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Gene profiling of high risk neuroblastoma.

Neuroblastoma, a cancer of young children, is well known for its diverse pattern of presentation. Approximately one-half of children have localized tumors that can be cured with surgery alone. The remaining children have widespread metastatic disease or quite large, aggressive, localized tumors. These children have a poor long-term survival rate of approximately 30%. We review the prognostically significant histologic and molecular features of high risk neuroblastoma and propose an algorithm to dissect further the differentially expressed genes that define the phenotype of this disease. Over the past 25 years, much effort has gone into establishing reliable prognostic indicators of high risk disease. For neuroblastoma, age, stage, and histopathology have time and again correlated well with outcomes. Chromosomal number, or ploidy, and amplification of the MYCN oncogene have proved to be equally as important and are commonly used to stratify patient risk. Other potentially lucrative markers include chromosome 1p deletion, chromosome 17q gain, receptor tyrosine kinases A and B (trk-A, trk-B), CD44, CXCR4, and multidrug resistance associated protein (MRP). With the onset of new technology, expression microarrays are now being used to profile advanced-stage neuroblastoma on a larger scale. Genes particular to cell cycle control, DNA/RNA replication, ribosomal synthesis, neuronal differentiation, and intracellular/extracellular signal transduction have been identified through differential expression analysis. We present our research on the MYCN transcription factor and target gene, MCM7, to show the utility of this approach.

Age Factors↗

Identification of genes expressed in human CD34(+) hematopoietic stem/progenitor cells by expressed sequence tags and efficient full-length cDNA cloning.

Hematopoietic stem/progenitor cells (HSPCs) possess the potentials of self-renewal, proliferation, and differentiation toward different lineages of blood cells. These cells not only play a primordial role in hematopoietic development but also have important clinical application. Characterization of the gene expression profile in CD34(+) HSPCs may lead to a better understanding of the regulation of normal and pathological hematopoiesis. In the present work, genes expressed in human umbilical cord blood CD34(+) cells were catalogued by partially sequencing a large amount of cDNA clones [or expressed sequence tags (ESTs)] and analyzing these sequences with the tools of bioinformatics. Among 9,866 ESTs thus obtained, 4,697 (47.6%) showed identity to known genes in the GenBank database, 2, 603 (26.4%) matched to the ESTs previously deposited in a public domain database, 1,415 (14.3%) were previously undescribed ESTs, and the remaining 1,151 (11.7%) were mitochondrial DNA, ribosomal RNA, or repetitive (Alu or L1) sequences. Integration of ESTs of known genes generated a profile including 855 genes that could be divided into different categories according to their functions. Some (8.2%) of the genes in this profile were considered related to early hematopoiesis. The possible function of ESTs corresponding to so far unknown genes were approached by means of homology and functional motif searches. Moreover, attempts were made to generate libraries enriched for full-length cDNAs, to better explore the genes in HSPCs. Nearly 60% of the cDNA clones of mRNA under 2 kb in our libraries had 5' ends upstream of the first ATG codon of the ORF. With this satisfactory result, we have developed an efficient working system that allowed fast sequencing of 32 full-length cDNAs, 16 of them being mapped to the chromosomes with radiation hybrid panels. This work may lay a basis for the further research on the molecular network of hematopoietic regulation.

ATPases Associated with Diverse Cellular Activitie↗

The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri.

The taxonomic position of the nitrogen-fixing rice isolate A15, previously classified as Alcaligenes faecalis, was reinvestigated. On the basis of its small subunit ribosomal RNA (16S rRNA) sequence this strain identifies as Pseudomonas stutzeri. Phenotyping and fatty acid profiling confirm this result. DNA:DNA hybridisations, using the optical renaturation rate method, between strain A15 and Pseudomonas stutzeri LMG 11199T revealed a mean DNA-binding of 77%. The identification was further corroborated by comparative sequence analysis of the oprF gene, which encodes the major outer membrane protein of rRNA homology group I pseudomonads. Furthermore we determined the nifH sequence of this strain and of two putative diazotrophic Pseudomonas spp. and made a comparative analysis with sequences of other diazotrophs. These Pseudomonas NifH sequences cluster with NifH sequences isolated from the rice rhizosphere by PCR and of proteobacteria from the beta and gamma subclasses.

