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PubMed2005

MR imaging of the diabetic foot: diagnostic challenges.

Pedal complications of diabetes have long presented a challenge for the clinician and radiologist predominately related to the difficulty in distinguishing infection from neuroarthropathy. The spectrum of diabetic foot infections is broad, ranging from callous and ulcer formation, to septic arthritis, abscess formation, and osteomyelitis. This article summarizes the MR imaging findings in the diabetic foot and the optimal pulse sequences. Focus is placed on aids in differentiating diabetic infection from other entities and increasing the specificity of diagnosing diabetic foot complications.

Abscess↗

PubMed1987

The pathogenesis of vascular changes in erythema nodosum-like lesions of Behçet's syndrome: an electron microscopic study.

The probable sequence of microvascular changes affecting endothelial cells in erythema nodosum-like lesions was examined by electron microscopy in 18 patients with typical Behçet's syndrome. Dark endothelial cells in the superficial and deep dermis exhibited degeneration with contraction changes. Consequently, degenerated endothelial cells showed nuclear and cytoplasmic condensation, vacuolization in the cytoplasm, and rich ribosomes. Moreover, blood vessels which were enveloped by cuffs of lymphocytes simultaneously exhibited both endothelial cell hypertrophy and endothelial cell necrosis. The implied associations between perivascular lymphocytic cuffs and blood vessels exhibiting endothelial cell alterations indicate that microvascular changes in erythema nodosum-like lesions may be closely associated with the delayed-type hypersensitivity reaction.

Behcet Syndrome↗

PubMed1992

Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases.

Astacin, a digestive zinc-endopeptidase from the crayfish Astacus astacus L., is the prototype for the 'astacin family', which includes mammalian metallo-endopeptidases and developmentally regulated proteins of man, fruitfly, frog and sea urchin. Here we report the X-ray crystal structure of astacin, which reveals a deep active-site cleft, with the zinc at its bottom ligated by three histidines, a water molecule and a more remote tyrosine. The third histidine (His 102) forms part of a consensus sequence, shared not only by the members of the astacin family, but also by otherwise sequentially unrelated proteinases, such as vertebrate collagenases. It may therefore represent the elusive 'third' zinc ligand in these enzymes. The amino terminus of astacin is buried forming an internal salt-bridge with Glu 103, adjacent to His 102. Astacin pro-forms extended at the N terminus, as observed for some 'latent' mammalian astacin homologues, did not exhibit this 'active' conformation, indicating an activation mechanism reminiscent of trypsin-like serine proteinases.

Amino Acid Sequence↗

PubMed2026

Integrating genetic predictors into subsequent breast cancer risk prediction in survivors of childhood cancer.

PURPOSE: Female survivors of childhood cancer are at high risk for developing breast cancer. The contributions of most general population primary breast cancer genetic predictors to this risk have not been explored. METHODS: Analyses included females who survived ≥5 years after their childhood cancer diagnosis with available array (N = 2096, subsequent breast cancer [SBC]=218) or whole-genome sequencing (WGS; N = 3292, SBC=101) data from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. We computed 99 externally-validated primary breast cancer polygenic risk scores (PRS). Using deep-coverage WGS, ClinVar-annotated pathogenic/likely pathogenic (P/LP) variants in breast cancer susceptibility genes were identified. Cox proportional hazards models assessed associations with SBC risk, adjusting for treatments and genetic ancestry. RESULTS: Among 5388 female survivors (genetic ancestry, European: N = 4,752; African: N = 444; East Asian: N = 192), 319 developed SBC. Most (90.9%) PRSs were nominally associated with SBC risk (P < 0.05), but effect sizes varied substantially. PRSs with superior discriminatory ability had greater genome-wide coverage (e.g., 6.4 million-variant PRS, HR per SD = 1.71, 95% CI = 1.43 to 2.05; P = 4.2x10-9) and 7.7-fold higher odds (P = 7.0x10-4) of including variants in multiple DNA damage repair pathways compared with PRSs with weaker risk associations. Among survivors with WGS, 1.6% carried P/LP variants in clinical testing panel genes, which was associated with a 7.4-fold greater risk (95% CI = 3.16 to 17.19). Including genetic factors improved SBC risk prediction by age 40 (P < 0.001) compared to treatment exposures alone. CONCLUSIONS: Externally-validated primary breast cancer genetic susceptibility predictors are relevant for SBC risk prediction and should be prioritized for risk stratification in survivors.

