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At least 1,441 records · Page 80Linked to original sources
PubMed2004

Cloning of a cDNA encoding an ETR2-like protein (Os-ERL1) from deep water rice (Oryza sativa L.) and increase in its mRNA level by submergence, ethylene, and gibberellin treatments.

A cDNA from deep water rice treated with ethylene, encoding an ethylene receptor homologous to Arabidopsis thaliana ETR2 and EIN4, was isolated using differential display and RACE techniques. The cDNA (2880 bp), corresponding to the Os-ERL1 gene (Oryza sativa ETHYLENE RESPONSE 2 like 1; GenBank accession number AB107219), contained an open reading frame of 2289 bp coding for 763 amino acids. The protein Os-ERL1 has 50% and 52% similarity to Arabidopsis ETR2 and EIN4, respectively. The Os-ERL1 gene was up-regulated by flooding, and by treatment with ethylene and gibberellin. These results suggest that deep water rice responds to flooding by increasing the number of its ethylene receptors.

Amino Acid Sequence↗
PubMedDate not supplied

Central pseudodefect of the talus: a potential ankle MR interpretation pitfall.

PURPOSE: The purpose of our study was to outline the MR features of the central pseudodefect of the talus (a normal finding that can simulate an osteochondral lesion on ankle MR studies), assess the prevalence of the central pseudodefect of the talus, and provide insight into the origin of this misleading MR appearance. METHOD: We retrospectively evaluated 31 ankle MR studies in 10 asymptomatic volunteers and 21 consecutive patients for the presence of the central pseudodefect of the talus. None of the patients had a history of trauma to the ankle. The signal, size, and shape of the pseudodefect were documented in each patient. The sagittal images were cross-referenced with the axial and coronal images in all patients in whom the central pseudodefect was identified. RESULTS: Six volunteers (60%) and 13 patients (62%) showed a curvilinear band in the middle third of the talus on far medial sagittal images, consistent with the central pseudodefect of the talus. The band measured 8-15 x 3-8 mm (mean 11 x 4 mm) and was hypointense on T1 and STIR pulse sequences. In two cases, the pseudodefect was subchondral; in the rest, it was found a few millimeters below the articular surface. On cross-referenced axial and coronal images, the band corresponded to the talar insertion site of the deep tibiotalar fibers of the deltoid ligament. CONCLUSION: The central pseudodefect of the talus is a common finding that is produced by the insertion of the tibiotalar fibers of the deltoid ligament into the talus. Familiarity with its appearance is necessary to avoid misinterpreting it as an osteochondral lesion of the talus.

Adult↗
PubMed2000

New psychrophilic and psychrotolerant Bacillus marinus strains from tropical and polar deep-sea sediments and emended description of the species.

In contrast to the current view that psychrophily combined with an absolute requirement for NaCl is connected with the Gram-negative cell wall type, psychrophilic and psychrotolerant, NaCl-requiring, Gram-positive bacteria have been isolated from tropical Atlantic, Arctic and Antarctic deep-sea sediments. Some of the isolates are even extremely psychrophilic, having maximum growth temperatures of 4 degrees C. On the basis of phenotypic characteristics, DNA base analyses, DNA-DNA hybridizations and partial and complete 16S rRNA gene sequence analyses, the strains from the three distinct geographical regions have been allocated to the obligately marine species Bacillus marinus. The distribution and origin of B. marinus are discussed and an emended description of the species is presented.

Antarctic Regions↗
PubMed1996

p53 expression patterns in colorectal adenomas and early carcinomas: a special reference to depressed adenoma and non-polypoid carcinoma.

