A comprehensive in silico analysis of putative outer membrane and secretory hydrolases from the pathogenic Leptospira: Possible implications in pathogenesis

Outer surface/membrane and virulent secretory proteins are primarily crucial for pathogenesis. Secreted and outer membrane hydrolases of many pathogens play an important role in attenuating the host immune system. Leptospira expresses many such proteins, and few have been characterized to display various roles, including host immune evasion. However, identification, classification, characterization, and elucidation of the possible role of Leptospira's outer membrane and secretory hydrolases have yet to be explored. In the present study, we used bioinformatics tools to predict exported proteins from the pathogenic Leptospira proteome. Moreover, we focused on secretory and outer membrane putative hydrolases from the exported proteins to generate a deeper understanding. Our analysis yielded four putative outer/secretory hydrolases, LIC_10995, LIC_11183, LIC_11463, and LIC_12988, containing α/β hydrolase fold and displayed similarity with lipase motif. Moreover, their conservation analysis of the predicted hydrolases across the spectrum of different Leptospira species showed high clustering with the pathogenic species. Outer membrane and secretory proteins with lipolytic activity may have a role in pathogenesis. This is the first bioinformatics analysis of secretory and outer membrane α/β hydrolases from leptospiral species. However, experimental studies are indeed required to unravel this possibility.

Bioremediation of rapid sand filters for removal of organic micropollutants during drinking water production

Rapid sand filtration (RSF) is used during drinking water production for removal of particles, possible harmful microorganisms, organic material and inorganic compounds such as iron, manganese, ammonium and methane. However, RSF can also be used for removal of certain organic micropollutants (OMPs). In this study, it was investigated if OMP removal in columns packed with sand from full scale RSFs could be stimulated by bioaugmentation (i.e. inoculating RSFs with sand from another RSF) and/or biostimulation (i.e. addition of nutrients, vitamins and trace-elements that stimulate microbial growth). The results showed that removal of PFOA, carbamazepine, 1-H benzotriazole, amidotrizoate and iopamidol in the columns was low (< 20 %). Propranolol and diclofenac removal was higher (50-60 %) and propranolol removal likely occurred via sorption processes, whereas for diclofenac it was unclear if removal was a combination of physical-chemical and biological processes. Moreover, bioaugmentation and biostimulation resulted in 99 % removal of gabapentin and metoprolol after 38 days and 99 % removal of acesulfame after 52 days of incubation. The bioaugmented column without biostimulation showed 99 % removal for gabapentin and metoprolol after 52 days, and for acesulfame after 80 days. In contrast, the non-bioaugmented column did not remove gabapentin, removed < 40 % metoprolol and showed 99 % removal of acesulfame only after 80 days of incubation. Removal of these OMPs was negatively correlated with ammonium oxidation and the absolute abundance of ammonia-oxidizing bacteria. 16S rRNA gene sequencing showed that OMP removal of acesulfame, gabapentin and metoprolol was positively correlated to the relative abundance of specific bacterial genera that harbor species with a heterotrophic and aerobic or denitrifying metabolism. These results show that bioaugmentation of RSF can be successful for OMP removal, where biostimulation can accelerate this removal.

Research on a Super-Resolution and Low-Complexity Positioning Algorithm Using FMCW Radar Based on OMP and FFT in 2D Driving Scene

Multitarget positioning technology, such as FMCW millimeter-wave radar, has broad application prospects in autonomous driving and related mobile scenarios. However, it is difficult for existing correlation algorithms to balance high resolution and low complexity, and it is also difficult to ensure the robustness of the positioning algorithm using an aging antenna. This paper proposes a super-resolution and low-complexity positioning algorithm based on the orthogonal matching pursuit algorithm that can achieve more accurate distance and angle estimation for multiple objects in a low-SNR environment. The algorithm proposed in this paper improves the resolving power by two and one orders of magnitude, respectively, compared to the classical FFT and MUSIC algorithms in the same signal-to-noise environment, and the complexity of the algorithm can be reduced by about 25-30%, with the same resolving power as the OMP algorithm. Based on the positioning algorithm proposed in our paper, we use the PSO algorithm to optimize the arrangement of an aging antenna array so that its angle estimation accuracy is equivalent to that observed when the antenna is intact, improving the positioning algorithm's robustness. This paper also further realizes the use of the proposed algorithm and a single-frame intermediate frequency signal to estimate the position angle information of the object and obtain its motion trajectory and velocity, verifying the proposed algorithm's estimation ability when it comes to these qualities in a moving scene. Furthermore, this paper designs and carries out simulations and experiments. The experimental results verify that the positioning algorithm proposed in this paper can achieve accuracy, robustness, and real-time performance in autonomous driving scenarios.

Implementation of One-Minute Preceptor for Clinical Teaching in Obstetrics and Gynaecology

Background

In absence of a dedicated teaching curriculum for non-PG residents in Obstetrics and Gynecology department, a concise teaching learning method, One-Minute Preceptor (OMP) with feedback being its core component may be introduced to translate their theoretical knowledge into clinical practice.

Methods

This descriptive cross-sectional study included four faculty members and 20 residents. Each resident was exposed to three OMP sessions pertaining to common gynecological case scenarios with a gap of at least two days in between the sessions with faculties acting as preceptor and as observer. After three OMP sessions, feedback from residents and faculty regarding their teaching and learning experience after implementing this tool was obtained through separate pre-validated questionnaires graded on Likert's scale.

