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HW 1: Using Wiki



J Infect Dis. 1991 Jan;163(1):1-6.

Mucosal immunity induced by enhance-potency inactivated and oral polio vaccines.

Onorato IM, Modlin JF, McBean AM, Thoms ML, Losonsky GA, Bernier RH.

Division of Immunization, Centers for Disease Control, Atlanta, Georgia 30333.

Oral polio vaccine (OPV) is recommended for routine immunization in the United
States in part because of its ability to induce intestinal and pharyngeal
immunity to reinfection. Mucosal immunity produced by OPV and enhanced-potency
inactivated polio vaccine (E-IPV) was compared by challenging vaccines with type
1 OPV. Fewer OPV (25%) than E-IPV (63%) vaccinees excreted OPV virus in stool
after challenge. The mean stool virus titer was higher and the duration of
shedding longer among E-IPV excreters. Only one E-IPV and three OPV vaccinees
shed virus in the pharynx after challenge. Prechallenge serum neutralizing
antibody levels were not statistically different among E-IPV vaccinees who did
and did not shed virus; these levels were much higher than those of OPV
vaccinees. Poliovirus-specific IgA levels in stool did not correlate with viral
excretion. E-IPV was less effective than OPV in preventing and limiting
intestinal infection, even though it induced higher postvaccination serum
antibody levels.

Publication Types:
    Clinical Trial
    Comparative Study
    Controlled Clinical Trial

PMID: 1845806 [PubMed - indexed for MEDLINE]

cis-acting sequence signals

Wikipedia:Cis-regulatory elements

Elements Description
Frameshift controls the frame mRNA is translated with using “slippery sequences” and choke points
Iron Response regulates iron associated genes and iron homeostasis in vertebrate cells
Internal Entry Site allows for translation initiation in the middle of mRNA during protein synthesis
Riboswitch gene regulation of the mRNA in which the element is situated in response to the concentrations of its target molecule

Bioinformatics Tools

protein structure prediction:

This is the prediction of the 3D protein structure from its primary structure. General methods include of using statistical probability in predicting secondary structures such as alpha helices and beta sheets as well as the evolutionary conservation of these secondary structures. eg. Chou-Fasman method, GOR method
  • Ab initio protein structure prediction software These methods try to predict the tertiary structures from the primary structure using general principles that govern protein folding energetics as well as statistical tendencies of conformational features that native structures acquire. This is accomplished without the use of templates.
  • Comparative protein structure modeling software These methods uses previously solved structures as a basis or as templates for the predictions. The premise for the method is the assumption that there exist only a limited set of tertiary structural motifs.

gene function

eg. GO EAST, Bio Cyc
  • Controlled vocabularies for gene/enzyme function (e.g. "EC numbers" or the "Gene Ontology") These methods unify the representation of gene and gene product attributes across all species.
  • Biochemical pathway databases To store and provide access to various biochemical pathways. These methods can be used for simulations of pathways, as an example.

structure analysis

eg. Auto Dock, Dock@Home via CHARMM
  • Protein/protein docking software These methods attempt to predict the preferred orientation of one molecule to a second when bound. Specifically, these would be between proteins.
  • Protein/small-molecule docking software On the other hand, these methods predict the preferred orientations when bound between small ligand molecules and their target proteins.

sequence analysis:

eg. Gap4/Gap5, ALL PATH
  • Sequence assembly software These methods align and merge fragments of DNA sequences to reconstruct the original sequence.
  • Gene-finding software These methods algorithmically identify stretches of sequences that are biologically functional. These methods identify if a sequence is functional but not its function.

RNA structure:

These tools examine and generate structural conformations of nucleic acid via the sequence. eg. VRNA, BARNACLE
  • RNA folding software This is to determine the secondary and tertiary structure of nucleic acid from its sequence.
  • RNA design software This is the process of generating a set of nucleic acid base sequence to generate a desired conformation.

-- KeithLicardo - 11 Sep 2010

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