Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Deep sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,801 records · Page 100Linked to original sources
PubMed2001

Bilateral subthalamic nucleus stimulation does not improve prolonged P300 latencies in Parkinson's disease.

Bilateral deep brain stimulation is an effective treatment for most motor signs of Parkinson's disease (PD), but the effects on cognitive functions are less clear. We therefore examined the effects of bilateral deep brain stimulation on central information processing, using the event-related auditory P300 potential as an electrophysiological index of mental chronometry. Eight PD patients with bilateral stimulators within the subthalamic nuclei (STN) and eight age-matched controls participated. Patients were examined after overnight withdrawal of antiparkinson medication, both "on" and "off" stimulation (in random sequence). The P300 and reaction times were recorded using an auditory oddball paradigm. P300 latencies were prolonged in PD patients off stimulation (440 +/- 45 ms) compared to controls (397 +/- 16 ms; P < 0.05). STN stimulation significantly reduced clinical disease severity (as indexed by the Unified Parkinson's Disease Rating Scale) and markedly improved reaction times, but did not improve the prolonged P300 latencies in PD patients (429 +/- 36 ms). These results confirm that P300 latencies are prolonged in PD. Significantly, bilateral STN stimulation did not improve this electrophysiological measure of cognitive impairment, even though motor disability was markedly reduced. This suggests that some dopa-responsive features are resistant to STN stimulation, possibly due to involvement of dopaminergic deficits outside the nigrostriatal pathway, which are not influenced by outflow from the STN.

Aged↗
PubMed2007

Chitinase gene diversity at a deep sea station of the east Pacific nodule province.

The Pacific nodule province covered about 4.5 million km(2) in the east tropical Pacific with an abundance of polymetallic nodules at the seafloor. In view of the environmental protection and resource preservation, the survey of biodiversity was important during the reconnaissance and exploitation in this area. As one of the important component of the deep sea ecosystem, the microbial community in the Pacific nodule province was still largely unknown. The chitinolytic bacteria diversity in deep-sea sediment of a station within the Pacific nodule province was examined by molecular technology. A total of 18 chitinase genes were detected by a set of degenerate PCR primer specific for chiA gene fragment of family 18 chitinase. Most of them belonged to the Serratia-like chitinase. Eight genes had different amino acid sequences in the conserved motif, encompassing the catalytic site among the ChiA protein of family 18 glycosyl hydrolases, and clustered in an independent clade on the phylygenetic tree.

Amino Acid Sequence↗
PubMed2006

Effect of laser modified surface microtopochemistry on endothelial cell growth.

The introduction of microelectronics technology in the area of biological sciences has brought forth previously unforeseeable applications such as DNA or protein biochips, miniaturized, multiparametric biosensors for high performance multianalyte assays, DNA sequencing, biocomputers, and substrates for controlled cell growth (i.e. tissue engineering). We developed and investigated a new method using "cold" excimer laser beam technology combined with microlithographical techniques to create surfaces with well defined 3D microdomains in order to delineate critical microscopic surface features governing cell-material interactions. Microfabricated surfaces with microgrooves 30-3 microm deep, 10 - 1 microm wide spaced 30 microm apart were obtained with micron resolution, by "microsculpturing" polymer model surfaces using a computer controlled laser KrF excimer beam coupled with a microlithographic projection technique. The laser beam after exiting a mask was focused onto the polymer target surface via an optical setup allowing for a 10-fold reduction of the mask pattern. Various 3D micropatterned features were obtained at the micron level. Reproducible submicron features could also be obtained using this method. Subsequently, model human umbilical endothelial cells (HUVEC) were cultured on the laser microfabricated surfaces in order to study the effects of specific microscopic surface features on cell deposition and orientation. Cell deposition patterns were found to be microstructure dependant, and showed cell orientation dependency for features in the cell range dimension, a behaviour significantly different from that of a previously studied cell model (osteoprogenitor cell). This model may be a promising in so far as it is very rapid (a time frame less than a second per square centimeter of micropatterned surface) and provides further insights into the effects of surface microtopography on cell response with possible applications in the field of biosensors, biomedical and/or pharmaceutical engineering sciences.