Results

The satisfaction index of the residents and faculties for OMP was found to be 96.3% and 95%, respectively. All residents and faculty members had consensus that OMP addressed the learning gaps (mean score 4.45 ± 0.51 and mean score 4.5 ± 0.57, respectively) and expressed being highly satisfied with OMP in busy clinical settings as compared to traditional method of teaching with mean score of 4.9 ± 0.30 and 4.75 ± 0.5, respectively. The faculties had consensuses that OMP can assess all domains of learning (mean score 4.75 ± 0.5). All residents and faculties opined that the time allotted to address all micro-skills was less and 60% residents advocated allotting at least 5 min time to the teaching encounter.

Conclusion

Our study indicates the beneficial role of OMP in time-constraint clinical environment and warrants further research to review the time frame keeping in view the learners' needs and the discipline.

Temperature Field Reconstruction Method for Acoustic Tomography Based on Multi-Dictionary Learning

A reconstruction algorithm is proposed, based on multi-dictionary learning (MDL), to improve the reconstruction quality of acoustic tomography for complex temperature fields. Its aim is to improve the under-determination of the inverse problem by the sparse representation of the sound slowness signal (i.e., reciprocal of sound velocity). In the MDL algorithm, the K-SVD dictionary learning algorithm is used to construct corresponding sparse dictionaries for sound slowness signals of different types of temperature fields; the KNN peak-type classifier is employed for the joint use of multiple dictionaries; the orthogonal matching pursuit (OMP) algorithm is used to obtain the sparse representation of sound slowness signal in the sparse domain; then, the temperature distribution is obtained by using the relationship between sound slowness and temperature. Simulation and actual temperature distribution reconstruction experiments show that the MDL algorithm has smaller reconstruction errors and provides more accurate information about the temperature field, compared with the compressed sensing and improved orthogonal matching pursuit (CS-IMOMP) algorithm, which is an algorithm based on compressed sensing and improved orthogonal matching pursuit (in the CS-IMOMP, DFT dictionary is used), the least square algorithm (LSA) and the simultaneous iterative reconstruction technique (SIRT).

Responses of selected biomarkers, female reproductive hormones and tissue changes in non-pregnant does challenged with Mannheimia haemolytica serotype A2 and its outer membrane protein (OMP) immunogen

BACKGROUND

Mannheimia haemolytica causative agent of pneumonic mannheimiosis, a common respiratory disease of goat and sheep, which cause huge economic losses to farmers worldwide. Pneumonic mannheimiosis caused by M. haemolytica serotype A2 has been reported among small ruminants in Malaysia. The lipopolysaccharide (LPS) and outer membrane protein (OMP) are major virulence determinants for M. haemolytica serotype A2. Although pneumonic mannheimiosis is known to cause poor reproductive performance in small ruminants under field conditions, there is a dearth of published information on the specific effects of M. haemolytica serotype A2 infection on the female reproductive physiology. In this experiment, we explored the impact of M. haemolytica serotype A2 and its OMP immunogen on selected pro-inflammatory cytokines, acute phase proteins, female reproductive hormones, and cellular changes in visceral and female reproductive organs of non-pregnant does.

METHODOLOGY

Twelve healthy, non-pregnant, Boer crossbreds does were divided equally into three groups (n = 4); Group 1 served as the negative control and was challenged with 2 ml of sterile PBS intranasally. Group 2 served as the positive control and was challenged with 2 ml of 10⁹ colonies forming unit (CFU) of M. haemolytica serotype A2 suspension intranasally. Group 3 was challenged with 2 ml of OMP extracted from 10⁹ CFU of M. haemolytica A2 intramuscularly. The experimental does were monitored for clinical signs and responses periodically. Blood samples were collected at 0, 1, 2, 4, 6, 12 and 24 h and 3, 7, 21, 35 and 56 days post treatment for serological analyses. All does were euthanised using the halal slaughter method on day 60 post challenge/treatment. Tissues from the uterus, liver, lung and associated bronchial lymph nodes were collected and fixed in 10% formalin for 14 days for histopathological study.

RESULTS

Compared to the control group, the challenged/treated groups showed significant (p < 0.05) increase in the rectal temperature, respiratory rate, heart rate, and rumen motility. Serum analyses revealed that the concentrations of progesterone and estrogen hormones were significantly (p < 0.05) decreased in groups 2 & 3. In contrast, the concentrations of pro-inflammatory cytokines (IL-1β and IL-6) and acute phase proteins (Hp and SAA) were significantly increased (p < 0.05) in the challenged/treated groups compared to the control group. Histopathological lesion scoring revealed mild to moderate cellular changes characterised by congestion, haemorrhage, degeneration, leucocytic cellular infiltration, and cellular necrosis in the tissues of does from the OMP treatment and bacterial challenge groups compared to the control group.

CONCLUSION

The findings from this study suggests that M. haemolytica serotype A2 and its OMP immunogen induced mild to moderate inflammatory and degenerative changes which may potentially interfere with fertilization through hormonal imbalances and cause temporary loss of fertility in infected does.

