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At least 1,315 records · Page 73Linked to original sources
PubMed2002

The 1.5 A crystal structure of a highly selected antiviral T cell receptor provides evidence for a structural basis of immunodominance.

Despite a potential repertoire of >10(15) alphabeta T cell receptors (TcR), the HLA B8-restricted cytolytic T cell response to a latent antigen of Epstein-Barr virus (EBV) is strikingly limited in the TcR sequences that are selected. Even in unrelated individuals this response is dominated by a single highly restricted TcR clonotype that selects identical combinations of hypervariable Valpha, Vbeta, D, J, and N region genes. We have determined the 1.5 A crystal structure of this "public" TcR, revealing that five of the six hypervariable loops adopt novel conformations providing a unique combining site that contains a deep pocket predicted to overlay the HLA B8-peptide complex. The findings suggest a structural basis for the immunodominance of this clonotype in the immune response to EBV.

Amino Acid Sequence↗
PubMed2004

A model of the ACE2 structure and function as a SARS-CoV receptor.

The angiotensin-converting enzyme 2 (ACE2) is an important regulator of the renin-angiotensin system and was very recently identified as a functional receptor for the SARS virus. The ACE2 sequence is similar (sequence identities 43% and 35%, and similarities 61% and 55%, respectively) to those of the testis-specific form of ACE (tACE) and the Drosophila homolog of ACE (AnCE). The high level of sequence similarity allowed us to build a robust homology model of the ACE2 structure with a root-mean-square deviation from the aligned crystal structures of tACE and AnCE less than 0.5A. A prominent feature of the model is a deep channel on the top of the molecule that contains the catalytic site. Negatively charged ridges surrounding the channel may provide a possible binding site for the positively charged receptor-binding domain (RBD) of the S-glycoprotein, which we recently identified [Biochem. Biophys. Res. Commun. 312 (2003) 1159]. Several distinct patches of hydrophobic residues at the ACE2 surface were noted at close proximity to the charged ridges that could contribute to binding. These results suggest a possible binding region for the SARS-CoV S-glycoprotein on ACE2 and could help in the design of experiments to further elucidate the structure and function of ACE2.

Amino Acid Sequence↗
PubMed1998

Melanopsin: An opsin in melanophores, brain, and eye.

We have identified an opsin, melanopsin, in photosensitive dermal melanophores of Xenopus laevis. Its deduced amino acid sequence shares greatest homology with cephalopod opsins. The predicted secondary structure of melanopsin indicates the presence of a long cytoplasmic tail with multiple putative phosphorylation sites, suggesting that this opsin's function may be finely regulated. Melanopsin mRNA is expressed in hypothalamic sites thought to contain deep brain photoreceptors and in the iris, a structure known to be directly photosensitive in amphibians. Melanopsin message is also localized in retinal cells residing in the outermost lamina of the inner nuclear layer where horizontal cells are typically found. Its expression in retinal and nonretinal tissues suggests a role in vision and nonvisual photoreceptive tasks, such as photic control of skin pigmentation, pupillary aperture, and circadian and photoperiodic physiology.

Amino Acid Sequence↗
PubMed1998

Crystal structure of the anti-fungal target N-myristoyl transferase.

N-myristoyl transferase (NMT) catalyzes the transfer of the fatty acid myristate from myristoyl-CoA to the N-terminal glycine of substrate proteins, and is found only in eukaryotic cells. The enzyme in this study is the 451 amino acid protein produced by Candida albicans, a yeast responsible for the majority of systemic infections in immuno-compromised humans. NMT activity is essential for vegetative growth, and the structure was determined in order to assist in the discovery of a selective inhibitor of NMT which could be developed as an anti-fungal drug. NMT has no sequence homology with other protein sequences and has a novel alpha/beta fold which shows internal two-fold symmetry, which may be a result of gene duplication. On one face of the protein there is a long, curved, relatively uncharged groove, at the center of which is a deep pocket. The pocket floor is negatively charged due to the vicinity of the C-terminal carboxylate and a nearby conserved glutamic acid residue, which separates the pocket from a cavity. These observations, considered alongside the positions of residues whose mutation affects substrate binding and activity, suggest that the groove and pocket are the sites of substrate binding and the floor of the pocket is the catalytic center.

