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PubMed2002

Intratumoral regional variations in copy number of the chromosomal part revealed by microdissection and combined ploidy and comparative genomic hybridization analyses in esophageal squamous cell carcinoma.

Intratumoral regional variations in the copy number of chromosomal material were analyzed to demonstrate the time sequence of chromosomal changes in progression of individual squamous cell carcinoma of the esophagus. We applied combined DNA ploidy and comparative genomic hybridization (CGH) analyses to multiple DNA samples extracted from microdissected, formalin-fixed, paraffin-embedded tissues, and amplified and labeled according to degenerate oligonucleotide-primed polymerase chain reaction. We examined two cases: one with a deep invasive tumor and the other with a superficial spreading tumor. We found that each sample had unique aberrations in addition to the ones common to all or some of the samples in a tumor. Based on previous studies (Okada et al., Cancer Genet Cytogenet 2000;118:99-107), we classified significant shifts of the green to red (G/R) ratio into small and large ones, which were within and beyond the range of 0.65 to 1.35, respectively. Most of the large-shift aberrations were found to be common to all or some of the samples in each case. These were thought to represent earlier events in the DNA-diploid stage, while small shifts may possibly reflect one-copy changes after tetraploidization or chromosomal instability. Based on the breakpoints and on the absolute copy numbers of altered chromosomal parts inferred from DNA ploidy and the shift size of the G/R ratio, we reconstructed the sequence of accumulation and divergence of chromosomal alterations as a dendrogram in each case. This method of temporal analysis may enable us to extract important early events from numerous aberrations screened by CGH in individual tumors.

Anatomy, Regional↗
PubMed2001

Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding?

Using a set of 372 proteins representative of a variety of 56 distinct globular folds, a statistical correlation was observed between two recently revealed features of protein structures: tightened end fragments or 'closed loops', i.e. sequence fragments that are able in three-dimensional (3D) space to nearly close their ends (a current parameter of polymer physics), and 'topohydrophobic positions', i.e. positions always occupied in 3D space by strong hydrophobic amino acids for all members of a fold family. Indeed, in sequence space, the distribution of preferred lengths for tightened end fragments and that for topohydrophobic separation match. In addition to this statistically significant similarity, the extremities of these 'closed loops' may be preferentially occupied by topohydrophobic positions, as observed on a random sample of various folds. This observation may be of special interest for sequence comparison of distantly related proteins. It is also important for the ab initio prediction of protein folds, considering the remarkable topological properties of topohydrophobic positions and their paramount importance within folding nuclei. Consequently, topohydrophobic positions locking the 'closed loops' belong to the deep cores of protein domains and might have a key role in the folding process.

Models, Molecular↗
PubMed2005

Survival of deep-sea shrimp (Alvinocaris sp.) during decompression and larval hatching at atmospheric pressure.

We report successful larval hatching of deep-sea shrimp after decompression to atmospheric pressure. Three specimens of deep-sea shrimp were collected from an ocean depth of 1157 m at cold-seep sites off Hatsushima Island in Sagami Bay, Japan, using a pressure-stat aquarium system. Phylogenetic analysis of Alvinocaris sp. based on cytochrome c oxidase subunit gene sequences confirmed that these species were a member of the genus Alvinocaris. All 3 specimens survived to reach atmospheric pressure conditions after stepwise 63-day decompression. Two of the specimens contained eggs, which hatched after 10 and 16 days, respectively, of full decompression. Although no molting of the shrimp larvae was observed during 74 days of rearing under atmospheric pressure, the larvae developed conventional dark-adapted eyes after 15 days.

Animals↗
PubMed1994

[Diprivan and full stomach].

On the basis of published data and our own experience, the procedure to be followed for general anaesthesia in a patient with a full stomach is that of a rapid sequence induction (induction-intubation) or "crash-induction". This technique which consists of the administration of atropine, a hypnotic and suxamethonium together with Sellick's manoeuvre, will provide the best conditions for intubation. In view of the characteristics of propofol (rapid effect, deep depression of pharyngo-laryngeal reflexes) it seems possible to use it as a first choice induction agent in patients who are haemodynamically stable. However, it should be noted, that there is, as yet, no evidence of the superiority of propofol over other induction agents.