Integrated age-related immunohistological changes occur in human olfactory epithelium and olfactory bulb

Olfactory epithelium (OE) is capable of lifelong regeneration due to presence of basal progenitor cells that respond to injury or neuronal loss with increased activity. However, this capability diminishes with advancing age and a decrease in odor perception in older individuals is well established. To characterize changes associated with age in the peripheral olfactory system, an in-depth analysis of the OE and its neuronal projections onto the olfactory bulb (OB) as a function of age was performed. Human olfactory tissue autopsy samples from 36 subjects with an average age of 74.1 years were analyzed. Established cell type-specific antibodies were used to identify OE component cells in whole mucosal sheets and epithelial sections as well as glomeruli and periglomerular structures in OB sections. With age, a reduction in OE area occurs across the mucosa progressing in a posterior-dorsal direction. Deterioration of the olfactory system is accompanied with diminution of neuron-containing OE, mature olfactory sensory neurons (OSNs) and OB innervation. On an individual level, the neuronal density within the epithelium appears to predict synapse density within the OB. The innervation of the OB is uneven with higher density at the ventral half that decreases with age as opposed to stable innervation at the dorsal half. Respiratory metaplasia, submucosal cysts, and neuromata, were commonly identified in aged OE. The finding of respiratory metaplasia and aneuronal epithelium with reduction in global basal cells suggests a progression of stem cell quiescence as an underlying pathophysiology of age-related smell loss in humans. KEY POINTS: A gradual loss of olfactory sensory neurons with age in human olfactory epithelium is also reflected in a reduction in glomeruli within the olfactory bulb. This gradual loss of neurons and synaptic connections with age occurs in a specific, spatially inhomogeneous manner. Decreasing mitotically active olfactory epithelium basal cells may contribute to age-related neuronal decline and smell loss in humans.

A Dictionary Optimization Method for Reconstruction of ECG Signals after Compressed Sensing

This paper presents a new approach for the optimization of a dictionary used in ECG signal compression and reconstruction systems, based on Compressed Sensing (CS). Alternatively to fully data driven methods, which learn the dictionary from the training data, the proposed approach uses an over complete wavelet dictionary, which is then reduced by means of a training phase. Moreover, the alignment of the frames according to the position of the R-peak is proposed, such that the dictionary optimization can exploit the different scaling features of the ECG waves. Therefore, at first, a training phase is performed in order to optimize the overcomplete dictionary matrix by reducing its number of columns. Then, the optimized matrix is used in combination with a dynamic sensing matrix to compress and reconstruct the ECG waveform. In this paper, the mathematical formulation of the patient-specific optimization is presented and three optimization algorithms have been evaluated. For each of them, an experimental tuning of the convergence parameter is carried out, in order to ensure that the algorithm can work in its most suitable conditions. The performance of each considered algorithm is evaluated by assessing the Percentage of Root-mean-squared Difference (PRD) and compared with the state of the art techniques. The obtained experimental results demonstrate that: (i) the utilization of an optimized dictionary matrix allows a better performance to be reached in the reconstruction quality of the ECG signals when compared with other methods, (ii) the regularization parameters of the optimization algorithms should be properly tuned to achieve the best reconstruction results, and (iii) the Multiple Orthogonal Matching Pursuit (M-OMP) algorithm is the better suited algorithm among those examined.

Effect of long-term intergenerational exposure to ocean acidification on ompa and ompb transcripts expression in European seabass (Dicentrarchus labrax)

Since sensory system allows organisms to perceive and interact with their external environment, any disruption in their functioning may have detrimental consequences on their survival. Ocean acidification has been shown to potentially impair olfactory system in fish and it is therefore essential to develop biological tools contributing to better characterize such effects. The olfactory marker protein (omp) gene is involved in the maturation and the activity of olfactory sensory neurons in vertebrates. In teleosts, two omp genes (ompa and ompb) originating from whole genome duplication have been identified. In this study, bioinformatic analysis allowed characterization of the ompa and ompb genes from the European seabass (Dicentrarchus labrax) genome. The European seabass ompa and ompb genes differ in deduced amino acid sequences and in their expression pattern throughout the tissues. While both ompa and ompb mRNA are strongly expressed in the olfactory epithelium, ompb expression was further observable in different brain areas while ompa expression was also detected in the eyes and in other peripheral tissues. Expression levels of ompa and ompb mRNA were investigated in adult seabass (4 years-old, F0) and in their offspring (F1) exposed to pH of 8 (control) or 7.6 (ocean acidification, OA). Under OA ompb mRNA was down-regulated while ompa mRNA was up-regulated in the olfactory epithelium of F0 adults, suggesting a long-term intragenerational OA-induced regulation of the olfactory sensory system. A shift in the expression profiles of both ompa and ompb mRNA was observed at early larval stages in F1 under OA, suggesting a disruption in the developmental process. Contrary to the F0, the expression of ompa and ompb mRNA was not anymore significantly regulated under OA in the olfactory epithelium of juvenile F1 fish. This work provides evidence for long-term impact of OA on sensorial system of European seabass as well as potential intergenerational acclimation of omp genes expression to OA in European seabass.