The purpose of the present study was to investigate the role of p53 in tumor progression of colorectal adenomas and early carcinomas, while especially focusing on flat tumors (depressed adenomas and non-polypoid carcinomas). Paraffin sections of 61 pure adenomas (33 polypoid, 28 depressed), 26 carcinomas in polypoid adenoma (CIA) and 63 pure carcinomas (36 polypoid, 27 non-polypoid) were examined for immunostaining using p53 monoclonal antibody (PAb 1801). All of the carcinomas were restricted to the mucosa. The number and distribution of the p53 positive tumor cells was evaluated, and then compared with tumor growth patterns and histological features. The incidence of p53 expression in carcinomas (58% in CIA and 51% in pure carcinomas) was significantly higher than that in polypoid adenoma (27% in CIA and 21% in pure adenomas). However, the same incidence in depressed adenomas (51%) was significantly higher than in polypoid adenomas. No correlation in carcinomas was observed between p53 expression and clinicopathologic data except for age. The distribution of p53 positive cells was different between adenomas and carcinomas. There tended to be fewer p53 positive cells in adenomas, even in depressed ones, than in carcinomas and they also tended to be confined to the superficial areas in adenomas, while they were diffusely distributed in carcinomas. Interestingly, the p53 positive cells were more frequently present in the deep mucosal areas than in the superficial areas of some non-polypoid carcinomas. In conclusion, the following hypotheses are suggested: (i) the increase of p53 expression from adenoma to carcinoma supports the hypothesis of an adenoma-carcinoma sequence in a polypoid tumor; (ii) the unique p53 expression in non-polypoid carcinoma suggests the existence of another type of carcinogenesis; and (iii) depressed adenomas are thus considered to have a high potential risk of carcinoma.

Adenoma↗
PubMed2002

Alpha-proteobacteria cultivated from marine sponges display branching rod morphology.

Most isolates recovered from marine environments are Gram-negative proteobacteria, even with the use of various media and media additions to enhance recoverability. Cultivation studies with two genera of deep-water sponges yielded nine isolates that demonstrated bulbous branching rod morphology, which is usually associated with microorganisms staining Gram-positive. Gram reactions indicated that the isolates were Gram-negative, which was confirmed by partial 16S rDNA sequencing. All nine isolates were shown to be alpha-proteobacteria most closely related to other alpha-proteobacteria isolated from various sponges.

Alphaproteobacteria↗
PubMed2001

Zooxanthellae of the Montastraea annularis species complex: patterns of distribution of four taxa of Symbiodinium on different reefs and across depths.

Corals of the Montastraea annularis complex host several different dinoflagellates in the genus Symbiodinium. Here we address two questions arising from our previous studies of these associations on an offshore reef. First, do the same taxa and patterns of association (Symbiodinium A and B found in higher irradiance habitats than Symbiodinium C) occur on an inshore reef? Second, does M. franksi at the limits of its depth range host only Symbiodinium C, as it does at intermediate depths? In both surveys, a new Symbiodinium taxon and different patterns of distribution (assayed by analyses of small ribosomal subunit RNA genes [srDNA]) were observed. Inshore, a taxon we name Symbiodinium E predominated in higher irradiance habitats in M. franksi and its two sibling species; the only other zooxanthella observed was Symbiodinium C. Offshore, M. franksi mainly hosted Symbiodinium C, but hosted Symbiodinium A, B, C, and E in shallow water and Symbiodinium E and C in very deep water. Symbiodinium E may be stress-tolerant. Observed srDNA heterogeneity within samples of Symbiodinium B, C, and E is interpreted as variation across copies within this multigene family. Experimental bleaching of Symbiodinium C supported this interpretation. Thus sequences from natural samples should be interpreted cautiously.

Animals↗
PubMed2001

Heparins and venous thromboembolism: current practice and future directions.

Unfractionated heparin (UFH) in adjusted doses and low-molecular-weight heparins (LMWH) in fixed doses are the chosen therapy for the initial treatment of venous thromboembolism. The use of UFH protocols ensures that virtually all patients will promptly achieve the therapeutic range for the activated partial thromboplastin time. However, proper use of UFH requires considerable expertise, can cause inconvenience and has limitations. Unmonitored therapy with subcutaneous LMWH is at least as effective and safe as adjusted-dose UFH, is associated with a considerable reduction of mortality in cancer patients, and permits the treatment of suitable patients in an outpatient setting. LMWH in high prophylactic doses is more effective than UFH and oral anticoagulants for prevention of postoperative venous thrombosis in major orthopedic surgery. Whether thromboprophylaxis should be continued for a few additional weeks after hospital discharge is controversial. LMWH and UFH are equally effective for prevention of postoperative deep-vein thrombosis in cancer patients. In a recent controlled randomized trial, enoxaparin in high prophylactic doses was an effective and safe measure of thromboprophylaxis in ordinary bedridden patients. The efficacy and safety of pentasaccharide (the smallest antithrombin binding sequence of heparin) in the treatment and prevention of venous thromboembolic disorders is currently under investigation.

