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Inventory of the proteins in Neisseria meningitidis serogroup B strain MC58.

A protein inventory of Neisseria meningitidis strain MC58, a meningococcal strain belonging to the serogroup B, was performed by proteomics. A differential extraction procedure was employed and 238 protein species were identified by 2D mini-maps and MALDI-ToF analyses. In this catalog, we detected protein products from 33 genes, which were not yet annotated in previous N. meningitidis proteomic studies. This approach is suitable for high-throughput studies on differential expression of N. meningitidis genomes.

Amino Acid Sequence↗
PubMed2006

Venom proteomes of closely related Sistrurus rattlesnakes with divergent diets.

The protein composition of the venoms of the three subspecies of Sistrurus catenatus (S. c. catenatus, tergeminus, and edwardsii) and a basal species, Sistrurus miliarius barbouri, were analyzed by RP-HPLC, N-terminal sequencing, MALDI-TOF peptide mass fingerprinting, and CID-MS/MS. The venoms of the four Sistrurus taxa contain proteins from 11 families. The protein family profile and the relative abundance of each protein group in the different venoms are not conserved. Myotoxins and 2-chain PLA2s were detected only in S.c. catenatus and S.c. tergeminus, whereas C-type BPP and Kunitz-type inhibitors were exclusively found in S.c. edwardsii and Sistrurus miliarius barbouri. Among major protein families, taxa were most similar in their metalloproteases (protein similarity coefficient value: 34%) and most divergent in PLA2s (12%), with values for disintegrins and serine proteases lying between these extremes (25 and 20%, respectively). The patterns of venom diversity points to either a gain in complexity in S. catenatus taxa or a loss of venom diversity occurring early on in the evolution of the group involving the lineage connecting S. milarius to the other taxa. The high degree of differentiation in the venom proteome among recently evolved congeneric taxa emphasizes the uniqueness of the venom composition of even closely related species that have different diets. Comparative proteomic analysis of Sistrurus venoms provides a comprehensive catalog of secreted proteins, which may contribute to a deeper understanding of the biology and ecology of these North American snakes and may also serve as a starting point for studying structure-function correlations of individual toxins.

Amino Acid Sequence↗
PubMed2005

Identification of 4-S-Cysteinyltetrodotoxin from the liver of the puffer fish, Fugu pardalis, and formation of thiol adducts of tetrodotoxin from 4,9-anhydrotetrodotoxin.

The metabolic pathway of tetrodotoxin (TTX), a powerful and specific voltage-gated sodium channel blocker, has not been well-clarified either in TTX-poisoned patients or in puffer fish. 4-S-CysteinylTTX (4-CysTTX) was isolated from the liver of the puffer fish, Fugu pardalis, as the first adduct of TTX with thiol. The structure was fully characterized by electrospray ionization-MS and two-dimensional NMR spectroscopy. The configuration of Cys in this compound was confirmed to be S (L-Cys) by application of the Marfey's method to cystine obtained from 4-CysTTX by iodine oxidation. We also found that 4-CysTTX was derived from 4,9-anhydroTTX by incubation with a large excess of Cys in aqueous buffer (pH 8.0) for 90 min at 40 degrees C in 33% yield by HPLC. GSH also reacted with 4,9-anhydroTTX to form 4-S-glutathionylTTX (4-GSTTX) in 39% yield under the same conditions, whereas TTX scarcely reacted with Cys and GSH. These reactions were strictly pH-dependent, giving the highest yield at pH 8.0. 4-GSTTX was converted to 4,9-anhydroTTX in 0.8 M sodium phosphate buffer (pH 8.0) at 25 degrees C. Its half-life was approximately 4 h. The minimum lethal doses of 4-CysTTX and 4-GSTTX to mice by ip injection were more than 140 and 860 microg/kg (n = 2), which were 14- and 86-fold larger than the LD(50) of TTX, respectively. 4-GSTTX was hydrolyzed to 4-CysTTX by gamma-glutamyltranspeptidase (Sigma, catalog no. G9270), which was supposed to contain cysteinylglycine dipeptidase. We also examined the effect of Cys or GSH coinjection (ip) with TTX to mice for detoxification of TTX and concluded that these coinjections did not reduce the toxicity of TTX.