Anesthesia, Intravenous↗
PubMed2001

Colonization, extinction, and phylogeographic patterning in a freshwater crustacean.

Phylogeographic analyses have revealed the importance of Pleistocene vicariance events in shaping the distribution of genetic diversity in freshwater fishes. However, few studies have examined the patterning of variation in freshwater organisms with differing dispersal syndromes and life histories. The present investigation addresses this gap, examining the phylogeography of Sida crystallina, a species whose production of diapausing eggs capable of passive dispersal was thought to constrain its regional genetic differentiation. By contrast, the present analysis has revealed deep allozyme and cytochrome oxidase I mitochondrial DNA divergence between populations from North America and Europe. Moreover, North American populations are separated into four allopatric assemblages, whose distribution suggests their derivation from different Pleistocene refugia. These lineages show higher haplotype diversity and deeper sequence divergence than those of any fish from temperate North America. Its distinctive life history traits have evidently sheltered lineages of Sida from extinction, contributing to a remarkably comprehensive and high resolution phylogeographic record.

Animals↗
PubMed2002

The early magnetic resonance imaging features of the knee in juvenile idiopathic arthritis.

AIMS: Early diagnosis of juvenile idiopathic arthritis (JIA) facilitates earlier more aggressive therapy, and improved outcome. Recognition of the features of early, untreated JIA on magnetic resonance imaging (MRI) will improve disease detection and expedite treatment. This study aims to highlight the relevant MRI features. METHODS: MRI examinations of the knee joint were performed on 11 children with clinically confirmed, early, untreated JIA. The MRI images were obtained at a mean of 2 months after symptom onset and independently evaluated by two consultant paediatric radiologists. RESULTS: Abnormalities were found on all MRI examinations. Synovial hypertrophy, joint effusions, popliteal lymph nodes and soft tissue swelling were present in all patients. Gadolinium DTPA enhancement improved the detection of synovial hyperplasia. Metaphyseal splaying and condylar overgrowth were seen in five cases (41%), oedema of the lateral collateral ligament in two cases (18%) and superficial cartilage thinning in one case. Bony erosions and deep cartilage destruction were not demonstrated. CONCLUSION: MRI of the knee joint identifies early joint changes which are distinct from those in later disease. The presence of these features should alert the radiologist to the possible diagnosis of JIA and post gadolinium DTPA sequences should be performed. Gadolinium DPTA enhancement increases the sensitivity for the detection of inflammatory changes in JIA.

Adolescent↗
PubMed2006

Low protein Z levels and risk of occurrence of deep vein thrombosis.

BACKGROUND: Protein Z (PZ) serves as a cofactor for activated factor X inhibition by the PZ-dependent protease inhibitor. In vivo and in vitro studies aimed at investigating the role of PZ levels in venous thombosis have produced conflicting results. OBJECTIVES: We investigated whether reduced PZ levels and PZ gene common variants are associated deep vein thrombosis (DVT). PATIENTS AND METHODS: In 197 patients with DVT and in 197 age-matched and sex-matched controls, PZ plasma levels and gene polymorphisms were evaluated by means of an enzyme-linked immunosorbent assay and direct cycle sequence analysis. RESULTS: Similar PZ levels were found in controls (1.44; SD 0.63 microg mL-1) and in patients (1.44; SD 0.96 microg mL-1). The incidence of PZ levels below the 5.0 (0.52 microg mL-1) or the 2.5 percentile of controls (0.47 microg mL-1) was higher in patients (10.2% and 8.7%, respectively) than in controls {4.1% [odds ratio (OR) 2.7, 95% confidence interval (CI) 1.2-7.3], and 2.0% (OR 4.6, 95% CI 1.5-13.9), respectively}. This relationship was independent of the effect of age, sex, and factor V Leiden and FII A(20210) alleles [OR 2.8 (95% CI 1.1-7.3), and OR 4.9 (95% CI 1.4-17.3)]. PZ levels were associated with the intron C G-42A and the intron F G79A polymorphisms in cases (r2=0.129) and in controls (r2=0.140). However, frequencies of the PZ gene polymorphisms were similar in the two groups and were not associated with very low PZ levels. CONCLUSIONS: The present data suggest an association between very low PZ plasma levels and the occurrence of DVT, with PZ gene polymorphisms contributing little to this relationship.

