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At least 1,441 records · Page 80Linked to original sources
PubMed2003

A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics.

A new matrix-assisted laser-desorption/ionization time-of-flight/time-of-flight mass spectrometer with the novel "LIFT" technique (MALDI LIFT-TOF/TOF MS) is described. This instrument provides high sensitivity (attomole range) for peptide mass fingerprints (PMF). It is also possible to analyze fragment ions generated by any one of three different modes of dissociation: laser-induced dissociation (LID) and high-energy collision-induced dissociation (CID) as real MS/MS techniques and in-source decay in the reflector mode of the mass analyzer (reISD) as a pseudo-MS/MS technique. Fully automated operation including spot picking from 2D gels, in-gel digestion, sample preparation on MALDI plates with hydrophilic/hydrophobic spot profiles and spectrum acquisition/processing lead to an identification rate of 66% after the PMF was obtained. The workflow control software subsequently triggered automated acquisition of multiple MS/MS spectra. This information, combined with the PMF increased the identification rate to 77%, thus providing data that allowed protein modifications and sequence errors in the protein sequence database to be detected. The quality of the MS/MS data allowed for automated de novo sequencing and protein identification based on homology searching.

Amino Acid Sequence↗
PubMed2006

Human chromosomal bands: nested structure, high-definition map and molecular basis.

In this paper, we report investigations on the nested structure, the high-definition mapping, and the molecular basis of the classical Giemsa and Reverse bands in human chromosomes. We found the rules according to which the approximately 3,200 isochores of the human genome are assembled in high (850-band) resolution bands, and the latter in low (400-band) resolution bands, so forming the nested mosaic structure of chromosomes. Moreover, we identified the borders of both sets of chromosomal bands at the DNA sequence level on the basis of our recent map of isochores, which represent the highest-resolution, ultimate bands. Indeed, beyond the 100-kb resolution of the isochore map, the guanine and cytosine (GC) profile of DNA becomes turbulent owing to the contribution of specific sequences such as exons, introns, interspersed repeats, CpG islands, etc. The isochore-based level of definition (100 kb) of chromosomal bands is much higher than the cytogenetic definition level (2-3 Mb). The major conclusions of this work concern the high degree of order found in the structure of chromosomal bands, their mapping at a high definition, and the solution of the long-standing problem of the molecular basis of chromosomal bands, as these could be defined on the basis of compositional DNA properties alone.

Base Composition↗
PubMed2003

Cloning and expression of a novel lipase gene from Bacillus sphaericus 205y.

A Bacillus sphaericus strain (205y) that produces an organic solvent-tolerant lipase was isolated in Port Dickson, Malaysia. The gene for the lipase was recovered from a genomic library and sequenced. Phylogenetic analysis was performed based on an alignment of thirteen microbial lipase sequences obtained from the NCBI database. The analysis suggested that the B. sphaericus lipase gene is a novel gene, as it is distinct from other lipase genes in Families I.4 and I.5 reported so far. Expression in Escherichia coli under the control of the lacZ promoter resulted in an eight-fold increase in enzyme activity after a 3-h induction with 1 mM IPTG. The crude enzyme thus obtained showed a slight (10%) enhancement in activity after a 30-min incubation in 25% (v/v) n-hexane at 37 degrees C, and retained 90% of its activity after a similar period in 25% (v/v) p-xylene.

Amino Acid Sequence↗
PubMed2005

Long-term prospective on-line real-time seizure prediction.