How Bacteria Change after Exposure to Silver Nanoformulations: Analysis of the Genome and Outer Membrane Proteome

OBJECTIVE

the main purpose of this work was to compare the genetic and phenotypic changes of E. coli treated with silver nanoformulations (E. coli BW25113 wt, E. coli BW25113 AgR, E. coli J53, E. coli ATCC 11229 wt, E. coli ATCC 11229 var. S2 and E. coli ATCC 11229 var. S7). Silver, as the metal with promising antibacterial properties, is currently widely used in medicine and the biomedical industry, in both ionic and nanoparticles forms. Silver nanoformulations are usually considered as one type of antibacterial agent, but their physical and chemical properties determine the way of interactions with the bacterial cell, the mode of action, and the bacterial cell response to silver.

METHODS

the changes in the bacterial genome, resulting from the treatment of bacteria with various silver nanoformulations, were verified by analyzing of genes (selected with mutfunc) and their conservative and non-conservative mutations selected with BLOSUM62. The phenotype was verified using an outer membrane proteome analysis (OMP isolation, 2-DE electrophoresis, and MS protein identification).

RESULTS

the variety of genetic and phenotypic changes in E. coli strains depends on the type of silver used for bacteria treatment. The most changes were identified in E. coli ATCC 11229 treated with silver nanoformulation signed as S2 (E. coli ATCC 11229 var. S2). We pinpointed 39 genes encoding proteins located in the outer membrane, 40 genes of their regulators, and 22 genes related to other outer membrane structures, such as flagellum, fimbria, lipopolysaccharide (LPS), or exopolysaccharide in this strain. Optical density of OmpC protein in E. coli electropherograms decreased after exposure to silver nanoformulation S7 (noticed in E. coli ATCC 11229 var. S7), and increased after treatment with the other silver nanoformulations (SNF) marked as S2 (noticed in E. coli ATCC 11229 var. S2). Increase of FliC protein optical density was identified in turn after Ag+ treatment (noticed in E.coli AgR).

CONCLUSION

the results show that silver nanoformulations (SNF) exerts a selective pressure on bacteria causing both conservative and non-conservative mutations. The proteomic approach revealed that the levels of some proteins have changed after treatment with appropriate SNF.

Intranasal administration of white tea alleviates the olfactory function deficit induced by chronic unpredictable mild stress

CONTEXT

White tea [Camellia sinensis (L) O.Ktze. (Theaceae)] is popular in Asia, but its benefits on olfactory injury are unknown.

OBJECTIVE

The present study explores the effects of white tea on the olfactory injury caused by chronic unpredictable mild stress (CUMS).

MATERIALS AND METHODS

C57BL/6J mice (WT) were exposed to CUMS. CUMS mice (CU) were intranasally treated with white tea extract [low tea (LT), 20 mg/kg; high tea (HT), 40 mg/kg] and fluoxetine (CF, 20 mg/kg) for 7 days. Several behavioural tests were conducted to assess depression and olfactory function. The transmission electron microscope (TEM) and semi-quantitative reverse transcription PCR were performed separately to observe the changes of related structures and genes transcription level.

RESULTS

The depressive behaviours of the LT and HT mice were reversed. The latency time of the buried food pellet test decreased from 280 s (CU) to 130 s (HT), while the olfactory sensitivity and olfactory avoidance test showed that the olfactory behaviours disorder of LT and HT mice were alleviated. The white tea increased the A_490 nm values of the cortisol treated cells from 0.15 to 1.4. Reduced mitochondrial and synaptic damage in the olfactory bulb (OB), enhanced expression of the brain-derived neurotrophic factor (BDNF) and olfactory marker protein (OMP) were observed in the LT and HT mice.

CONCLUSIONS AND DISCUSSION

White tea has the potential in curing the olfactory deficiency related to chronic stress. It lays the foundation for the development of new and reliable drug to improve olfactory.

Sparse Analyzer Tool for Biomedical Signals

The virtual (software) instrument with a statistical analyzer for testing algorithms for biomedical signals' recovery in compressive sensing (CS) scenario is presented. Various CS reconstruction algorithms are implemented with the aim to be applicable for different types of biomedical signals and different applications with under-sampled data. Incomplete sampling/sensing can be considered as a sort of signal damage, where missing data can occur as a result of noise or the incomplete signal acquisition procedure. Many approaches for recovering the missing signal parts have been developed, depending on the signal nature. Here, several approaches and their applications are presented for medical signals and images. The possibility to analyze results using different statistical parameters is provided, with the aim to choose the most suitable approach for a specific application. The instrument provides manifold possibilities such as fitting different parameters for the considered signal and testing the efficiency under different percentages of missing data. The reconstruction accuracy is measured by the mean square error (MSE) between original and reconstructed signal. Computational time is important from the aspect of power requirements, thus enabling the selection of a suitable algorithm. The instrument contains its own signal database, but there is also the possibility to load any external data for analysis.