Adult↗
PubMed1999

Dissimilatory Fe(III) reduction by Clostridium beijerinckii isolated from freshwater sediment using Fe(III) maltol enrichment.

A microorganism which reduces Fe(III) during the fermentation of glucose was isolated from freshwater sediment. The Fe(III) was supplied to enrichment cultures as a soluble complex with the bidentate ligand maltol (3-hydroxy-2-methyl-4-pyrone). Advantages that were afforded by the use of Fe(III)(maltol)3 over previously published methods included negation of the requirement for assays of Fe(II) formation. Because Fe(III)(maltol)3 has a characteristic deep red colour, Fe(III) reduction could be quantified spectrophotometrically by monitoring the disappearance of the complex in liquid cultures. Furthermore, Fe(III) reduction on agar plates containing the complex was apparent by zones of decolourisation around the bacterial colonies. 16S rRNA gene sequencing indicated the isolate to be a strain of Clostridium beijerinckii. Growth experiments were performed on the isolate in batch cultures with varying concentrations of Fe(III) citrate and 50 mM glucose. Increasing the level of Fe(III) citrate present was found to alter the fermentation balance, with less acidic products being formed. The presence of Fe(III) led to increases in the growth rate and growth yield, which were both approximately doubled when the supply of the cation reached 25 mM. A NAD(P)H-dependent Fe(III) reductase activity was localised to the bacterial membrane and found not to be sensitive to respiratory inhibitors. Taken together, these data suggest that dissimilatory Fe(III) reduction by the isolate provides a means of utilising the cation as an electron sink, thus facilitating pyridine nucleotide to be recycled during fermentative metabolism.

Anaerobiosis↗
PubMed2001

Two types of neurons in the rat cerebellar nuclei as distinguished by membrane potentials and intracellular fillings.

Classically, three classes of neurons in the cerebellar nuclei (CN), defined by different projection targets and content of transmitters, have been distinguished. However, evidence for different types of neurons based on different intrinsic properties is lacking. The present study reports two types of neurons defined mainly by their intrinsic properties, as determined by whole-cell patch recordings. The majority of cells (type I, n = 63) showed cyclic burst firing whereas a small subset (type II, n = 7) did not. Burst firing was used to distinguish the two types of neurons because, as it turned out, pharmacological interference could not be used to convert the non-bursting cells to bursting ones. Some of the membrane potentials exclusively present in type I neurons, such as sodium and calcium plateau potentials, low-threshold calcium spikes, and a slow calcium-dependent afterhyperpolarization, were found to contribute to the generation of burst firing. Other membrane potentials of type I neurons were not obviously related to the generation of bursts. These were 1) the lower amplitude and width of the action potential during spontaneous activity, 2) a sequence of afterhyperpolarization-afterdepolarization-afterhyperpolarization following each spike, and 3) the high spontaneous firing rate. In contrast, type II neurons lacked slow plateau potentials and low threshold spikes. Their action potentials showed higher amplitude and width and were followed by a single deep afterhyperpolarization. Furthermore, they showed a lower firing rate at rest. In both types of neurons, a delayed inward rectification was present. Neurons filled with neurobiotin revealed that the sizes of the somata and dendritic fields of type I neurons comprised the whole range known from Golgi studies, whereas those of the few type II neurons recovered were found to be in the lowest range. In view of their size and scarcity, we propose that type II neurons may correspond to CN interneurons.