Acyl Coenzyme A↗
PubMed1996

Two mathematically defined expressive language structures in humans and chimpanzees.

Two expressive language structures have been identified mathematically in humans and chimpanzees. The first was found by measuring the waiting times between the invocation of new words or symbols, which consistently yielded individually characteristic rate constants and descending exponential curves that reflect a stochastically lawful Poisson process. The second was discovered by calculating the cumulative informational complexity (entropy) of word usage, which in all cases was a deterministically lawful logarithmic function of the number of words used to a given point in a communicative sequence. Individual and species differences in how this law is obeyed also characterized the sample. The results from the apes resembled those from the works of human poets like Shakespeare. The findings speak for deep, natural, unlearned expressive language structures in apes that are comparable to those seen in humans.

Animals↗
PubMed2000

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae).

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution.

Animals↗
PubMedDate not supplied

Evaluation of magnetic resonance imaging techniques in the equine digit.

An anatomic study of the equine digit using magnetic resonance imaging (MRI) was performed. Seventeen isolated forelimbs and one hindleg of nine warmblood horses were imaged in transverse, sagittal, and dorsal planes with a 1.5 Tesla magnet using T1-, T2- proton density-weighted spin echo sequences as well as T2 gradient echo sequences. One scan plane in each horse was compared with corresponding anatomic and histologic sections. The best imaging planes to visualize various anatomic structures were determined. Fibrocartilage was visualized in the insertion of the deep digital flexor tendon and the suspensory ligament as well as in the distal sesamoidean ligaments. The correlation of MRI images with anatomic and histologic sections confirmed that all of the anatomic structures in the equine digit could be evaluated in PD and T2 studies.

Animals↗
PubMed1998

Genotypic characterization of Actinobacillus actinomycetemcomitans isolated from periodontitis patients by arbitrarily primed polymerase chain reaction.

Actinobacillus actinomycetemcomitans is one of the most suspected pathogens in the initiation and progression of juvenile periodontitis and severe adult periodontitis. The aim of the present study was to investigate the genotypic characterization of A. actinomycetemcomitans using arbitrarily primed polymerase chain reaction (AP-PCR). AP-PCR was applied to 143 A. actinomycetemcomitans strains, including 8 reference strains and 135 clinical strains isolated from 43 unrelated Japanese periodontitis patients. The DNA fragment patterns obtained using a single 10-mer primer with random sequence (OPA-07) for these strains allowed the recognition of 10 distinct AP-PCR groups that correlated to some extent with serotypes. AP-PCR group VIII was significantly (P < 0.05) observed in deep (> 5 mm) periodontal pockets. Group II was exclusively detected in deep pockets. However, a clear relationship was not observed between AP-PCR genotypes and various periodontal status. Only one genotype was found within individual oral cavity/single-infected site, except one case in which the patient harbored two AP-PCR genotypes. The AP-PCR patterns of the A. actinomycetemcomitans isolates recovered from the site after periodontal treatment remained identical. These results demonstrate genetic diversity among the investigated population and a clonal nature in a periodontal patient of A. actinomycetemcomitans by AP-PCR. Furthermore, it could be inferred that a certain AP-PCR genotype(s) of A. actinomycetemcomitans is more important in the pathogenesis of periodontal diseases.

Adolescent↗
PubMedDate not supplied

Mast cells in the murine oral mucosa are of the connective tissue-type.

