Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Deep sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,153 records · Page 64Linked to original sources
PubMed2005

Feasibility of in vivo structural analysis of high-resolution magnetic resonance images of the proximal femur.

Previously, high resolution MRI to assess bone structure of deep-seated regions of the skeleton such as the proximal femur was substantially limited by signal-to-noise ratio (SNR). With the advent of new optimized pulse sequences in MRI at 1.5 T and 3 T, it may now be possible to depict and quantify the trabecular microarchitecture in the proximal femur. The purpose of this study was to investigate the feasibility of assessing trabecular microstructure of the human proximal femur in vivo with MR imaging at 1.5 T and 3 T. MR images of six young, healthy male and female subjects were acquired using standard clinical 1.5-T and high-field 3-T whole-body MR scanners. Using a T2/T1-weighted 3D FIESTA sequence (and a 3D FIESTA-C sequence at 3 T to avoid susceptibility artifacts) a resolution of 0.234 x 0.234 x 1.5 mm(3) was achieved in vivo. Structural parameters analogous to standard bone histomorphometry were determined in femoral head and trochanter regions of interest. Bone mineral density (BMD) measurements were also obtained using dual-energy X-ray absorptiometry (DXA) for the femoral trochanter in the same subjects. The bone structure of the proximal femur is substantially better depicted at 3 T than at 1.5 T. Correlation between the structural parameters obtained at both field strengths was up to R =0.86 for both the femoral head and the trochanteric region. However, the resolution of the images limits the application of 3D structural analysis, making the assessment more akin to 2D textural measures, which may be correlated to histomorphometric but are not identical measures. This feasibility study establishes the potential of MRI as a means of imaging proximal femur structure, and improvements in technique and resolution enhancements are warranted.

Adult↗
PubMed1999

The prevalence and distribution of white-matter changes on different MRI pulse sequences in a post-stroke cohort.

No uniform criteria currently exist for rating white-matter (WM) high-signal foci on MRI. Ratings are based on descriptive terms, different pulse sequences and different WM areas. Reports on the prevalence and clinical correlates of high-signal foci have been contradictory. We wanted to examine the contribution of the pulse sequence and WM area on rating WM changes. We analysed WM changes separately on T2-, protondensity (PD)- and T1-weighted images in periventricular, subcortical, watershed area and deep WM. The difference between T2- and PD-weighted images was significant for frontal caps, counting small foci or analysing subcortical changes. T1-weighted images showed significantly less change, but the number of foci detected was greater than previously thought. The prevalence of WM high-signal foci was greatest in the watershed zone and smallest in the subcortical area. There was a significant correlation between foci in different areas.

Aged↗
PubMed2006

Piezophilic adaptation: a genomic point of view.

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. As oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. One of the key environment variables that influences the life and evolution of deep-sea organisms is high pressure. This extreme widespread condition requires specific adaptations, the nature of which remains largely unknown. Recent advances in genomic approaches, such as in sequencing technologies and global expression profiling, are rapidly increasing the data available to understand microbial evolution, biochemistry, physiology and diversity. This review summarises the analysis of the results published so far about microbial high pressure adaptation from a genomic point of view. Understanding high pressure adaptation mechanisms is not just a scientific exercise but has important biotechnological implications. For example, hydrostatic pressure is a reality for food science and technology, both for food preparation and preservation. An understanding of the effects of pressure on biomolecules will expand its use in the medical, industrial and biotechnological fields.

Acclimatization↗
PubMed2002

Structure and phylogeny of the crustacean hyperglycemic hormone and its precursor from a hydrothermal vent crustacean: the crab Bythograea thermydron.

The structure of a well-known neurohormone involved in homeostasis regulation and stress response, the crustacean hyperglycemic hormone, was investigated in the deep-sea hydrothermal vent crab Bythograea thermydron. The neuropeptide was isolated from neurohemal organs (sinus glands) and its biological activity checked using an homologous bioassay. Partial amino acid sequence was established by a combination of Edman chemistry and mass spectrometry. Then, the sequence of the cDNA encoding the hormone precursor was determined. The preprohormone is composed of a 29 amino acid signal peptide, followed by a 41 amino acid associated peptide flanking the 72 amino acid hyperglycemic hormone. Comparison of these data with other known crab hyperglycemic hormone and prohormone sequences was performed using phylogenetic analysis methods.