Action Potentials↗
PubMed2005

Prophylaxis for and treatment of deep venous thrombosis after stroke: the Post-Stroke Rehabilitation Outcomes Project (PSROP).

Deep venous thrombosis (DVT) is a common and preventable complication after a stroke. Although the treatment of DVT is simple and straightforward, its prevention remains controversial. The Post-Stroke Rehabilitation Outcomes Project (PSROP) database was used to describe the incidence and temporal sequence of DVT and trends in the prevention and treatment of DVT. Of the 1,161 patients in the PSROP database, 383 (32.99%) patients without DVT and 8 (0.69%) with DVT had no documented orders for anticoagulant medications. Sixty-five (5.60%) patients had DVTs during the inpatient rehabilitation facility stay. Of 10 (0.86%) patients with DVTs in the common femoral vein, 4 (40%) were diagnosed within 24 hours of admission. Nine (90%) of these 10 patients were classified as moderate or severe strokes. All patients with common femoral DVT received appropriate therapy. Although much is known about the prevention, diagnosis, and treatment of poststroke DVT, clinicians need to learn and apply treatment protocols to prevent DVTs and allow more quality time for rehabilitation.

Age Factors↗
PubMed2006

The kidney: imaging with microbubble contrast agents.

Conventional ultrasonography of the kidney is faced by limitations due to the poor contrast of B-mode imaging for parenchymal disease and limited sensitivity of color Doppler for the detection of intracortical capillaries and deep pedicular vessels. Ultrasound contrast agents (USCAs) overcome these limitations, allowing the development of new applications for renal blood flow imaging and quantification. These improvements result from the increased acoustic response obtained from the microbubbles, as well as from the development of pulse sequences for bubble-specific imaging. In radiology, the liver has been considered as the primary target for contrast because USCAs allow both detection and characterization of focal lesions. The kidney has been less studied because USCA kinetics do not provide the same obvious potential for tumor characterization, and most clinical trials for contrast-enhanced renal imaging were conducted using color Doppler. Despite this, the kidney offers promising applications as USCAs improve the detection of abnormal microvascular and macrovascular disorders. Contrast-enhanced US may become the modality of choice for diagnosis of renal artery stenosis and detection of a perfusion deficit, as well as for characterization of indeterminate renal lesions, atypical cystic lesions, and the identification of acute pyelonephritis.

Contrast Media↗
PubMed2002

Modeling the transmembrane arrangement of the uncoupling protein UCP1 and topological considerations of the nucleotide-binding site.

The uncoupling protein from brown adipose tissue (UCP1) is a mitochondrial proton transporter whose activity is inhibited by purine nucleotides. UCP1, like the other members of the mitochondrial transporter superfamily, is an homodimer and each subunit contains six transmembrane segments. In an attempt to understand the structural elements that are important for nucleotide binding, a model for the transmembrane arrangement of UCP1 has been built by computational methods. Biochemical and sequence analysis considerations are taken as constraints. The main features of the model include the following: (i) the six transmembrane alpha-helices (TMHs) associate to form an antiparallel helix bundle; (ii) TMHs have an amphiphilic nature and thus the hydrophobic and variable residues face the lipid bilayer; (iii) matrix loops do not penetrate in the core of the bundle; and (iv) the polar core constitutes the translocation pathway. Photoaffinity labeling and mutagenesis studies have identified several UCP1 regions that interact with the nucleotide. We present a model where the nucleotide binds deep inside the bundle core. The purine ring interacts with the matrix loops while the polyphosphate chain is stabilized through interactions with essential Arg residues in the TMH and whose side chains face the core of the helix bundle.

Adipose Tissue, Brown↗
PubMed1998

Evidence for three adult fast myosin heavy chain isoforms in type II skeletal muscle fibers in pigs.