Blood Loss, Surgical↗
PubMed1989

Central nervous system pathology in pediatric AIDS: an autopsy study.

The neuropathologic findings of brains and spinal cords removed at autopsy from 26 infants and children with AIDS is described; in two cases, only the spinal cords were available. The most common finding in the brains was dystrophic calcification of blood vessels of all calibers in the basal ganglia and deep cerebral white matter (21 og 24 cases). The next most frequent finding was subacute encephalitis (SE) (15 of 24 cases) with microglial nodules and multinulceated giant cells. Immunocytochemical and in situ hybridization studies showed HIV antigen or genetic sequences only in the brains of cases with SE. Multinucleated giants cells (MGC) were the most frequent cells with reaction products. MGC were labeled with ricinus lectin (RCA), but not with leukocyte common antigen (LCA) or glial fibrillary acidic protein. Many cells in microglial nodules were labeled with RCA, but not LCA; cells in the perivascular compartment were labeled with LCA, but not RCA. Corticospinal tract degeneration was noted in 15 of 20 spinal cords. In six cases tract degeneration was consistent with delayed myelination, and the remaining cases had axonal injury consistent with Wallerian degeneration. Opportunistic infections were rare (three cases). Central nervous system lymphoma occurred in three children and was the most common mass lesion. In two cases lymphoma occurred in the setting of a systemic polyclonal immunoproliferation possibly related to Epstein-Barr virus infection. Cerebrovascular accidents were noted in seven cases. Two cases had hemorrhage associated with immune thrombocytopenia; one hemorrhage was catastrophic. Two children had large vessel arteriopathy with multiple encephalomalacias. Two children had a necrotizing encephalopathy with encephalomalacia and vascular changes suggestive of a mitochondrial cytopathy.(ABSTRACT TRUNCATED AT 250 WORDS)

Acquired Immunodeficiency Syndrome↗
PubMed2007

Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site.

Dipeptidyl peptidase 4 (DP4) inhibitors are currently under intensive investigation in late-stage clinical trials as a treatment for type II diabetes. Lack of selectivity toward the related enzymes DP8 and DP9 has recently emerged as a possible source of drug-induced toxicity. Unlike DP4, X-ray structures of DP8 and DP9 are not yet available. As an aid to understanding the structural basis for selectivity, the authors have constructed homology models of DP8 and DP9 based on the X-ray coordinates of DP4. Accurate sequence alignment reveals common structural features indicative for a well-preserved overall fold comprising two domains, namely, a hydrolase domain and a so-called beta-propeller, which together form the active site deeply buried within the protein. The conformation of two loops inside this deep cavity is particularly relevant for the active sites. The authors used a published protocol for loop prediction based on conformational sampling and energy analysis to generate plausible solutions for these two loops. The predictive power of the approach was successfully evaluated for the template protein DP4 and two additional known structures from the same protein family, namely, FAP and DPX. The authors also show that inclusion of the covalent ligand NVP-728 greatly enhances the refinement. Based on the established evaluation protocol, the corresponding loops of DP8 and DP9 were predicted and the resulting active sites were compared with DP4. In particular, the authors conclude that differences in the P2-pocket are relevant for the design of selective DP4 inhibitors. The loss of key interactions in DP8 and DP9 as predicted from their models is consistent with the selectivity profile of the DP4 clinical candidate MK-431.

Adenosine Deaminase↗
PubMed2002

Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.

To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.

Amino Acid Sequence↗
PubMed2002

A strong signature of balancing selection in the 5' cis-regulatory region of CCR5.

