse effects on human normal flora and metabolism. However, the effects of H. pylori on human metabolism have not been fully elucidated. The 13 C breathing test was used as the basis for distinguishing negative and positive groups. Serum samples were collected from the two groups for targeted quantitative metabolomics detection; multidimensional statistics were used, including partial least squares discriminant analysis (PLS-DA), principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and differential metabolites were screened. Unidimensional statistics combined with multidimensional statistics were used to further screen potential biomarkers, and finally pathway analysis was performed. SPSS 21.0 software package was used for statistical analysis of experimental data. Multivariate statistical analysis such as PLS-DA, PCA, and OPLS-DA was performed using Simca-P 13.0 to search for differential metabolites. This study confirmed that H. pylori caused significant changes in human metabolism. In this experiment, 211 metabolites were detected in the serum of the two groups. Multivariate statistical analysis showed that PCA of metabolites was not significantly different between the two groups. PLS-DA indicated that the serum of the two groups was well clustered. There were significant differences in metabolites between OPLS-DA groups. By setting the variable importance in projection (VIP) threshold as one and the corresponding P-value <0.05, a total of 40 metabolites were screened in this study. P <0.05 and ∣log2FC∣>0 (where FC is the fold change) were used together as a unidimensional statistical filter condition. The analysis found that the expression of 15 metabolites such as propionic acid, acetic acid, adipic acid increased, and the metabolism of six products such as deoxycholic acid (DCA), 4-hydroxyphenylpyruvic acid, pyruvic acid decreased. P <0.05, false discovery rate <0.5, ∣log2FC∣>1, and OPLSDA_VIP>1 were used together as a condition for filter screening potential biomarkers. Four potential biomarkers were screened, which were sebacic acid, isovaleric acid, DCA, and indole-3-carboxylic acid. Finally, the different metabolites were added to the pathway-associated metabolite sets (SMPDB) library for the corresponding pathway enrichment analysis. The significant abnormal metabolic pathways were taurine and subtaurine metabolism, tyrosine metabolism, glycolysis or gluconeogenesis, pyruvate metabolism, etc. This study shows that H. pylori has an impact on human metabolism. Not only a variety of metabolites have significant changes, but also metabolic pathways are abnormal, which may be the reason for the high risk of H. pylori causing gastric cancer.

Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Seed-Shattering-Related Genes in Common Buckwheat.

Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the F2 population of Gr (green-flower mutant and shattering resistance) and UD (white flower and susceptible to shattering), which included eight linkage groups with 174 loci, and detected seven QTLs of pedicel strength. RNA-seq analysis of pedicel in two parents revealed 214 differentially expressed genes DEGs that play roles in phenylpropanoid biosynthesis, vitamin B6 metabolism, and flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) was performed and screened out 19 core hub genes. Untargeted GC-MS analysis detected 138 different metabolites and conjoint analysis screened out 11 DEGs, which were significantly associated with differential metabolites. Furthermore, we identified 43 genes in the QTLs, of which six genes had high expression levels in the pedicel of common buckwheat. Finally, 21 candidate genes were screened out based on the above analysis and gene function. Our results provided additional knowledge for the identification and functions of causal candidate genes responsible for the variation in seed-shattering and would be an invaluable resource for the genetic dissection of common buckwheat resistance-shattering molecular breeding.

Fast and Efficient Atmospheric NO2 Collection for Isotopic Analysis by a 3D-Printed Denuder System.