New insights into transport capability of sugars and its impact on growth from novel mutants of Escherichia coli

The fast-growing capability of Escherichia coli strains used to produce industrially relevant metabolites relies on their capability to transport efficiently glucose or potential industrial feedstocks such as sucrose or xylose as carbon sources. E. coli imports extracellular glucose into the periplasmic space across the outer membrane porins: OmpC, OmpF, and LamB. As the internal membrane is an impermeable barrier for sugars, the cell employs several primary and secondary active transport systems, and the phosphoenolpyruvate (PEP)-sugar phosphotransferase (PTS) system for glucose transport. PTS:glucose is the preferred system by E. coli to transport and phosphorylate the periplasmic glucose; nevertheless, PTS imposes a strict metabolic control mechanism on the preferential consumption of glucose over other carbon sources in sugar mixtures such as glucose and xylose resulting from the hydrolysis of lignocellulosic biomass, by the carbon catabolite repression. In this contribution, we summarize the major sugar transport systems for glucose and disaccharide transport, the exhibited substrate plasticity, and their impact on the growth of E. coli, highlighting the relevance of PTS in the control of the expression of genes for the transport and catabolism of other sugars as xylose. We discuss the strategies developed by evolved mutants of E. coli during adaptive laboratory evolution experiments to overcome the nutritional stress condition imposed by inactivation of PTS as a strategy for the selection of fast-growing derivatives in glucose, xylose, or mixtures of glucose:xylose. This approach results in the recruitment of other primary and secondary active transporters, demonstrating relevant sugar plasticity in derivative-evolved mutants. Elucidation of the molecular and biochemical basis of sugar-transport substrate plasticity represents a consistent approach for sugar-transport system engineering for the design of efficient E. coli derivative strains with improved substrate assimilation for biotechnological purposes.

Transmembrane β-barrels: Evolution, folding and energetics

The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.

5HTR3A-driven GFP labels immature olfactory sensory neurons

The ionotropic serotonin receptor, 5-HT₃ , is expressed by many developing neurons within the central nervous system. Since the olfactory epithelium continues to generate new olfactory sensory neurons (OSNs) throughout life, we investigated the possibility that 5-HT₃ is expressed in the adult epithelium. Using a transgenic mouse in which the promoter for the 5-HT_3a subunit drives expression of green fluorescent protein (GFP), we assessed the expression of this marker in the olfactory epithelium of adult mice. Both the native 5-HT_3a mRNA and GFP are expressed within globose basal cells of the olfactory and vomeronasal epithelium in adult mice. Whereas the 5-HT_3a mRNA disappears relatively quickly after final cell division, the GFP label persists for about 5 days, thereby labeling immature OSNs in both the main olfactory system and vomeronasal organ. The GFP-labeled cells include both proliferative globose basal cells as well as immature OSNs exhibiting the hallmarks of ongoing differentiation including GAP43, PGP9.5, but the absence of olfactory marker protein. Some of the GFP-labeled OSNs show characteristics of more mature yet still developing OSNs including the presence of cilia extending from the apical knob and expression of NaV1.5, a component of the transduction cascade. These findings suggest that 5-HT_3a is indicative of a proliferative or developmental state, regardless of age, and that the 5-HT_3A GFP mice may prove useful for future studies of neurogenesis in the olfactory epithelium. J. Comp. Neurol. 525:1743-1755, 2017. © 2016 Wiley Periodicals, Inc.

Immunoprotective Efficacy of Acinetobacter baumannii Outer Membrane Protein, FilF, Predicted In silico as a Potential Vaccine Candidate

Acinetobacter baumannii is emerging as a serious nosocomial pathogen with multidrug resistance that has made it difficult to cure and development of efficacious treatment against this pathogen is direly needed. This has led to investigate vaccine approach to prevent and treat A. baumannii infections. In this work, an outer membrane putative pilus assembly protein, FilF, was predicted as vaccine candidate by in silico analysis of A. baumannii proteome and was found to be conserved among the A. baumannii strains. It was cloned and expressed in E. coli BL21(DE3) and purified by Ni-NTA chromatography. Immunization with FilF generated high antibody titer (>64,000) and provided 50% protection against a standardized lethal dose (10⁸ CFU) of A. baumannii in murine pneumonia model. FilF immunization reduced the bacterial load in lungs by 2 and 4 log cycles, 12 and 24 h post infection as compared to adjuvant control; reduced the levels of pro-inflammatory cytokines TNF-α, IL-6, IL-33, IFN-γ, and IL-1β significantly and histology of lung tissue supported the data by showing considerably reduced damage and infiltration of neutrophils in lungs. These results demonstrate the in vivo validation of immunoprotective efficacy of a protein predicted as a vaccine candidate by in silico proteomic analysis and open the possibilities for exploration of a large array of uncharacterized proteins.

Analyzing the Role of Periplasmic Folding Factors in the Biogenesis of OMPs and Members of the Type V Secretion System

The outer membrane (OM) of gram-negative bacteria is highly packed with OM proteins (OMPs) and the trafficking and assembly of OMPs in gram-negative bacteria is a subject of intense research. Structurally, OMPs vary in the number of β-strands and in the size and complexity of extra-membrane domains, with extreme examples being the members of the type V protein secretion system (T5SS), such as the autotransporter (AT) and intimin/invasin families of secreted proteins, in which a large extracellular "passenger" domain is linked to a β-barrel that inserts in the OM. Despite their structural and functional diversity, OMPs interact in the periplasm with a relatively small set of protein chaperones that facilitate their transport from the inner membrane (IM) to the β-barrel assembly machinery (BAM complex), preventing aggregation and assisting their folding in various aspects including disulfide bond formation. This chapter is focused on the periplasmic folding factors involved in the biogenesis of integral OMPs and members of T5SS in E. coli, which are used as a model system in this field. Background information on these periplasmic folding factors is provided along with genetic methods to generate conditional mutants that deplete these factors from E. coli and biochemical methods to analyze the folding, surface display, disulfide formation and oligomerization state of OMPs/T5SS in these mutants.