Cell Culture Techniques↗
PubMed2005

When space merges into language.

We present data from right brain-damaged patients, with and without spatial heminattention, which show the influence of hemispatial deficits on spoken language processing. We explored the findings of a previous study, which used an emphatic stress detection task and suggested spatial transcoding of a spoken active sentence in a 'language line'. This transcoding was impaired in its initial portion (the subject-word) when the neglect syndrome was present. By expanding the original methodology, the present study provides a deeper understanding of the level of spoken language processing involved in the heminattentional bias. To ascertain the role played by syntactic structure, active and passive sentences were compared. Sentences comprised of musical notes and of a sequence of unrelated nouns were also compared to determine whether the bias was manifest with any sequence of events (not only linguistic ones) deployed over time, and with a sequence of linguistic events not embedded in a structured syntactic frame. Results showed that heminattention exerted an influence only when a syntactically structured linguistic input (=sentence with agent of action, action and recipient of action) was processed, and that it did not interfere when a sequence of non-linguistic sounds or unrelated words was presented. Furthermore, when passing from active to passive sentences, the heminattentional bias was inverted, suggesting that heminattention primarily involves the logical subject of the sentence, which has an inverted position in passive sentences. These results strongly suggest that heminattention acts on the spatial transcoding of the deep structure of spoken language.

Adult↗
PubMed1999

Primary effusion lymphoma after heart transplantation: a new entity associated with human herpesvirus-8.

Deep immunosuppression and Epstein-Barr virus (EBV) infection promote the emergence of lymphoproliferative disorders in patients undergoing solid organ transplantation. In the last few years a new herpesvirus, named human herpesvirus-8 (HHV-8), has been identified in Kaposi's sarcoma and primary effusion lymphoma (PEL) developing in AIDS patients. Subsequently, the same viral DNA sequences have been identified in almost all cases of Kaposi's sarcoma emerged outside HIV infection, thus suggesting their possible pathogenetic role in this tumor. Similarly, the association between HHV-8 and PEL also emerged in cases without HIV infection, even though the total number of these patients is still limited. Here, we focus on the emergence of this unusual lymphoma in patients undergoing solid organ transplant and underline once again its association with the HHV-8. Moreover, despite the characteristic local growth of this peculiar type of lymphoma, we demonstrate at the molecular level, an early neoplastic spread to the bone marrow suggesting the need to investigate in more detail the origin of the disease, as well as the molecular mechanisms controlling its systemic dissemination.

Aged↗
PubMed2003

Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge.

We report here a molecular survey based on 16S rRNA genes of the bacterial diversity found in two deep-sea vent niches at the Mid-Atlantic Ridge: hydrothermal sediment (Rainbow site), and microcolonizers made of three different substrates (organic-rich, iron-rich and pumice) that were exposed for 15 days to a vent emission. Bacterial diversity in sediment samples was scattered through many bacterial divisions. The most abundant and diverse environmental sequences (phylotypes) in our libraries corresponded to the Gammaproteobacteria, followed by the Acidobacteria. We detected members of all the subdivisions within the Proteobacteria. Myxobacterial lineages were the most represented within the delta subdivision. Phylotypes ascribing to the Cytophaga-Flavobacterium-Bacteroides, Planctomycetales, high and low G + C Gram-positives, Nitrospirae, and the candidate division TM7 were also identified. Compared to this broad taxonomic coverage, microcolonizers were almost exclusively colonized by epsilonproteobacteria, although these exhibited considerable morphological and phylogenetic in-group diversity. No specificity for any of the substrates tested was seen. This observation further supports the idea of the ecological dominance of epsilonproteobacteria in the fluid-seawater interface environment. Because oxidation of reduced S species and/or sulphur-reduction is thought to be essential for their energetic metabolism in these areas, we mapped different oxidation states of S in individual bacterial filaments from the iron-rich microcolonizer. For this, we used high-resolution, non-destructive synchrotron micro-X-ray Absorption Near-Edge Spectroscopy (micro-XANES), which revealed the co-existence of different S oxidation states, from sulphide to sulphate, at the level of individual cells. This suggests that these cells were metabolizing sulphur in situ.