Alcaligenes↗

Insulin effects on protein synthesis and secretion in primary cultures of amphibian hepatocytes.

The objective of the present study was to determine the effects of insulin on amphibian hepatocytes in primary culture. Hepatocytes were isolated from adult bullfrogs by collagenase perfusion and maintained as monolayers in serum-free medium. Cells cultured in the continuous presence of insulin exhibited a relatively constant rate of protein secretion over the first four to five days, whereas controls showed an almost three-fold decrease over the same time period. The decline in secreted proteins was equally represented in most exported proteins, except that serum albumin secretion showed twice as much of a decrease relative to the other proteins. The maintenance of protein secretion by insulin was the result of its effect on protein synthesis. The rate of protein synthesis was measured by the incorporation of (3H)-leucine into protein using culture medium containing 0.5 mM leucine, a condition where the specific radioactivity of leucyl-tRNA was shown to be equal to that of (3H)-leucine in the medium. Cultures maintained with insulin for 60 hours synthesized protein at two to three times the rate found in non-insulin treated controls whose rate of protein synthesis was first detectably decreased after nine hours of culture in the insulin-free medium. Sedimentation profiles of polyribosomes from hepatocytes maintained for 60 hours without insulin showed proportionately fewer ribosomes in large polysomes and more in monosomes and free ribosomal subunits than ribosomes from cells cultured with insulin. This result suggests that the decrease in protein synthesis found in the absence of insulin is due to a defect in initiation. Insulin does not exert its effect by regulating cellular levels of ATP; no change in ATP content was found in cells maintained with or without insulin. The results show that insulin maintains high levels of protein synthesis and secretion in amphibian hepatocytes. The hepatocytes in monlayer culture provide a system to study the molecular mechanisms involved in the translational control of protein synthesis by insulin.

Albumins↗

Transcriptome-Wide Analysis of the 5' Cap Status of RNA Using 5' Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing.

Eukaryotic mRNAs carry an N7-methylguanosine (m7G) cap structure at their 5' extremity, which protects them from the degradation by 5'-3' exoribonucleases and plays a pivotal role in mRNA metabolism, promoting splicing, nuclear export, and translation. Decapping, the enzymatic process that removes this structure, is a key event during cytoplasmic mRNA 5'-3' decay, leading to the degradation of the transcript body by Xrn1. In this chapter, we describe a procedure to assess the cap status of RNA at the transcriptome level. It is based on a treatment of total RNA extracts with a 5' monophosphate-dependent exonuclease, which like Xrn1 specifically degrades decapped RNAs harboring 5' monophosphate extremities, but not RNAs with intact m7G cap. The digested RNAs are then analyzed by RNA sequencing.

Exoribonucleases↗

Chromosomal and nuclear distribution of the HindIII 1.9-kb human DNA repeat segment.

A human interspersed repetitive DNA cloned in pBR322, the HindIII 1.9-kb (kilobase pair) sequence, was labeled with biotinylated dUTP and hybridized to acid-fixed chromosomes and paraformaldehyde-fixed whole cells in situ. Using our most sensitive detection techniques this probe highlighted on the order of 200 discrete loci, in punctate or banded arrays, that resembled a Giemsa-dark band pattern on chromosome arms. Interphase cells also displayed many discrete punctate spots of hybridization along chromosome fibers. The ubiquitous Alu sequence repeat also appeared to be concentrated in specific regions of the chromosome and predominantly highlighted Giemsa-light bands. Centromeric or ribosomal spacer DNA repeats used as controls in all studies gave the expected hybridization profiles and showed no non-specific labeling of chromosome arms. Cohesive groups of centromeric DNA arrays and rDNA clusters were observed in interphase nuclei. Refinements in methods for detecting biotin-labeled probes in situ were developed during these studies and calculations indicated that about 20 kb or more of the 1.9-kb repeat were present at each hybridization site. The chromosomal distribution of the 1.9-kb repeat suggests that this sequence may reflect, or participate in defining, ordered structural domains along the chromosome.

Base Composition↗

Electrophoretic karyotyping and gene mapping of seven formae speciales in Fusarium solani.

