Epitope mapping.

Epitope mapping can be used to identify areas of a protein that an antibody recognizes and binds to. Monoclonal antibodies are easier to characterize, but epitope maps can also be produced for polyclonal antisera.

Strand bias in oligonucleotide-mediated dystrophin gene editing.

Defects in the dystrophin gene cause the severe degenerative muscle disorder, Duchenne muscular dystrophy (DMD). Among the gene therapy approaches to DMD under investigation, a gene editing approach using oligonucleotide vectors has yielded encouraging results. Here, we extend our studies of gene editing with self-pairing, chimeric RNA/DNA oligonucleotides (RDOs) to the use of oligodeoxynucleotides (ODNs) to correct point mutations in the dystrophin gene.

Indoprofen upregulates the survival motor neuron protein through a cyclooxygenase-independent mechanism.

Most patients with the pediatric neurodegenerative disease spinal muscular atrophy have a homozygous deletion of the survival motor neuron 1 (SMN1) gene, but retain one or more copies of the closely related SMN2 gene. The SMN2 gene encodes the same protein (SMN) but produces it at a low efficiency compared with the SMN1 gene. We performed a high-throughput screen of approximately 47,000 compounds to identify those that increase production of an SMN2-luciferase reporter protein, but not an SMN1-luciferase reporter protein.

Monitoring of recombinant survival motor neuron protein using fiber-optic surface plasmon resonance.

Spinal muscular atrophy (SMA) is the leading genetic cause of infant mortality. SMA is caused by the homozygous loss of the survival motor neuron 1 (SMN1) gene. A nearly identical copy gene exists known as SMN2, however, due to an aberrant splicing event, the SMN2 gene fails to produce sufficient full-length protein to protect against disease development in the absence of SMN1.

Projected benefits of active surveillance for vancomycin-resistant enterococci in intensive care units.

Hospitals use many strategies to control nosocomial transmission of vancomycin-resistant enterococci (VRE). Strategies include "passive surveillance," with isolation of patients with known previous or current VRE colonization or infection, and "active surveillance," which uses admission cultures, with subsequent isolation of patients who are found to be colonized with VRE. We created a mathematical model of VRE transmission in an intensive care unit (ICU) using data from an existing active surveillance program; we used the model to generate the estimated benefits associated with active surveillance.

A lamin A/C beta-strand containing the site of lipodystrophy mutations is a major surface epitope for a new panel of monoclonal antibodies.

Using a phage-displayed peptide library, we have identified the epitope recognized by a new panel of five monoclonal antibodies (mAbs) raised against full-length recombinant human lamin A. The mAbs were found to recognize both lamin A and C by Western blotting and immunolocalization at the nuclear rim. A nine-amino acid consensus sequence PLLTYRFPP in the common immunoglobulin-like (Ig-like) domain of lamin A/C contains the binding site for all five mAbs.

Assessment of evolution of pandemic Vibrio parahaemolyticus by multilocus sequence typing.

The genetic relatedness of 81 isolates of Vibrio parahaemolyticus was assessed by multilocus sequence typing. The strain with serotype O3:K6 emerged as a pandemic pathogen in 1996, with subsequent expansion to include strains having serotypes O1:KUT, O4:K68, and O1:K25. Sequence data from gyrB, recA, dnaE, and gnd revealed that 16 distinct serogroups isolated prior to the pandemic were highly variable and only isolates of serogroup O3:K6 shared two alleles with the pandemic strains.

Colonic bacterial flora: changing understandings in the molecular age.

The human intestinal microbiota is a complex bacterial consortium that is critical to normal health. The microflora is present at concentrations of 10(11)-10(12) cells/g of intestinal contents; the number of species present may exceed 500, although exact numbers remain to be defined, due in part to the fact that <30% of microorganisms are culturable with current microbiologic methods. Molecular tools based on 16S rDNA sequence similarities such as fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), quantitative dot blot hybridization, restriction fragment length polymorphism (RFLP) and large scale 16S rDNA sequencing have helped to overcome limitations of conventional microbiological plating methods in studying the fecal microflora composition.

Comparative analysis of multilocus sequence typing and pulsed-field gel electrophoresis for characterizing Listeria monocytogenes strains isolated from environmental and clinical sources.

One hundred seventy-five Listeria monocytogenes strains were characterized by serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) based on loci in actA, betL, hlyA, gyrB, pgm, and recA. One hundred twenty-two sequence types (STs) were identified by MLST based on allelic profiles of the four housekeeping genes (betL, gyrB, pgm, and recA), and 34 and 38 alleles were identified for hlyA and actA, respectively. Several actA and hlyA alleles appeared to be predominantly associated with clinical isolates.

Two-dimensional and Doppler transesophageal echocardiographic delineation and flow characterization of anomalous coronary arteries in adults.

Objectives: The purpose of this study was to examine the use of transesophageal echocardiography (TEE) in the identification and flow characterization of congenital coronary anomalies.

Background: Congenital coronary anomalies in adults are rare but may cause serious cardiac complications. The use of TEE in evaluation of this entity has not been well defined.

Epidemiological risk factors for isolation of ceftriaxone-resistant versus -susceptible citrobacter freundii in hospitalized patients.

Antimicrobial resistance is an emerging problem among nosocomial bacteria. Risk factors for the recovery of ceftriaxone-resistant (CRCF) or -susceptible (CSCF) Citrobacter freundii in clinical cultures from hospitalized patients were determined by using a case-case-control study design. CRCF was isolated from 43 patients (case group 1) and CSCF was isolated from 87 patients (case group 2) over a 3-year period.

Cholera and other types of vibriosis: a story of human pandemics and oysters on the half shell.