Animals↗
PubMed1999

Implementing a multiple-isolator unit for centralized preparation of cytotoxic drugs in a cancer center pharmacy.

Due to numerous reasons: assuring safety (technicians, patients, nurses, environment), preventing medication errors, cost, maintaining pharmaceutical quality, rules and regulations, it was decided to create a dedicated room within the pharmacy for the preparation of intravenous cytotoxic drugs. After a preliminary study, the following choices were made: isolator unit instead of a vertical laminar air-flow hood, rigid surface instead of flexible film, a multiple-unit structure (one half suit unit for storage and one isolator unit for passthrough, two preparation units, each with four double-gloving portals) instead of a single-unit structure. After the equipment was installed, the physical and microbiological processes were validated and a medical/pharmaceutical catalog of protocols was created. Then the technicians were trained and the standard operating procedures were written. Updated every six months, they describe the general organization, gaseous sterilization of the isolators, the drugs and the medical devices, prescription analysis and circuit, preparation of nominative forms and labels, double checking the preparations delivery, cleaning and maintenance, documentation and reports, waste disposal, safety and protection and instructions for emergency. The pharmacists, pharmacy staff, physicians and nurses were all included in a work group responsible for the isolator unit project. The unit was opened in January 1997.

Antineoplastic Agents↗
PubMed1999

Regional mapping panels for human chromosomes 1, 2, and 7.

The NIGMS Human Genetic Cell Repository has assembled regional mapping panels for human chromosomes 1, 2, and 7 from human rodent somatic cell hybrids submitted to the collection by researchers from 14 different laboratories. All hybrids were characterized initially by the submitters and verified by the Repository. Each hybrid carries a stable defined human segment as a derivative or deletion chromosome. These panels define 8-10 intervals for each chromosome. The panel for chromosome 2 is a new resource. The panels for chromosomes 1 and 7 complement previously published panels. The Repository distributes these regional mapping panels as cell cultures or as DNA. Information about these panels as well as for panels for chromosomes 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 22, and X may be viewed in the NIGMS Repository electronic catalog (http://locus.umdnj.edu/nigms).

Animals↗
PubMed2003

Methodological and statistical techniques: what do residents really need to know about statistics?

The purpose of this study was to catalog the statistical methods used in six journals two each from the fields of Family Practice, Emergency Medicine, and Obstetrics and Gynecology. We reviewed the quantitative articles from January 1998 through December 2000 from the Journal of Family Practice, the Journal of Family Medicine, the Annals of Emergency Medicine, the Journal of Academic Emergency Medicine. Articles from January 2000 through December 2000 of Obstetrics and Gynecology and the American Journal of Obstetrics and Gynecology were also included. Case reports and editorials were not included in this analysis. There were a total of 1828 articles reviewed (666 from Emergency Medicine articles, 380 from Family Practice, and 782 from Obstetrics and Gynecology). The distribution of study types (cross-sectional or survey, retrospective, or prospective) did not differ between the selected journals within Emergency Medicine, Family Practice, or Obstetrics and Gynecology. Pearson's chi-square/Fisher's Exact test was the statistic of choice overall (47.5%) followed by Student's t-test (33.1%). Analysis-of-variance was used in 23.3% of the studies, nonparametric methods (8.1%), linear regression (17.6%), and odds ratios/logistic regression (17.4%). Other statistical procedures were used less than 10% of the time. These results show that a physician who comfortably comprehends the appropriate use of descriptive statistics Student's t-test, Pearson's chi-square/Fisher's Exact test will be able to read and interpret at least 70% of the published medical literature. Educational efforts should focus on appropriate study design and analysis.