Chromosomal DNAs of 22 strains in 7 formae speciales (f. spp.) of Fusarium solani were compared by pulsed field gel electrophoresis (PFGE) and gene mapping on the chromosomes. Using PFGE, complete separation of the full components of the genome was not attained, due to the limited resolution of large chromosomes, but 5-12 chromosomes with sizes of 0.6-5.7 Mbp were resolvable for every strain. Although each strain had a unique banding profile, similarity in the banding profile was noticed among strains of the same (f. sp.). In gene mapping, the ribosomal RNA gene (rDNA) and putative pathogenesis-related genes encoding kievitone hydratase (khs), pisatin demethylase (pda) and pectate-degrading enzyme (pelA) were located on the chromosomes separated by PFGE. rDNA was always detected on the stacked large bands of 5.2-5.7 Mbp. The khs gene was detected on a chromosome of 2.8-5.4 Mbp in all f. sp. phaseoli strains and one strain of f. sp. pisi. The pda gene was detected on a chromosome of 1.4-5.6 Mbp in f. sp. pisi and pelA was localized on a chromosome of 2.3-2.9 Mbp in f. spp. pisi, xanthoxyli, batatas and mori. The results of PFGE and Southern blot hybridization supported the idea that each f. sp. of F. solani (or mating population of the teleomorph Nectria haematococca) has a distinctive genomic organization, as previously inferred from molecular phylogenetic analyses.

Chromosome Mapping↗

Sequential alterations of neuronal architecture in nucleus magnocellularis of the developing chicken: an electron microscope study.

The development of the auditory nerve endings and their target cells in nucleus magnocellularis was studied by electron microscopy of perfusion-fixed brains from embryonic day 12 to hatching. Embryonic days 12-13: somatic processes extend from the perikaryon. The cytoplasm of the soma and processes contains free ribosomes, mitochondria, lysosomes, rough endoplasmic reticulum, Golgi apparatus and an eccentric, heterochromatic nucleus. Small profiles of auditory nerve fibers containing round, clear vesicles make specialized contacts, including some synapses, on distal somatic processes but rarely on proximal somatic processes or on the soma. The postsynaptic zones contain a flocculent matrix. Days 15-17: somatic processes disappear and occasional attachment plaques are seen between cell bodies. The nucleus appears euchromatic. Cytoplasmic organelles form a dense matrix indicative of intense metabolic activity. Somatic spines are evident. The afferent axons form large, vesiculated profiles located, increasingly, on the cell body and somatic spines, with many points of synaptic contact. Opposite each ending a band of amorphous, flocculent material fills the postsynaptic cytoplasm. Embryonic day 18-hatching: the somatic cytoplasm becomes less dense; stacks of rough endoplasmic reticulum start to condense. Afferent axon terminals mature, especially the synaptic membrane complex and associated densities. The postsynaptic flocculent material diminishes in extent until it is found associated only with somatic spines. The ultrastructural observations on the maturation of nucleus magnocellularis closely corroborate and extend previous results with the Golgi methods. Developing auditory nerve fibers initially synapse on the distal parts of the somatic processes of the immature cells. As the somatic processes disappear or retract, axonal endings move to the soma and develop into large axosomatic end-bulbs. Possibly, the somatic processes as they retract drag the auditory nerve endings to the cell body. The findings also suggest a role of the transiently appearing, flocculent material of the postsynaptic regions in the formation of synapses.

Animals↗

Electron microscopic immunocytochemical study of somatostatin neurons in the periventricular nucleus of the rat hypothalamus with special reference to their relationships with homologous neuronal processes.

The neurons containing somatostatin in the rat periventricular nucleus were studied by using a modified electron microscopic immunocytochemical technique that improves both the penetration of immunoreagents into unembedded immunostained tissues and the preservation of ultrastructural morphology. Inside perikarya and dendrites, immunostaining was not only associated with neurosecretory granules but also with ribosomes and saccules of the cis face of the Golgi apparatus. In the axonal profiles found in this region the labeling was observed both on neurosecretory granule cores and on the limiting membrane of small synaptic-like vesicles. Throughout the periventricular nucleus, both non-synaptic and synaptic relationships were shown between labeled neurons. Non-synaptic relationships mainly consisted of direct apposition of the membranes of neighboring neurons by dendrosomatic, somasomatic or dendrodendritic contacts. These labeled perikarya and dendrites were also synaptically contacted by labeled axonal endings containing numerous aggregated synaptic-like vesicles. The physiological significance of the synaptic and non-synaptic relationships between somatostatinergic neurons is discussed in terms of possible synchronization between homologous neurons of the somatostatin neuroendocrine system and control of these neurons by a central ultra-short loop feedback mechanism.