Atlantic Ocean↗
PubMed2004

An analysis of chest wall and diaphragm motions in patients with idiopathic scoliosis using dynamic breathing MRI.

STUDY DESIGN: The motions of chest wall and diaphragm were measured in patients with scoliosis and healthy individuals using dynamic breathing magnetic resonance imaging. OBJECTIVES: To investigate the motions of the chest wall and the diaphragm during deep breathing in patients with idiopathic scoliosis. SUMMARY OF BACKGROUND DATA: Despite the central role of the respiratory motions in maintaining ventilation, it is difficult to measure and describe the motions because of the limited methods available. The kinematics of respiration in scoliosis have not yet been clarified. METHODS: Dynamic fast spoiled gradient-recalled echo sequences were used for 18 patients with idiopathic scoliosis and 9 healthy individuals. The chest wall and diaphragm motions were evaluated using a cineloop view and a fusion display of maximal inspiratory and expiratory images. The data were analyzed quantitatively by measuring displacements. RESULTS: Respiratory chest wall movements were significantly restricted in patients with scoliosis, although the diaphragm motion was normal. An analysis of the fusion magnetic resonance displays superimposed with the maximal inspiratory and expiratory images facilitated the understanding of the abnormal respiratory motion in patients with scoliosis. There was some correlation between the values of respiratory motions and pulmonary function tests. CONCLUSIONS: The present technique is useful for assessing respiratory mechanisms dynamically and noninvasively. One of the distinguishing features of respiratory dysfunction in patients with scoliosis is their limited chest wall motion.

Adolescent↗
PubMed2004

Combined use of cultivation-dependent and cultivation-independent methods indicates that members of most haloarchaeal groups in an Australian crystallizer pond are cultivable.

Haloarchaea are the dominant microbial flora in hypersaline waters with near-saturating salt levels. The haloarchaeal diversity of an Australian saltern crystallizer pond was examined by use of a library of PCR-amplified 16S rRNA genes and by cultivation. High viable counts (10(6) CFU/ml) were obtained on solid media. Long incubation times (> or =8 weeks) appeared to be more important than the medium composition for maximizing viable counts and diversity. Of 66 isolates examined, all belonged to the family Halobacteriaceae, including members related to species of the genera Haloferax, Halorubrum, and Natronomonas. In addition, isolates belonging to a novel group (the ADL group), previously detected only as 16S rRNA genes in an Antarctic hypersaline lake (Deep Lake), were cultivated for the first time. The 16S rRNA gene library identified the following five main groups: Halorubrum groups 1 and 2 (49%), the SHOW (square haloarchaea of Walsby) group (33%), the ADL group (16%), and the Natronomonas group (2%). There were two significant differences between the organisms detected in cultivation and 16S rRNA sequence results. Firstly, Haloferax spp. were frequently isolated on plates (15% of all isolates) but were not detected in the 16S rRNA sequences. Control experiments indicated that a bias against Haloferax sequences in the generation of the 16S rRNA gene library was unlikely, suggesting that Haloferax spp. readily form colonies, even though they were not a dominant group. Secondly, while the 16S rRNA gene library identified the SHOW group as a major component of the microbial community, no isolates of this group were obtained. This inability to culture members of the SHOW group remains an outstanding problem in studying the ecology of hypersaline environments.

Archaea↗
PubMed2000

Ataxia caused by mutations in the alpha-tocopherol transfer protein gene.

A 48 year old woman with ataxia with vitamin E deficiency is described. Gene analysis identified two point mutations in exon 1 of the alpha-tocopherol transfer protein (alpha-TTP) gene, one missense mutation and an upstream initiation codon mutation in the 5'-untranslated region (Kozak sequence). The latter mutation is the first one identified in the translation regulatory region. This mutation decreased the level of alpha-TTP protein expression. The clinical features included uncommon urinary disturbance and deafness and relatively rare retinitis pigmentosa. Supplementary therapy increased her serum vitamin E concentration to the normal range with mild improvement of the deep senses.

