scholarly journals Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Yunyun Zhou ◽  
Douglas R. Call ◽  
Shira L. Broschat
Keyword(s):  
Open Source Software ◽  
Protein Profile ◽  
Correlation Filter ◽  
New Taxon ◽  
Optimal Alignment ◽  
Gram Negative ◽  
Protein Clusters ◽  
Bacterial Plasmids ◽  
Insertion Algorithm ◽  
Ab Initio Approach

In this paper we present a new ab initio approach for constructing an unrooted dendrogram using protein clusters, an approach that has the potential for estimating relationships among several thousands of species based on their putative proteomes. We employ an open-source software program called pClust that was developed for use in metagenomic studies. Sequence alignment is performed by pClust using the Smith-Waterman algorithm, which is known to give optimal alignment and, hence, greater accuracy than BLAST-based methods. Protein clusters generated by pClust are used to create protein profiles for each species in the dendrogram, these profiles forming a correlation filter library for use with a new taxon. To augment the dendrogram with a new taxon, a protein profile for the taxon is created using BLASTp, and this new taxon is placed into a position within the dendrogram corresponding to the highest correlation with profiles in the correlation filter library. This work was initiated because of our interest in plasmids, and each step is illustrated using proteomes from Gram-negative bacterial plasmids. Proteomes for 527 plasmids were used to generate the dendrogram, and to demonstrate the utility of the insertion algorithm twelve recently sequenced pAKD plasmids were used to augment the dendrogram.

scholarly journals An Aerogenic Pasteurella-Like Organism Isolated from Horses

1989 ◽  
Vol 1 (1) ◽  
pp. 3-5 ◽  
Author(s):  
Linda R. K. Schlater
Keyword(s):  
Taxonomic Position ◽  
Respiratory Pathogen ◽  
New Taxon ◽  
Case Histories ◽  
Genetic Studies ◽  
Gram Negative ◽  
Biochemical Characteristics ◽  
Secondary Role ◽  
The Family ◽  
Clinical Conditions

Thirteen strains of a gram-negative, fermentative bacterium that produced gas from glucose were isolated from horses with a variety of clinical conditions. The morphological and biochemical characteristics of this bacterium are similar to those described for the family Pasteurellaceae. These strains appear to constitute a new taxon within the genus Pasteurella; however, the final taxonomic position of this group depends upon more detailed genetic studies. Case histories indicate that this bacterium may be a primary respiratory pathogen and may play a secondary role in various other disease conditions.

Genetic relationships among 527 Gram-negative bacterial plasmids

Plasmid ◽  
2012 ◽  
Vol 68 (2) ◽  
pp. 133-141 ◽  
Author(s):  
Yunyun Zhou ◽  
Douglas R. Call ◽  
Shira L. Broschat
Keyword(s):  
Genetic Relationships ◽  
Gram Negative ◽  
Bacterial Plasmids

A Freeze-Etch Study of Acinetobacter SP. Grown on a Hydrocarbon Substrate

1974 ◽  
Vol 32 ◽  
pp. 174-175
Author(s):  
C. L. Scott ◽  
W. R. Finnerty
Keyword(s):  
Membrane System ◽  
Structural Distortion ◽  
Intracytoplasmic Membrane ◽  
Gram Negative ◽  
Sectioned Material ◽  
Acinetobacter Sp

Acinetobacter sp. HO-1-N, a gram-negative hydrocarbon oxidizing bacterium previously designated Micrococcus cerificans, has been shown to sequester the hydrocarbon into intracytoplasmic pools as a result of growth on this substrate. In hydrocarbon grown cells, an intracytoplasmic membrane system was also observed along with a doubling of cellular phospholipids (Z). However, using conventional dehydration and embedding procedures in preparing thin sectioned material, the hydrocarbon is extracted from the cells. This may lead to structural distortion, consequently, the freeze-etch technique was applied to preserve the integrity of the cell.

Bacterial-Mucosal Cell Junctional Complexes

1974 ◽  
Vol 32 ◽  
pp. 144-145
Author(s):  
Roger C. Wagner
Keyword(s):  
Intestinal Wall ◽  
Rat Colon ◽  
Mucosal Cell ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Mucosal Cells ◽  
Mucosal Lining ◽  
Degenerative Alterations ◽  
Junctional Complexes ◽  
Intestinal Mucosal Cells

Bacteria exhibit the ability to adhere to the apical surfaces of intestinal mucosal cells. These attachments either precede invasion of the intestinal wall by the bacteria with accompanying inflammation and degeneration of the mucosa or represent permanent anchoring sites where the bacteria never totally penetrate the mucosal cells.Endemic gram negative bacteria were found attached to the surface of mucosal cells lining the walls of crypts in the rat colon. The bacteria did not intrude deeper than 0.5 urn into the mucosal cells and no degenerative alterations were detectable in the mucosal lining.