Animals↗

Molecular detection and direct enumeration of methanogenic Archaea and methanotrophic Bacteria in domestic solid waste landfill soils.

Methane oxidizing and producing activities of cover soil (10, 30 cm depth) and burial waste (1, 3 m depth) were evaluated: top cover soil (10 cm) had the highest methane oxidizing activity, while 1 m depth buried waste showed the highest methane producing potential. All the sequences of the 1 m sample were found to be closely related to 16S rDNAs of mainly hydrogenotrophic methanogens known, such as genera Methanosarcina, Methanoculleus, and Methanobacterium. We developed a modified fluorescence in situ hybridization (FISH) direct counting method for landfill samples, resulting in the detection of approx. 1% of total cells as archaeal cells (presumably methanogens). However, probe-positive cells could not be found with probes for methanotrophs by the methods.

Archaea↗

Development and validation of an instrument to measure the effects of a mistletoe preparation on quality of life of cancer patients: the Life Quality Lectin-53 (LQL-53) Questionnaire.

Mistletoe preparations standardised to the content of mistletoe lectin are supposed to improve quality of life (QoL) in patients with cancer. To obtain a validated and sensitive research instrument, the Life Quality Lectin-53 (LQL-53) Questionnaire was developed in three phases: item generation via interviews with 42 patients, item selection by means of a study with 109 cancer patients, and psychometric testing. The LQL-53 includes 46 items assigned to the subscales 'General well-being', 'Emotional well-being', 'Vitality' 'Hope', 'Locus of control', Social relationships', and 'Physical complaints', plus seven items dealing with possible adverse effects of mistletoe treatment. Psychometric testing was carried out in a study with 112 patients with solid tumours who were treated with a mistletoe preparation standardised to mistletoe lectins for 12 weeks. Internal consistency (Cronbach's alpha) was between 0.72 and 0.94. Test-retest reliability was > or = r of 0.72. Subscales correlated highly with external criteria. Construct validity, as determined by Multitrait Scaling Analysis, resulted in an optimal assignment of items to subscales (scaling success) for four of the subscales. During the course of the therapy, significant improvement in QoL was found in all subscales. In two of the subscales, effect size was high (>0.80), and in five other subscales it varied between 0.53 and 0.78.

Adjuvants, Immunologic↗

Biogenesis of the crystalloid endoplasmic reticulum in UT-1 cells: evidence that newly formed endoplasmic reticulum emerges from the nuclear envelope.

The crystalloid endoplasmic reticulum (ER), a specialized smooth ER of the compactin-resistant UT-1 cell, is composed of multiple membrane tubules packed together in a hexagonal pattern. This membrane contains large amounts of 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, an integral membrane protein that enzymatically regulates endogenous cholesterol biosynthesis. Using morphological and immunocytochemical techniques, we have traced the sequence of events in the biogenesis of this ER when compactin-withdrawn UT-1 cells, which do not have a crystalloid ER, are incubated in the presence of compactin. After 15 h of incubation in the presence of compactin, many cells had profiles of ER cisternae that were juxtaposed to the nuclear envelope and studded with ribosomes on their outer membrane. Both the outer nuclear membrane and the ER membrane contained HMG CoA reductase; however, there was little or no detectable enzyme in rough ER that was free in the cytoplasm. With longer times of incubation in the presence of compactin, these cells had lamellar stacks of smooth ER next to the nuclear envelope that contained HMG CoA reductase. Coordinate with the appearance of the smooth ER, crystalloid ER appeared in the same cell. Often regions of continuity were found between the membrane of the smooth ER and the membrane of the crystalloid ER tubules. These studies suggest that HMG CoA reductase is synthesized along the outer nuclear membrane and in response to increased enzyme synthesis, a membrane emerges from the outer nuclear membrane as smooth ER cisternae, which then transforms into crystalloid ER tubules.