Ataxia↗
PubMed1990

[Infection of the hand: a specific disease picture].

Certain anatomical and physiological features are responsible for the specific clinical presentations of hand infections: The dorsum of the hand possesses a loose mobile areolar layer, whereas the gripping function of the palm has determined the development of a dense, firmly anchored sheet layer of connective tissue. It follows that infections of the dorsum of the hand can spread easily and give rise to extensive cellulitis. This cannot occur on the palmar aspect, where infection always tracks along the path of least resistance into the deep tissues, rapidly reaching the functionally important structures of the flexor compartments, including the subfascial compartments of the deep palmar space and the space of Parona in the forearm. A similar chain of events characterizes infections of the thenar and hypothenar eminences. Distal finger infections around the nail are a separate clinical entity with a considerable risk of running a chronic course and involving bone or the distal interphalangeal joint. In this case the sequence leads form subcutaneous infection or paronychia via bone infection to joint sepsis. There is considerable scope for misdiagnosis of hand infections, and inappropriate conclusions may lead to serious consequences for future function of the hand. The treatment of hand infections is demanding, time-consuming and not infrequently requires the infrastructure of a hospital clinic; therefore, in cases of doubt, early referral is always advisable.

Bacterial Infections↗
PubMed1998

A new Tetrahymena actin-binding protein is localized in the division furrow.

Using an F-actin affinity column, a 60 kDa fragment of a 71 kDa F-actin-binding protein was partially purified from Tetrahymena pyriformis. After digestion of the 60 kDa fragment with cyanogen bromide, the N-terminal 21-amino acid sequence of one of the resulting peptides was found to show sequence similarity to a region near the actin-binding site (amino acid residues 260-281) of yeast fimbrin. An antibody prepared against a synthesized 21-mer oligopeptide reacted with the 71 kDa proteins in T. pyriformis and T. thermophila cell extracts, suggesting that the 60 kDa fragment was produced from the 71 kDa protein through partial digestion occurring during isolation. The 60 kDa fragment bound to Tetrahymena F-actin as well as to rabbit skeletal muscle F-actin, and induced the bundling of Tetrahymena F-actin. Indirect immunofluorescence revealed colocalization of the 71 kDa protein and actin in the oral apparatus and the deep fiber bundles in T. pyriformis. On the other hand, in T. thermophila, the 71 kDa protein was localized in the oral apparatus and the contractile vacuole pores during the interphase. During cytokinesis, the 71 kDa protein was localized in the division furrow. Therefore, the 71 kDa protein seems to associate with the actin cytoskeleton, and to regulate the actin filament organization during phagocytosis and cytokinesis in Tetrahymena.

Actins↗
PubMed2000

The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae.

Aspergillus flavus is a common filamentous fungus that produces aflatoxins and presents a major threat to agriculture and human health. Previous phylogenetic studies of A. flavus have shown that it consists of two subgroups, called groups I and II, and morphological studies indicated that it consists of two morphological groups based on sclerotium size, called "S" and "L." The industrially important non-aflatoxin-producing fungus A. oryzae is nested within group I. Three different gene regions, including part of a gene involved in aflatoxin biosynthesis (omt12), were sequenced in 33 S and L strains of A. flavus collected from various regions around the world, along with three isolates of A. oryzae and two isolates of A. parasiticus that were used as outgroups. The production of B and G aflatoxins and cyclopiazonic acid was analyzed in the A. flavus isolates, and each isolate was identified as "S" or "L" based on sclerotium size. Phylogenetic analysis of all three genes confirmed the inference that group I and group II represent a deep divergence within A. flavus. Most group I strains produced B aflatoxins to some degree, and none produced G aflatoxins. Four of six group II strains produced both B and G aflatoxins. All group II isolates were of the "S" sclerotium phenotype, whereas group I strains consisted of both "S" and "L" isolates. Based on the omt12 gene region, phylogenetic structure in sclerotium phenotype and aflatoxin production was evident within group I. Some non-aflatoxin-producing isolates of group I had an omt12 allele that was identical to that found in isolates of A. oryzae.