Being major species of atmospheric reactive nitrogen, nitrogen oxides (NOx = NO + NO2) have important implications for ozone and OH radical formation in addition to nitrogen cycles. Stable nitrogen isotopes (δ15N) of NOx have been sought to track NOx emissions and NOx chemical reactivities in the atmosphere. The current atmospheric NOx collection methods for isotopic analysis, however, largely suffer from unverified collection efficiency and/or low collection speed (<10 L/min). The latter makes it difficult to study δ15N(NOx) in pristine regions with low NOx concentrations. Here, we present a three-dimensional (3D)-printed honeycomb denuder (3DP-HCD) system, which can effectively collect atmospheric NO2 (a major part of NOx) under a variety of laboratory and field conditions. With a coating solution consisting of 10% potassium hydroxide (KOH) and 25% guaiacol in methanol, the denuder system can collect NO2 with nearly 100% efficiency at flow rates of up to 70 L/min, which is 7 times higher than that of the existing method and allows high-resolution (e.g., diurnal or finer resolution) NO2 collection even in pristine sites. Besides, the δ15N of NO2 collected by the 3DP-HCD system shows good reproducibility and consistency with the previously tested method. Preliminary results of online NO oxidation by a chrome trioxide (CrO3) oxidizer for simultaneous NO and NO2 collection are also presented and discussed.

Ionic Strength-Dependent Attachment of Pseudomonas aeruginosa PAO1 on Graphene Oxide Surfaces.

Graphene oxide (GO) is a widely used antimicrobial and antibiofouling material in surface modification. Although the antibacterial mechanisms of GO have been thoroughly elucidated, the dynamics of bacterial attachment on GO surfaces under environmentally relevant conditions remain largely unknown. In this study, quartz crystal microbalance with dissipation monitoring (QCM-D) was used to examine the dynamic attachment processes of a model organism Pseudomonas aeruginosa PAO1 onto GO surface under different ionic strengths (1-600 mM NaCl). Our results show the highest bacterial attachment at moderate ionic strengths (200-400 mM). The quantitative model of QCM-D reveals that the enhanced bacterial attachment is attributed to the higher contact area between bacterial cells and GO surface. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and atomic force microscopy (AFM) analysis were employed to reveal the mechanisms of the bacteria-GO interactions under different ionic strengths. The strong electrostatic and steric repulsion at low ionic strengths (1-100 mM) was found to hinder the bacteria-GO interaction, while the limited polymer bridging caused by the collapse of biopolymer layers reduced cell attachment at a high ionic strength (600 mM). These findings advance our understanding of the ionic strength-dependent bacteria-GO interaction and provide implications to further improve the antibiofouling performance of GO-modified surfaces.

Inheritance and QTL Mapping for Flower Color in Salvia miltiorrhiza Bunge.

Salvia miltiorrhiza Bunge is an outcross-pollinated plant with diverse flower colors, ranging from white to purple. To clarify the genetic basis of S. miltiorrhiza flower color, we crossed white-flowered S. miltiorrhiza f. alba with dark violet-flowered S. miltiorrhiza, and selfed F1 to obtain an F2 population. The RGB color system was used to describe the flower color of the parents, F1 progeny, and F2 individuals. Afterward, we used genotyping-by-sequencing technology to construct a high-density linkage map of S. miltiorrhiza based on the F2 population. Finally, the linkage map was used to locate the QTLs of the genes that control flower color in S. miltiorrhiza. Through measurement and cluster analysis of the R, G, and B values of flowers from the parents, F1, and F2 individuals, it was found that the purple flower color of S. miltiorrhiza is a quantitative trait controlled by 2 loci of major genes. The genetic map contained 605 SNPs with a total length of 738.3 cM in 8 linkage groups (LGs), and the average distance between 2 markers was 1.22 cM. Based on the constructed genetic map and the flower R, G, B, and R+G+B values, 2 QTLs were detected for flower color, located on LG4 and LG5. The results of this study lay the foundation for cloning genes that control flower color and studying the molecular mechanism of flower color regulation in S. miltiorrhiza.

Effect of Ca2+ binding states of calmodulin on the conformational dynamics and force responses of myosin lever arm.