Immunohistochemical and lectin histochemical studies on the developing olfactory organs of fetal camel

Little is known about the development of the olfactory organs of camel. In this study, prenatal development and neuronal differentiation of the vomeronasal organ (VNO) and the olfactory epithelium (OE) of the one-humped camel were studied by immunohistochemistry and lectin histochemistry. A neuronal marker, protein gene product (PGP) 9.5, but not a marker of fully differentiated olfactory receptor cells, olfactory marker protein, intensely labeled the olfactory receptor cells of the VNO and OE at 395 mm, 510 mm, and 530 mm fetal ages, indicating that the olfactory receptor cells are differentiated, but not fully matured both in the VNO and the OE. In 187 mm and 190 mm fetuses, PGP 9.5 yielded faint immunoreactive signals in the VNO, but not in the OE, although the presence of olfactory receptor cells were demonstrated in both tissues by intense WGA and LEL stainings. We conclude that the camel VNO and OE bear differentiated, but still immature receptor cells; in addition, the onset of neuronal differentiation seems to be somewhat earlier in the VNO than in the OE till half of the prenatal life.

Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein-protein interactions

The most severe form of malaria is caused by the obligate parasite Plasmodium falciparum. Orotate phosphoribosyltransferase (OPRTase) is the fifth enzyme in the de novo pyrimidine-synthesis pathway in the parasite, which lacks salvage pathways. Among all of the malaria de novo pyrimidine-biosynthesis enzymes, the structure of P. falciparum OPRTase (PfOPRTase) was the only one unavailable until now. PfOPRTase that could be crystallized was obtained after some low-complexity sequences were removed. Four catalytic dimers were seen in the asymmetic unit (a total of eight polypeptides). In addition to revealing unique amino acids in the PfOPRTase active sites, asymmetric dimers in the larger structure pointed to novel parasite-specific protein-protein interactions that occlude the catalytic active sites. The latter could potentially modulate PfOPRTase activity in parasites and possibly provide new insights for blocking PfOPRTase functions.

Summary and Future Directions

β-barrel outer membrane proteins (OMPs) are found in the outer membranes (OMs) of all gram-negative bacteria, yet exactly how they are folded and inserted remains unknown. The last decade has provided a wealth of discovery including the identification of the BAM complex, a multicomponent complex responsible for the biogenesis of all OMPs into the OM. It is anticipated that the next decade will further advance our knowledge of how the BAM complex is able to perform its unique and interesting function.

The Role of a Destabilized Membrane for OMP Insertion

Here we describe the procedures used in our laboratory for the in vitro investigation of the apparent folding kinetics as well as the folding efficiencies of outer membrane proteins (OMPs). Because microbial OMPs display a change in their gel migration upon folding, the usage of traditional gel electrophoresis is a standard method of folding analysis. Additional aspects of the method we detail herein include the preparation and storage of OMP stocks, the setup procedures for a folding reaction, and the analysis of fraction folded from scanned gel images.

Heat Modifiability of Outer Membrane Proteins from Gram-Negative Bacteria

β-barrel membrane proteins are somewhat unique in that their folding states can be monitored using semi-native SDS-PAGE methods to determine if they are folded properly or not. This property, which is commonly referred to as heat modifiability, has been used for many years on both purified protein and on whole cells to monitor folded states of proteins of interest. Additionally, heat modifiability assays have proven indispensable in studying the BAM complex and its role in folding and inserting β-barrel membrane proteins into the outer membrane. Here, we describe the protocol our lab uses for performing the heat modifiability assay in our studies on outer membrane proteins.

Small Angle X-ray Scattering (SAXS) Characterization of the POTRA Domains of BamA

BamA is the central component of the BAM complex and contains a C-terminal β-barrel domain embedded in the outer membrane, and a soluble, periplasmic domain, made out of five polypeptide transport associated (POTRA) motifs. Structural characterization of the POTRA domains was carried out by a combination of crystallographic, NMR and solution Small Angle X-ray Scattering (SAXS) approaches. Despite its limited resolution, SAXS is an excellent complement to NMR and crystallography. It is well suited to validate high-resolution models in solution and is particularly useful to characterize flexible systems such as the POTRA domains of BamA. Here we present a protocol for sample preparation and discuss the considerations of SAXS data collection and quality control, which is applicable to most soluble proteins.

Proteoglycan abnormalities in olfactory epithelium tissue from subjects diagnosed with schizophrenia

