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At least 775 records · Page 43Linked to original sources
PubMed1993

Keratosis of the tympanic membrane and deep external auditory canal. A defect of auditory epithelial migration.

We have previously described the pathways of movement of epithelium on the tympanic membrane, showing that there are two discrete and separate zones. Four cases of keratosis of the tympanic membrane and deep external auditory canal are here reported. All patients complained of tinnitus and other aural symptoms. Sequences of otoscopic photography of daubs of dye placed on the tympanic membrane showed an abnormal anterior movement over the whole tympanic membrane in two cases and complete paralysis of movement in the two others. These findings suggest that the disorder arises from damage to basal epidermal cells caused by inflammation, which is probably due to infection. Treatment is by suction-stripping of keratin from the eardrum. Careful examination of the eardrum under magnification is required in all cases of tinnitus so as to detect this condition.

Aged↗
PubMedDate not supplied

Pitfalls in staging uterine neoplasm with imaging: a review.

This review analyzes current pitfalls in pretreatment staging of endometrial and cervical carcinoma with magnetic resonance imaging (MRI) based on a critical review of the literature. Technical, patient, and tumor-related characteristics were analyzed to improve further staging of uterine neoplasm with MRI. For endometrial carcinoma staging, contrast-enhanced dynamic imaging appears essential to avoid false-positive findings for deep myometrial invasion by better delineating tumor from normal myometrium. However, leiomyomas, adenomyosis, and grade 3 tumors provide difficulties in staging for pathologists and radiologists. Slice orientation perpendicular to the long axis of the cervical channel might improve false-negative findings for deep stromal invasion on T2-weighted images in endometrial and cervical cancer. Contrast-enhanced sequences do not improve diagnosis of parametrial or vaginal invasion in cervical cancer. Assessment of lymph node invasion by any imaging modality has limited sensitivity in detecting lymph node metastasis smaller than 5 mm. Knowledge of diagnostic criteria is critical to avoid false-negative findings for bladder wall invasion. Higher spatial resolution with dedicated multichannel pelvic phase array coils, smaller fields of view and section thickness, and careful comparison of T2-weighted and contrast-enhanced sequences are strategies that might avoid misinterpretation of pelvic MRI in staging uterine neoplasm.

Aged↗
PubMed2005

New MHC class Ia domain lineages in rainbow trout (Oncorhynchus mykiss) which are shared with other fish species.

Major histocompatibility complex (MHC) class Ia genes in salmonid fishes are encoded by a single locus with probably the highest allelic diversity ever described. Various combinations of very different domain lineages contribute to the diversity of alleles. An extensive PCR survey distinguishing most domain lineages and their combinations was established. This survey has practical value for researchers investigating salmonid MHC class Ia variation. In the present study it was used to find new domain lineages. Applied for 24 hatchery strains in Japan, the survey identified two new rainbow trout alpha1 lineages and one new rainbow trout alpha2 lineage. The alpha2 lineage and one of the alpha1 lineages had been described in Atlantic salmon, but the other alpha1 lineage is novel. The newly identified trout alpha1 lineages are evolutionary very old. The present study should be the most extensive description of very deep MHC class Ia lineages to date: six trout alpha1 lineages cluster with non-salmonid sequences whereas previous studies mentioned this for only two salmonid alpha1 lineages. Although exon-shuffling events significantly contributed to salmonid MHC class Ia variation, analysis of 800 trout siblings did not detect such events within a single generation.

Alleles↗
PubMed2025

A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.

PURPOSE: The Undiagnosed Diseases Network is a National Institutes of Health funded research study that aims to solve a broad clinical spectrum of challenging rare disease cases. Participants receive care from multiple clinical specialists, who collaborate to perform deep phenotyping and state-of-the-art multiomics analyses. As bioinformatics of short-read sequencing has matured, the discovery of repeat expansion disorders (REDs) is accelerating. REDs comprise approximately 60 characterized disorders, which exhibit a broad spectrum of phenotypes. Thus, a largely unbiased genome-wide approach in a phenotypically diverse sample will add to the diagnostic depth, explore the limits of short-read genome analysis, and establish novel candidate RED loci. METHODS: Here, we present a genome-wide analysis of repeat expansions conducted on 1018 genomes from the Undiagnosed Diseases Network. By leveraging 2 distinct bioinformatics tools, ExpansionHunter Denovo and STRling, we showed that repeat expansions can be accurately detected in short-read genomes. RESULTS: We demonstrated that a genotype-first approach can diagnose atypical cases of known REDs and provide valuable clinical insights. We present clinical details on participants with expansions in ATXN7, DMPK, FMR1, GLS, HTT, RFC1, AFF3, and MARCH6. Importantly, we highlight 2 cases of juvenile Huntington disease that were discovered through our analysis. Finally, we present a list of novel candidate short tandem repeats (TR) that could potentially be pathogenic if expanded. CONCLUSION: Importantly, our approach showcases the bioinformatic advancements in genome analysis for RED detection and highlights its practical applications.