The mechanochemical coupling and biological function of myosin motors are regulated by Ca2+ concentrations. As one of the regulation pathways, Ca2+ binding induces a conformational change of the light chain calmodulin and its binding modes with a myosin lever arm, which can affect the stiffness of the lever arm and force transmission. However, the underlying molecular mechanism of the Ca2+ regulated stiffness change is not fully understood. Here, we study the effect of Ca2+ binding on the conformational dynamics and stiffness of the myosin VIIa lever arm bound with a calmodulin by performing molecular dynamics simulations and dynamic correlation network analysis. The results showed that the calmodulin bound lever arm at an apo state can sample three different conformations. In addition to the conformation observed in a crystal structure, a calmodulin bound lever arm at the apo condition can also adopt other two conformations featured by different extents of small-angle bending of the lever arm. However, large-angle bending is strongly prohibited. Such results suggest that the calmodulin bound lever arm without Ca2+ binding is plastic for small-angle deformation but shows high stiffness for large-angle deformation. In comparison, after the binding of Ca2+, although the calmodulin bound lever arm is locally more rigid, it can adopt largely deformed or even unfolded conformations, which may render the lever arm incompetent for force transmission. The conformational plasticity of the lever arm for small-angle deformation at the apo condition may be used as a force buffer to prevent the lever arm from unfolding during the power stroke action of the motor domain.

HaCYC2c regulating the heteromorphous development and functional differentiation of florets by recognizing HaNDUA2 in sunflower.

KEY MESSAGE: The overexpression of HaCYC2c and its regulation on HaNDUA2 through transcriptional recognition are important for regulating the heteromorphous development and functional differentiation of ray and disc florets in sunflower. Flower symmetry is closely related to pollinator recruitment and individual fecundity for higher plants and is the main feature used to identify flower type in angiosperms. In sunflower, HaCYC2c regulates floral organ development and floral symmetry, but the specific detail remains unclear. In this study, sunflower long petal mutant (lpm) with HaCYC2c insertion mutation was used to investigate the regulating role of HaCYC2c in the morphogenesis of florets and the transformation of floral symmetry through phenotype, transcriptome, qRT-PCR, and possible protein-gene interactions analyses. Results showed that HaCYC2c was overexpressed after an insertion into the promoter region. This gene could recognize the cis-acting element GGTCCC in the promoter region of HaNDUA2 that might regulate HaNDUA2 and affect other related genes. As a consequence, the abnormal elongation of disc petals and the degradation of male reproductive system occurred at the early development of floral organ in sunflower. Furthermore, this insertion mutation resulted in floral symmetry transformation, from actinomorphy to zygomorphy, thereby making the tubular disc florets transformed into ray-like disc florets in sunflower lpm. The findings suggested that the overexpression of HaCYC2c and its control of HaNDUA2 through transcriptional recognition might be an important regulating node of the heteromorphous development and functional differentiation for ray and disc florets in sunflower. This node contributes to the understanding of the balance between pollinator recruitment capacity of ray florets and fertility of disc florets for the optimization of reproductive efficiency and enhancement of species competitiveness in sunflower.

Design and Implementation of an Indoor Warning System with Physiological Signal Monitoring for People Isolated at Home.

Due to the recent COVID-19 pandemic, many people have faced in-home isolation, as every suspected patient must stay at home. The behavior of such isolated people needs to be monitored to ensure that they are staying at home. Using a camera is a very practical method. However, smart bracelets are more convenient when personal privacy is a concern or when the blood oxygen value or heart rate must be monitored. In this study, a low-cost indoor positioning system that uses a Bluetooth beacon, a smart bracelet, and an embedded system is proposed. In addition to monitoring whether a person living alone is active in a specific environment and tracking the heart rate or blood oxygen value under particular conditions, this system can also send early warning signals to specific observation units or relatives through instant messaging software.

Development of Joint Activity Angle Measurement and Cloud Data Storage System.

In this study, we developed a range of motion sensing system (ROMSS) to simulate the function of the elbow joint, with errors less than 0.76 degrees and 0.87 degrees in static and dynamic verification by the swinging and angle recognition modules, respectively. In the simulation process, the É£ correlation coefficient of the Pearson difference between the ROMSS and the universal goniometer was 0.90, the standard deviations of the general goniometer measurements were between ±2 degrees and ±2.6 degrees, and the standard deviations between the ROMSS measurements were between ±0.5 degrees and ±1.6 degrees. With the ROMSS, a cloud database was also established; the data measured by the sensor could be uploaded to the cloud database in real-time to provide timely patient information for healthcare professionals. We also developed a mobile app for smartphones to enable patients and healthcare providers to easily trace the data in real-time. Historical data sets with joint activity angles could be retrieved to observe the progress or effectiveness of disease recovery so the quality of care could be properly assessed and maintained.