Journal Article↗

PubMed2003

The PlantsP and PlantsT Functional Genomics Databases.

PlantsP and PlantsT allow users to quickly gain a global understanding of plant phosphoproteins and plant membrane transporters, respectively, from evolutionary relationships to biochemical function as well as a deep understanding of the molecular biology of individual genes and their products. As one database with two functionally different web interfaces, PlantsP and PlantsT are curated plant-specific databases that combine sequence-derived information with experimental functional-genomics data. PlantsP focuses on proteins involved in the phosphorylation process (i.e., kinases and phosphatases), whereas PlantsT focuses on membrane transport proteins. Experimentally, PlantsP provides a resource for information on a collection of T-DNA insertion mutants (knockouts) in each kinase and phosphatase, primarily in Arabidopsis thaliana, and PlantsT uniquely combines experimental data regarding mineral composition (derived from inductively coupled plasma atomic emission spectroscopy) of mutant and wild-type strains. Both databases provide extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. The databases incorporate a unique user annotation and review feature aimed at acquiring expert annotation directly from the plant biology community. PlantsP is available at http://plantsp.sdsc.edu and PlantsT is available at http://plantst.sdsc.edu.

Arabidopsis↗

PubMed1995

A phylogenetic analysis of micro-organisms isolated from subsurface environments.

Three methods were used to provide information on the identity and phylogenetic relatedness of 19 aerobic, chemoheterotrophic bacteria isolated from topsoil and deep subsurface sediments at a site in South Carolina. These methods were (i) analysis of selected physiological traits, (ii) restriction endonuclease analysis (REA) of genomic DNA, and (iii) analysis of 16S ribosomal RNA sequences. When the 16S rRNA sequences were compared with those for 12 standard strains, two topsoil isolates and six subsurface strains formed a tight group with the high-G+C Gram-positive bacteria and appeared to be most closely related to Arthrobacter globiformis--a coryneform-actinomycete bacterium with unusually effective survival capabilities. The rest of the subsurface isolates were scattered among the standard strains from the Proteobacteria-including the pseudomonads and Agrobacterium tumefaciens--or the low-G+C Gram-positive bacteria.

Agrobacterium tumefaciens↗

PubMed1990

Value of diagnostic tests for deep venous thrombosis: a decision analysis model.

A decision analysis model and data pooled from more than 12,000 patients were used to help elucidate conflicting results about the preferred method for diagnosing deep venous thrombosis (DVT). The prevalence of DVT in symptomatic legs is 40%, a value at which venography followed by Doppler ultrasound (in cases of nondiagnostic or unsuccessful venography) is preferred over the sequence of Doppler-plethysmography, provided that the sensitivity of the latter is less than 94%. If the prevalence of DVT decreases to 25% or the sensitivity of Doppler is 95% or higher, then the sequences of Doppler-plethysmography and venography-Doppler are equivalent in helping minimize resulting morbidity and mortality. Because of the greater clinical significance of proximal DVT, the analysis was modified to reflect changes in prevalence, sensitivity of noninvasive tests, and rate of pulmonary embolus due to DVT extending above the knee. In this case, performing plethysmography is slightly better than performing venography followed by Doppler or plethysmography.

Decision Support Techniques↗

PubMed2003

Epileptic nystagmus and its possible relationship with PGO spikes.