Amino Acid Sequence↗
PubMed2002

Crystal structure of the human TbetaR2 ectodomain--TGF-beta3 complex.

Transforming growth factor-beta (TGF-beta) is the prototype of a large family of structurally related cytokines that play key roles in maintaining cellular homeostasis by signaling through two classes of functionally distinct Ser/Thr kinase receptors, designated as type I and type II. TGF-beta initiates receptor assembly by binding with high affinity to the type II receptor. Here, we present the 2.15 A crystal structure of the extracellular ligand-binding domain of the human TGF-beta type II receptor (ecTbetaR2) in complex with human TGF-beta3. ecTbetaR2 interacts with homodimeric TGF-beta3 by binding identical finger segments at opposite ends of the growth factor. Relative to the canonical 'closed' conformation previously observed in ligand structures across the superfamily, ecTbetaR2-bound TGF-beta3 shows an altered arrangement of its monomeric subunits, designated the 'open' conformation. The mode of TGF-beta3 binding shown by ecTbetaR2 is compatible with both ligand conformations. This, in addition to the predicted mode for TGF-beta binding to the type I receptor ectodomain (ecTbetaR1), suggests an assembly mechanism in which ecTbetaR1 and ecTbetaR2 bind at adjacent positions on the ligand surface and directly contact each other via protein--protein interactions.

Amino Acid Sequence↗
PubMed2001

Deep-Earth reactor: nuclear fission, helium, and the geomagnetic field.

Geomagnetic field reversals and changes in intensity are understandable from an energy standpoint as natural consequences of intermittent and/or variable nuclear fission chain reactions deep within the Earth. Moreover, deep-Earth production of helium, having (3)He/(4)He ratios within the range observed from deep-mantle sources, is demonstrated to be a consequence of nuclear fission. Numerical simulations of a planetary-scale geo-reactor were made by using the SCALE sequence of codes. The results clearly demonstrate that such a geo-reactor (i) would function as a fast-neutron fuel breeder reactor; (ii) could, under appropriate conditions, operate over the entire period of geologic time; and (iii) would function in such a manner as to yield variable and/or intermittent output power.

Earth, Planet↗
PubMed2001

Neural activity profiles of the neocortex and superior colliculus after bimodal sensory stimulation.

Current efforts at functional mapping of multisensory neurons are hampered by the need for both cellular-level resolution and the separate visualization of activity by different sensory cues. We have used a recently developed technique that exploits the differential time course of zif268 mRNA versus protein induction in neurons after sensory stimulation. Adult male rats were visually and acoustically deprived and then exposed to one of the following stimulation sequences: (i) no sensory stimulation; (ii) 2 h visual stimulation followed by 30 min auditory stimulation; (iii) 2 h auditory stimulation followed 30 min of visual stimulation; and (iv) 2 h compound visual and auditory stimulation. The neocortex and superior colliculus (SC) were then processed for fluorescent immunocytochemistry and in situ hybridization for staining of Zif268 protein and mRNA products. We have found that activity patterns in primary visual and auditory cortices were in accord with the sequence of the compound stimulus. We also show that SC superficial layers contained a pool of exclusively unimodal neurons, similar to that of visual cortex. Activity patterns of deep SC layers contained multimodal neurons with varying degrees of visual and auditory convergence. The deep SC layers also showed that auditory processing was largely carried out by a small, bimodal group of neurons whereas visual processing was coordinated by both a large unimodal and a small bimodal pool of neurons.

Acoustic Stimulation↗
PubMed2003

Dialister invisus sp. nov., isolated from the human oral cavity.

Six strains of anaerobic, Gram-negative coccobacilli isolated from the root canals of patients with endodontic infections (five strains) and from a deep periodontal pocket (one strain) were subjected to a comprehensive range of phenotypic and genetic tests and were found to comprise a homogeneous group. Following 16S rRNA gene sequence analysis, they were found to be most closely related to Dialister pneumosintes, with 93 % sequence similarity between the two taxa. A novel species, Dialister invisus sp. nov., is proposed. Biochemically, the species is largely unreactive and is asaccharolytic, with only traces of acetate and propionate detected as metabolic end-products. The G+C content of the DNA of D. invisus strains is 45-46 mol%. The type strain is E7.25(T) (=CCUG 47026(T)=DSM 15470(T)).