The distribution, histochemistry, and functional properties of oral (cheeks, soft palate, and tongue) mast cells (MC) was compared to those of peritoneal, cutaneous, and intestinal MC. The ultrastructure of oral MC was also studied. Fresh tissue and peritoneal cells were fixed either in absolute ethanol or in periodate lysine 2% paraformaldehyde and embedded in paraffin. For electron microscopy, specimens were fixed in 1% glutaraldehyde in formol and embedded in epon. Serial paraffin sections were stained with Giemsa, toluidine blue (0.5% and 0.005%), astra blue/safranin, alcian blue/safranin, berberine sulfate, safranin alone, and fluorescein-labelled avidin to determine the staining properties, incidence, and distribution of both connective tissue-type MC and mucosal-type MC at these sites. Oral, peritoneal, and cutaneous MC granules stained positively with Giemsa, toluidine blue (0.5 and 0.005%), alcian blue, astra blue, berberine sulfate, safranin used alone, and avidin-FITC, but failed to stain with safranin when used in sequence with alcian blue or astra blue. Intestinal MC stained with the same dyes as oral MC except for 0.005% toluidine blue, berberine sulfate, and safranin. Oral and lingual MC are located in the deep lamina propria, around blood vessels and salivary secretory ducts, in close association with nerve endings, and between muscle fibers. In the cheeks and soft palate, but rarely in the tongue, MC were also found around and between glandular acini. MC constitute a predominant immune component in oral tissues, being more numerous in the soft palate and cheek-labial junction (4800/mm3) and in the tongue (4000/mm3), than in the duodenal mucosa (2650/mm3).(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1989

[The dilemma of the 2d primary molar].

Extensive carious lesions in primary molars often confront the dentist with a dilemma: extraction or restoration. The primary molar constitutes an important element in the development of the dentition. If extraction is considered, the dentist should be aware of the possible risks towards malocclusion or malposition. In order to understand these consequences a brief summary of normal dentition development is given, followed by a description of factors influencing development of dentition after premature extraction of a second primary molar. Premature extraction causes a disturbance in the eruption of the successor and migration of the neighbouring teeth. The eruption of the bicuspid can be delayed or accelerated according to the stage of root formation. The rate, amount and direction of migration depends on the extracted element, time of loss, spacing or crowding, eruption sequence, dental relationship, intercuspation, interaction of soft tissues and dental arch, supra-occlusion and the leeway space. To conclude the treatment modalities of pulp pathologies in primary molars are outlined. In children with deep carious lesions a treatment plan involves the child's medical history and social development as well as orthodontic, preventive and restorative aspects.

Child↗
PubMed1998

Molecular systematics of shrimp (Decapoda: Bresiliidae) from deep-sea hydrothermal vents, I: Enigmatic "small orange" shrimp from the Mid-Atlantic Ridge are juvenile Rimicaris exoculata.

Independent species descriptions of a "small orange" caridean shrimp found at deep-sea hydrothermal vents along the Mid-Atlantic Ridge have created the synonymous names Iorania concordia Vereshchaka 1996b and Rimicaris aurantiaca Martin et al. 1997. Our genetic analyses involving allozymes and mitochondrial DNA sequences reveal that the "small orange" shrimp described in these studies are a juvenile form of Rimicaris exoculata Williams and Rona, a species commonly found at these sites. In light of this result, we reconsider the life history and ecologic characteristics of juvenile and adult stages of Rimicaris exoculata.

Animals↗
PubMed1997

TGF-beta receptor type II and fetuin in the developing sheep neocortex.

Fetuin shows a characteristic pattern of distribution in the developing neocortex in many mammalian species. Its expression is confined to early-appearing cortical-plate and later subplate neurons. A short 19 amino-acid sequence of fetuin shows a degree of homology to an 18 amino-acid sequence of the TGF-beta type II receptor (TbetaR-II) and in vitro fetuin binds to members of the TGF-beta family of cytokines. It has been suggested that fetuin is the biologically significant antagonist of these cytokines. We have compared, using immunocytochemistry, the distribution pattern of TbetaR-II and fetuin in the developing neocortex of foetal sheep. TbetaR-II immunoreactivity first appears at around 40 days of gestation in the fetal sheep (E40, term in sheep is 150 days from conception), localised in two discreet bands: one just outside the cortical plate in the inner part of the marginal zone and one deep in the cortical plate in what becomes the transient subplate zone. By E70-E80, TbetaR-II is prominent in a population of subplate cells, whereas, by E120 only small patches of TbetaR-II-positive cells are visible, principally in pyramidal cells in layer VI. The developmental sequence of the staining pattern for TbetaR-II in the neocortex is complementary to that for fetuin, rather than overlapping with it. Double-labelling of fetuin and TbetaR-II shows some cellular co-localisation, especially at E60, but most fetuin-positive cells are not immunoreactive for TbetaR-II. Thus, fetuin's proposed role as an antagonist of TGF-beta cytokines and mimic of TbetaR-II is not consistent with the observed distribution of these two molecules in the developing neocortex of the foetal sheep.