A simultaneous video-EEG on a waking 6-year-old male revealed rapid horizontal and then vertical eye movements and 10 sec later showed ictal rhythms maximal on the occipital areas, quickly spreading to all other areas. A second ictal event during wakefulness was very similar to the first. During sleep interictal discharges were seen from the right frontal-temporal area and one more ictal event was noted. This latter seizure in the NREM sleep record did not show any eye movements, but showed ictal activity on the right frontal-temporal area, which later became generalized. We propose that the interictal discharges on the right frontal-temporal area likely arose from the amygdala, which activated the pontine nuclei responsible for PGO (ponto-geniculo-occipital) spikes and the rapid eye movements seen in our patient. The PGO spikes activated the occipital areas, which then showed clear ictal rhythms to complete the sequence of events. This case demonstrates a sequence of rapid eye movements without ictal patterns, followed by seizure rhythms, but may still be an example of "epileptic nystagmus," assuming that the eye movements arose from an ictal activation of the deep subcortical portion of the PGO system.

Brain↗

PubMed1989

[Treatment of patients with 1B-stage cervical cancer].

An analysis of a more than 40-year experience of management of stage Ib, T1bN0M0 cervical cancer (611 cases) followed the development of combined treatment of the disease: Until 1970-ies, irradiation plus surgery was preferred. During the seventies no correlation between effectiveness and sequence of these component procedures was established. According to data on 33 surgical cases, extended extirpation of the uterus may be recommended in patients with stage Ib cervical cancer less than 5 mm deep and free from such adverse prognostic factors as concomitant pregnancy, poor cell differentiation and blood and lymph vascular microembolism by tumor.

Cervix Uteri↗

PubMed1994

Vertical transmission of a chemoautotrophic symbiont in the protobranch bivalve, Solemya reidi.

Invertebrates that contain endosymbiotic chemoautotrophic bacteria are widely distributed in a variety of reducing marine habitats (i.e., hydrothermal vents and cold seeps). The mechanisms of symbiont transmission and incorporation during early host development are poorly understood primarily because these critical early life stages have not been procured. Solemya reidi is a gutless protobranch bivalve found inhabiting pulpmill effluent and sewage outfall sites. Endosymbiotic sulfur oxidizing bacteria are contained within specialized host cells of the gill filaments. These bivalves have the advantage over their deep-sea counterparts in that they can be spawned and cultured axenically, providing the opportunity to examine the ontogenetic process of symbiont incorporation. The 16S rDNA of the symbiont from Solemya reidi was sequenced from a PCR product obtained using two bacterial-specific primers. Phylogenetic analysis of this sequence identified a hypervariable region of the molecule that was unique to this symbiont. An 18-base oligonucleotide probe was synthesized and tested for specificity and sensitivity to detect its symbiont-specific target. Immobilized cellular RNAs from a range of taxa were used to screen the specificity of the Solemya probe. At high stringency, the symbiont-specific probe hybridized only to RNA extracted from gill tissue of S. reidi. When matched with a bacterial-specific forward primer in PCR amplifications, the symbiont-specific probe successfully amplified S. reidi symbiont 16S rDNA genes in genomic DNA isolated from the host ovary, eggs, and 1- and 4-day-old larvae. Amplifications detected the presence of symbiont target in the germ tissue and larvae. Nonradioactive in situ hybridizations were performed on 3-day-old larvae with the symbiont-specific probe. Detection of hybrids localized the symbionts to the epithelial test cells of the larvae. These results suggest that the symbionts are vertically transmitted with the egg and are incorporated as a post-metamorphosis event.

Animals↗

PubMedDate not supplied

Phylogenetic identification of hypermastigotes, Pseudotrichonympha, Spirotrichonympha, Holomastigotoides, and parabasalian symbionts in the hindgut of termites.