Energy landscape remodeling mechanism of Hsp70-chaperone-accelerated protein folding.

Hsp70 chaperone is one of the key protein machines responsible for the quality control of protein production in cells. Facilitating in vivo protein folding by counteracting misfolding and aggregation is the essence of its biological function. Although the allosteric cycle during its functional actions has been well characterized both experimentally and computationally, the mechanism by which Hsp70 assists protein folding is still not fully understood. In this work, we studied the Hsp70-mediated folding of model proteins with rugged energy landscape by using molecular simulations. Different from the canonical scenario of Hsp70 functioning, which assumes that folding of substrate proteins occurs spontaneously after releasing from chaperones, our results showed that the substrate protein remains in contacts with the chaperone during its folding process. The direct chaperone-substrate interactions in the open conformation of Hsp70 tend to shield the substrate sites prone to form non-native contacts, which therefore avoids the frustrated folding pathway, leading to a higher folding rate and less probability of misfolding. Our results suggest that in addition to the unfoldase and holdase functions widely addressed in previous studies, Hsp70 can facilitate the folding of its substrate proteins by remodeling the folding energy landscape and directing the folding processes, demonstrating the foldase scenario. These findings add new, to our knowledge, insights into the general molecular mechanisms of chaperone-mediated protein folding.

Modulation of locomotor behaviors by location-specific epileptic spiking and seizures.

INTRODUCTION: Epilepsy is a debilitating neurological condition characterized by spontaneous seizures as well as significant comorbid behavioral abnormalities. In addition to seizures, epileptic patients exhibit interictal spikes far more frequently than seizures, often, but not always observed in the same brain areas. The exact relationship between spiking and seizures as well as their respective effects on behavior are not well understood. In fact, spiking without overt seizures is seen in various psychiatric conditions including attention-deficit hyperactivity disorder. METHODS: In order to study the effects of spiking and seizures on behavior in an epileptic animal model, we used long-term video-electroencephalography recordings at six cortical recording sites together with behavioral activity monitoring. Animals received unilateral injections of tetanus toxin into either the somatosensory or motor cortex. RESULTS: Somatosensory cortex-injected animals developed progressive spiking ipsilateral to the injection site, while those receiving the injection into the motor cortex developed mostly contralateral spiking and spontaneous seizures. Animals with spiking but no seizures displayed a hyperactive phenotype, while animals with both spiking and seizures displayed a hypoactive phenotype. Not all spikes were equivalent as spike location strongly correlated with distinct locomotor behaviors including ambulatory distance, vertical movements, and rotatory movement. CONCLUSIONS: Together, our results demonstrate relationships between brain region-specific spiking, seizures, and behaviors in rodents that could translate into a better understanding for patients with epileptic behavioral comorbidities and other neuropsychiatric disorders.

Application of Simulated Arms with Real-Time Pressure Monitor in Casting and Splinting by Physiological Sensors.

In the real condition, the small sensor found it difficult to detect the position of the pressure sore because of casting displacement clinically. The large sensor will detect the incorrect pressure value due to wrinkles without close to arm. Hence, we developed a simulated arm with physiological sensors combined with an APP and a cloud storage system to detect skin pressure in real time when applying a short arm cast or splint. The participants can apply a short arm cast or splint on the simulative arm and the pressure in the cast or splint could be immediately displaced on the mobile application. The difference of pressure values from six pressure detection points of the simulated arm between the intern and the attending physician with 20-year working experience were 22.8%, -7.3%, 25.0%, 8.6%, 38.2%, 49.6%, respectively. It showed that the difference of pressure values in two farthest points, such as radius stab and ulnar styloid, was maximal. The pressures on the skin surface of the short arm cast were within acceptable range. Doctors would obtain reliable reference data and instantly understand the tightness of the swathed cast which would enable them to adjust it at any time to avoid complications.