Three main fiber types (one slow [type I] and two fast [type IIA and IIB] can be distinguished using conventional actomyosin ATPase (AM-ATPase) histochemistry after acidic pretreatment in mature pig skeletal muscle. We report the isolation, characterization, and identification of four adult 3'-untranslated regions corresponding to types I, IIA, IIB, and IIX myosin heavy chains (MyHC) from a cDNA library. Identification of different type II clones was based on sequence homology, in situ hybridizations (ISH), AM-ATPase histochemistry, and immunocytochemistry. Enzyme histochemistry, immunocytochemistry, and ISH were performed on serial transverse sections of longissimus and red portion of semitendinosus muscle. Results showed that all three fast MyHC transcripts were expressed in the longissimus, whereas only type IIA and IIX transcripts were present in deep red semitendinosus muscle. Type I and IIA fibers contained mostly type I and IIA transcripts, respectively, whereas type IIB fibers contained a heterogeneous population of transcripts. In longissimus muscle, 18, 31, and 51% of conventional IIB fibers were pure IIX, hybrid IIX/IIB, and pure IIB fibers, respectively. Conversely, conventional IIB fibers were actually IIX in deep red semitendinosus muscle. Expression of the three fast adult MyHC isoforms in longissimus was spatially regulated around the typical islets of type I fibers encountered in pig skeletal muscle. Thus, IIA fibers were contiguous to type I fibers, pure IIX fibers were in the direct vicinity of type I and IIA fibers, and hybrid IIX/IIB fibers were located mostly within primary fascicles between the islets of type I fibers; however, pure IIB fibers were located mainly at the periphery of the rosettes near the edges of primary fascicles. In light of the present study, conventional IIB fibers, as defined with AM-ATPase staining, are a heterogeneous population that should be split into pure IIX, hybrid IIX/ IIB, and pure IIB fibers for a more accurate fiber typing.

Amino Acid Sequence↗
PubMed1997

Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea.

Several strains of a strictly anaerobic, vibrio-shaped or sigmoid, sulfate-reducing bacterium were isolated from deep marine sediments (depth, 80 and 500 m) obtained from the Japan Sea (Ocean Drilling Program Leg 128, site 798B). This bacterium was identified as a member of the genus Desulfovibrio on the basis of the presence of desulfoviridin and characteristic phospholipid fatty acids (iso 17:1 omega 7 and iso 15:0), the small number of growth substrates utilized (lactate, pyruvate, and hydrogen), and 16S rRNA gene sequence analysis data. Based on data for 16S rRNA sequences (1,369 bp), all of the Japan Sea strains were identical to each other and were most closely related to Desulfovibrio salexigens and less closely related to Desulfovibrio desulfuricans (levels of similarity, 91 and 89.6%, respectively). There were, however, considerable phenotypic differences (in temperatures, pressures, and salinities tolerated, growth substrates, and electron donors) between the Japan Sea isolates and the type strains of previously described desulfovibrios, as well as important differences among the Japan Sea isolates. The Japan Sea isolates were active (with sulfide production) over a wide temperature range (15 to 65 degrees C) and a wide sodium chloride concentration range (0.2 to 10%) (moderate halophile), and they were barophiles that were active at pressures up to about 40 MPa (400 atm). The optimum pressures for activity corresponded to the calculated pressures at the depths from which the organisms were isolated (for isolates obtained at depths of 80 and 500 m the optimum activities occurred at 10 and 15 MPa, respectively [100 and 150 atm, respectively]). This confirms that the organisms came from deep sediments and indicates that they are well-adapted for deep sediment conditions, which is consistent with other characteristics (utilization of hydrogen, fermentation, and utilization of ferric iron and organic sulfonates as electron acceptors). We propose that Japan Sea isolate 500-1 is the type strain of a new species, Desulfovibrio profundus.

Base Sequence↗
PubMed2006

Diversity of actinomycetes isolated from Challenger Deep sediment (10,898 m) from the Mariana Trench.

