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At least 883 records · Page 49Linked to original sources
PubMed2003

High-resolution methylation analysis and in vivo protein-DNA binding at the promoter of the viral oncogene LMP2A in B cell lines carrying latent Epstein-Barr virus genomes.

Latency protein LMP2A of Epstein-Barr virus (EBV) has been implicated in EBV related tumorigenesis. To understand the host cell dependent expression of the LMP2A gene, it is necessary to analyse the regulatory mechanisms of the LMP2A promoter (LMP2Ap). By transient transfection and in vitro binding analyses two CBF1 sites have previously been shown to be involved in the regulation of LMP2Ap. However, the promoter structure has not been examined at the nucleotide level in vivo. Therefore we undertook a comprehensive analysis of in vivo protein binding and of CpG-methylation patterns at LMP2Ap in a panel of B cell lines carrying latent EBV genomes. The presence of characteristic footprints on two CBF1 and further binding-sites, together with overall hypomethylation of CpG dinucleotides correlated well with promoter activity. In contrast, the absence of several genomic footprints, as well as the presence of patches of highly methylated CpG dinucleotides were characteristic of silent LMP2Aps.

B-Lymphocytes↗
PubMed1999

Metabolic flux analysis: a powerful tool for monitoring tissue function.

In recent years, metabolic flux analysis has been widely used in bioprocess engineering to monitor cell viability and improve strain activity. Metabolic flux analysis refers to a methodology for investigating cellular metabolism whereby intracellular fluxes are calculated using a stoichiometric model for the major intracellular reactions and applying mass balances around intracellular metabolites. A powerful feature of this methodology is its ability to consider cellular biochemistry in terms of reaction networks. By considering the stoichiometry of biochemical reactions, it is possible to estimate the degree of engagement of each pathway participating in overall cellular activity, and hence obtain a comprehensive view of a cell s metabolic state. Given the potential impact of cellular energy metabolism on the function of engineered tissues, such comprehensive analysis of metabolic activity can be an extremely useful tool for tissue engineers. Estimates of intracellular fluxes under various environmental conditions could be used to optimize function in vivo as well as culture conditions in vitro. In this review, we provide a brief theoretical background of metabolic flux analysis and summarize the most widely used experimental approaches to obtain flux data. This review is intended as an overview of the field and as a starting point for tissue engineers wishing to learn about and eventually employ this methodology.

Animals↗
PubMed2025

Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.

BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types. RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings. CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.

Animals↗
PubMed2006

[Effect analysis of surgery for treating abnormal styloid process].

OBJECTIVE: To analyze the relationship between pharyngeal paraesthesia and abnormal styloid process, and to evaluate the surgery outcome. METHODS: One hundred and four patients with styloid process abnormality, especially those with pharyngeal paraesthesia were studied preoperatively and postoperatively. RESULTS: Among 104 patients who complained about foreign body sensation of the pharynx and a sore throat, after partial removal of styloid process, 71.2% (74/104) cured (symptoms disappeared), 12.5% (13/104) improved, while 16.3% (17/104) had no improvement. The responding rate was 83.7% (87/104). CONCLUSIONS: Not all abnormality of styloid process subjects would have pharyngeal paraesthesia, so for this kind of cases a more comprehensive analysis is necessary. Surgery via mouth is preferable.

Adult↗
PubMed2004

[Cardiovascular whole-body MRI: possibilities and limitations in prevention].

Cardiovascular disease is a major challenge to the healthcare with increasing prevalence in western societies. Hence, early detection of cardiovascular pathologies and preventative strategies will experience growing relevance in the future. Magnetic resonance imaging (MRI) nowadays allows a comprehensive analysis of the cardiovascular system. By combining separate examinations of brain, arterial vasculature, and heart the technique permits early detection of pathological changes with high diagnostic accuracy void of adverse events. Such a protocol has been proven feasible and technically robust and can be performed within 45 min. Inherent limitations are low spatial resolution of whole-body MR angiography and lack of functional stress testing of the heart. However, while being suitable as a fast and comprehensive imaging technique for cardiovascular screening purposes, medical consequences and socioeconomic relevance must further be elucidated.

Adult↗
PubMed2005

Transcriptional analysis of in vivo Plasmodium yoelii liver stage gene expression.

