scholarly journals Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies

Microbiology ◽  
2010 ◽  
Vol 156 (2) ◽  
pp. 287-301 ◽  
Author(s):  
Weiwen Zhang ◽  
Feng Li ◽  
Lei Nie
Keyword(s):  
Cellular Systems ◽  
Biological Molecules ◽  
Omics Analysis ◽  
Online Databases ◽  
Quantitative Monitoring ◽  
Integrated Omics ◽  
Genomic Scale ◽  
A Cell ◽  
Micro Organisms ◽  
Microbial Systems

Recent advances in various ‘omics’ technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular ‘omics’ platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single ‘omics’ analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-‘omics’ approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous ‘omics’ datasets in various microbial systems and the results have demonstrated that the multi-‘omics’ approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental ‘omics’ approaches, recent application of the integrated ‘omics’ for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated ‘omics’ analyses. Online databases and bioinformatic infrastructure available for integrated ‘omics’ analyses are also briefly discussed.

Fabrication of Nanoscale Hydrophobic Regions on Anodic Alumina for Selective Adhesion of Biologic Molecules

2003 ◽  
Vol 773 ◽  
Author(s):  
Xiefan Lin ◽  
Anthony S. W. Ham ◽  
Natalie A. Villani ◽  
Whye-Kei Lye ◽  
Qiyu Huang ◽  
...  
Keyword(s):  
Anodic Alumina ◽  
Biological Molecules ◽  
Spatial Density ◽  
Length Scale ◽  
Adhesion Sites ◽  
A Cell ◽  
Adhesive Molecules ◽  
Receptor Clusters ◽  
Molecular Bonding ◽  
Fabrication Parameters

AbstractStudies of selective adhesion of biological molecules provide a path for understanding fundamental cellular properties. A useful technique is to use patterned substrates, where the pattern of interest has the same length scale as the molecular bonding sites of a cell, in the tens of nanometer range. We employ electrochemical methods to grow anodic alumina, which has a naturally ordered pore structure (interpore spacing of 40 to 400 nm) controlled by the anodization potential. We have also developed methods to selectively fill the alumina pores with materials with contrasting properties. Gold, for example, is electrochemically plated into the pores, and the excess material is removed by backsputter etching. The result is a patterned surface with closely separated islands of Au, surrounded by hydrophilic alumina. The pore spacing, which is determined by fabrication parameters, is hypothesized to have a direct effect on the spatial density of adhesion sites. By attaching adhesive molecules to the Au islands, we are able to observe and study cell rolling and adhesion phenomena. Through the measurements it is possible to estimate the length scale of receptor clusters on the cell surface. This information is useful in understanding mechanisms of leukocytes adhesion to endothelial cells as well as the effect of adhesion molecules adaptation on transmission of extracellular forces. The method also has applications in tissue engineering, drug and gene delivery, cell signaling and biocompatibility design.

scholarly journals Integrated ‘omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes

2018 ◽  
Vol 289 ◽  
pp. 1-13 ◽  
Author(s):  
Jarno E.J. Wolters ◽  
Simone G.J. van Breda ◽  
Jonas Grossmann ◽  
Claudia Fortes ◽  
Florian Caiment ◽  
...  
Keyword(s):  
Human Hepatocytes ◽  
Drug Induced ◽  
New Drug ◽  
Omics Analysis ◽  
Integrated Omics

The Biology of Bacteria

2019 ◽  
Author(s):  
Armine Sefton
Keyword(s):  
Cell Wall ◽  
Bacterial Infections ◽  
Genetic Material ◽  
Gram Positive ◽  
Dna And Rna ◽  
Gram Staining ◽  
Genetic Features ◽  
Potential Pathogen ◽  
A Cell ◽  
Micro Organisms

Bacterial infections and infestations of man can be caused by both microbes and non-microbes. Microbes include bacteria, viruses, fungi, and protozoa. Non-microbes include worms, insects, and arachnids. This chapter concentrates on the basic biology of bacteria. A pathogen is an organism that is able to cause disease in its host and the pathogenicity of any organism is its ability to produce disease. Microbes express their pathogenicity by means of their virulence. The virulence of any pathogen is determined by any of its structural, biochemical, or genetic features that enable it to cause disease in the host. The relationship between a host and a potential pathogen is non- static; the likelihood of any pathogen causing disease in its host depends both on the virulence of the pathogen and the degree of resistance or susceptibility of the host, due mainly to the effectiveness of the host’s defence mechanisms. Two of the main factors influencing a bacteria’s pathogenicity are its ability to invade and it ability to produce toxins—either exotoxins or endotoxins. Bacteria are unicellular prokaryotic micro-organisms, unlike human cells, which are eukaryotic. Fungi, protozoa, helminths, and arthropods are also eukaryotic. Prokaryotic organisms contain both DNA and RNA, but their genetic material exists unbound in the cytoplasm of the cell as, unlike eukaryotic cells, they have no nuclear membrane. Sometimes bacteria contain additional smaller circular DNA molecules, called plasmids. The main features of a bacterium are the cell wall, cytoplasm, and cell membrane. However, some bacteria have additional features such as spores, capsules, fimbriae (pili), and flagellae. The construction of the cell wall is different in different bacteria, but all cell walls contain peptidoglycan. The structure of the cell wall determines the staining characteristics when stained using the Gram stain. Although its first use was over a hundred and fifty years ago, is still the standard method for primary classification of bacteria. Occasionally, bacteria do not have a cell wall. Gram staining of a fixed smear of bacteria is used to separate bacteria into Gram positive or Gram negative, and also to demonstrate their shape. Bacteria with a thick peptidoglycan layer but with no outer membrane stain purple and are called Gram positive.