CCR5 encodes a cell surface chemokine receptor molecule that serves as the principal coreceptor, with CD4, for HIV-type 1 (HIV-1). Varied HIV-1 susceptibility and time to progression to AIDS have been associated with polymorphisms in CCR5. Many of these polymorphisms are located in the 5' cis-regulatory region of CCR5, suggesting that it may have been a target of natural selection. We characterized CCR5 sequence variation in this region in 400 chromosomes from worldwide populations and compared it to a genome-wide analysis of 100 Alu polymorphisms typed in the same populations. Variation was substantially higher than expected and characterized by an excess of intermediate-frequency alleles. A genealogy of CCR5 haplotypes had deep branch lengths despite markedly little differentiation among populations. This finding suggested a deviation from neutrality not accounted for by population structure, which was confirmed by tests for natural selection. These results are strong evidence that balancing selection has shaped the pattern of variation in CCR5 and suggest that HIV-1 resistance afforded by CCR5 5' cis-regulatory region haplotypes may be the consequence of adaptive changes to older pathogens.

Alleles↗
PubMed1999

Non-visual photoreception by a variety of vertebrate opsins.

Extraretinal photoreceptors in animals are involved in a variety of physiological functions such as photo-entrainment of circadian rhythm, photoperiodicity and body colour change. We have identified pinopsin in the chicken pineal gland as a typical 'non-visual' photoreceptive molecule. Pinopsin with bound 11-cis-retinal shows a blue-light sensitivity (lambda max = 468 nm), and it may play a role in synchronizing the phase of the endogenous circadian oscillator with an environmental dark-light cycle. Pinopsin is not a unique pineal opsin in animals. In the zebrafish, we have detected expression of two rhodopsin genes, the nucleotide sequences of which are very similar but distinct from each other. One is canonical rhodopsin expressed in the retina, and the other is expressed in the pineal gland. The latter gene is widely distributed among teleosts, and we named it 'exo-rhodopsin' after extraocular rhodopsin. On the other hand, our effort to identify the 'deep brain opsin' responsible for the photoperiodic gonadal response resulted in the identification of two kinds of opsins; pinopsin in the toad anterior preoptic nucleus and rhodopsin in the pigeon lateral septum. Both of these opsins are localized in the cerebrospinal fluid-contacting neurons in the brain of the two animals. We also identified VAL opsin in zebrafish retinal horizontal cells, which have not been considered as photoreceptive cells. It has become evident that animals employ a wide variety of photoreceptive molecules for 'non-visual' purposes.

Amino Acid Sequence↗
PubMed2025

Armenian Hamsters (Nothocricetulus migratorius): A New Host Susceptible to Corynebacterium bovis Infection and Disease.

Corynebacterium bovis causes skin disease in immunocompromised mice and possibly rats. In 2022, scaly skin and mortality were observed in 7- to 11-d-old neonates (n = 8) from a primiparous Armenian (Nothocricetulus migratorius) hamster breeding pair in a newly established colony. C. bovis was detected by culture and PCR, and affected animals had moderate to severe acanthotic, hyperkeratotic lesions with intralesional C. bovis confirmed by in situ hybridization. Intrafollicular Demodex cricetuli mites, an ectoparasite found in all laboratory-maintained Armenian hamsters, were also identified in affected animals. To elucidate the role of D. cricetuli on C. bovis-associated disease and maintain adult hamsters without the need for sustained mite treatment, a D. cricetuli-free colony was generated by treating breeding pairs and their 1- to 3-d-old neonates with topical fluralaner (35 mg/kg), and a prospective study was undertaken to compare C. bovis-associated pup mortality in D. cricetuli-free and D. cricetuli-infested hamsters. During the ensuing 22 mo, 4 of 96 (4.2%) litters born exhibited C. bovis-associated disease and/or mortality. The litters were born to 4 different nulliparous breeding pairs (n = 47, 9%). Of the 4 affected litters, 2 were D. cricetuli-infested while 2 were D. cricetuli-free. C. bovis was routinely cultured with a variable bacterial burden that had no association with mortality or skin lesion severity from all hamsters, independent of their D. cricetuli status. The severity of histologic pathology appeared to correlate with clinical presentation and mortality in neonates. Whole genome sequencing was performed on 4 hamster C. bovis isolates, which revealed a close genetic association among the isolates as well as with previously characterized mouse and rat C. bovis isolates.

