scholarly journals Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 374
Author(s):  
Wieslaw Swietnicki ◽  
Ron Caspi
Keyword(s):  
Experimental Data ◽  
Porphyromonas Gingivalis ◽  
Lipid A ◽  
Structural Data ◽  
Bioinformatic Analysis ◽  
Biosynthetic Pathways ◽  
Human Pathogen ◽  
Dental Tissue ◽  
Type Antigen ◽  
Core Components

Porphyromonas gingivalis is an oral human pathogen. The bacterium destroys dental tissue and is a serious health problem worldwide. Experimental data and bioinformatic analysis revealed that the pathogen produces three types of lipopolysaccharides (LPS): normal (O-type), anionic (A-type), and capsular (K-type). The enzymes involved in the production of all three types of lipopolysaccharide have been largely identified for the first two and partially for the third type. In the current work, we use bioinformatics tools to predict biosynthetic pathways for the production of the normal (O-type) lipopolysaccharide in the W50 strain Porphyromonas gingivalis and compare the pathway with other putative pathways in fully sequenced and completed genomes of other pathogenic strains. Selected enzymes from the pathway have been modeled and putative structures are presented. The pathway for the A-type antigen could not be predicted at this time due to two mutually exclusive structures proposed in the literature. The pathway for K-type antigen biosynthesis could not be predicted either due to the lack of structural data for the antigen. However, pathways for the synthesis of lipid A, its core components, and the O-type antigen ligase reaction have been proposed based on a combination of experimental data and bioinformatic analyses. The predicted pathways are compared with known pathways in other systems and discussed. It is the first report in the literature showing, in detail, predicted pathways for the synthesis of selected LPS components for the model W50 strain of P. gingivalis.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Synthetic tetra-acylated derivatives of lipid A from Porphyromonas gingivalis are antagonists of human TLR4

2008 ◽  
Vol 6 (18) ◽  
pp. 3371 ◽  
Author(s):  
Yanghui Zhang ◽  
Jidnyasa Gaekwad ◽  
Margreet A. Wolfert ◽  
Geert-Jan Boons
Keyword(s):  
Porphyromonas Gingivalis ◽  
Lipid A ◽  
Derivatives Of

scholarly journals Development of a rabies virus-based retrograde tracer with high trans-monosynaptic efficiency by reshuffling glycoprotein

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Fan Jia ◽  
Li Li ◽  
Haizhou Liu ◽  
Pei Lv ◽  
Xiangwei Shi ◽  
...  
Keyword(s):  
Experimental Data ◽  
Rabies Virus ◽  
Oncolytic Virus ◽  
Neural Circuits ◽  
Bioinformatic Analysis ◽  
Cell Engineering ◽  
Bias Score ◽  
Codon Pair Bias ◽  
Codon Pair

AbstractRabies virus (RV) is the most widely used vector for mapping neural circuits. Previous studies have shown that the RV glycoprotein can be a target to improve the retrograde transsynaptic tracing efficiency. However, the current versions still label only a small portion of all presynaptic neurons. Here, we reshuffled the oG sequence, a chimeric glycoprotein, with positive codon pair bias score (CPBS) based on bioinformatic analysis of mouse codon pair bias, generating ooG, a further optimized glycoprotein. Our experimental data reveal that the ooG has a higher expression level than the oG in vivo, which significantly increases the tracing efficiency by up to 12.6 and 62.1-fold compared to oG and B19G, respectively. The new tool can be used for labeling neural circuits Therefore, the approach reported here provides a convenient, efficient and universal strategy to improve protein expression for various application scenarios such as trans-synaptic tracing efficiency, cell engineering, and vaccine and oncolytic virus designs.

scholarly journals The status of CMV as a human pathogen

1988 ◽  
Vol 100 (1) ◽  
pp. 1-15 ◽  
Author(s):  
P. D. Griffiths ◽  
J. E. Grundy
Keyword(s):  
Experimental Data ◽  
Human Body ◽  
Primary Infection ◽  
Immune Surveillance ◽  
Infectious Agent ◽  
Human Pathogen ◽  
The Status

Cytomegalovirus (CMV) is a common infectious agent which is well adapted to its host. Following primary infection, which is almost always asymptomatic in people with normal immunity, the virus establishes latency at sites which are unknown. The virus is probably maintained in this latent state by immune surveillance mechanisms since immunosuppression frequently leads to reactivation of virus.Cytomegalovirus has been identified in most anatomical areas of the human body. The aim of this article is to define criteria for pathogenicity so that clinical and experimental data can be reviewed to determine if CMV is likely to cause disease at these various clinical sites. Thus, patients have been shown to die frequentlywithCMV but do they diefromit?

scholarly journals The Activity of Lipid A and Core Components of Bacterial Lipopolysaccharides in the Prevention of the Hypersensitive Response in Pepper

1997 ◽  
Vol 10 (7) ◽  
pp. 926-928 ◽  
Author(s):  
Mari-Anne Newman ◽  
Michael J. Daniels ◽  
J. Maxwell Dow
Keyword(s):  
Hypersensitive Response ◽  
Xanthomonas Campestris ◽  
Lipid A ◽  
Enteric Bacteria ◽  
Core Oligosaccharide ◽  
The Core ◽  
Minimal Structure ◽  
Core Components ◽  
Pre Treatment ◽  
Bacterial Lipopolysaccharides