Clinical Competence↗
PubMed2000

Mammary cancer in humans and mice: a tutorial for comparative pathology. The CD-ROM.

This article introduces a CD-ROM containing whole-mount and histological images of normal growth and development of both the mouse mammary gland and the human breast. It also covers nonneoplastic lesions and neoplasias in both species including a catalog of lesions in genetically engineered mice. Instructions, with examples, on techniques such as whole-mount preparation, immunohistochemistry, in situ hybridization, and common histological stains are provided. The images are based on full-scale 1996 x 1640 pixel images at 300 pixels/ inch and are annotated. Every genetically engineered model has one or more accompanying citations. Tables are provided for orientation and organization. The CD includes zoom capabilities, a search engine, and a help mode.

Animals↗
PubMed2004

A molecular description of brain trauma pathophysiology using microarray technology: an overview.

It has been estimated that 50% of human transcriptome, the collection of mRNA in a cell, is expressed in the brain, making it one of the most complex organs to understand in terms of genomic responses to injury. The availability of genome sequences for several organisms coupled with the increasing affordability of microarray technologies makes it feasible to monitor the mRNA levels of thousands of genes simultaneously. In this paper, we provide an overview of findings using both cDNA- and oligonucleotide-based microarray analyses after experimental traumatic brain injury (TBI). Specifically, the utility of this methodology as a means of cataloging the biochemical sequelae of brain trauma and elucidating novel genes or pathways for further study is discussed. Furthermore, we offer future directions for the continued evaluation of microarray results and discuss the usefulness of microarray techniques as a testing format for determining the efficacy of mechanism-based therapies.

Animals↗
PubMed2003

Molecular fingerprinting of TGFbeta-treated embryonic maxillary mesenchymal cells.

The transforming growth factor-beta (TGF(beta)) family represents a class of signaling molecules that plays a central role in normal embryonic development, specifically in development of the craniofacial region. Members of this family are vital to development of the secondary palate where they regulate maxillary and palate mesenchymal cell proliferation and extracellular matrix synthesis. The function of this growth factor family is particularly critical in that perturbation of either process results in a cleft of the palate. While the cellular and phenotypic effects of TGF(beta) on embryonic craniofacial tissue have been extensively cataloged, the specific genes that function as downstream mediators of TGF(beta) in maxillary/palatal development are poorly defined. Gene expression arrays offer the ability to conduct a rapid, simultaneous assessment of hundreds to thousands of differentially expressed genes in a single study. Inasmuch as the downstream sequelae of TGF(beta) action are only partially defined, a complementary DNA (cDNA) expression array technology (Clontech's Atlas Mouse cDNA Expression Arrays), was utilized to delineate a profile of differentially expressed genes from TGF(beta)-treated primary cultures of murine embryonic maxillary mesenchymal cells. Hybridization of a membrane-based cDNA array (1178 genes) was performed with 32P-labeled cDNA probes synthesized from RNA isolated from either TGF(beta)-treated or vehicle-treated embryonic maxillary mesenchymal cells. Resultant phosphorimages were subject to AtlasImage analysis in order to determine differences in gene expression between control and TGF(beta)-treated maxillary mesenchymal cells. Of the 1178 arrayed genes, 552 (47%) demonstrated detectable levels of expression. Steady state levels of 22 genes were up-regulated, while those of 8 other genes were down-regulated, by a factor of twofold or greater in response to TGF(beta). Affected genes could be grouped into three general functional categories: transcription factors and general DNA-binding proteins; growth factors/signaling molecules; and extracellular matrix and related proteins. The extent of hybridization of each gene was evaluated by comparison with the abundant, constitutively expressed mRNAs: ubiquitin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ornithine decarboxylase (ODC), cytoplasmic beta-actin and 40S ribosomal protein. No detectable changes were observed in the expression levels of these genes in-response to TGF(beta) treatment. Gene expression profiling results were verified by Real-Time quantitative polymerase chain reaction. Utilization of cDNA microarray technology has enabled us to delineate a preliminary transcriptional map of TGF(beta) responsiveness in embryonic maxillary mesenchymal cells. The profile of differentially expressed genes offers revealing insights into potential molecular regulatory mechanisms employed by TGF(beta) in orchestrating craniofacial ontogeny.