Microanatomy of the Periplasm of Bacillus Licheniformis

1971 ◽  
Vol 29 ◽  
pp. 262-263
Author(s):  
B.K. Ghosh
Keyword(s):  
Cell Wall ◽  
Plasma Membrane ◽  
Bacillus Licheniformis ◽  
External Environment ◽  
Permeability Barrier ◽  
Periplasmic Space ◽  
Modified Technique ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria

Periplasm of bacteria is the space outside the permeability barrier of plasma membrane but enclosed by the cell wall. The contents of this special milieu exterior could be regulated by the plasma membrane from the internal, and by the cell wall from the external environment of the cell. Unlike the gram-negative organism, the presence of this space in gram-positive bacteria is still controversial because it cannot be clearly demonstrated. We have shown the importance of some periplasmic bodies in the secretion of penicillinase from Bacillus licheniformis.In negatively stained specimens prepared by a modified technique (Figs. 1 and 2), periplasmic space (PS) contained two kinds of structures: (i) fibrils (F, 100 Å) running perpendicular to the cell wall from the protoplast and (ii) an array of vesicles of various sizes (V), which seem to have evaginated from the protoplast.

Rapid demonstration of septic or infectious arthritis due to Gram-negative bacteria

1992 ◽  
Vol 50 (1) ◽  
pp. 686-687
Author(s):  
Jacob S. Hanker ◽  
Paul R. Gross ◽  
Beverly L. Giammara
Keyword(s):  
Chronic Arthritis ◽  
Blood Cultures ◽  
Gram Negative Bacteria ◽  
Infectious Arthritis ◽  
Bacterial Arthritis ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria

Blood cultures are positive in approximately only 50 per cent of the patients with nongonococcal bacterial infectious arthritis and about 20 per cent of those with gonococcal arthritis. But the concept that gram-negative bacteria could be involved even in chronic arthritis is well-supported. Gram stains are more definitive in staphylococcal arthritis caused by gram-positive bacteria than in bacterial arthritis due to gram-negative bacteria. In the latter situation where gram-negative bacilli are the problem, Gram stains are helpful for 50% of the patients; they are only helpful for 25% of the patients, however, where gram-negative gonococci are the problem. In arthritis due to gram-positive Staphylococci. Gramstained smears are positive for 75% of the patients.

Ultrastructure of periplasmic bodies in gram-negative bacteria

1990 ◽  
Vol 48 (3) ◽  
pp. 640-641
Author(s):  
Xie Nianming ◽  
Ding Shaoqing ◽  
Wang Luping ◽  
Yuan Zenglin ◽  
Zhan Guolai ◽  
...  
Keyword(s):  
Electron Microscope ◽  
Campylobacter Jejuni ◽  
Proteus Mirabilis ◽  
Shigella Flexneri ◽  
Morphological Description ◽  
Gram Negative Bacteria ◽  
Periplasmic Space ◽  
Clostridium Tetani ◽  
Gram Negative ◽  
Brucella Canis

Perhaps the data about periplasmic enzymes are obtained through biochemical methods but lack of morphological description. We have proved the existence of periplasmic bodies by electron microscope and described their ultrastructures. We hope this report may draw the attention of biochemists and mrophologists to collaborate on researches in periplasmic enzymes or periplasmic bodies with each other.One or more independent bodies may be seen in the periplasmic space between outer and inner membranes of Gram-negative bacteria, which we called periplasmic bodies. The periplasmic bodies have been found in seven species of bacteria at least, including the Pseudomonas aeroginosa. Shigella flexneri, Echerichia coli. Yersinia pestis, Campylobacter jejuni, Proteus mirabilis, Clostridium tetani. Vibrio cholerae and Brucella canis.

Dual stain kit for the microscopic gram classification of ocular infection bacteria

1993 ◽  
Vol 51 ◽  
pp. 248-249
Author(s):  
Jacob S. Hanker ◽  
Dale N. Holdren ◽  
Kenneth L. Cohen ◽  
Beverly L. Giammara
Keyword(s):  
Contact Lenses ◽  
Ocular Infection ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Gram Staining ◽  
Ocular Infections ◽  
Different Types ◽  
Culture Positive ◽  
Increased Susceptibility

Keratitis and conjunctivitis (infections of the cornea or conjunctiva) are ocular infections caused by various bacteria, fungi, viruses or parasites; bacteria, however, are usually prominent. Systemic conditions such as alcoholism, diabetes, debilitating disease, AIDS and immunosuppressive therapy can lead to increased susceptibility but trauma and contact lens use are very important factors. Gram-negative bacteria are most frequently cultured in these situations and Pseudomonas aeruginosa is most usually isolated from culture-positive ulcers of patients using contact lenses. Smears for staining can be obtained with a special swab or spatula and Gram staining frequently guides choice of a therapeutic rinse prior to the report of the culture results upon which specific antibiotic therapy is based. In some cases staining of the direct smear may be diagnostic in situations where the culture will not grow. In these cases different types of stains occasionally assist in guiding therapy.

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