Bacterial Proteins↗
PubMed1998

Evolutionary origins of the vertebrate dentition: phylogenetic patterns and developmental evolution.

The theory that teeth evolved from dermal denticles linked with the origin of jaws no longer accounts for the diversity of new data emerging from the fossil record. We have reviewed oropharyngeal dental patterns in all fossil groups of early vertebrates to establish the primitive condition, in order to understand the polarity of change. The evolutionary precedence of dermal denticles before teeth now seems less likely; both may be alternative manifestations of a common morphogenetic system. This developmental system involves regulatory changes affecting the odontode, a fundamental exoskeletal unit, and can explain skeletal diversity. However, tooth and denticle differences may have diverged at loci deep within vertebrate phylogeny, as real differences exist between them. Teeth were conceived as evolving from non-growing odontodes with regulation of precise increase in size, position, sequence of time of development, and polarity of shape. A characteristic feature of teeth is the ability to replace from a developing sequence, programmed with these parameters, prior to demand. Tooth whorls, a feature of denticles in the oropharyngeal region, may be regarded as a preadaptation of this tooth replacement mechanism. The new fossil evidence suggests that teeth may have evolved from these more specialised oropharyngeal denticles in agnathan vertebrates.

Animals↗
PubMed2007

Calcium indicators based on calmodulin-fluorescent protein fusions.

Calmodulin (CaM) is an ubiquitous protein involved in Ca2+-mediated signal transduction. On Ca2+ influx, CaM acquires a strong affinity to various cellular proteins with one or more CaM recognition sequences, resulting in the onset or termination of Ca2+-regulated cascades. Through nuclear magnetic resonance and crystallographic structural studies of these Ca2+-CaM complexes, we have gained a deep understanding of CaM target recognition mechanisms. One immediate application is the creation of protein-based Ca2+ sensors using CaM complexes and green fluorescent proteins, previously named "chameleon." The major advantage of chameleons is that they can be expressed in single cells and targeted to the specific organelles or tissues to measure localized Ca2+ changes. This chapter describes the methods involved in cloning chameleons, characterizing their biochemical and biophysical properties, and imaging them in single cells using a digital fluorescence microscope.

Calcium↗
PubMed2000

Barriers to gene flow in Embiotoca jacksoni, a marine fish lacking a pelagic larval stage.

Marine species generally show high dispersal capabilities, which should be accompanied by high levels of gene flow and low speciation rates. However, studies that focused on the relationship between dispersal and gene flow in marine fishes have been inconclusive. This study focuses on the black surfperch, Embiotoca jacksoni, a temperate reef fish that lacks a pelagic larval stage and lives on almost continuous reefs along the California and Baja California coasts. Mitochondrial control-region sequences from 240 individuals were obtained, and phylogeographic patterns were analyzed. A major phylogeographic break was found at Santa Monica Bay, a sandy expanse that prevents adult dispersal. Deep water separating the southern California Channel Islands was also found to be a major barrier to gene flow. Minor phylogeographic breaks were also detected in the Big Sur/Morro Bay and in the Punta Eugenia/Guerrero Negro regions, but none in the Point Conception region. Gene flow levels in E. jacksoni were found to be almost identical to those of another species with limited dispersal, Acanthochromis polyacanthus, thus indicating that the lack of a pelagic larval stage combined with barriers to adult dispersal may have had similar effects on these two species.

Animals↗
PubMed2002

[The Top Wire Appliance bracket: tooth movement and friction].

The TWA (Top Wire Appliance) bracket enables a vertical insertion of the rectangular orthodontic archwire. This updated biomechanical evolution of the TWA technique promotes corrections during the first therapeutic stages of a fixed treatment. This bracket has been designed to take full advantage of the properties of shape memory archwires, reducing chairtime and making deep bite correction easier, dental rotations, alignment, leveling and stabilization, thanks to the rigidity of the vertically inserted arch, working heightwise. Progressive tightening ligature, adapted to the therapeutic sequence in progress is an element of biomechanics in TWA technique.