Animals↗
PubMed1998

The genetic sequence of retinal development in the ciliary margin of the Xenopus eye.

The ciliary marginal zone is a perpetually self-renewing proliferative neuroepithelium at the perimeter of the retina in amphibians and fish. In the ciliary marginal zone (CMZ), cells are spatially ordered with respect to cellular development, deep stem cells being most peripheral and differentiating retinal progenitors being most central. This spatial gradient in the CMZ recapitulates embryonic retinogenesis and provides a powerful system to examine the relative order of gene expression during this process. A number of neurogenic and proneural genes have been described to have interacting roles in the development of the vertebrate nervous system, and so it is of major importance to put these genes in a hierarchical pathway. In no other system yet described are the developmental stages of neurogenesis arrayed so clearly in a spatial pattern as in the CMZ. We have therefore taken advantage of this system, using double in situ hybridizations on cross sections of the CMZ, to compare the spatial patterns of 15 proneural, neurogenic, and other genes involved in early and late phases of retinal development. In addition, we have positioned these expression patterns with respect to cell division. What emerges from this work is a spatial ordering of gene expression that predicts a genetic hierarchy governing vertebrate retinogenesis. By injecting messenger RNA for some of these genes into blastomeres of the Xenopus embryo and examining the effects on expression of the putative downstream genes, we have been able to corroborate some of the relationships between genes predicted to act sequentially.

Animals↗
PubMed2003

Digging deep--structure-function relationships in the melatonin receptor family.

The melatonin receptor family is a small group of receptors within the G protein-coupled receptor (GPCR) superfamily. The group comprises of three subtypes which bind melatonin and one member, the melatonin related receptor (MRR), that shares >40% sequence identity with the other melatonin receptors but does not bind melatonin. Identification of two subtypes expressed in the mouse suprachiasmatic nucleus, one of which (MT1) inhibits neuronal firing and the other (MT2) mediating the phase advancing properties of melatonin has given renewed interest to the development of subtype specific compounds for each of the mammalian melatonin receptors. Towards this goal site-directed and chimaeric receptor mutagenesis studies have been performed which have provided some insight into the structure-function relationships of the melatonin receptors. Furthermore, these studies may lead to the identification of the ligand for the orphan MRR.

Amino Acid Sequence↗
PubMedDate not supplied

Fatal group A Streptococcal toxic shock-like syndrome in a child with varicella: report of the first well documented case with detection of the genetic sequences that code for exotoxins spe A and B, in São Paulo, Brazil.

A previously healthy seven-year-old boy was admitted to the intensive care unit because of toxaemia associated with varicella. He rapidly developed shock and multisystem organ failure associated with the appearance of a deep-seated soft tissue infection and, despite aggressive treatment, died on hospital day 4. An M-non-typable, spe A and spe B positive Group A Streptococcus was cultured from a deep soft tissue aspirate. The criteria for defining Streptococcal toxic shock-like syndrome were fulfilled. The authors discuss the clinical and pathophysiological aspects of this disease as well as some unusual clinical findings related to this case.

Bacterial Toxins↗
PubMed2005

The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths.