The transcriptional repertoire of the in vivo liver stage of Plasmodium has remained largely unidentified and seemingly not amenable to traditional molecular analysis because of the small number of parasites and large number of uninfected hepatocytes. We have overcome this obstruction by utilizing laser capture microdissection to provide a high quality source of parasite mRNA for the construction of a liver stage cDNA library. Sequencing and annotation of this library demonstrated expression of 623 different Plasmodium yoelii genes during development in the hepatocyte. Of these genes, 25% appear to be unique to the liver stage. This is the first comprehensive analysis of in vivo gene expression undertaken for the liver stage of P. yoelii, and provides insights into the differential expression of P. yoelii genes during this critical stage of development.

Animals↗
PubMedDate not supplied

[Better quality of medical care in patients with trauma before hospitalization].

The psychological stability of traveling emergency care teams was under consideration. Reasons affecting, essentially, the human factor under the conditions of time deficit are presented on the basis of an analysis of the experience of the Research Center for Emergency Medical Care as well as on the basis of published data. The acting model of the dispatcher's service, whose activity is targeted at implementing a set of appropriate measures ensuring an optimal decision in a complicated professional situation, is described. It is concluded that a higher quality of medical care before hospitalization demands a balanced approach towards the discussed issue, which should be based on a comprehensive analysis of the positive experience accumulated in other countries and on searching for the mechanisms of adaptation of such experience to the principles existing in Russia.

Decision Making↗
PubMed1995

Internal controls as performance monitors and quantitative standards in the detection by polymerase chain reaction of herpes simplex virus and cytomegalovirus in clinical specimens.

Internal controls (IC) were produced and characterized for an HSV and a CMV PCR assay which serve both as test performance monitors and as quantitative standards. In each of the PCR assays the IC and native targets were amplified with equal efficiency and were detected with the same sensitivity, i.e. < 10 target copies. An algorithm was developed for the use of IC as a quantitative standard which entailed coamplifying a test specimen with four two-fold dilutions of the respective IC target (63-500 copies), followed by regression analysis of the relative yield of amplification products. This approach allowed the determination of both the initial virus genome copy number and the variability of the results, which provided a confidence index for the PCR assay. The relative yields of PCR products were determined by Southern blot and probe hybridization and by densitometry of digitized ethidium bromide-stained gels. Both methods produced estimations of the initial target copy numbers within +/- 40% of the expected value. Such a comprehensive analysis of an internal control for a PCR assay provides a rigorous control of test performance and permits reliable quantitative interpretation of a PCR assay result.

AIDS-Related Opportunistic Infections↗
PubMed2004

Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis.

AIMS: To investigate the potential of amplified fragment length polymorphism (AFLP) profiling for genotyping Arcobacter butzleri and to obtain further data on the genetic diversity of this organism. METHODS AND RESULTS: Seventy-three isolates of Danish, British, Turkish, Swedish, Nigerian and North American origin from human infections, chickens, turkeys, ducks, sheep and poultry abbatoir effluent were studied by use of a protocol that involved stringent PCR amplification of fragments derived from digestion of genomic DNA with restriction enzymes BglII and Csp6I. The mean similarity value of duplicate profiles of 10 isolates was 91.15%, indicating the method to be reproducible. Numerical analysis of all 73 isolates distinguished 51 subtypes at the 91% similarity level, of which 39 comprised single strains. The remaining 34 isolates were distributed among 12 subtypes, each of which contained strains homogeneous with respect to their respective source of isolation. However, contemporaneous strains from the same source could also be distinguished. CONCLUSIONS: AFLP profiling is an effective method for typing the genetically diverse organism A. butzleri. SIGNIFICANCE AND IMPACT OF THE STUDY: The study represents a comprehensive analysis of the genetic diversity of A. butzleri by use of isolates from six countries spanning three continents and also shows that several distinct A. butzleri genotypes may be found in a given environment. AFLP profiling appears to have considerable potential for molecular epidemiological studies of this ubiquitous emerging pathogen that is implicated as a causative agent of both human and animal disease.

Abattoirs↗
PubMedDate not supplied

[Two-parameter flow fluorescence analysis of human chromosomes. Quantitative processing].