Biomechanical Phenomena↗
PubMed1994

Application of a valveless anesthesia circuit for deep diving.

The Mapleson E breathing circuit used in anesthesia has no valves or CO2-absorbent canisters and thus entails low resistance to breathing and has low requirements for fresh gas flow (FGF). The authors investigated whether these advantages would make a circuit, modified for hyperbaric use, able to support ventilation during heavy work on the surface and at deep depths with reduced FGF rates. The current recommended FGF for free-flowing diving circuits is 170 liters/min. Six Navy divers participated in 10-min graded exercise sequences, peak workload 220 W. Measurements were made of inspired and end-tidal concentrations of CO2, tidal volume, respiratory rate, and CO2 production at both sea level and 2.7 MPa dry environment. At sea level, all six divers were able to finish their exercises using the modified circuit with all tested rates of FGF. At 2.7 MPa the exercise sequence could be finished by all subjects when FGF was 170 liter/min and by five subjects when FGF was 127.5 liter/min, but high end-tidal CO2 measurements and hypercapnia symptoms were common at 127.5 liter/min. None of the subjects was able or allowed to finish the exercise sequence when FGF was 85 liter/min. Lower work-loads of 75 and 150 W for up to 4 min were completed easily by all subjects at all three rates of FGF. We conclude that this circuit concept warrants further study because it requires lower FGF than is currently used with open-circuit helmets and is valveless; how much of a reduction in FGF could be tolerated with heavy work at depths such as 2.7 MPa requires further study.

Adult↗
PubMed1998

Epidermolysis bullosa, pyloric atresia, aplasia cutis congenita: histopathological delineation of an autosomal recessive disease.

The simultaneous appearance of epidermolysis bullosa and pyloric atresia (EB-PA) is recognized as an autosomal recessive disease; however, the coappearance of EB-PA and aplasia cutis congenita (ACC) has not been delineated as a defined entity. The aim of this study was to analyze clinically and histopathologically eight cases with EB-PA-ACC belonging to an extended Bedouin family to gain insight into the cause and pathophysiology of the disease. All affected infants were found to have mixed skin lesions, including blisters and patchy lack of skin. Almost all of them (seven of eight) also had intestinal obstructions, especially pyloric atresia or stenosis. Skin lesions involved all skin layers with marked dystrophic changes. The intestinal obstruction was the result of overproliferation of connective tissue. In view of the clinical and histopathological findings, it is postulated that the condition is caused by an autosomal recessive gene affecting the integrity of the basement membrane and hemidesmosomes and the control of the normal process of fibrosis occurring during the course of wound healing. The sequence of events is initiated by the separation of the epidermis or the intestinal mucosal layer. Then, inflammatory reaction takes place and proceeds with massive fibrosis penetrating the deep layers and causing damage of skin and obstruction of the intestinal lumen. In view of the recent findings regarding the molecular basis of EB-PA, the described phenotype may result from a mutation in one of the integrin genes.

Ectodermal Dysplasia↗
PubMed1994

Molecular basis for sequence selective DNA alkylation by (+)- and ent-(-)-CC-1065 and related agents: alkylation site models that accommodate the offset AT-rich adenine N3 alkylation selectivity.