The phylogenetic diversity of parabasalian flagellates was examined based on the sequences of small subunit ribosomal RNA genes amplified directly from the mixed population of flagellates in the hindgut of lower termites. In total, 33 representative sequences of parabasalids were recovered from eight termite species. Fluorescent-labeled oligonucleotide probes specific for certain sequences were designed and used for the in situ identification of parabasalian species by whole-cell hybridization. The hypermastigotes, Pseudotrichonympha grassii, Spirotrichonympha leidyi, and Holomastigotoides mirabile in the hindgut of Coptotermes formosanus, and Spirotrichonympha sp. and Trichonympha spp. in Hodotermopsis sjoestedti were identified. In the phylogenetic tree constructed, the sequences from the termites were dispersed within the groups of known members of parabasalids, reflecting the presence of diverse parabasalids in the hindgut of termites. There were three paraphyletic lineages of hypermastigotes represented by Pseudotrichonympha, Trichonympha, and Spirotrichonympha, in agreement with the morphology-based taxonomic groups. The analysis of the tree-root suggested that the Pseudotrichonympha group is the most probable ancient lineage of parabasalids and that the Trichonympha group is the secondly deep-branching lineage. The Spirotrichonympha group and the Trichomonadida may have emerged later.

Animals↗

PubMed2005

Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency.

On encountering low oxygen conditions, DosR activates the transcription of 47 genes, promoting long-term survival of Mycobacterium tuberculosis in a non-replicating state. Here, we report the crystal structures of the DosR C-terminal domain and its complex with a consensus DNA sequence of the hypoxia-induced gene promoter. The DosR C-terminal domain contains four alpha-helices and forms tetramers consisting of two dimers with non-intersecting dyads. In the DNA-bound structure, each DosR C-terminal domain in a dimer places its DNA-binding helix deep into the major groove, causing two bends in the DNA. DosR makes numerous protein-DNA base contacts using only three amino acid residues per subunit: Lys179, Lys182, and Asn183. The DosR tetramer is unique among response regulators with known structures.

Amino Acid Sequence↗

PubMed1998

NADP-dependent bacterial alcohol dehydrogenases: crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii.

We have determined the X-ray structures of the NADP(H)-dependent alcohol dehydrogenase of Clostridiim beijerinckii (CBADH) in the apo and holo-enzyme forms at 2.15 A and 2.05 A resolution, respectively, and of the holo-alcohol dehydrogenase of Thermoanaerobacter brockii (TBADH) at 2.5 A. These are the first structures of prokaryotic alcohol dehydrogenase to be determined as well as that of the first NADP(H)-dependent alcohol dehydrogenase. CBADH and TBADH 75% have sequence identity and very similar three-dimensional structures. Both are tetramers of 222 symmetry. The monomers are composed of two domains: a cofactor-binding domain and a catalytic domain. These are separated by a deep cleft at the bottom of which a single zinc atom is bound in the catalytic site. The tetramers are composed of two dimers, each structurally homologous to the dimer of alcohol dehydrogenases of vertebrates. The dimers form tetramers by means of contacts between surfaces opposite the interdomain cleft thus leaving it accessible from the surface of the tetramer. The tetramer encloses a large internal cavity with a positive surface potential. A molecule of NADP(H) binds in the interdomain cleft to the cofactor-binding domain of each monomer. The specificity of the two bacterial alcohol dehydrogenases toward NADP(H) is determined by residues Gly198, Ser199, Arg200 and Tyr218, with the latter three making hydrogen bonds with the 2'-phosphate oxygen atoms of the cofactor. Upon NADP(H) binding to CBADH, Tyr218 undergoes a rotation of approximately 120 degrees about chi1 which facilitates stacking interactions with the adenine moiety and hydrogen bonding with one of the phosphate oxygen atoms. In apo-CBADH the catalytic zinc is tetracoordinated by side-chains of residues Cys37, His59, Asp150 and Glu60; in holo-CBADH, Glu60 is retracted from zinc in three of the four monomers whereas in holo-TBADH, Glu60 does not participate in Zn coordination. In both holo-enzymes, but not in the apo-enzyme, residues Ser39 and Ser113 are in the second coordination sphere of the catalytic zinc. The carboxyl group of Asp150 is oriented with respect to the active carbon of NADP(H) so as to form hydrogen bonds with both pro-S and pro-R hydrogen atoms.