Humans↗
PubMed2002

"Staphylococcus pettenkoferi," a novel staphylococcal species isolated from clinical specimens.

In this report we describe a novel species of coagulase-negative novobiocin susceptible staphylococci obtained from an epidemiologically unrelated blood culture and a wound infection. These isolates significantly differed from all other validated Staphylococcus species based on phenotypic characteristics and 16S rRNA gene sequencing. Both isolates had identical 16S rRNA sequences and phylogenetic trees constructed from evolutionary distances showed that this species formed a distinct and deep subline that was most closely related to members of the Staphylococcus saprophyticus cluster group (S. kloosii, S. gallinarum, S. arlettae, S. saprophyticus, S. xylosus, S. equorum, S. succinus and S. cohnii) and Staphylococcus auricularis. Furthermore these strains could each be distinguished from all other staphylococci based on at least one phenotypic trait. Therefore we propose the designation of "Staphylococcus pettenkoferi" a novel species of coagulase-negative staphylococci.

Adult↗
PubMed2004

The effect of information and behavioural training on endoscopy patients' clinical outcomes.

This study was designed to examine the effects of preparatory information and behavioural training on patients about to undergo an endoscopy procedure. Forty-five first-time endoscopy patients (aged 20-70 years), were randomly assigned to one of three groups (cognitive, cognitive/behavioural and control group). The cognitive group received a 12 min preparation with sensory and procedural information relating to the sensations and sequence of events associated with the endoscopy procedure. The cognitive/behavioural group received, in addition, instruction in deep breathing exercises, tongue depressor task and swallowing technique. Results indicated that patients in the two experimental conditions experienced significantly fewer signs of behavioural distress during endoscopy. The cognitive group required a significantly shorter time to induce the scope. There were no statistical differences between the groups however, for mood, physiological and anxiety measures, although a positive trend was evident for the two intervention groups.

Adult↗
PubMed2002

Genetic subdivision and biogeography of the Danubian rheophilic barb Barbus petenyi inferred from phylogenetic analysis of mitochondrial DNA variation.

The barb Barbus petenyi is a cyprinid widely distributed throughout the mountain regions in the Danube River basin. Phylogenetic analysis of the DNA sequence variation at the mitochondrial cytochrome b gene over much of this range yielded three deep-branching (5.9-9.4% average divergence), well-supported haplotype clades with mutually exclusive geographic distributions and divergence times estimated to be in the Tertiary. The clades did not form an altogether monophyletic group as the most divergent one coalesced more recently with haplotypes of phylogenetically close species than with the other B. petenyi haplotypes. This pattern was supported by bootstrap and log-likelihood Shimodaira-Hasegawa tests. The other two were sister clades, but their distinctiveness was supported by previous allozyme data. Hence, from a taxonomic point of view, the current recognition of B. petenyi is erroneous, as it does not represent a single evolutionary lineage, and we suggest that three species be recognized instead. Substantial phylogeographic differences were evident among the three putative species, the two more southerly ones displaying significant structure, which suggested that they each survived in several glacial refugia throughout the Pleistocene. The phylogeographic pattern of multiple populations of rheophilic barbs with a history of long-term persistence and separation within the Danube River basin is novel within fishes and provides a hypothesis against which phylogeographic patterns among other similarly distributed rheophilic species may be compared.

Animals↗
PubMed2005

Topography of diphtheria toxin A chain inserted into lipid vesicles.