A detailed evaluation of the DNA alkylation selectivity of (+)-CC-1065, ent-(-)-CC-1065 and a series of aborted and extended analogs possessing the CPI alkylation subunit is detailed and the refinement of a model that accommodates the offset AT-rich adenine N3 alkylation selectivity of the enantiomeric agents is presented. The natural enantiomers bind in the minor groove in the 3'-->5' direction starting from the adenine N3 alkylation site across a 2 base (N-BOC-CPI; i.e. 5'-AA), 3.5 base (CPI-CDPI1/CPI-PDE-I1; i.e. 5'-AAA), 5 base (CC-1065/CPI-CDPI2; i.e. 5'-AAAAA) or 6.5 base (CPI-CDPI3; i.e. 5'-AAAAAA) AT-rich site. In contrast, the unnatural enantiomers bind in the reverse 5'-->3' direction in the minor groove and the binding site necessarily starts at the first 5' base preceding the adenine N3 alkylation site and extends across the alkylation site to the adjacent 3' bases covering an AT-rich site of 2 bases (N-BOC-CPI; e.g., 5'-AA), 5 bases (CC-1065/CPI-CDPI2; eg. 5'-AAAAA), or 6.5 bases (CPI-CDPI3; e.g. 5'-AAAAAA). Notably, the model accommodates the unusual observation that both enantiomers of N-BOC-CPI alkylate the same sites within duplex DNA (5'-AA > 5'-TA) and the required reversed binding orientation of the enantiomeric agents. The reversed binding orientation is required to permit access to the electrophilic cyclopropane and the resulting offset AT-rich alkylation selectivity is the natural consequence of the diastereomeric relationship of the adducts. Three dimensional models of the natural and unnatural enantiomer alkylations are presented which clearly illustrate the offset binding sites. A fundamentally simple model for the CC-1065 DNA alkylation reaction, that accommodates the behavior of both enantiomers, is provided in which the sequence selectivity is derived from the noncovalent binding selectivity of the agents preferentially in the narrower, sterically more accessible AT-rich minor groove, the inherent steric accessibility to the adenine N3 alkylation site that accompanies deep penetration of the agent into the minor groove within an AT-rich site, and the 2 base-pair (N-BOC-CPI), 3.5 base-pair (CPI-PDE-I1/CPI-CDPI1), 5 base-pair (CC-1065/CPI-CDPI2), or 6.5 base-pair (CPI-CDPI3) site size required to permit agent binding in the minor groove at the alkylation site.(ABSTRACT TRUNCATED AT 400 WORDS)

Alkylation↗
PubMed2006

Deep biosphere-related bacteria within the subsurface of tidal flat sediments.

Biogeochemical and microbiological processes in the upper sediment layers of tidal flats were analysed in many investigations, while deeper zones remained largely unexplored. Therefore, denaturant gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments along the depth profile of up to 5.5 m-long sediment cores was performed in comparison with lithological and geochemical parameters. The investigation revealed that different compartments of the sediment columns were characterized by specific microbial communities. These compartments were analysed by sequencing of 113 DGGE bands. The upper layers down to 160-200 cm were dominated by gamma- and delta-Proteobacteria representing more than 60% of the total number of phylotypes. Underneath, a striking shift in community composition was observed, as the Proteobacteria were replaced by Chloroflexi with more than 60% of all sequences. As sulfate was still available as an electron acceptor in these layers, the abundance of Chloroflexi might be promoted by the electron donor or the quality of the carbon source. The dominance of this group, previously known as green non-sulfur bacteria, indicates the presence of a typical deep-biosphere microbial community in relatively young subsurface sediments. Thus, tidal flats might offer a convenient possibility to study and understand certain aspects of the deep biosphere in general.

Bacteria↗
PubMed2005

Fastidiosipila sanguinis gen. nov., sp. nov., a new Gram-positive, coccus-shaped organism from human blood.

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6 % O(2). Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al., Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15 % or more were observed between the unidentified bacterium and all other recognized species within this and related rRNA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp. nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (=CIP 108292(T)).

Aged↗
PubMed2003

Recognition of accessory protein motifs by the gamma-adaptin ear domain of GGA3.

Adaptor proteins load transmembrane protein cargo into transport vesicles and serve as nexuses for the formation of large multiprotein complexes on the nascent vesicles. The gamma-adaptin ear (GAE) domains of the AP-1 adaptor protein complex and the GGA adaptor proteins recruit accessory proteins to these multiprotein complexes by binding to a hydrophobic motif. We determined the structure of the GAE domain of human GGA3 in complex with a peptide based on the DFGPLV sequence of the accessory protein Rabaptin-5 and refined it at a resolution of 2.2 A. The leucine and valine residues of the peptide are partly buried in two contiguous shallow, hydrophobic depressions. The anchoring phenylalanine is buried in a deep pocket formed by the aliphatic portions of two conserved arginine residues, along with an alanine and a proline, illustrating the unusual function of a cluster of basic residues in binding a hydrophobic motif.

ADP-Ribosylation Factors↗