Thirty-eight actinomycetes were isolated from sediment collected from the Mariana Trench (10,898 m) using marine agar and media selective for actinomycetes, notably raffinose-histidine agar. The isolates were assigned to the class Actinobacteria using primers specific for members of this taxon. The phylogenetic analysis based on 16S rRNA gene sequencing showed that the isolates belonged to the genera Dermacoccus, Kocuria, Micromonospora, Streptomyces, Tsukamurella and Williamsia. All of the isolates were screened for genes encoding nonribosomal peptide and polyketide synthetases. Nonribosomal peptide synthetase sequences were detected in more than half of the isolates and polyketide synthases type I (PKS-I) were identified in five out of 38 strains. The Streptomyces isolates produced several unusual secondary metabolites, including a PKS-I associated product. In initial testing for piezotolerance, the Dermacoccus strain MT1.1 grew at elevated hydrostatic pressures.

Actinobacteria↗
PubMed2004

Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench.

Two strains of obligately piezophilic bacteria were isolated from sediment collected from the bottom surface of a small canyon on the seaward slope of the Japan Trench at a depth of 6278 m. The isolated strains, Y223GT and Y251E, are closely affiliated with members of the genus Colwellia on the basis of 16S rRNA gene sequence analysis. The G + C contents of both strains were about 39 mol%. DNA-DNA hybridization values between these strains and Colwellia reference strains were significantly lower than those accepted as the phylogenetic definition of a species. The novel strains are Gram-negative, polarly flagellated and facultatively anaerobic. The optimal pressure for growth was 60 MPa at both 4 and 10 degrees C; the most rapid growth rate was observed at 10 degrees C and 60 MPa. No growth occurred at 15 degrees C under any pressure studied. The major isoprenoid quinone is Q-8. The predominant cellular fatty acids are C16 : 0 and C16 : 1. Based on the taxonomic differences observed, the isolated strains appear to represent a novel obligately piezophilic Colwellia species. The name Colwellia piezophila sp. nov. (type strain Y223GT = JCM 11831T = ATCC BAA-637T) is proposed.

Anaerobiosis↗
PubMed2002

BIGH3 mutation spectrum in corneal dystrophies.

PURPOSE: To investigate the molecular pathology underlying BIGH3-related corneal dystrophies (CDs) and to further delineate genotype-phenotype specificity. METHODS: Sixty-one index patients with CDs were subjected to phenotypic and genotypic characterization. The corneal phenotypes of all patients were assessed by biomicroscopy and documented by slit lamp photography. The BIGH3 gene was amplified exon by exon from constitutional DNA to perform single-strand conformation polymorphism (SSCP) analysis, followed by direct bidirectional sequencing of abnormal conformers. RESULTS: The phenotypes of CDs were classified as lattice CD in 30 patients, Groenouw type I in 12 (CDGGI), Avellino in 7 (CDA), Reis-Bückler in 8 (CDRB), and Thiel-Behnke in 4 (CDTB). Fifty occurrences of 16 distinct mutations were identified, including 8 novel mutations responsible for lattice type IIIA in three patients (CDLIIA), intermediate type I/IIIA (CDLI/IIIA) in four patients, and atypical CDL with deep deposits in one patient (CDL-deep). CONCLUSIONS: Disease-causing mutations were identified in 80% of the patients (50/61). All mutations localize in two regions of kerato-epithelin: the amino acid R124 and BIGH3 fasc domain 4. This study also confirms the mutation hot spot at positions R124 and R555 with nearly 50% of the mutations targeting these two amino acids (24/50). In addition the corneal phenotypes induced by changes at R124 and R555 are amino acid specific: R124C in CDLI, R555W and R124S in CDGGI, R124H in CDA, R124L in CRRB, and R555Q in CDTB. In CDLIIIA, CDLI/IIIA, and CDL-deep the genotype-phenotype correlation is domain specific, with all changes occurring at the boundary or within the fasc4 domain.

Amino Acid Sequence↗