The membrane-inserting T domain of diphtheria toxin aids the low-pH-triggered translocation of the catalytic A chain of the toxin across endosomal membranes. To evaluate the role of the isolated A chain in translocation, the topography of isolated A chain inserted into model membrane vesicles was investigated using a mixture either of dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol (DOPG) or of dimyristoleoylphosphatidylcholine (DMoPC) and DOPG. The latter mixture was previously found to promote deep insertion of the T domain. A series of single Cys mutants along the A chain sequence were labeled with bimane or BODIPY groups. After A chain insertion into model membranes, the location of these groups within the lipid bilayer was determined via bimane fluorescence emission lambda(max), binding of externally added anti-BODIPY antibodies, and a novel technique involving the comparison of the quenching of bimane fluorescence by aqueous iodide and membrane-associated 10-doxylnonadecane. The results show that in both DOPC- and DMoPC-containing bilayers, membrane-inserted residues all along the A chain sequence occupy shallow locations that are relatively exposed to the external solution. There were only small differences between A chain topography in the two different types of lipid mixtures. However, the behavior of the A chain in the two different lipid mixtures was distinct in that it strongly oligomerized in DMoPC-containing vesicles as judged by Trp fluorescence. In addition, A chain selectively induced fusion of the DMoPC-containing vesicles, and this may aid oligomerization by increasing the A chain/vesicle ratio. Fusion may also explain why A chain also selectively induced leakage of the contents of DMoPC-containing vesicles. We propose that isolated A chain is unlikely to be inserted in a transmembrane orientation, and thus its interaction with the T domain is likely to be critical for properly orienting the A chain within the bilayer in a fashion that allows translocation.

4-Chloro-7-nitrobenzofurazan↗
PubMed2005

Role of the unique peptide tail in hyperthermostable Aquifex aeolicus cochaperonin protein 10.

All known cochaperonin protein 10 (cpn10) molecules are heptamers of seven identical subunits noncovalently linked by beta-strand interactions. Cpn10 from the deep-branching, hyperthermophilic bacterium Aquifex aeolicus (Aacpn10) shows high homology with mesophilic and other thermophilic cpn10 sequences, except for a 25-residue C-terminal extension not found in any other cpn10. Prior to atomic structure information, we here address the role of the tail by biophysical means. A tail-lacking variant (Aacpn10-del25) also adopts a heptameric structure in solution and exhibits nativelike substrate-refolding activity. Thermal and chemical perturbations of both Aacpn10 and Aacpn10-del25, probed by far-UV circular dichroism, demonstrate that both proteins have high thermodynamic stability. Heptamer-monomer dissociation midpoints were defined by isothermal titration calorimetry; at 25 degrees C, the values for Aacpn10 and Aacpn10-del25 are within 2-fold of each other and close to reported midpoints for mesophilic cpn10 proteins. In contrast, the monomer stabilities for the A. aeolicus proteins are significantly higher than those of mesophilic homologues at 30 degrees C; thus, heptamer thermophily is a result of more stable monomers. Electron microscopy data reveals that Aacpn10-del25 heptamers are prone to stack on top of each other forming chainlike molecules; the electrostatic surface pattern of a structural model can explain this behavior. Taken together, the unique tail in Aacpn10 is not required for heptamer structure, stability, or function; instead, it appears to be an ancient strategy to avoid cochaperonin aggregation at extreme temperatures.

Bacteria↗
PubMed2005

Pre-oxygenation in the obese patient: effects of position on tolerance to apnoea.

BACKGROUND: In obese patients, reduced functional residual capacity exacerbated by supine position might decrease the effectiveness of pre-oxygenation and the tolerance to apnoea. The aim of this study was to compare the effect of body posture during pre-oxygenation, sitting or supine, on its effectiveness in obese patients. METHODS: Forty obese patients (BMI > or =35 kg m(-2)) undergoing surgery with general anaesthesia were randomly assigned to one of two groups: Group 1 (sitting, n=20) or Group 2 (supine, n=20). In the predetermined body position, pre-oxygenation was achieved with eight deep breaths within 60 s and an oxygen flow of 10 litre min(-1). After rapid sequence induction of anaesthesia in decubitus position, the trachea was intubated and the patient was left apneic and disconnected from the anaesthesia circuit until Sp(o2) decreased to 90%. The time taken for desaturation to 90% from the end of induction of anaesthesia was recorded. Arterial blood oxygen tension was measured before (baseline) and after pre-oxygenation. Values were compared with two-way anova and unpaired Student's t-test. RESULTS: Oxygen and carbon dioxide tensions were similar between groups, both at baseline and after pre-oxygenation. However, the mean time to desaturation to 90% was significantly longer in the sitting group compared with the supine group [mean (SD): 214 (28) vs 162 (38) s, P<0.05]. CONCLUSIONS: Pre-oxygenation in sitting position significantly extends the tolerance to apnoea in obese patients when compared with the supine position.

