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PubMed1996

Structure of the human cytomegalovirus protease catalytic domain reveals a novel serine protease fold and catalytic triad.

Proteolytic processing of capsid assembly protein precursors by herpesvirus proteases is essential for virion maturation. A 2.5 A crystal structure of the human cytomegalovirus protease catalytic domain has been determined by X-ray diffraction. The structure defines a new class of serine protease with respect to global-fold topology and has a catalytic triad consisting of Ser-132, His-63, and His-157 in contrast with the Ser-His-Asp triads found in other serine proteases. However, catalytic machinery for activating the serine nucleophile and stabilizing a tetrahedral transition state is oriented similarly to that for members of the trypsin-like and subtilisin-like serine protease families. Formation of the active dimer is mediated primarily by burying a helix of one protomer into a deep cleft in the protein surface of the other.

Amino Acid Sequence↗

PubMed2002

Small subunit ribosomal DNA phylogeny of microsporidia that infect Daphnia (Crustacea: Cladocera).

Glugoides intestinalis, Microsporidium sp., Ordospora colligata, Gurleya vavrai, Larssonia obtusa and Flabelliforma magnivora are microsporidian parasites of planctonic freshwater crustaceans Daphnia spp. We performed a phylogenetic analysis of the small subunit ribosomal DNA which revealed their positions as polyphyletic. G. intestinalis, Microsporidium sp. and O. colligata, which are horizontally transmitted gut parasites with small spores and low virulence, group with different lineages. G. intestinalis is related to 2 microsporidia infecting lepidopterans and to Vittaforma corneae, which has been described as a human pathogen. It is thought that V. corneae may have an invertebrate as its natural host. Microsporidium sp. is a relative of the genera Enterocytozoon and Nucleospora, pathogens of man and fish respectively. O. colligata is the first species found to be closely related to the genus Encephalitozoon, which is comprised of 3 species that are parasites of homeothermic vertebrates. G. vavrai and L. obtusa are sister taxa that branch close to the Amblyosporidae, the only microsporidia with known intermediate hosts. This finding supports the presumption of secondary hosts for G. vavrai and L. obtusa, as it has not been possible to maintain these species in Daphnia in the laboratory. F. magnivora roots deep at the base of the phylum microsporidia with no close relative found so far.

Animals↗

PubMed1993

Auditory evoked magnetic fields in stroke.

Auditory magnetic fields evoked by noise/square-wave sequences, presented once every 2.2 s, were recorded in eight subjects who had had a stroke in the auditory cortex or in its vicinity. In two subjects with large temporoparietal lesions, the magnetic 100 ms deflection (N100m) was absent over the damaged side. In one subject with a large but less deep temporoparietal lesion, a small N100m could be discerned on the defective side. The latency of N100m was increased in patients with frontal lesions. Small damages in the vicinity of the supratemporal plane had no effect on N100m. Magnetoencephalography is particularly applicable to outpatient studies of stroke.

Cerebrovascular Disorders↗

PubMed2003

A supertree of early tetrapods.

A genus-level supertree for early tetrapods is built using a matrix representation of 50 source trees. The analysis of all combined trees delivers a long-stemmed topology in which most taxonomic groups are assigned to the tetrapod stem. A second analysis, which excludes source trees superseded by more comprehensive studies, supports a deep phylogenetic split between lissamphibian and amniote total groups. Instances of spurious groups are rare in both analyses. The results of the pruned second analysis are mostly comparable with those of a recent, character-based and large-scale phylogeny of Palaeozoic tetrapods. Outstanding areas of disagreement include the branching sequence of lepospondyls and the content of the amniote crown group, in particular the placement of diadectomorphs as stem diapsids. Supertrees are unsurpassed in their ability to summarize relationship patterns from multiple independent topologies. Therefore, they might be used as a simple test of the degree of corroboration of nodes in the contributory analyses. However, we urge caution in using them as a replacement for character-based cladograms and for inferring macroevolutionary patterns.

Animals↗

PubMed2006

Molecular characterization of clinical isolates of M non-typable group A streptococci from invasive disease cases.