DSS, deep skin scrape↗
PubMed2004

Expression of bone morphogenetic protein-6 and -2 and a bone morphogenetic protein antagonist in horses with naturally acquired osteochondrosis.

OBJECTIVE: To determine the mRNA expression of bone morphogenetic protein (BMP)-6 and -2 and a BMP antagonist (Noggin) in horses with osteochondrosis. SAMPLE POPULATION: Samples of articular cartilage from affected stifle or shoulder joints of 10 immature horses with naturally acquired osteochondrosis and corresponding joints of 9 clinically normal horses of similar age; additionally, samples of distal femoral growth plate cartilage and distal femoral articular cartilage were obtained from a normal equine fetus. PROCEDURE: Cartilage specimens were snap-frozen in liquid nitrogen, and total RNA was isolated. Adjacent specimens were fixed in 4% paraformaldehyde for histologic examination. Expression of BMP-6, BMP-2, and Noggin mRNA was evaluated by real-time quantitative polymerase chain reaction (PCR) assays. Spatial tissue mRNA expression of BMP-6 was determined by in situ hybridization. RESULTS: Nucleotide sequences were obtained for portions of the BMP-6 propeptide and mature peptide region, as well as the signal and mature peptide region of Noggin. Expression of BMP-6, BMP-2, and Noggin mRNA was found to be similar in cartilage from normal and osteochondrosis-affected horses. Spatial expression of BMP-6 correlated with the middle and deep layers of articular cartilage; no differences were observed in overall expression between cartilage specimens from the 2 groups of horses. No expression of BMP-6 was found in the superficial layer, subchondral bone, or osteochondrosis-affected cleft fibrous tissue. CONCLUSIONS AND CLINICAL RELEVANCE: Although these signaling peptides may play important roles in cartilage differentiation, results did not provide evidence to suggest that they are involved in the disease process of osteochondrosis.

Animals↗
PubMed1992

Do the ends justify the mean? Proline mutations at the ends of the keratin coiled-coil rod segment are more disruptive than internal mutations.

Intermediate filament (IF) assembly is remarkable, in that it appears to be self-driven by the primary sequence of IF proteins, a family (40-220 kd) with diverse sequences, but similar secondary structures. Each IF polypeptide has a central 310 amino acid residue alpha-helical rod domain, involved in coiled-coil dinner formation. Two short (approximately 10 amino acid residue) stretches at the ends of this rod are more highly conserved than the rest, although the molecular basis for this is unknown. In addition, the rod is segmented by three short nonhelical linkers of conserved location, but not sequence. To examine the degree to which different conserved helical and nonhelical rod sequences contribute to dimer, tetramer, and higher ordered interactions, we introduced proline mutations in residues throughout the rod of a type I keratin, and we removed existing proline residues from the linker regions. To further probe the role of the rod ends, we introduced more subtle mutations near the COOH-terminus. We examined the consequences of these mutations on (a) IF network formation in vivo, and (b) 10-nm filament assembly in vitro. Surprisingly, all proline mutations located deep in the coiled-coil rod segment showed rather modest effects on filament network formation and 10-nm filament assembly. In addition, removing the existing proline residues was without apparent effect in vivo, and in vitro, these mutants assembled into 10-nm filaments with a tendency to aggregate, but with otherwise normal appearance. The most striking effects on filament network formation and IF assembly were observed with mutations at the very ends of the rod. These data indicate that sequences throughout the rod are not equal with respect to their role in filament network formation and in 10-nm filament assembly. Specifically, while the internal rod segments seem able to tolerate considerable changes in alpha-helical conformation, the conserved ends seem to be essential for creating a very specific structure, in which even small perturbations can lead to loss of IF stability and disruption of normal cellular interactions. These findings have important implications for the disease Epidermolysis Bullosa Simplex, arising from point mutations in keratins K5 or K14.

Amino Acid Sequence↗
PubMed2004

Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough.

A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16 : 1omega7c, 15 : 0 iso, 16 : 0 and 13 : 0 iso. The G+C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98 %), Shewanella oneidensis (97 %) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were <20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella. Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (=DSM 15900(T)=JCM 12080(T)) as the type strain.

Anaerobiosis↗