Aflatoxins↗
PubMed1998

A truncated species of apolipoprotein B (B-38.7) in a patient with homozygous hypobetalipoproteinemia associated with diabetes mellitus.

Familial hypobetalipoproteinemia is caused by mutations in the apolipoprotein (apo) B gene. We identified a 57-year-old woman whose plasma total cholesterol and apoB levels were 2.17 mmol/L and 0.03 g/L, respectively. Separation of plasma lipoproteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the absence of apoB-100 and the presence of a faster-migrating form of apoB with an apparent Mr of 195 kDa. Direct sequencing of a polymerase chain reaction-amplified fragment of the patient's apoB gene DNA revealed a single C-->T transition at nucleotide 5472 that converts glutamine 1755 (CAA) to a stop codon (TAA). We predict this novel nonsense mutation of the apoB gene to produce a truncated protein that contains 1754 amino-terminal amino acid residues of apoB-100. We designated this mutant form of apoB apoB-38.7 by following the centile nomenclature of the apoB species. The same mutation was found in both of her children. The proband revealed clinical findings of retinitis pigmentosa, acanthocytosis, and loss of deep tendon reflexes that are characteristic of severe hypobetalipoproteinemia. In addition, the proband had type II diabetes mellitus with nephropathy, anemia, cholelithiasis, hepatic hemangioma, bronchiectasis, and extensive calcification of major arteries including, the celiac, splenic, and renal. In summary, we have found a novel truncated apoB, apoB-38.7, in a patient with an unusual presentation of hypobetalipoproteinemia that includes diabetes mellitus and extensive arterial calcification.

Apolipoproteins B↗
PubMed2024

Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.

Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the characteristics, variants, expression levels of the alternative proteome, in addition to already annotated proteins (RefProts). To obtain a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific total RNA-sequencing profiles and customized protein databases were generated. In total, 128 RefProts and 30 AltProts were identified exclusively in SKOV-3 and PEO-4 cells. Among them, an AltProt variant of IP_715944, translated from DHX8, was found mutated (p.Leu44Pro). We show high variation in protein expression levels of RefProts and AltProts in different subcellular compartments. The presence of 117 RefProt and two AltProt variants was described, along with their possible implications in the different physiological/pathological characteristics. To identify the possible involvement of AltProts in cellular processes, cross-linking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt interactions. This approach revealed an interaction between POLD3 and the AltProt IP_183088, which after molecular docking, was placed between POLD3-POLD2 binding sites, highlighting its possibility of the involvement in DNA replication and repair.

Humans↗
PubMed1997

Molecular diagnosis of deep nodular bacillary angiomatosis and monitoring of therapeutic success.

A 51-year-old human immunodeficiency virus (HIV)-positive male patient (CDC stage 3C) had had a painful nodule on his external ankle joint for 10 months. A biopsy suggested bacillary angiomatosis, but Kaposi's sarcoma could not be excluded. Rods were detectable in lesional skin by a Warthin-Starry stain. A 298 base pair (bp) gene fragment specific for Bartonella species was amplified from lesional skin and direct nucleotide sequence analysis of the amplification product clearly identified Bartonella quintana. Kaposi's sarcoma-associated herpes virus specific DNA was not amplifiable by polymerase chain reaction (PCR) in our patient, suggesting that the lesion represented bacillary angiomatosis alone, despite clinical and histopathological features which suggested the coexistence of bacillary angiomatosis and Kaposi's sarcoma. The lesion regressed after erythromycin was prescribed. However, 4 and 9 weeks after initiation of therapy, PCR still yielded a positive result in material obtained by a swab. After complete healing, following 12 weeks of antibiotic therapy, PCR became consistently negative. The optimal length of antibiotic treatment in HIV-positive patients with bacillary angiomatosis is not yet known and inadequate therapy may be followed by disseminated disease and a fatal outcome. PCR-based monitoring of the success of treatment is valuable for determining the duration of treatment resulting in a cure.

AIDS-Related Opportunistic Infections↗
PubMed2001

Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers.