Currently there are 93 validated M serotypes of Streptococcus pyogenes, Lancefield group A streptococcus (GAS), and >130 emm genotypes. A marked increase in the number of non-typable GAS isolates (2 % in 2000, 4 % in 2001 and 9 % in 2002) from invasive disease cases referred to the authors' reference laboratory was noted during 2000-2002. A total of 217 (92 %) were from blood cultures, 14 (6 %) from deep abscesses and five (2 %) from aspirates. The clinical manifestations included bacteraemia, septicaemia, cellulitis, meningitis, necrotizing fasciitis and toxic-shock syndrome. In order to establish whether this increase was due to the emergence of novel types or the unavailability of M-typing sera, these isolates were subjected to emm sequencing. A total of 144 isolates (61 %) belonged to M types for which sera were no longer available; 112 (48 %) belonged to higher M types, including emm83.1 (9 %), emm94 (8 %) emm87 (6 %) and emm89 (6 %); and 32 (13 %) belonged to lower M types that were not commonly isolated in the UK, and included M25, M43, M49, M64, M73 and M74. Sixty-six (28 %) of the isolates belonged to newly designated emm types. Other isolates belonged to the novel emm types st2147, STNS1033 and st854, recently registered in the Centers for Disease Control (CDC) database by other laboratories. One novel emm type, st2161, was isolated from an injecting drug user. There were differences in the type distribution of these isolates according to geographic location. However, 90 % of emm93, one of seven predominant emm types identified amongst the collection of M non-typable (MNT) isolates, were isolated from the London region.

Abscess↗

PubMed2003

Magnetic resonance imaging of the equine foot: 15 horses.

REASONS FOR PERFORMING STUDY: Foot pain is a common cause of equine lameness and there have been significant limitations of the methods available for the diagnosis of the causes of foot pain (radiography, nuclear scintigraphy and ultrasonography). Until recently, magnetic resonance imaging (MRI) in the horse has been limited to examination of cadaver limbs. OBJECTIVES: Our purpose was to 1) describe MRI of the foot in live horses, 2) describe MRI findings in horses with foot pain in which a definitive diagnosis could not be established by alternative means and 3) correlate MRI findings with other methods of clinical investigation. METHODS: The feet of 15 horses with unilateral (12) or bilateral (3), forelimb (14) or hindlimb (1) lameness associated with foot pain of previously ill-defined origin were examined using MRI. The horses were examined in right lateral recumbency under general anaesthesia, with the feet positioned in the isocentre of a flared end 1.5 Tesla GE Signa Echospeed magnet. Images were obtained in sagittal, transverse and dorsal planes using 3-dimensional (3D) T2* gradient echo (GRE), spoiled gradient echo, fat-saturated 3D T2* GRE and short inversion recovery sequences. Image acquisition took approximately 1 h. RESULTS: Abnormalities of the distal interphalangeal joint (DIP) cartilage and/or subchondral bone, periarticular osteophyte formation, distension of the DIP joint capsule with or without synovial proliferation, distension of the navicular bursa with or without evidence of chronic inflammation, surface and core lesions in the deep digital flexor tendon, abnormal signal within the navicular bone, evidence of mineralised fragments in the distal sesamoidean impar ligament, irregular outline of and signal in the medial cortex of the distal phalanx, and an abnormal signal on the dorsal aspect of the distal phalanx consistent with laminitis were identified. CONCLUSIONS: MRI permits the diagnosis of a variety of lesions involving different structures within the foot that cannot be diagnosed using other means, thus enhancing our knowledge of the causes of foot pain. POTENTIAL RELEVANCE: With further experience it is likely that lesions involving other structures will also be identified. Long-term follow-up data is required to determine the prognosis for the injuries described.

Animals↗

PubMed2004

Characterization of iron- and sulphide mineral-oxidizing moderately thermophilic acidophilic bacteria from an Indonesian auto-heating copper mine waste heap and a deep South African gold mine.

Iron- and chalcopyrite-oxidizing enrichment cultures were obtained at 50 degrees C from acidic, high-temperature, copper/gold mine environments in Indonesia and South Africa. Over 90% copper yield was obtained from chalcopyrite concentrate with the Indonesian enrichment in 3 months with 2% solids concentration, when pH was maintained at around 2. Neither addition of silver cations nor an enhanced nutrient concentration influenced chalcopyrite leaching. Excision and sequencing of bands from denaturing gradient gel electrophoresis of the amplified partial 16S rRNA gene showed that the enrichment cultures from different environments in South Africa and Indonesia were very simple, and similar. Chalcopyrite concentrate supported a simpler and different community than Fe2+. The members of the enrichment cultures were closely related to Sulfobacillus yellowstonensis and Sulfobacillus acidophilus.