Adult↗
PubMed2002

Preparation of a crystallizable mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.

SelB is a bacterial elongation factor required for the decoding of a UGA stop codon together with a specific mRNA hairpin to selenocysteine. In attempts to crystallize Moorella thermoacetica SelB, a proteolysis process occurred and crystals of a proteolytic fragment were observed. The crystals, which appeared after a year, contained a C-terminal 30 kDa fragment containing the mRNA-binding domain. This fragment was reproduced through recloning. Crystals diffracting to 2.7 A were obtained.

Amino Acid Sequence↗
PubMed1995

Characterization of the endosymbiont of a deep-sea bivalve, Calyptogena soyoae.

We have purified DNA from gill tissue of a marine bivalve, Calyptogena soyoae, collected from the deep-sea cold seep communities in Sagami Bay, Japan. An rRNA gene was amplified, cloned, and sequenced. In situ hybridization revealed that the sequence is that of a bacterial endosymbiont within the gill of C. soyoae.

Animals↗
PubMed2001

Characterization of a highly thermostable alkaline phosphatase from the euryarchaeon Pyrococcus abyssi.

This work reports the first isolation and characterization of an alkaline phosphatase (AP) from a hyperthermophilic archaeon. An AP gene from Pyrococcus abyssi, a euryarchaeon isolated from a deep-sea hydrothermal vent, was cloned and the enzyme expressed in Escherichia coli. Analysis of the sequence showed conservation of the active site and structural elements of the E. coli AP. The recombinant AP was purified and characterized. Monomeric and homodimeric active forms were detected, with a monomer molecular mass of 54 kDa. Apparent optimum pH and temperature were estimated at 11.0 and 70 degrees C, respectively. Thus far, P. abyssi AP has been demonstrated to be the most thermostable AP, with half-lives at 100 and 105 degrees C of 18 and 5 h, respectively. Enzyme activity was found to be dependent on divalent cations: metal ion chelators inhibited activity, whereas the addition of exogenous Mg(II), Zn(II), and Co(II) increased activity. The enzyme was inhibited by inorganic phosphate, but not by molybdate and vanadate. Strong inhibitory effects were observed in the presence of thiol-reducing agents, although cysteine residues of the P. abyssi AP were not found to be incorporated within intra- or interchain disulfide bonds. In addition, P. abyssi AP was demonstrated to dephosphorylate linear DNA fragments with dephosphorylation efficiencies of 93.8 and 84.1% with regard to cohesive and blunt ends, respectively.

Alkaline Phosphatase↗
PubMedDate not supplied

In vitro and in vivo MR imaging of hyaline cartilage: zonal anatomy, imaging pitfalls, and pathologic conditions.

Hyaline cartilage plays an essential role in the maintenance of normal synovial joint function by reducing friction and distributing loads. Histologic analysis of hyaline cartilage reveals zonal variation in cellular morphology, proteoglycan concentration, and collagen fiber size and orientation. High-resolution magnetic resonance (MR) imaging reveals an analogous laminar anatomy that is often visible on clinical images obtained with proper attention to technique. In vitro and in vivo pulse sequences show three distinct laminae: a hypointense superficial lamina, a hyperintense intermediate lamina, and a heterogeneous deep lamina that consists of alternating hyperintense and hypointense bands perpendicular to the subchondral bone. Imaging pitfalls include magic angle effects, truncation artifact, partial volume effect, regional anatomic variation, chemical shift, and magnetic susceptibility effects. Pathologic conditions that affect articular cartilage include chondromalacia patellae, osteoarthritis, and localized traumatic lesions. Although detection of early cartilage disease remains elusive, MR imaging can demonstrate intermediate and advanced lesions.

Adult↗
PubMed1982

Opioid peptides in human plasma: evidence for multiple forms.