Vibrios are ubiquitous in the aquatic environment and are commonly present in or on shellfish and other seafood. A small subset of strains/species are able to cause human disease, including the cholera toxin-producing strains of Vibrio cholerae that are responsible for epidemic/pandemic cholera; thermostable direct hemolysin-producing strains of Vibrio parahaemolyticus; and Vibrio vulnificus, which can cause fulminant sepsis. Cholera outbreaks can be initiated by transmission of "epidemic" V.

Functional amounts of dystrophin produced by skipping the mutated exon in the mdx dystrophic mouse.

As a target for gene therapy, Duchenne muscular dystrophy (DMD) presents many obstacles but also an unparalleled prospect for correction by alternative splicing. The majority of mutations in the dystrophin gene occur in the region encoding the spectrin-like central rod domain, which is largely dispensable. Thus, splicing around mutations can generate a shortened but in-frame transcript, permitting translation of a partially functional dystrophin protein.

Inflammatory cytokine response to Vibrio vulnificus elicited by peripheral blood mononuclear cells from chronic alcohol users is associated with biomarkers of cellular oxidative stress.

Vibrio vulnificus is the leading cause of death in the United States associated with the consumption of raw seafood, particularly oysters. In epidemiological studies, primary septicemia and inflammation-mediated septic shock caused by V. vulnificus is strongly associated with liver disease, often in the context of chronic alcohol abuse.

The color of hamburger: slow steps toward the development of a science-based food safety system in the United States.

Concerns about food safety have played a key role in the emergence of the public health system in the United States. Unfortunately, the food safety regulatory system that was established in the early part of the 20th century in response to these concerns has not kept pace with our advancing scientific knowledge. In 1995, basic changes were made in the structure of the U.

Effect of pathogenic mis-sense mutations in lamin A on its interaction with emerin in vivo.

Mutations in lamin A/C can cause Emery-Dreifuss muscular dystrophy (EDMD) or a related cardiomyopathy (CMD1A). Using transfection of lamin-A/C-deficient fibroblasts, we have studied the effects of nine pathogenic mutations on the ability of lamin A to assemble normally and to localize emerin normally at the nuclear rim. Five mutations in the rod domain (L85R, N195K, E358K, M371K and R386K) affected the assembly of the lamina.

Emerin interacts in vitro with the splicing-associated factor, YT521-B.

Emerin is a nuclear membrane protein that interacts with lamin A/C at the nuclear envelope. Mutations in either emerin or lamin A/C cause Emery-Dreifuss muscular dystrophy (EDMD). The functions of emerin are poorly understood, but EDMD affects mainly skeletal and cardiac muscle.

Multilocus sequence typing has better discriminatory ability for typing Vibrio cholerae than does pulsed-field gel electrophoresis and provides a measure of phylogenetic relatedness.

Twenty-two Vibrio cholerae isolates, including some from "epidemic" (O1 and O139) and "nonepidemic" serogroups, were characterized by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) by using three housekeeping genes, gyrB, pgm, and recA; sequence data were also obtained for the virulence-associated genes tcpA, ctxA, and ctxB. Even with the small number of loci used, MLST had better discriminatory ability than did PFGE. On MLST analysis, there was clear clustering of epidemic serogroups; much greater diversity was seen among tcpA- and ctxAB-positive V.

Characterization of microbial communities from coastal waters using microarrays.

Molecular methods, including DNA probes, were used to identify and enumerate pathogenic Vibrio species in the Chesapeake Bay; our data indicated that Vibrio vulnificus exhibits seasonal fluctuations in number. Our work included a characterization of total microbial communities from the Bay; development of microarrays that identify and quantify the diversity of those communities; and observation of temporal changes in those communities. To identify members of the microbial community, we amplified the 16S rDNA gene from community DNA isolated from a biofilm sample collected from the Chesapeake Bay in February, 2000.

Changes in myotonic dystrophy protein kinase levels and muscle development in congenital myotonic dystrophy.

Myotonic dystrophy (DM1) is caused by the expansion of a CTG repeat in the noncoding region of a protein kinase, DMPK, expressed in skeletal and cardiac muscles. The aim of the present study was to determine the effects of very large CTG expansions on DMPK expression and skeletal muscle development. In fetuses suffering from the severe congenital form of DM1 with large CTG expansions (1800 to 3700 repeats), the skeletal muscle level of DMPK was reduced to 57% of control levels and a similar reduction was observed in cultured DM1 muscle cells relative to control cultures.

Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis.

Escherichia coli O157:H7 is a major cause of foodborne illness in the United States. Pulsed-field gel electrophoresis (PFGE) is the molecular epidemiologic method mostly commonly used to identify food-borne outbreaks. Although PFGE is a powerful epidemiologic tool, it has disadvantages that make a DNA sequence-based approach potentially attractive.

A 4-year study of the epidemiology of Vibrio cholerae in four rural areas of Bangladesh.

How Vibrio cholerae spreads around the world and what determines its seasonal peaks in endemic areas are not known. These features of cholera have been hypothesized to be primarily the result of environmental factors associated with aquatic habitats that can now be identified. Since 1997, fortnightly surveillance in 4 widely separated geographic locations in Bangladesh has been performed to identify patients with cholera and to collect environmental data.

Long-term persistence of donor nuclei in a Duchenne muscular dystrophy patient receiving bone marrow transplantation.

Duchenne muscular dystrophy (DMD) is a severe progressive muscle-wasting disorder caused by mutations in the dystrophin gene. Studies have shown that bone marrow cells transplanted into lethally irradiated mdx mice, the mouse model of DMD, can become part of skeletal muscle myofibers. Whether human marrow cells also have this ability is unknown.