Pre-treatment of leaves of pepper (Capsicum annuum) with lipopolysaccharide (LPS) preparations from enteric bacteria and Xanthomonas campestris could prevent the hypersensitive response caused by an avirulent X. campestris strain. By use of a range of deep-rough mutants, the minimal structure in Salmonella LPS responsible for the elicitation of this effect was determined to be lipid A attached to a disaccharide of 2-keto-3-deoxyoctulosonate; lipid A alone and the free core oligosaccharide from a Salmonella Ra mutant were not effective. For Xanthomonas, the core oligosaccharide alone had activity although lipid A was not effective. The results suggest that pepper cells can recognize different structures within bacterial LPS to trigger alterations in plant response to avirulent pathogens.

The physical properties of ThCr2Si2-type superconductors MPd2P2 (M = Y, La): A theoretical investigation

2018 ◽  
Vol 32 (28) ◽  
pp. 1850312
Author(s):  
Md. Lokman Ali ◽  
Md. Tosaddek Hossen ◽  
Shahin Alam ◽  
Md. Sadek Hossain ◽  
Jakiul Islam ◽  
...  
Keyword(s):  
Experimental Data ◽  
Elastic Constants ◽  
Structural Data ◽  
Computer Code ◽  
Generalized Gradient ◽  
Generalized Gradient Approximation ◽  
Anisotropic Factor ◽  
Optical Functions ◽  
Debye Temperatures ◽  
Ductile Behavior

The structural stability, elastic, mechanical, optical characteristics and Debye temperature of single crystalline superconductors MPd2P2 (M = Y, La) were investigated by using the ab initio technique. We have carried out the plane wave pseudopotential within the generalized gradient approximation (GGA) implemented in the CASTEP computer code. Our investigated results of structural data are in well consistent with the previous experimental data. The bulk modulus B, shear modulus G, Young’s modulus E, Poisson’s ratio v, hardness H, and anisotropic factor A of MPd2P2 (M = Y, La) compounds were evaluated from the calculated elastic constants. The analysis of ratio B/G shows that the MPd2P2 superconductors are in ductile behavior. The Debye temperatures are also investigated from the elastic constants. Finally, the optical functions including reflectivity, absorption coefficient, loss function, conductivity, refractive index, dielectric function are calculated and analyzed.

scholarly journals Discovery and Biosynthesis of Natural Products from New Zealand Soil Metagenome Libraries

2021 ◽  
Author(s):  
◽  
Luke Stevenson
Keyword(s):  
Natural Products ◽  
New Zealand ◽  
Heterologous Expression ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Coli Strain ◽  
Functional Screening ◽  
Functional Difference ◽  
Biosynthetic Pathways ◽  
New Members

<p>Antibiotic discovery rates dramatically declined following the “golden age” of the 1940’s to the 1960’s. The platforms that underpinned that age of discovery rested upon laboratory cultivation of a small clade of bacteria, the actinomycetes, primarily isolated from soil environments. Fermentation extracts of these isolated bacteria have provided the majority of antibiotics and anticancer small molecules still used today. By applying modern genetic analysis techniques to these same environmental sources that have previously yielded such success, we can uncover new biosynthetic pathways, and bioactive compounds. The work described in this thesis investigated New Zealand soil metagenomes for this purpose.  Four large metagenome libraries were constructed from the microbiomes of diverse soil environments. These were then interrogated by a functional screening approach in a knockout Escherichia coli strain, to recover a large collection of the biosynthetic gene clusters responsible for bacterial secondary metabolite production. Using different modes of bioinformatic analysis, these gene clusters were demonstrated to have both phylogenetic divergence, and functional difference from bacterial biosynthesis pathways previously discovered from culture based studies.  Two additional biosynthetic pathways were recovered from one of these metagenome libraries, and in each case found to have novel genetic features. These gene clusters were further studied by heterologous expression within Streptomyces albus production hosts. One of these gene clusters produced small aromatic polyketide compounds, the structure of one of which was solved by chemical analytic techniques, and found to be a new chemical entity.  The second gene cluster was demonstrated to have similarity to known aureolic acid biosynthesis gene clusters – a class of potent anticancer natural products. Heterologous expression resulted in the production of many metabolites, two of which were characterised and found to be new members of this chemical class.  The research in this thesis both validates the use of metagenomic analysis for future natural product discovery efforts, and adds to a growing body of evidence that understudied clades of bacteria have an untapped biosynthetic potential that can be accessed by metagenomic methods.</p>

scholarly journals Differential modulation of human β-defensins expression in human gingival epithelia by Porphyromonas gingivalis lipopolysaccharide with tetra- and penta-acylated lipid A structures

2009 ◽  
Vol 15 (6) ◽  
pp. 325-335 ◽  
Author(s):  
Qian Lu ◽  
Richard P. Darveau ◽  
Lakshman P. Samaranayake ◽  
Cun-Yu Wang ◽  
Lijian Jin
Keyword(s):  
Porphyromonas Gingivalis ◽  
Lipid A ◽  
Differential Modulation ◽  
Porphyromonas Gingivalis Lipopolysaccharide
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