Studies were designed to assess whether the enkephalin-containing peptides and proteins present in the chromaffin granules of the adrenal medulla and in other secretory tissues, such as the neurohypophysis, could be found circulating in human blood. We analyzed human plasma acid acetone extracts chromatographed on Sephadex G-75 in acetic acid and found evidence for the existence of opioid peptides of several different molecular weights and a large number of peptides and small proteins which generate opioid activity after tryptic digestion. These compounds are different from and present in much greater quantities than previously described opioid peptides in human plasma, and are separate from dynorphin-immunoreactive compounds, which we also report in the blood. Expressed in leucine-enkephalin equivalents on a radioreceptor assay, we found 63.2 +/- 6.5 (n = 4; mean +/- SEM) pmol/ml plasma. One active peak from the Sephadex G-75 chromatography of human plasma (apparent mol wt, 3000) was examined by reverse phase high pressure liquid chromatography, tryptic digestion, and Sephadex G-50 chromatography. The results were consistent with the notion that this opioid active peptide contains an enkephalin sequence at its N-terminal, followed by a basic residue. Mild stress (2 min of deep knee bends) produced a 2-fold elevation in overall circulating opioid activity. The possibility is considered that the large enkephalin-containing peptides may have an endocrine function, independent of a role as enkephalin precursors.

Adult↗
PubMed2025

Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom.

Fungal genome sizes exhibit more than a 100-fold variation, largely driven by the expansion of repetitive sequences such as transposable elements (TEs). Silencing mechanisms targeting TEs at the epigenetic or transcript level have independently evolved in many lineages. In fungi, repeat-induced point mutation (RIP) targets TEs by recognizing repetitive sequences and inducing mutagenesis. However, the prevalence of RIP across the fungal kingdom and the fidelity of the canonical C-to-T mutation signatures remain unclear. In this study, we address these gaps by tracking shifts in genome architecture across the fungal kingdom. We find that a striking approximately 30-fold increase in genome size within a clade of leotiomycetes is associated with the absence of several RIP-related genes, suggesting a relaxation of genome defense mechanisms during this expansion. To track the impact of genome defenses, we designed a quantitative screen for RIP-like mutation signatures. The phylum of ascomycetes was unique in showing enrichment in mutation signatures in non-coding and repetitive sequences, consistent with a phylogenetically restricted occurrence of RIP-like genome defense systems. Then, we performed a phylogeny-aware association study to identify gene functions associated with RIP-like mutation signatures. We identified a zinc-finger protein as the strongest candidate underpinning a novel mechanism of genome defenses. Our findings reveal the multifaceted drivers of genome defense systems and their close ties to genome size evolution in fungi, particularly in lineages with evidence for recent RIP activity, highlighting how proximate molecular mechanisms can shape genome evolution on deep phylogenetic scales.

Genome, Fungal↗
PubMed1994

Hereditary elliptocytosis associated with spectrin Le Puy in a Japanese family: ultrastructural aspect of the red cell skeleton.

A dominantly-inherited hereditary elliptocytosis of intermediate severity was recorded in a Japanese family from Yamagata. The condition was associated with a spectrin truncated beta-chain (MW: 214 kD; 31% of total beta-spectrin), and a defect of mutant spectrin as regards tetramerization and phosphorylation. cDNA analysis revealed skipping of exon X, the third-to-last exon of the spectrin beta-gene. At the gene level, a one-base substitution (A-->G) changed position +4 of the 5' donor splice site consensus sequence of intron X. This mutation has been described before in a French kindred, defining spectrin Le Puy. Electron micrographs following quick-freeze deep-etching showed that the skeletal network was disorganized.

Base Sequence↗
PubMed2006

Deep mixing of 3He: reconciling Big Bang and stellar nucleosynthesis.

Low-mass stars, approximately 1 to 2 solar masses, near the Main Sequence are efficient at producing the helium isotope 3He, which they mix into the convective envelope on the giant branch and should distribute into the Galaxy by way of envelope loss. This process is so efficient that it is difficult to reconcile the low observed cosmic abundance of 3He with the predictions of both stellar and Big Bang nucleosynthesis. Here we find, by modeling a red giant with a fully three-dimensional hydrodynamic code and a full nucleosynthetic network, that mixing arises in the supposedly stable and radiative zone between the hydrogen-burning shell and the base of the convective envelope. This mixing is due to Rayleigh-Taylor instability within a zone just above the hydrogen-burning shell, where a nuclear reaction lowers the mean molecular weight slightly. Thus, we are able to remove the threat that 3He production in low-mass stars poses to the Big Bang nucleosynthesis of 3He.

Journal Article↗