Animals↗
PubMed2001

Scarring alopecia and the dermatopathologist.

BACKGROUND: The evaluation of patients with cicatricial alopecia is particularly challenging, and dermatopathologists receive little training in the interpretation of scalp biopsy specimens. Accurate interpretation of specimens from patients with hair disease requires both qualitative (morphology of follicles, inflammation, fibrosis, etc.) and quantitative (size, number, follicular phase) information. Much of this data can only be obtained from transverse sections. In most cases, good clinical/pathologic correlation is required, and so clinicians should be expected to provide demographic information as well as a brief description of the pattern of hair loss and a clinical differential diagnosis. RESULTS: The criteria used to classify the various forms of cicatricial alopecia are relatively imprecise, and so classification is controversial and in a state of evolution. There are five fairly distinctive forms of cicatricial alopecia: 1) chronic, cutaneous lupus erythematosus (discoid LE); 2) lichen planopilaris; 3) dissecting cellulitis (perifolliculitis abscedens et suffodiens); 4) acne keloidalis; and 5) central, centrifugal scarring alopecia (follicular degeneration syndrome, folliculitis decalvans, pseudopelade). Not all patients with cicatricial alopecia can be confidently assigned to one of these five entities, and "cicatricial alopecia, unclassified" would be an appropriate label for such cases. CONCLUSION: The histologic features of five forms of cicatricial alopecia are reviewed. Dermatopathologists can utilize a "checklist" to catalog the diagnostic features of scalp biopsy specimens. In many, but not all, cases the information thus acquired will "match" the clinical and histologic characteristics of a form of cicatricial alopecia. However, because of histologic and clinical overlap between the forms of cicatricial alopecia, a definitive diagnosis cannot always be rendered.

Alopecia↗
PubMed2003

Hair keratin pattern in human hair follicles grown in vitro.

The keratin family includes epithelial (soft) keratins and hair (hard) keratins, and can be divided into acidic type I and basic to neutral type II subfamilies. Recently, nine type I and six type II hair keratin genes have been characterized through the screening of a human PAC library. The expression of these genes in the hair follicle was determined in vivo and a combined catalog of acidic and basic hair keratins was established. In this study, we investigated the expression and localization of most of the human hair keratin members of both types in human hair grown in vitro. We show that in vitro growth of hair follicles for 10 days in complete William's E culture medium did not alter the expression pattern of hair keratins. Similarly to the in vivo situation, each hair keratin was localized in precise and discrete compartments of the follicle, ranging from the matrix to the upper cortex and/or the hair cuticle. This study shows that the increase in length of in vitro grown follicles was accompanied by the proper hair shaft keratinization process. It also shows that hair follicle integrity was maintained in vitro, both in terms of gross morphology and molecular organization despite the complexity of the keratin expression pattern.

Culture Techniques↗
PubMed1996

Hippocampus and memory in a food-storing and in a nonstoring bird species.

Food-storing birds maintain in memory a large and constantly changing catalog of the locations of stored food. The hippocampus of food-storing black-capped chickadees (Parus atricapillus) is proportionally larger than that of nonstoring dark-eyed juncos (Junco hyemalis). Chickadees perform better than do juncos in an operant test of spatial non-matching-to-sample (SNMTS), and chickadees are more resistant to interference in this paradigm. Hippocampal lesions attenuate performance in SNMTS and increase interference. In tests of continuous spatial alternation (CSA), juncos perform better than chickadees. CSA performance also declines following hippocampal lesions. By itself, sensitivity of a given task to hippocampal damage does not predict the direction of memory differences between storing and nonstoring species.