Bacteria↗

PubMed2006

Critical role for a single leucine residue in leukemia induction by E2A-PBX1.

In roughly 5% of cases of acute lymphoblastic leukemia, a chromosomal translocation leads to expression of the oncogenic protein E2A-PBX1. The N-terminal portion of E2A-PBX1, encoded by the E2A gene, is identical in sequence to the corresponding portion of the E proteins E12/E47 and includes transcriptional activation domains. The C terminus consists of most of the HOX interacting transcription factor PBX1, including its DNA-binding homeodomain. Structure-function correlative experiments have suggested that oncogenesis by E2A-PBX1 requires an activation domain, called AD1, at the extreme N terminus. We recently demonstrated that a potentially helical portion of AD1 interacts directly with the transcriptional coactivator protein cyclic AMP response element-binding protein (CBP) and that this interaction is essential in the immortalization of primary bone marrow cells in tissue culture. Here we show that a conserved LXXLL motif within AD1 is required in the interaction between E2A-PBX1 and the KIX domain of CBP. We show by circular dichroism spectroscopy that the LXXLL-containing portion of AD1 undergoes a helical transition upon interacting with the KIX domain and that amino acid substitutions that prevent helix formation prevent both the KIX interaction and cell immortalization by E2A-PBX1. Perhaps most strikingly, substitution of a single, conserved leucine residue (L20) within the LXXLL motif impairs leukemia induction in mice after transplantation with E2A-PBX1-expressing bone marrow. The KIX domain of CBP mediates well-characterized interactions with several transcription factors of relevance to leukemia induction. Circumstantial evidence suggests that the side chain of L20 might interact with a deep hydrophobic pocket in the KIX domain. Therefore, our results serve to identify a potential new drug target.

Amino Acid Motifs↗

PubMed2001

Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus.

The relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock-reef fish, throughout its range in the Gulf of California. A 408-bp fragment of the mitochondrial control region was sequenced from 105 individuals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation-by-distance. A significant habitat-by-geographical-distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.

Animals↗

PubMed2006

Sequence of information processing for emotions based on the anatomic dialogue between prefrontal cortex and amygdala.

The prefrontal cortex and the amygdala have synergistic roles in regulating purposive behavior, effected through bidirectional pathways. Here we investigated the largely unknown extent and laminar relationship of prefrontal input-output zones linked with the amygdala using neural tracers injected in the amygdala in rhesus monkeys. Prefrontal areas varied vastly in their connections with the amygdala, with the densest connections found in posterior orbitofrontal and posterior medial cortices, and the sparsest in anterior lateral prefrontal areas, especially area 10. Prefrontal projection neurons directed to the amygdala originated in layer 5, but significant numbers were also found in layers 2 and 3 in posterior medial and orbitofrontal cortices. Amygdalar axonal terminations in prefrontal cortex were most frequently distributed in bilaminar bands in the superficial and deep layers, by columns spanning the entire cortical depth, and less frequently as small patches centered in the superficial or deep layers. Heavy terminations in layers 1-2 overlapped with calbindin-positive inhibitory neurons. A comparison of the relationship of input to output projections revealed that among the most heavily connected cortices, cingulate areas 25 and 24 issued comparatively more projections to the amygdala than they received, whereas caudal orbitofrontal areas were more receivers than senders. Further, there was a significant relationship between the proportion of 'feedforward' cortical projections from layers 2-3 to 'feedback' terminations innervating the superficial layers of prefrontal cortices. These findings indicate that the connections between prefrontal cortices and the amygdala follow similar patterns as corticocortical connections, and by analogy suggest pathways underlying the sequence of information processing for emotions.

Amygdala↗

PubMed1998

Extended local access fibers: adjustable treatment of deep sites in the brain.