We determined the whole mitochondrial genome sequence for Indonesian coelacanth Latimeria menadoensis. The genome content and organization were identical to that of typical vertebrates including Comoran coelacanth, Latimeria chalumnae. The overall nucleotide differences between the two species (excluding the control region) was 4.28%. The divergence time between the two species was estimated using whole mitochondrial genome data from the two coelacanths and 26 actinopterygians that represent major actinopterygian lineages plus an outgroup. Partitioned Bayesian analyses were conducted with the two data sets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding ND6 gene) and concatenated nucleotide sequences from 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The molecular clock analysis was also conducted with the concatenated amino acid sequences from the 12 protein-coding genes after removing faster or more slowly evolving sequences. Using the sarcopterygian-actinopterygian split as a calibration point (450 Mya), divergence time estimation between L. menadoensis and L. chalumnae fell in the range of 40-30 Mya, which is much older than those of the previous studies (<6.3 Mya). Assuming that the most recent ancestor of Latimeria was distributed continuously along the deep coasts of Africa through Eurasia, our estimate is in agreement with the hypothesis that the collision of India with Eurasia (50 Mya) and the subsequent siltation caused by the formation of major rivers resulted in a coelacanth habitat disjunction that allowed populations on either side of India to diverge.

Amino Acid Sequence↗
PubMed2006

Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin.

The community compositions of Bacteria and Archaea were investigated in deep, sub-seafloor sediments from the highly productive Peru Margin (ODP Leg 201, sites 1228 and 1229, c. 25 km apart) down to nearly 200 m below the seafloor using taxonomic (16S rRNA) and functional (mcrA and dsrA) gene markers. Bacterial and archaeal groups identified from clone libraries of 16S rRNA gene sequences at site 1229 agreed well with sequences amplified from bands excised from denaturing gradient gel electrophoresis (DGGE) depth profiles, with the exception of the Miscellaneous Crenarchaeotic Group (MCG). This suggested that the prokaryotic community at site 1228, obtained from DGGE profiling alone, was reliable. Sites were dominated by Bacteria in the Gammaproteobacteria, Chloroflexi (green non-sulphur bacteria) and Archaea in the MCG and South African Gold Mine Euryarchaeotic Group, although community composition changed with depth. The candidate division JS1 was present throughout both sites but was not dominant. The populations identified in the Peru Margin sediments consisted mainly of prokaryotes found in other deep subsurface sediments, and were more similar to communities from the Sea of Okhotsk (pelagic clays) than to those from the low organic carbon Nankai Trough sediments. Despite broad similarities in the prokaryotic community at the two sites, there were some differences, as well as differences in activity and geochemistry. Methanogens (mcrA) within the Methanosarcinales and Methanobacteriales were only found at site 1229 (4 depths analysed), whereas sulphate-reducing prokaryotes (dsrA) were only found at site 1228 (one depth), and these terminal-oxidizing prokaryotes may represent an active community component present at low abundance. This study clearly demonstrates that the deep subsurface sediments of the Peru Margin have a large diverse and metabolically active prokaryotic population.

Archaea↗
PubMed2005

Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae).

The importance of the cyanobacteria Prochlorococcus and Synechococcus in marine ecosystems in terms of abundance and primary production can be partially explained by ecotypic differentiation. Despite the dominance of eukaryotes within photosynthetic picoplankton in many areas a similar differentiation has never been evidenced for these organisms. Here we report distinct genetic [rDNA 18S and internal transcribed spacer (ITS) sequencing], karyotypic (pulsed-field gel electrophoresis), phenotypic (pigment composition) and physiological (light-limited growth rates) traits in 12 Ostreococcus strains (Prasinophyceae) isolated from various marine environments and depths, which suggest that the concept of ecotype could also be valid for eukaryotes. Internal transcribed spacer phylogeny grouped together four deep strains isolated between 90 m and 120 m depth from different geographical origins. Three deep strains displayed larger chromosomal bands, different chromosome hybridization patterns, and an additional chlorophyll (chl) c-like pigment. Furthermore, growth rates of deep strains show severe photo-inhibition at high light intensities, while surface strains do not grow at the lowest light intensities. These features strongly suggest distinct adaptation to environmental conditions encountered at surface and the bottom of the oceanic euphotic zone, reminiscent of that described in prokaryotes.

Chlorophyll↗