Animals↗
PubMed2000

Route choices, anticipated forgetting, and interface design for on-line reference documents.

Preference and usability are imperfectly correlated when choice among procedures depends on anticipating cognitive difficulties. Navigation choices were explored by offering 2 routes through an on-line price catalog. The harder route never varied, but interface features of the easier route varied across readers. In Experiment 1, readers chose the easier route (82% trials) when it was visually salient but otherwise preferred the harder route from the active window. This suggested that visual factors influenced decisions. Experiment 2 equated visual factors, but choice of the easier route fell significantly when it needed an activation click. Navigating the harder route increased readers' use of an on-line notebook (i.e., people more often anticipated forgetting prices while reading). People choose easier procedures unless interface design miscues anticipated effort. Thus, usability evaluation needs to include factors influencing choices among methods.

Adult↗
PubMed2001

Influence of performance evaluation rating segmentation on motivation and fairness perceptions.

This study investigated the impact of rating segmentation (i.e., the number of alternative appraisal categories available for rating employee performance) on motivation and perceptions of fairness. Participants were 305 student volunteers who performed a catalog search task. A 2 x 4 factorial design with 2 performance rating systems-low segmentation (3 categories) and moderate segmentation (5 categories)--and 4 performance levels was used. Overall, the results indicated that the 5-category system resulted in higher self-efficacy regarding participants' ability to reach the next higher rating category. higher goals for rating improvement, and higher rating improvements than the 3-category system. The effects of rating system and performance rating on rating improvement were partially mediated by self-efficacy and personal goals. The rating system and the performance rating affected perceptions of distributive and procedural justice.

Adult↗
PubMed2003

Self-organization of cognitive performance.

Background noise is the irregular variation across repeated measurements of human performance. Background noise remains after task and treatment effects are minimized. Background noise refers to intrinsic sources of variability, the intrinsic dynamics of mind and body, and the internal workings of a living being. Two experiments demonstrate 1/f scaling (pink noise) in simple reaction times and speeded word naming times, which round out a catalog of laboratory task demonstrations that background noise is pink noise. Ubiquitous pink noise suggests processes of mind and body that change each other's dynamics. Such interaction-dominant dynamics are found in systems that self-organize their behavior. Self-organization provides an unconventional perspective on cognition, but this perspective closely parallels a contemporary interdisciplinary view of living systems.

Adult↗
PubMed2005

Probabilistic model of the human protein-protein interaction network.

A catalog of all human protein-protein interactions would provide scientists with a framework to study protein deregulation in complex diseases such as cancer. Here we demonstrate that a probabilistic analysis integrating model organism interactome data, protein domain data, genome-wide gene expression data and functional annotation data predicts nearly 40,000 protein-protein interactions in humans-a result comparable to those obtained with experimental and computational approaches in model organisms. We validated the accuracy of the predictive model on an independent test set of known interactions and also experimentally confirmed two predicted interactions relevant to human cancer, implicating uncharacterized proteins into definitive pathways. We also applied the human interactome network to cancer genomics data and identified several interaction subnetworks activated in cancer. This integrative analysis provides a comprehensive framework for exploring the human protein interaction network.

Chromosome Mapping↗
PubMed2005

Discovery of regulatory elements in vertebrates through comparative genomics.

We have analyzed issues of reliability in studies in which comparative genomic approaches have been applied to the discovery of regulatory elements at a genome-wide level in vertebrates. We point out some potential problems with such studies, including difficulties in accurately identifying orthologous promoter regions. Many of these subtle analytical problems have become apparent only when studying the more complex vertebrate genomes. By determining motif reliability, we compared existing tools when applied to the discovery of vertebrate regulatory elements. We then used a statistical clustering method to produce a computational catalog of high quality putative regulatory elements from vertebrates, some of which are widely conserved among vertebrates and many of which are novel regulatory elements. The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques.

Algorithms↗