We describe a minimally invasive method for administering diffusible substances to computer-targeted regions of the primate brain. Treatments enter the brain by diffusion or under pressure from the portion of a curvilinear implant that lies within the region of interest. During the implantation surgery, a guide-tube cannula is passed through a cranial burr-hole and concentric, telescoping needles are extended from the cannula in sequence to trace a pre-planned course through brain tissue. After the leading end of the longest needle emerges through another burr-hole, the surgeon fastens a hollow dialysis fiber to its tip and draws the fiber into the brain by retracting the telescoping device in an orderly sequence. The surgery affects brain tissue only along the course of the fiber, causing about the same acute damage as the stereotactic introduction of an ordinary straight needle. The 'extended local access fiber' is relatively soft, flexible, and biocompatible. It remains permanently in the brain, with its semipermeable portion lodged in the target region. Leading and trailing portions are accessible from outside the brain. Experiments indicate a broad range of possible trajectories and confirm that substances delivered by access fiber can have physiological effects even 10 weeks after implantation.

Animals↗

PubMed1998

Cospeciation of chemoautotrophic bacteria and deep sea clams.

Vesicomyid clams depend entirely on sulfur-oxidizing endosymbiotic bacteria for their nutriment. Endosymbionts that are transmitted cytoplasmically through eggs, such as these, should exhibit a phylogenetic pattern that closely parallels the phylogeny of host mitochondrial genes. Such parallel patterns are rarely observed, however, because they are obscured easily by small amounts of horizontal symbiont transmission or occasional host switching. The present symbiont genealogy, based on bacterial small subunit (16S) rDNA sequences, was closely congruent with the host genealogy, based on clam mitochondrial cytochrome oxidase subunit I and large subunit (16S) rDNA sequences. This phylogenetic evidence supports the hypothesis of cospeciation and a long term association between the participants in this symbiosis.

Animals↗

PubMed2004

How does angiogenesis develop in pediatric moyamoya disease after surgery? A prospective study with MR angiography.

OBJECT: The dynamic process of neovascularization seen in patients with moyamoya disease who have received bypass surgery has not been sufficiently elucidated. Magnetic resonance angiography (MRA)is expected to disclose this process since it can be conducted frequently because of its non-invasive nature. In this study, we prospectively investigated postoperative neovascularization using repeated MRA. METHODS: We studied 14 pediatric patients (23 sides) who have received both direct bypass surgery of the superficial temporal artery (STA) to middle cerebral artery and indirect surgery of encephalo-duro-arterio-myo-synangiosis during the past 3 years. MRA was performed using a 1.5-T machine, image sequences of 512 x 256 resolution, and the time-of-flight method. MRA was prospectively performed preoperatively and repeated 1, 3, and 6 months after surgery. CONCLUSIONS: A tendency toward a decrease in moyamoya vessels and the development of the STA was observed 1 month after the surgery. Development of the deep temporal artery and the middle meningeal artery was observed 3 months after the surgery. The progression of stenotic change was apparently accelerated after the surgery. A reciprocal relation between neovascularization artificially induced by bypass surgery and moyamoya vessels, which are supposed to compensate for the stenotic change of the internal carotid artery, was disclosed.

Cerebral Revascularization↗

PubMedDate not supplied

Close relationship between equine and human molluscum contagiosum virus demonstrated by in situ hybridisation.

To determine whether the virus responsible for human molluscum contagiosum (MCV) is the causal agent of a similar disease in horses, in situ hybridisations using cloned fragments of human MCV DNA labelled with digoxigenin were carried out on formalin-fixed biopsy sections of lesions from two horses with molluscum contagiosum-like skin lesions. In both instances there was evidence of specific hybridisation of the labelled probe to target DNA in the sections under high stringency conditions, identified by the development of a deep blue-purple stain in the cytoplasm of cells in the stratum spinosum and stratum granulosum of the lesions and the absence of non-specific hybridisation in adjacent non-lesional areas of the epidermis. These results indicate that on the basis of very close homology of their viral DNA sequences, the causative virus of equine molluscum contagiosum is either identical with, or very closely related to, its human equivalent.

Animals↗

PubMed1996

Role of venous duplex scanning in patients with suspected pulmonary embolism.