Outer Membrane c-Type Cytochromes OmcA and MtrC Play Distinct Roles in Enhancing the Attachment of Shewanella oneidensis MR-1 Cells to Goethite.

The outer membrane c-type cytochromes (c-Cyts) OmcA and MtrC in Shewanella are key terminal reductases that bind and transfer electrons directly to iron (hydr)oxides. Although the amounts of OmcA and MtrC at the cell surface and their molecular structures are largely comparable, MtrC is known to play a more important role in dissimilatory iron reduction. To explore the roles of these outer membrane c-Cyts in the interaction of Shewanella oneidensis MR-1 with iron oxides, the processes of attachment of S. oneidensis MR-1 wild type and c-type cytochrome-deficient mutants (the ΔomcA, ΔmtrC, and ΔomcA ΔmtrC mutants) to goethite are compared via quartz crystal microbalance with dissipation monitoring (QCM-D). Strains with OmcA exhibit a rapid initial attachment. The quantitative model for QCM-D responses reveals that MtrC enhances the contact area and contact elasticity of cells with goethite by more than one and two times, respectively. In situ attenuated total reflectance Fourier transform infrared two-dimensional correlation spectroscopic (ATR-FTIR 2D-CoS) analysis shows that MtrC promotes the initial interfacial reaction via an inner-sphere coordination. Atomic force microscopy (AFM) analysis demonstrates that OmcA enhances the attractive force between cells and goethite by about 60%. As a result, OmcA contributes to a higher attractive force with goethite and induces a rapid short-term attachment, while MtrC is more important in the longer-term interaction through an enhanced contact area, which promotes interfacial reactions. These results reveal that c-Cyts OmcA and MtrC adopt different mechanisms for enhancing the attachment of S. oneidensis MR-1 cells to goethite. It improves our understanding of the function of outer membrane c-Cyts and the influence of cell surface macromolecules in cell-mineral interactions.IMPORTANCEShewanella species are one group of versatile and widespread dissimilatory iron-reducing bacteria, which are capable of respiring insoluble iron minerals via six multiheme c-type cytochromes. Outer membrane c-type cytochromes (c-Cyts) OmcA and MtrC are the terminal reductases in this pathway and have comparable protein structures. In this study, we elucidate the different roles of OmcA and MtrC in the interaction of S. oneidensis MR-1 with goethite at the whole-cell level. OmcA confers enhanced affinity toward goethite and results in rapid attachment. Meanwhile, MtrC significantly increases the contact area of bacterial cells with goethite and promotes the interfacial reaction, which may explain its central role in extracellular electron transfer. This study provides novel insights into the role of bacterial surface macromolecules in the interfacial interaction of bacteria with minerals, which is critical to the development of a comprehensive understanding of cell-mineral interactions.

The attachment process and physiological properties of Escherichia coli O157:H7 on quartz.

BACKGROUND: Manure application and sewage irrigation release many intestinal pathogens into the soil. After being introduced into the soil matrix, pathogens are commonly found to attach to soil minerals. Although the survival of mineral-associated Escherichia coli O157:H7 has been studied, a comprehensive understanding of the attachment process and physiological properties after attachment is still lacking. RESULTS: In this study, planktonic and attached Escherichia coli O157:H7 cells on quartz were investigated using RNA sequencing (RNA-seq) and the isobaric tagging for relative and absolute quantitation (iTRAQ) proteomic method. Based on the transcriptomic and proteomic analyses and gene knockouts, functional two-component system pathways were required for efficient attachment; chemotaxis and the Rcs system were identified to play determinant roles in E. coli O157:H7 attachment on quartz. After attachment, the pyruvate catabolic pathway shifted from the tricarboxylic acid (TCA) cycle toward the fermentative route. The survival rate of attached E. coli O157:H7 increased more than 10-fold under penicillin and vancomycin stress and doubled under alkaline pH and ferric iron stress. CONCLUSIONS: These results contribute to the understanding of the roles of chemotaxis and the Rcs system in the attachment process of pathogens and indicate that the attachment of pathogens to minerals significantly elevates their resistance to antibiotics and environmental stress, which may pose a potential threat to public health.