Alcohol Oxidoreductases↗

PubMed2000

Arg133Cys mutation of Notch3 in two unrelated Japanese families with CADASIL.

OBJECTIVE: More than 80 unrelated, but all Caucasian, patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), originating from various communities around the world, have been molecularly identified. To clarify the occurrence of CADASIL in Orientals, we investigated Japanese families presenting as CADASIL. METHODS: We performed the PCR-SSCP and sequence analyses using genomic DNA, isolated from venous blood of participants under informed consent. PATIENTS: We identified two unrelated Japanese families with CADASIL, including 5 affected members through 2 generations. RESULTS: Each of the affected individuals developed recurrent strokes without risk factors resulting in progressive dementia, pseudobulbar palsy, and gait disturbances which started after the fifth decade of life. Although affected individuals had no vascular risk factors, they showed various degrees of narrowing of retinal arteries. Their MRI/CTs showed characteristics of the disease; bilateral small infarcts in the thalamus, basal ganglia, brain stem, and deep white matter in addition to the findings of leukoaraiosis. On SPECT imaging, there was severe hypoperfusion in the cortex as well as in the white matter. Ultrastructural studies revealed an abnormal deposition of granular osmiophilic materials (GOM) within the basal lamina of pericytes in muscular capillaries. On PCR-SSCP and sequence analyses, a heterozygous Arg133Cys mutation was present, in the affected individuals, in the exon 4 of Notch3 gene which is the hot spot region for CADASIL mutations in Caucasian families. None of the non-affected members nor the 50 Japanese normal controls revealed this mutation. CONCLUSION: Thus, our results confirm that CADASIL is a geographically widespread disorder caused by a Notch3 mutation.

Arginine↗

PubMed1997

Comparison of T2-weighted and fluid-attenuated inversion-recovery fast spin-echo MR sequences in intracerebral AIDS-associated disease.

PURPOSE: To compare the value of fast fluid-attenuated inversion-recovery (FLAIR) with T2-weighted fast spin-echo MR imaging in the detection of acquired immunodeficiency virus (AIDS)-related lesions of the brain. METHODS: Forty-four human immunodeficiency virus (HIV)-positive patients were examined with both sequences on either a 1.0-T or a 1.5-T MR system. The number, size, location, and conspicuity of the lesions were evaluated by two independent observers. Contrast ratios between lesions and normal brain/cerebrospinal fluid were determined, and contrast-to-noise ratios were calculated. RESULTS: FLAIR was found to be superior to T2-weighted fast spin-echo in detection of small lesions and of lesions located in cortical/subcortical regions and deep white matter. The two techniques were equal in delineation of lesions larger than 2 cm and for lesions located in the basal ganglia and posterior fossa. In 24 patients, more lesions were detected with the FLAIR fast spin-echo technique. Lesion/cerebrospinal fluid contrast ratios and contrast-to-noise ratios were significantly higher for the FLAIR fast spin-echo sequences than for the T2-weighted fast spin-echo sequences. CONCLUSION: FLAIR allows early detection of small lesions in subcortical and cortical locations, especially in HIV encephalitis. Because of its improved lesion detection rate and greater overall lesion conspicuity, we believe FLAIR is useful in the evaluation of subtle changes in the brains of AIDS patients with central nervous system disease, and could even replace the T2-weighted fast spin-echo technique.

AIDS Dementia Complex↗

PubMed1997

Ultrastructural changes in the deep cortical pyramidal cells of infant rats with inherited hydrocephalus and the effect of shunt treatment.