A procedure for the quantitative analysis of the results of fluorimetric studies on human chromosomes in a flow is described. The procedure enables one to simultaneously follow two parameters by using two fluorochromes, one of which is selective to the GC-, and the other, to AT base pairs of DNA. Thus, it becomes possible to derive from the experimentally obtained distributions an information on the relative DNA content in individual chromosomes, differences in DNA content between homologous chromosomes, the relative number of chromosomes of each type in the sample tested, as well as on the percent ratio of AT and GC base pairs in a particular chromosome. In addition, the procedure enables one to assign, with a high degree of accuracy, the peaks on experimental distributions to the objects of analysis chromosomes. The analysis cutting off the extreme combines the method of components with the least square method, as applied to the peaks of the Gaussian shape. The first step involves the filtration of the starting experimental data from contaminating signals from both the parts of degraded chromosomes and stained cytoplasm fragments, and from chromosome aggregates. The procedure is realized as a package of programs for IBM-compatible PC/AT computers (486 and later versions), which permits one to perform a comprehensive analysis of two-parameter distributions of chromosome fluorescence signals to solve a number of problems, such as the identification of chromosome aberrations in cell lines tested, quantitative comparison of distinguishing features of homologous chromosomes and whole chromosome sets.

Chromosomes, Human↗
PubMed2006

Multidimensional chromatographic techniques for hydrophilic copolymers II. Analysis of poly(ethylene glycol)-poly(vinyl acetate) graft copolymers.

A large variety of hydrophilic copolymers is applied in different fields of chemical industry including bio, pharma and pharmaceutical applications. For example, poly(ethylene glycol)-poly(vinyl alcohol) graft copolymers that are used as tablet coatings are responsible for the controlled release of the active compounds. These copolymers are produced by grafting of vinyl acetate onto polyethylene glycol (PEG) and subsequent hydrolysis of the poly(ethylene glycol)-poly(vinyl acetate) graft copolymers. The poly(ethylene glycol)-poly(vinyl acetate) copolymers are distributed with regard to molar mass and chemical composition. In addition, they frequently contain the homopolymers polyethylene glycol and polyvinyl acetate. The comprehensive analysis of such complex systems requires hyphenated analytical techniques, including two-dimensional liquid chromatography and combined LC and nuclear magnetic resonance spectroscopy. The development and application of these techniques are discussed in the present paper.

Chromatography, Liquid↗
PubMed2005

Glycosphingolipid structural analysis and glycosphingolipidomics.

Sphingosines, or sphingoids, are a family of naturally occurring long-chain hydrocarbon derivatives sharing a common 1,3-dihydroxy-2-amino-backbone motif. The majority of sphingolipids, as their derivatives are collectively known, can be found in cell membranes in the form of amphiphilic conjugates, each composed of a polar head group attached to an N-acylated sphingoid, or ceramide. Glycosphingolipids (GSLs), which are the glycosides of either ceramide or myo-inositol-(1-O)-phosphoryl-(O-1)-ceramide, are a structurally and functionally diverse sphingolipid subclass; GSLs are ubiquitously distributed among all eukaryotic species and are found in some bacteria. Since GSLs are secondary metabolites, direct and comprehensive analysis (metabolomics) must be considered an essential complement to genomic and proteomic approaches for establishing the structural repertoire within an organism and deducing its possible functional roles. The glycosphingolipidome clearly comprises an important and extensive subset of both the glycome and the lipidome, but the complexities of GSL structure, biosynthesis, and function form the outlines of a considerable analytical problem, especially since their structural diversity confers by extension an enormous variability with respect to physicochemical properties. This chapter covers selected developments and applications of techniques in mass spectrometric (MS) that have contributed to GSL structural analysis and glycosphingolipidomics since 1990. Sections are included on basic characteristics of ionization and fragmentation of permethylated GSLs and of lithium-adducted nonderivatized GSLs under positive-ion electrospray ionization mass spectrometry (ESI-MS) and collision-induced mass spectrometry (CID-MS) conditions; on the analysis of sulfatides, mainly using negative-ion techniques; and on selected applications of ESI-MS and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to emerging GSL structural, functional, and analytical issues. The latter section includes a particular focus on evolving techniques for analysis of gangliosides, GSLs containing sialic acid, as well as on characterizations of GSLs from selected nonmammalian eukaryotes, such as dipterans, nematodes, cestodes, and fungi. Additional sections focus on the issue of whether it is better to leave GSLs intact or remove the ceramide; on development and uses of thin-layer chromatography (TLC) blotting and TLC-MS techniques; and on emerging issues of high-throughput analysis, including the use of flow injection, liquid chromatography mass spectrometry (LC-MS), and capillary electrophoresis mass spectrometry (CE-MS).