scholarly journals A cell-based simulation software for multi-cellular systems

2010 ◽  
Vol 26 (20) ◽  
pp. 2641-2642 ◽  
Author(s):  
Stefan Hoehme ◽  
Dirk Drasdo
Keyword(s):  
Simulation Software ◽  
Cellular Systems ◽  
A Cell

scholarly journals Mutations in the Lipopolysaccharide Biosynthesis Pathway Interfere with Crescentin-Mediated Cell Curvature in Caulobacter crescentus

2010 ◽  
Vol 192 (13) ◽  
pp. 3368-3378 ◽  
Author(s):  
Matthew T. Cabeen ◽  
Michelle A. Murolo ◽  
Ariane Briegel ◽  
N. Khai Bui ◽  
Waldemar Vollmer ◽  
...  
Keyword(s):  
Cell Wall ◽  
Caulobacter Crescentus ◽  
Cell Envelope ◽  
Cellular Systems ◽  
Biosynthesis Pathway ◽  
Cell Morphogenesis ◽  
Division Site ◽  
Growth Properties ◽  
A Cell ◽  
Cellular Components

ABSTRACT Bacterial cell morphogenesis requires coordination among multiple cellular systems, including the bacterial cytoskeleton and the cell wall. In the vibrioid bacterium Caulobacter crescentus, the intermediate filament-like protein crescentin forms a cell envelope-associated cytoskeletal structure that controls cell wall growth to generate cell curvature. We undertook a genetic screen to find other cellular components important for cell curvature. Here we report that deletion of a gene (wbqL) involved in the lipopolysaccharide (LPS) biosynthesis pathway abolishes cell curvature. Loss of WbqL function leads to the accumulation of an aberrant O-polysaccharide species and to the release of the S layer in the culture medium. Epistasis and microscopy experiments show that neither S-layer nor O-polysaccharide production is required for curved cell morphology per se but that production of the altered O-polysaccharide species abolishes cell curvature by apparently interfering with the ability of the crescentin structure to associate with the cell envelope. Our data suggest that perturbations in a cellular pathway that is itself fully dispensable for cell curvature can cause a disruption of cell morphogenesis, highlighting the delicate harmony among unrelated cellular systems. Using the wbqL mutant, we also show that the normal assembly and growth properties of the crescentin structure are independent of its association with the cell envelope. However, this envelope association is important for facilitating the local disruption of the stable crescentin structure at the division site during cytokinesis.

scholarly journals Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA

PLoS ONE ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. e0210910 ◽  
Author(s):  
Bobak D. Kechavarzi ◽  
Huanmei Wu ◽  
Thompson N. Doman
Keyword(s):  
Breast Cancer ◽  
Bottom Up ◽  
Omics Analysis ◽  
Integrated Omics

scholarly journals Endothelin receptors: what's new and what do we need to know?

2010 ◽  
Vol 298 (2) ◽  
pp. R254-R260 ◽  
Author(s):  
Stephanie W. Watts
Keyword(s):  
Biological Effect ◽  
Receptor Agonist ◽  
Biological Molecules ◽  
Endothelin Receptors ◽  
Receptor Interaction ◽  
Pharmacological Studies ◽  
Receptor Pharmacology ◽  
A Cell ◽  
And Function ◽  
Receptor Family

Receptors are at the heart of how a molecule transmits a signal to a cell. Two receptor classes for endothelin (ET) are recognized, the ETAand ETBreceptors. Intriguing questions have arisen in the field of ET receptor pharmacology, physiology, and function. For example, a host of pharmacological studies support the interaction of the ETAand ETBreceptor in tissues (veins, arteries, bronchus, arterioles, esophagus), but yet few have been able to demonstrate direct ETA/ETBreceptor interaction. Have we modeled this interaction wrong? Do we have a truly selective ETAreceptor agonist such that we could selectively stimulate this important receptor? What can we learn from the recent phylogenic studies of the ET receptor family? Have we adequately addressed the number of biological molecules with which ET can interact to exert a biological effect? Recent mass spectrometry studies in our laboratory suggest that ET-1 interacts with other hereto unrecognized proteins. Biased ligands (ligands at the same receptor that elicit distinct signaling responses) have been discovered for other receptors. Do these exist for ET receptors and can we take advantage of this possibility in drug design? These and other questions will be posed in this minireview on topics on ET receptors.

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