OBJECTIVE: Epilepsy, one of the most common neurological disorders, constitutes a unique opportunity to study the dynamics of spatiotemporal state transitions in real, complex, nonlinear dynamical systems. In this study, we evaluate the performance of a prospective on-line real-time seizure prediction algorithm in two patients from a common database. METHODS: We previously demonstrated that measures of chaos and angular frequency, estimated from electroencephalographic (EEG) signals recorded at critical sites in the cerebral cortex, progressively converge (i.e. become dynamically entrained) as the epileptic brain transits from the asymptomatic interictal state to the ictal state (seizure) (Iasemidis et al., 2001, 2002a, 2003a). This observation suggested the possibility of developing algorithms to predict seizures well ahead of their occurrences. One of the central points in those investigations was the application of optimization theory, specifically quadratic zero-one programming, for the selection of the critical cortical sites. This current study combines that observation with a dynamical entrainment detection method to prospectively predict epileptic seizures. The algorithm was tested in two patients with long-term (107.54h) and multi-seizure EEG data B and C (Lehnertz and Litt, 2004). RESULTS: Analysis from the 2 test patients resulted in the prediction of up to 91.3% of the impending 23 seizures, about 89+/-15min prior to seizure onset, with an average false warning rate of one every 8.27h and an allowable prediction horizon of 3h. CONCLUSIONS: The algorithm provides warning of impending seizures prospectively and in real time, that is, it constitutes an on-line and real-time seizure prediction scheme. SIGNIFICANCE: These results suggest that the proposed seizure prediction algorithm could be used in novel diagnostic and therapeutic applications in epileptic patients.

Brain Mapping↗
PubMed2004

In vivo measurement and mapping of skin redox stress induced by ultraviolet light exposure.

Exposure of skin to UV light presents a potent oxidative stress and this could alter the skin redox state. In this context, we evaluated the ability of electron paramagnetic resonance (EPR) imaging to provide noninvasive in vivo mapping of the redox status of the skin of living rats. The redox status was measured using a topically applied nitroxyl spin probe, (15)N-PDT. The nitroxyl intensity profile obtained across the skin layers showed that the concentration of the probe was higher in the epidermis and lower in the dermis and hypodermis. Skin permeability and reduction metabolism were evaluated in the skin exposed to UVB (312 nm) radiation. Exposure of skin to UVB decreased the overall reduction rate constant of the nitroxyl probe to 25 +/- 6% of the value obtained in the untreated skin. EPR imaging data showed that after the UVB treatment, the reduction rate constant decreased to 41 +/- 1% in epidermis, 28 +/- 1% in dermis, and 21 +/- 8% in hypodermis layers. The data suggested that UVB decreased the overall reducing capability of the skin with a larger decrease in the dermis and hypodermis. In summary, in vivo EPR imaging measurements showed significant alterations in the redox state of the skin exposed to UV light.

Animals↗
PubMed2004

Trials and tribulations: a primer on successfully navigating the waters of the Food and Drug Administration.

Conducting clinical trials in a regulated environment constitutes unfamiliar territory for most physicians. There exists no formal training in this subject, so many clinicians lack even a basic understanding of the procedures required by the Federal Food, Drug, and Cosmetic Act and their implications vis-à-vis clinical practice. The authors distill drug regulation to relevant applications and elucidate the rationale and procedures for submitting an Investigational New Drug application by providing a user-friendly road map of the process.

Clinical Trials as Topic↗
PubMed2005

Atypical language representation in epilepsy: implications for injury-induced reorganization of brain function.

This review addresses language function and reorganization associated with various forms of epilepsy. Longstanding epilepsy, particularly types with onset early in life, may be associated with changes in the representation of language function in the brain. As a result of this reorganization, language function may be relatively spared despite injury to areas of the brain that normally subserve these functions. We examine the changes seen in language function in two types of epilepsy: hemispheric epilepsy of childhood and focal epilepsies. Findings from behavioral studies, intracarotid amytal testing, intraoperative cortical testing, and more recent functional imaging studies are reviewed. Studying changes in the representation of language function seen in some forms of epilepsy provides information about brain plasticity with implications for other neurologic diseases, as well as for the neuroscientific understanding of how and when functional reorganization may occur.

Animals↗
PubMed1998

Genomic organisation, alternative splicing and primary structure of human matrilin-4.