Recent studies on the diversity and ubiquity of Fe(III)-reducing organisms in different environments led to the isolation and identification of four new dissimilatory Fe(III)-reducers (strains H-2T, 172T, TACP-2T and TACP-5). All four isolates are non-motile, Gram-negative, freshwater, mesophilic, strict anaerobes with morphology identical to that of Geobacter metallireducens strain GS-15T. Analysis of the 16S rRNA sequences indicated that the new isolates belong to the genus Geobacter, in the delta-Proteobacteria. Significant differences in phenotypic characteristics, DNA-DNA homology and G+C content indicated that the four isolates represent three new species of the genus. The names Geobacter hydrogenophilus sp. nov. (strain H-2T), Geobacter chapellei sp. nov. (strain 172T) and Geobacter grbiciae sp. nov. (strains TACP-2T and TACP-5) are proposed. Geobacter hydrogenophilus and Geobacter chapellei were isolated from a petroleum-contaminated aquifer and a pristine, deep, subsurface aquifer, respectively. Geobacter grbiciae was isolated from aquatic sediments. All of the isolates can obtain energy for growth by coupling the oxidation of acetate to the reduction of Fe(III). The four isolates also coupled Fe(III) reduction to the oxidation of other simple, volatile fatty acids. In addition, Geobacter hydrogenophilus and Geobacter grbiciae were able to oxidize aromatic compounds such as benzoate, whilst Geobacter grbiciae was also able to use the monoaromatic hydrocarbon toluene.

Base Composition↗
PubMed2006

False-negative factor V Leiden genetic testing in a patient with recurrent deep venous thrombosis.

False-negative genetic testing of the factor V Leiden (fVL) mutation is unusual. We report a case of a young woman with a history of deep venous thrombosis tested for the fVL at four separate laboratories on four separate dates. Two laboratories reported the patient to be heterozygous for the fVL, while the other two reported no evidence of a mutation. Testing methods of the various laboratories were reviewed, and additional testing was performed on stored and newly drawn DNA samples, including sequencing of the fVL gene segment. The preponderance of evidence indicates the patient to be heterozygous for the fVL mutation. Dissection of data suggests that either sample misidentification or faulty allele specific amplification methods could have led to false-negative results in two laboratories. In one of the two laboratories, misinterpretation of results and clerical error could not be excluded. There is a need for standardization of optimized fVL genetic testing methods. Further education of ordering physicians on the limitations of genetic testing is necessary.

Adolescent↗
PubMed1985

Form and function of the masticatory musculature in the tree sloths, Bradypus and Choloepus.

The tree sloths, Bradypus and Choloepus, show unusual masticatory specializations, compared to each other and to other mammals. Both have an incomplete zygomatic arch with descending jugal process, a complex superficial masseter, a large temporalis and medial pterygoid musculature, and a lateral pterygoid with two heads. In Choloepus the deep masseter and zygomaticomandibularis are typical when compared to other mammals. However, in Bradypus there is an ascending jugal process from which enlarged and vertically oriented deep masseter and zygomaticomandibularis muscles originate. Although both sloths are folivores, the anterior teeth in Choloepus are caniniform, while those of Bradypus have lost such elongation. In both sloths the glenoid cavity is similarly located; however, in Bradypus the craniomandibular joint is raised above the occlusal plane, and the pterygoid flanges are elongated. Prediction of the evolutionary sequence of cranial changes from Choloepus-like (primitive) to Bradypus-like (derived) morphology is based upon the most parsimonious model of masseter-medial pterygoid complex changes for masticatory efficiency improvement. The model proposes that the condylar neck in Bradypus was elongated and that this single change predicated a series of other structural changes. Mandibular movement patterns in both sloths showed anteromedially directed unilateral power strokes as in other mammals. Puncture-crushing, tooth-sharpening, and chewing cycles are distinct in Choloepus, less so in Bradypus. The masticatory rate is slow in sloths compared to other mammals of similar body size, averaging 590 ms per cycle for Choloepus and 510 ms for Bradypus.

Animals↗

Refine your search to explore more results.