Emerging evidence points to proteoglycan abnormalities in the pathophysiology of schizophrenia (SZ). In particular, markedly abnormal expression of chondroitin sulfate proteoglycans (CSPGs), key components of the extracellular matrix, was observed in the medial temporal lobe. CSPG functions, including regulation of neuronal differentiation and migration, are highly relevant to the pathophysiology of SZ. CSPGs may exert similar functions in the olfactory epithelium (OE), a continuously regenerating neural tissue that shows cell and molecular abnormalities in SZ. We tested the hypothesis that CSPG expression in OE may be altered in SZ. CSPG-positive cells in postmortem OE from non-psychiatric control (n=9) and SZ (n=10) subjects were counted using computer-assisted light microscopy. 'Cytoplasmic' CSPG (c-CSPG) labeling was detected in sustentacular cells and some olfactory receptor neurons (c-CSPG+ORNs), while 'pericellular' CSPG (p-CSPG) labeling was found in basal cells and some ORNs (p-CSPG+ORNs). Dual labeling for CSPG and markers for mature and immature ORNs suggests that c-CSPG+ORNs correspond to mature ORNs, and p-CSPG+ORNs to immature ORNs. Previous studies in the same cohort demonstrated that densities of mature ORNs were unaltered (Arnold et al., 2001). In the present study, numerical densities of c-CSPG+ORNs were significantly decreased in SZ (p<0.025; 99.32% decrease), suggesting a reduction of CSPG expression in mature ORNs. Previous studies showed a striking increase in the ratios of immature neurons with respect to basal cells. In this study, we find that the ratio of p-CSPG+ORNs/CSPG+basal cells was significantly increased (p=0.03) in SZ, while numerical density changes of p-CSPG+ORNs (110.71% increase) or CSPG+basal cells (53.71% decrease), did not reach statistical significance. Together, these results indicate that CSPG abnormalities are present in the OE of SZ and specifically point to a reduction of CSPG expression in mature ORNs in SZ. Given the role CSPGs play in OE cell differentiation and axon guidance, we suggest that altered CSPG expression may contribute to ORN lineage dysregulation, and olfactory identification abnormalities, observed in SZ.

High prevalence of IgA class anti-neutrophil cytoplasmic antibodies (ANCA) is associated with increased risk of bacterial infection in patients with cirrhosis

BACKGROUND & AIMS

Anti-neutrophil cytoplasmic antibodies (ANCA) are a non-uniform family of antibodies recognizing diverse components of neutrophil granulocytes. ANCA formation might be induced by protracted bacterial infections or probably reflect an abnormal immune response to commensal microorganisms. Bacterial infections are common complications in cirrhosis with high incidence of episodes caused by enteric organisms, therefore, we sought to study the presence and clinical importance of ANCA in cirrhosis.

METHODS

Sera of 385 patients with cirrhosis of different etiologies were assayed for ANCA of IgG, IgA, IgA1, IgA2, and secretory IgA subtypes by indirect immunofluorescence and ELISAs. The control group comprised 202 patients with chronic liver diseases without cirrhosis and 100 healthy subjects. In cirrhosis, a 2-year follow-up, observational study was conducted to assess a possible association between the presence of ANCA and clinically significant bacterial infections.

RESULTS

Prevalence of ANCA IgA was significantly higher in cirrhosis (52.2%) compared to chronic liver diseases (18.6%) or healthy controls (0%, p<0.001 for both). ANCA IgA subtyping assays revealed marked increase in the proportion of IgA2 subtype (46% of total ANCA IgA) and presence of the secretory component concurrently. Presence of ANCA IgA was associated with disease-specific clinical characteristics (Child-Pugh stage and presence of ascites, p<0.001). During a 2-year follow-up period, risk of infections was higher among patients with ANCA IgA compared to those without (41.8% vs. 23.4%, p<0.001). ANCA IgA positivity was associated with a shorter time to the first infectious complication (pLogRank <0.001) in Kaplan-Meier analysis and was identified as an independent predictor in multivariate Cox-regression analysis (HR:1.74, 95% CI: 1.18-2.56, p=0.006).

CONCLUSIONS

Presence of IgA type ANCA is common in cirrhosis. Involvement of gut mucosal immune system is in center of their formation and probably reflects sustained exposure to bacterial constituents.

Mechanisms of permanent loss of olfactory receptor neurons induced by the herbicide 2,6-dichlorobenzonitrile: effects on stem cells and noninvolvement of acute induction of the inflammatory cytokine IL-6

We explored the mechanisms underlying the differential effects of two olfactory toxicants, the herbicide 2,6-dichlorobenzonitrile (DCBN) and the anti-thyroid drug methimazole (MMZ), on olfactory receptor neuron (ORN) regeneration in mouse olfactory epithelium (OE). DCBN, but not MMZ, induced inflammation-like pathological changes in OE, and DCBN increased interleukin IL-6 levels in nasal-wash fluid to much greater magnitude and duration than did MMZ. At 24h after DCBN injection, the population of horizontal basal cells (HBCs; reserve, normally quiescent OE stem cells) lining the DMM became severely depleted as some of them detached from the basal lamina, and sloughed into the nasal cavity along with the globose basal cells (GBCs; heterogeneous population of stem and progenitor cells), neurons, and sustentacular cells of the neuroepithelium. In contrast, the layer of HBCs remained intact in MMZ-treated mice, as only the mature elements of the neuroepithelium were shed. Despite the respiratory metaplasia accompanying the greater severity of the DCBN lesion, residual HBCs that survived intoxication were activated by the injury and contributed to the metaplastic respiratory epithelium, as shown by tracing their descendants in a K5CreEr(T2)::fl(stop)TdTomato strain of mice in which recombination causes HBCs to express TdTomato in advance of the lesion. But, contrary to published observations with MMZ, the HBCs failed to form ORNs. A role for IL-6 in suppressing ORN regeneration in DCBN-treated mice was rejected by the failure of the anti-inflammatory drug dexamethasone to prevent the subsequent respiratory metaplasia in the DMM, suggesting that other factors lead to HBC neuro-incompetence.