We have recently cloned a cDNA for mouse matrilin-4. By sequence comparison we identified the 12 kb long human matrilin-4 gene as a part of a high-throughput genomic sequence (HS453C12) in the databases. Additionally we found a human matrilin-4 expressed sequence tag (H54037) in the database that had been mapped to chromosome 20q13.1-2. The gene contains 10 exons and, like the matrilin-1 gene, the human matrilin-4 gene contains an AT-AC intron between the two exons encoding the coiled-coil domain. The cDNA sequence of human matrilin-4 was determined by sequencing of RT-PCR products obtained from mRNA of the human embryonic kidney cell line HEK 293. At the amino acid level it showed an overall sequence identity to the mature mouse matrilin-4 of 91% with a maximum of 97% in the second vWFA-like module. Alternative splicing leads to three different mRNAs. They all encode the putative signal peptide, the two vWFA-like domains and the potential coiled-coil alpha-helical oligomerisation domain but differ in that either one, two or three EGF-like domains are retained in the mature mRNA. Due to a G to A mutation at the splice donor site of intron C, the third exon encodes an untranslated pseudo-exon specifying the first EGF-like domain when compared to mouse matrilin-4.

Alternative Splicing↗
PubMed1998

Development of long PCR techniques to analyze deletion mutations of the human hprt gene.

DNA primers and reaction conditions for long polymerase chain reaction amplification (PCR) of portions of the human hprt gene are presented. Use of these primers with DNA from previously defined hprt deletion mutants demonstrated production of the expected smaller size products as compared to DNA from wild type cells. These primers will be of value in the rapid analysis and subsequent sequencing of hprt deletion mutations in human cells.

Base Sequence↗
PubMed1999

Evaluation of DNA-based typing procedures for strain categorization of Candida spp.

DNA-based procedures have replaced earlier epidemiologic methodologies that relied on nonreproducible and insensitive measurements of phenotypic characteristics to identify a specific strain as the source of infection. The reliability (interlaboratory percent agreement for strain delineation) and sensitivity (recognition of subtle strain-to-strain variation) of similar DNA-based typing systems by different laboratories were evaluated. Ten isolates (five epidemiologic-related and five unrelated strains each) of Candida albicans, C. lusitaniae, C. parapsilosis, C. tropicalis, and Candida (Torulopsis) glabrata were characterized in a blinded fashion by three laboratories. All 50 isolates were subtyped in each laboratory by electrophoretic karyotyping (EK) analysis using contour-clamped homogenous electric field (CHEF) electrophoresis protocols. In addition, two laboratories also performed restriction endonuclease analysis of genomic DNA (REAG) using the restriction endonucleases SfiI and BssHII followed by CHEF electrophoresis separation of resulting fragments. DNA strain identification of the 50 isolates by the three different laboratories using similar CHEF methodologies demonstrated the following species-dependent, interlaboratory reproducibility: C. tropicalis (82%), C. parapsilosis (83%), C. albicans (90%), C. lusitaniae (93%), and C. glabrata (100%). In addition, agreement was higher by the CHEF method (83 to 100%), when compared with the strain types identified by the REAG (60 to 100%) method. Five to seven strains of each Candida species evaluated were detected by the different methodologies used for this study. This study indicates that these procedures are relatively discriminatory and reliable tools to study strain-to-strain variations in epidemiologic evaluations of these yeasts.

Candida↗
PubMed2002

A simple nomenclature for a complex proton pump: VHA genes encode the vacuolar H(+)-ATPase.

The vacuolar-type H(+)-ATPase acidifies intracellular compartments and is essential for many processes, including cotransport, guard cell movement, development, and tolerance to environmental stress. We have identified at least 26 genes encoding subunits of the vacuolar-type H(+)-ATPase in the Arabidopsis thaliana genome, although inconsistent nomenclature of these genes is confusing. The pump consists of subunits A through H of the peripheral V(1) complex, and subunits a, c, c" and d of the V(o) membrane sector. Most V(1) subunits are encoded by a single gene, whereas V(o) subunits are encoded by multiple genes found in duplicated segments of the genome. We propose to name these genes VHA-x, where x represents the letter code for each subunit. Applying a consistent nomenclature will help us to understand how the expression, assembly and activity of this pump are integrated with plant growth, signaling, development and adaptation.

Adaptation, Physiological↗
PubMedDate not supplied

Statistical methods for QTL mapping in cereals.

This paper gives an overview of the statistical theory suitable for mapping quantitative trait loci in experimental populations derived from inbred parents, with a particular emphasis on methodology for cereal crops. The basic theory is described, and some new areas of statistical research appropriate for mapping in cereal crops are discussed.

Chromosome Mapping↗