PURPOSE: We examined the use of venous duplex scanning (VDS) in the diagnosis of pulmonary embolism (PE) at our institution. METHODS: Patients undergoing lower extremity VDS from October 1988 through June 1995 were cross-referenced with those who underwent ventilation perfusion (V/Q) scans and pulmonary angiography (PA) for PE. RESULTS: A total of 664 of 3534 VDS were for "rule out PE." Deep venous thrombosis was found in 13%. A total of 256 VDS were in conjunction with V/Q scans in 249 patients, with only 8% undergoing PA. Deep venous thrombosis was present in 18% for those with both V/Q and VDS compared with 10% (p < 0.01) for those with VDS as the sole study. The order in which V/Q, VDS, and PA were obtained and the relationship of positive studies was examined. CONCLUSION: We found no pattern to the sequence of tests ordered. V/Q scan rather than VDS should be the first study in the evaluation of PE. PE was diagnosed or excluded in nearly one third of patients based on V/Q as the initial study. A total of 29% of VDS could have been avoided. Treatment could be determined on the basis of VDS as the initial study in only 13%. We found only 14% incidence of positive PA in patients with nondiagnostic V/Q scans. We advocate judicious use of diagnostic tests in a stepwise fashion to appropriately treat patients with suspected PE.

Algorithms↗

PubMed1993

Immunohistochemical study of p53 expression in endometrial carcinomas: correlation with markers of proliferating cells and clinicopathologic features.

Using anti-p53 (PAb1801 and PAb240), anti-DNA polymerase alpha and Ki-67 monoclonal antibodies, the expression of p53 was studied in 11 normal endometria, 14 endometrial hyperplasias and 27 endometrial carcinomas and its relationship to the proliferative activity of the tumors was examined. Normal endometria and simple hyperplasias were completely negative for p53. The PAb1801 indices of complex hyperplasias and complex atypical hyperplasias were 2.5+/-1.8% and 5.0+/-3.2%, respectively. The PAb1801 indices of grade 1, grade 2 and grade 3 endometrial carcinomas were 10.2+/-14.2%, 44.4+/-29/0% and 45.0+/-32.5%, respectively. These results indicate a progressively enhanced p53 expression in the sequence from normal endometrium, through hyperplasia to carcinoma. A significant correlation between p53 expression and labeling indices of Ki-67 and DNA polymerase alpha was observed in endometrial carcinomas. The endo-metrial carcinomas with p53 overexpression developed mainly in post-menopausal patients and were frequently high-grade tumors with deep myometrial invasion. These findings may indicate that overexpression of p53 protein contributes to the proliferative activity of the tumor cells.

Journal Article↗

PubMed1987

The 20-Hz signals of finback whales (Balaenoptera physalus).

The 20-Hz signals of finback whales (Balaenoptera physalus) were analyzed from more than 25 years of recordings at a variety of geographic locations on near-surface hydrophones close to whales and on deep hydrophone systems. These signals were composed of 1-s pulses of sinusoidal waveform with downward sweeping frequency from approximately 23 to 18 Hz at variable source levels up to 186 dB (re: 1 microPa at 1 m), usually with slightly lower levels for the pulses at the beginning and end of sequences. These "20-Hz" pulses were produced in signal bouts (separated by more than 2 h) lasting as long as 32.5 h. Bouts were composed of regularly repeated pulses at intervals of 7-26 s (typically), either at one nominal pulse rate or at two alternating (doublet) pulse intervals. Signal bouts were interrupted by rests of 1-20 min at roughly 15-min intervals and by irregular gaps lasting between 20 and 120 min. The distribution of these signals throughout the year and their temporal sequence were analyzed from the continuous drum records of the Bermuda SOFAR Station. Signal bouts occurred during winter, sometimes beginning in September and ending in May. The sound sequences were never exactly replicated. Direct association of the bouts with the reproductive season for this species points to the 20-Hz signals as possible reproductive displays by finback whales.

Acoustics↗

PubMed1985

Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins.

A 2.7 angstrom resolution x-ray diffraction analysis of a trypsin-modified form of the Escherichia coli elongation factor Tu reveals that the GDP-binding domain has a structure similar to that of other nucleotide-binding proteins. The GDP ligand is located at the COOH-terminal end of the beta sheet and is linked to the protein via a Mg2+ ion salt bridge. The location of the guanine ring is unusual; the purine ring is located on the outer edge of the domain, not deep within a hydrophobic pocket. The amino acids from Pro10 to Arg44 and from Gly59 to Glu190 have been assigned to the electron density with computer graphic techniques, and the resulting model is consistent with all known biochemical data. An analysis of the structure reveals that four regions of the amino acid sequence that are homologous with the family of ras oncogene proteins, termed p21, are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the proteins interact directly with the GDP ligand.

Amino Acid Sequence↗