Dissecting the effects of periplasmic chaperones on the in vitro folding of the outer membrane protein PagP

Although many periplasmic folding factors have been identified, the mechanisms by which they interact with unfolded outer membrane proteins (OMPs) to promote correct folding and membrane insertion remain poorly understood. Here, we have investigated the effect of two chaperones, Skp and SurA, on the folding kinetics of the OMP, PagP. Folding kinetics of PagP into both zwitterionic diC12:0PC (1,2-dilauroyl-sn-glycero-3-phosphocholine) liposomes and negatively charged 80:20 diC12:0PC:diC12:0PG [1,2-dilauroyl-sn-glycero-3-phospho-(1'-rac-glycerol)] liposomes were investigated using a combination of spectroscopic and SDS-PAGE assays. The results indicate that Skp modulates the observed rate of PagP folding in a manner that is dependent on the composition of the membrane and the ionic strength of the buffer used. These data suggest that electrostatic interactions play an important role in Skp-assisted substrate delivery to the membrane. In contrast, SurA showed no effect on the observed folding rates of PagP, consistent with the view that these chaperones act by distinct mechanisms in partially redundant parallel chaperone pathways that facilitate OMP assembly. In addition to delivery of the substrate protein to the membrane, the ability of Skp to prevent OMP aggregation was investigated. The results show that folding and membrane insertion of PagP can be restored, in part, by Skp in conditions that strongly favour PagP aggregation. These results illustrate the utility of in vitro systems for dissecting the complex folding environment encountered by OMPs in the periplasm and demonstrate the key role of Skp in holding aggregation-prone OMPs prior to their direct or indirect delivery to the membrane.

Relationship between periodontal disease, Porphyromonas gingivalis, peripheral vascular resistance markers and coronary artery disease in Asian Indians

INTRODUCTION

A close association exists between oral health and cardiovascular disease. Periodontal disease induces early vascular changes while oral pathogens have been detected in sub gingival and atheromatous plaques. We examined the interrelationship between Periodontal disease, oral bacteria, surrogate sub-clinical markers and coronary artery disease (CAD) in a representative Asian Indian cohort.

MATERIALS AND METHODS

532 Gingivitis cases and 282 Periodontitis cases were assessed for early peripheral vascular changes, namely pulse wave velocity (PWV), arterial stiffness index (ASI) and ankle brachial index (ABI) using computerized oscillometry method. Relative quantitation (RQ) of Porphyromonas gingivalis (Pg) was estimated in saliva samples of 54 Periodontitis, 25 Gingivitis and 51 CAD cases (38 also had oral disease) by Taqman assay by amplifying pathogen-specific gene targets, 16srRNA and IktA, respectively, and 16s universal bacterial rRNA as endogenous control.

RESULTS

PWV and ASI were elevated in Periodontitis compared to Gingivitis cases (p<0.0001) and in those with diabetes and hypertension. Cases with Periodontitis showed higher mean expression of Pg than Gingivitis (0.37±0.05 versus 0.15±0.04, p<0.0001), while CAD patients with oral disease (N=38) showed lower mean Pg expression than those without oral disease (N=13) (0.712±0.119 versus 1.526±0.257, p=0.008). Higher Pg expression was recorded in subjects with diabetes and hypertension.

CONCLUSION

Oral disease induces early changes in the peripheral blood vessels. Further, common presence of Pg in subjects with oral disease, in those with established cardiovascular risk factors and in patients with symptomatic CAD reflects the importance of oral hygiene in the development of Coronary Artery Disease in Asian Indians.

SIGLOCPRED: an algorithm to predict bacterial signal peptides and OMPS

There is a growing interest in Biological investigation to determine the location of proteins, to identify new potentially accessible drug targets. Signal peptide directs the transport of the protein to its location. Bacterial OMPs are essential for their survival in the host organism. SIGLOCPRED a signal peptide predictor for the bacterial proteins as well as OMP prediction has been developed. The signal peptide prediction is done based on the influence of the flanking residues on the signal peptide cleavage. A dataset of proteins with confirmed outer membrane location has being created, and the probable OMP polypeptide sequence is predicted. Since the algorithm uses confirmed datasets the prediction is more reliable and efficient. SIGLOCPRED is as efficient as many of the existing signal peptide predictors and can also predict OMPs in addition.

Comparative analysis of Wolbachia surface protein in D. melanoagster, A. tabida and B. malayi

Wolbachia surface protein (WSP) is an eight beta-barrel transmembrane structure which participates in host immune response, cell proliferation, pathogenicity and controlled cell death program. The protein has four extracellular loops containing hyper variable regions separated by conserved regions. The WSP structure is homologous to Neisseria surface protein (Nsp A) which has about 34% similarity including antigenic variation and hydrophilicity. Recombination has a large impact on diversity of this protein including positive selection which is major constraint on protein evolution. The molecular mechanism through which Wolbachia induces various reproductive anomalies is unclear; a key feature observed for such anomalies might be because of Wolbachia undergoing extensive recombination. In Wolbachia, increased recombination is observed in ankyrin proteins, surface proteins and in some hypothetical proteins. Genetic divergence is extensive in the WSP gene, WSP is known to be a chimeric protein involved in host-symbiont interactions. Here we predicted the structural and functional variations in WSP sequences of Wolbachia present in D. melanogaster, A. tabida and in B. malayi.