Animals↗
PubMed1993

Isolation and identification of six Pneumocystis carinii genes utilizing codon bias.

Pneumocystis carinii pneumonia (PCP) is a leading cause of death among AIDS patients in the United States. Our analysis of P. carinii protein-coding genes has revealed a significant A + T codon bias. Polymerase chain reaction (PCR) was utilized to isolate and identify the genes encoding calmodulin, beta-tubulin, DNA polymerase II, and RNA polymerases I, II and III from P. carinii. Primer pairs were designed to incorporate P. carinii codon preference to known conserved protein regions from other organisms. This strategy should be useful for a large variety of P. carinii genes and assist in the comprehensive analysis of the genomic structure of this important pathogen.

Amino Acid Sequence↗
PubMed2001

Attentional processes in autism.

Attentional processes in individuals with high-functioning autism were compared with a matched control group. Participants for the study were 103 children and adults with autism and 103 control subjects. Measures administered corresponded to Mirsky et al.'s (1991) factor analysis of tests of attention. Diminished performance was noted on measures that loaded on the Focus-Execute and Shift factors, but not on the Sustain and Encode factors. For tests in which psychomotor speed was used as the score, and the difference between groups was significant, covariance analyses were performed, using tests of basic motor functions as covariates. This procedure led to attenuation to the point of nonsignificant differences in the case of some of the attention tests. Thus, this comprehensive analysis of attention in individuals with high-functioning autism only found differences on measures in which the task placed demands on cognitive flexibility or psychomotor speed. Thus, purported attention deficits in autism may actually be primary deficits in complex decision making or psychomotor abilities.

Adolescent↗
PubMed1998

Particle beam therapy (hadrontherapy): basis for interest and clinical experience.

The particle or hadron beams deployed in radiotherapy (protons, neutrons and helium, carbon, oxygen and neon ions) have physical and radiobiological characteristics which differ from those of conventional radiotherapy beams (photons) and which offer a number of theoretical advantages over conventional radiotherapy. After briefly describing the properties of hadron beams in comparison to photons, this review discusses the indications for hadrontherapy and analyses accumulated experience on the use of this modality to treat mainly neoplastic lesions, as published by the relatively few hadrontherapy centres operating around the world. The analysis indicates that for selected patients and tumours (particularly uveal melanomas and base of skull/spinal chordomas and chondrosarcomas), hadrontherapy produces greater disease-free survival. The advantages of hadrontherapy are most promisingly realised when used in conjunction with modern patient positioning, radiation delivery and focusing techniques (e.g. on-line imaging, three-dimensional conformal radiotherapy) developed to improve the efficacy of photon therapy. Although the construction and running costs of hadrontherapy units are considerably greater than those of conventional facilities, a comprehensive analysis that considers all the costs, particularly those resulting from the failure of less effective conventional radiotherapy, might indicate that hadrontherapy could be cost effective. In conclusion, the growing interest in this form of treatment seems to be fully justified by the results obtained to date, although more efficacy and dosing studies are required.

Central Nervous System Neoplasms↗
PubMed1982

Analysis of enzymatically released peptides by reverse-phase high performance liquid chromatography from picomole amounts of apolipoproteins separated on polyacrylamide isoelectric focusing gels.

Methods were developed for the peptide analysis of individual isoproteins of human apolipoproteins separated on urea-polyacrylamide isoelectric focusing (IEF) gels. After IEF the proteins were fixed in the gel matrix by trichloroacetic acid precipitation. Low molecular weight contaminants, including ampholytes, were removed and the proteins were chemically desialylated. Enzymatic digestions with L-1-tosyl-2-phenylethylchloromethyl ketone - trypsin, chymotrypsin, or with thermolysin were accomplished within the gel matrix. The proteolytically released peptides were analyzed by reverse-phase high performance liquid chromatography. These methods facilitated the comprehensive analysis of protein structural differences between individual isoproteins of apolipoproteins in duplicate with as little as 1-2 nmol of each isoprotein, without the use of radiolabels. Human apolipoproteins A-I, C, and E were analysed by these methods.