Pathological changes in the cortical gray matter in infantile hydrocephalus vary with the age at onset and may not be reversible with shunt treatment. We have used electron microscopy to investigate the sequence of pathological change and the effect of shunt treatment on layer VI pyramidal cells from infant H-Tx rats with inherited early-onset hydrocephalus. Tissue was prepared from the frontal and visual cortex of control and hydrocephalic rats at 4, 11, and 21 days after birth, together with 21-day rats previously treated with ventriculosubcutaneous shunts at 4-5 or 10-11 days after birth. Both cortical regions gave similar results but the effects were more severe in the visual cortex. In the early stages of hydrocephalus, the pyramidal cells were in clusters with fewer mature dendrites and less cytoplasmic organization than those in control rats, and some neuronal processes were vacuolated. In intermediate hydrocephalus the changes were more severe, with vacuolated cytoplasm, fewer cytoplasmic organelles, frequent swollen processes, and infrequent synapses. In advanced hydrocephalus at 21 days, many neurons showed degenerative changes, with edematous Golgi and dilated endoplasmic reticulum, distorted mitochondria, and single ribosomes. The neuropil contained many spongy areas with distended profiles. Shunt treatment prevented most of the changes if carried out at 4 days. Shunt treatment at 11 days also gave a dramatic recovery at the cellular level, but there were more immature pyramidal cells and edematous processes in the neuropil than in the 4-day-treated rats. The changes in hydrocephalus are consistent with progressive neuronal damage, which is largely prevented by early shunt treatment.

Animals↗

PubMed2004

Phylogenetic and physiological diversity of microorganisms isolated from a deep greenland glacier ice core.

We studied a sample from the GISP 2 (Greenland Ice Sheet Project) ice core to determine the diversity and survival of microorganisms trapped in the ice at least 120,000 years ago. Previously, we examined the phylogenetic relationships among 16S ribosomal DNA (rDNA) sequences in a clone library obtained by PCR amplification from genomic DNA extracted from anaerobic enrichments. Here we report the isolation of nearly 800 aerobic organisms that were grouped by morphology and amplified rDNA restriction analysis patterns to select isolates for further study. The phylogenetic analyses of 56 representative rDNA sequences showed that the isolates belonged to four major phylogenetic groups: the high-G+C gram-positives, low-G+C gram-positives, Proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. The most abundant and diverse isolates were within the high-G+C gram-positive cluster that had not been represented in the clone library. The Jukes-Cantor evolutionary distance matrix results suggested that at least 7 isolates represent new species within characterized genera and that 49 are different strains of known species. The isolates were further categorized based on the isolation conditions, temperature range for growth, enzyme activity, antibiotic resistance, presence of plasmids, and strain-specific genomic variations. A significant observation with implications for the development of novel and more effective cultivation methods was that preliminary incubation in anaerobic and aerobic liquid prior to plating on agar media greatly increased the recovery of CFU from the ice core sample.

Bacteria↗

PubMed2004

Ancient phylogenetic separation between Pacific and Atlantic cephalochordates as revealed by mitochondrial genome analysis.

The subphylum Cephalochordata (lancelets) is a relatively small taxonomic group in contrast to the subphyla Urochordata and Vertebrata. As an initial step to determine whether lancelets exhibit small genetic divergence in keeping with their conservative body organization or large genetic variation, four Branchiostoma species from the Pacific (B. belcheri and B. malayanum) and Atlantic (B. floridae and B. lanceolatum) Oceans were genetically compared using partial mitochondrial DNA sequences of the cytochrome oxidase c subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes. In both genes, large genetic differences were revealed between the Pacific and Atlantic species, as well as within the former. Two maximum-likelihood trees from the COI and 16S rRNA genes showed that the Pacific and Atlantic lancelets were reciprocally clustered into different clades. Furthermore, both gene trees consistently exhibited deep phylogenetic separation between the two oceans. The estimated divergence time suggested that differentiation may have followed the migration of ancestral lancelets from the Pacific to the Atlantic Oceans via the Tethys Sea.

Animals↗