The exopolysaccharide-eDNA interaction modulates 3D architecture of Bacillus subtilis biofilm.

BACKGROUND: Bacterial biofilms are surface-adherent microbial communities in which individual cells are surrounded by a self-produced extracellular matrix of polysaccharides, extracellular DNA (eDNA) and proteins. Interactions among matrix components within biofilms are responsible for creating an adaptable structure during biofilm development. However, it is unclear how the interactions among matrix components contribute to the construction of the three-dimensional (3D) biofilm architecture. RESULTS: DNase I treatment significantly inhibited Bacillus subtilis biofilm formation in the early phases of biofilm development. Confocal laser scanning microscopy (CLSM) and image analysis revealed that eDNA was cooperative with exopolysaccharide (EPS) in the early stages of B. subtilis biofilm development, while EPS played a major structural role in the later stages. In addition, deletion of the EPS production gene epsG in B. subtilis SBE1 resulted in loss of the interaction between EPS and eDNA and reduced the biofilm biomass in pellicles at the air-liquid interface. The physical interaction between these two essential biofilm matrix components was confirmed by isothermal titration calorimetry (ITC). CONCLUSIONS: Biofilm 3D structures become interconnected through surrounding eDNA and EPS. eDNA interacts with EPS in the early phases of biofilm development, while EPS mainly participates in the maturation of biofilms. The findings of this study provide a better understanding of the role of the interaction between eDNA and EPS in shaping the biofilm 3D matrix structure and biofilm formation.

Responses of Exogenous Bacteria to Soluble Extracellular Polymeric Substances in Wastewater: A Mechanistic Study and Implications on Bioaugmentation.

Compared with the chemically defined synthetic wastewater (SynWW), real wastewater has been reported to exhibit distinct effects on microbial community development. Whether and how soluble microbial products in real wastewater contribute to different effects of synthetic and real wastewater on the fate of exogenous bacteria remains elusive. In this study, using a model wastewater bacterium Comamonas testosteroni, we first examined the influences of microfiltration filter-sterilized real wastewater (MF-WW) and SynWW on the retention of C. testosteroni in established wastewater flocs during bioaugmentation. In bioreactors fed with MF-WW, augmentation of C. testosteroni to wastewater flocs resulted in a substantially higher abundance of the augmented bacterial cells than those fed with SynWW. To identify the soluble microbial products in MF-WW contributing to the observed differences between bioaugmentation reactors fed with MF-WW and SynWW, we examined the effect of MF-WW and SynWW on the growth, floc formation, and biofilm development of C. testosteroni. When C. testosteroni grew in MF-WW, visible flocs formed within 2 h, which is in contrast to cell growth in SynWW where floc formation was not observed. We further demonstrated that the observed differences were mainly attributed to the high molecular weight fraction of the soluble extracellular polymeric substances (EPS) in MF-WW, in particular, proteins and extracellular DNA. The DLVO analysis suggested that, in the presence of soluble EPS, the bacterial cell surface exhibits an increased hydrophobicity and a diminished energy barrier, leading to irreversible attachment of planktonic cells and floc formation. The RNA-seq based transcriptional analysis revealed that, in the presence of soluble EPS, genes involved in nonessential metabolisms were downregulated while genes coding for Cco (cbb3-type) and Cox (aa3-type) oxidases with different oxygen affinities were upregulated, facilitating bacterial survival in flocs. Taken together, this study reveals the mechanisms underlying the contribution of soluble EPS in real wastewater to the recruitment of exogenous bacteria by microbial aggregates and provides implications to bioaugmentation.