Animals↗
PubMed2004

New cytokine-dependent acute myeloid leukemia cell line MUTZ-11 with disomic chromosome rearrangement t(16;17).

Continuous human leukemia-lymphoma (LL) cell lines represent a rich resource of abundant, accessible and manipulable living cells contributing significantly to a better understanding of the pathophysiology of hematopoietic tumors. In particular, classical and molecular cytogenetics have benefitted enormously from the availability of LL cell lines with specific chromosomal abnormalities. Such aberrations may be the portal to the discovery of novel oncogene rearrangements for which positive cell lines provide a resource for both discovery and functional studies. The new continuous leukemia cell line MUTZ-11 was established in 1994 from the peripheral blood of a 60-year-old woman with acute myeloid leukemia (AML) M4 (following 2 years with myelodysplastic syndromes). DNA fingerprinting confirmed the authenticity and derivation of the cell line. The immunoprofile as determined by flow cytometry was as follows: positive for myelocytic markers (CD13, CD15, CD33, CD65 and CD68), negative for T-cell (except for CD4 and CD7), B-cell and erythroid-megakaryocytic markers. The cell line is constitutively cytokine-dependent and growth depends on externally added cytokines. With regard to cytokine receptor expression, the cell line was found to be positive for GM-CSFRalpha (granulocyte-macrophage colony-stimulating factor receptor, CD116), Kit (CD117) and IL-3Ralpha (interleukin-3 receptor, CD123). The cytokine response profiles as determined by [(3)H]-thymidine incorporation assay were: 2-to-12 fold growth stimulation of MUTZ-11 by GM-CSF, IFN-alpha (interferon), IFN-beta, IFN-gamma, IL-3 and SCF (stem cell factor); growth inhibition by TGF-beta1 (transforming growth factor), TNF-alpha (tumor necrosis factor) and TNF-beta. Cytogenetic analysis showed the following consensus karyotype: 46, XX, der(16)t(16;17)(p13.3;q23)x2. Previous molecular biological analysis documented that MUTZ-11 cells carry both an FLT3 internal tandem duplication (ITD) and an MLL partial tandem duplication (PTD). The scientific significance of MUTZ-11 lies (i). in the absolute cytokine-dependency and the proliferative response to various cytokines, (ii). in the unique cytogenetic (disomic t(16;17)) and (iii). molecular biological alterations (FLT3 ITD + MLL PTD). In summary, the new cytokine-dependent AML-derived cell line MUTZ-11 displays unique novel features and emphasizes the need for comprehensive analysis of new LL cell lines which may lead to the discovery of important pathogenetic alterations.

Cell Division↗
PubMed2004

Rice proteomics: recent developments and analysis of nuclear proteins.

Rice is the most important cereal crop in Asia, and is considered as a model cereal plant for genetic and molecular studies. An immense progress has been made in rice genome sequence analysis during the last decade. This prompted the researcher to identify the functions, modifications, and regulations of every encoded protein. Proteome analysis provides information to predict the translation and relative concentration of gene products, including the extent of modification, none of which can be accurately predicted from the nucleic acid sequence alone. During the last couple of years, considerable researches were conducted to analyze rice proteome, and only recently a remarkable progress has been made to systematically analyze and characterize the functional role of various tissues and organelles in rice. In this review, the rice proteomic research has been compiled and also presented a comprehensive analysis of rice nuclear proteins. In rice nucleus, 549 proteins were resolved using 2D-PAGE. Among them, 257 proteins were systematically analyzed by Edman sequencing and mass spectrometry and identified 190 proteins following database searching (http://gene64.dna.affrc.go.jp/RPD/main.html). The identified proteins were sorted into different functional categories. In these data, the proteins involved in signaling and gene regulations dominated others, reflecting the role of nucleus in gene expression and regulation.

Cell Nucleus↗