Acyl Coenzyme A↗

Fine structural aspects of the anterior necrotic zone in the leg bud of the chick embryo.

A fine structural study was undertaken on the area called the anterior necrotic zone of leg buds of the chick embryo at stages 22-29. Physiologically dying cells, which were distributed in the mesenchymal area, were characterized by increased electron density of the cytoplasm, appearance of electron lucent vacuoles and condensed chromatin pattern. Many of the dying cells seemed to be fragmented into several pieces of cell debris during the necrotic process. Two kinds of cells were observed to take up the necrotic cells; one type, large cells 15 microns or more in size and irregular in shape, which had lysosomes, extended microvillus-like cytoplasmic projections and pseudopods, took up pieces of necrotic cells by phagocytosis and stored them in acid phosphate-negative and -positive vacuoles. The other type was several microns in diameter with numerous free ribosomes and stored a small number of vacuoles containing cell debris. At stage 29, profiles of necrotic cells lying free in the mesenchymal area, and cells containing one or two vacuoles filled with cell debris decreased in number as well as large cells containing numerous vacuoles, whose contents seemed to be degraded. When pieces of the anterior portion of chick leg buds at stage 24 were organ-cultured for 3 days after glutaraldehyde-fixed mouse red blood cells were injected, the red blood cells were taken up into cells in the mesenchymal area. Formation of large cells containing numerous vacuoles stuffed with red blood cells was rare. These findings may imply that most necrotic cells in the anterior necrotic zone are disposed of by macrophages and that some are endocytosed by mesenchymal cells.

Acid Phosphatase↗

[Kinetics of the in vivo synthesis of the polypeptide chain; the effect of translation inhibitors].

Effects of aurinetricarbonic acid and cycloheximide on kinetics of polypeptide chain synthesis and polyribosome protile in mouse liver cell in vivo are studied. Both compounds are found to decrease the absolute rate of protein synthesis and to increase the time of polypeptide synthesis. Cycloheximide changed the ratio of translating and non-translating ribosomes and different in size polyribosome types. Aurinetricarbonic acid exerts no effect on polyribosome profile. Effects of cycloheximide and aurinetricarbonic acid on kinetic parameters of translation and a mechanism of action of these compounds are studied.

Animals↗

Fine structure of the retinal pigment epithelium of the mallard duck (Anas platyrhynchos).

As part of a comparative morphological study, the fine structure of the retinal pigment epithelium (RPE), the choriocapillaris and Bruch's membrane (complexus basalis) has been investigated by light and electron microscopy in the mallard (Anas platyrhynchos). In this species the RPE consists of a single layer of cuboidal cells which display numerous very deep basal (scleral) infoldings and extensive apical (vitreal) processes which enclose photoreceptor outer segments. The RPE cells are joined laterally by prominent basally-located tight junctions. Internally smooth endoplasmic reticulum is the most abundant cell organelle with only small amounts of rough endoplasmic reticulum present. Polysomes are abundant as are basally-located mitochondria which often displayed a ring-shaped profile. The cell nucleus is large and vesicular. Melanosomes are plentiful only within the apical processes of the RPE cells in the light-adapted state. Myeloid bodies are large and numerous and very often have ribosomes on their outer surface. Bruch's membrane (complexus basalis) shows a pentalaminate structure but with only a poorly represented central elastic lamina. Profiles of the choriocapillaris are relatively small and the endothelium of these capillaries while extremely thin facing the retinal epithelium is but minimally fenestrated.

Animals↗

Expression profiling of translation-associated genes in sporulating Bacillus subtilis and consequence of sporulation by gene inactivation.

A DNA microarray technique was used to demonstrate global changes in the transcription pattern of translation-associated genes that encode fifty-four ribosomal proteins including a putative ribosomal gene, and eleven translation factors in sporulating B. subtilis. We found that the mRNA levels of nine genes involved in the translation system, which include the genes for three ribosomal proteins (rpmA, rpmGB, and ctc) and two translation factors (efp, and frr), were maintained at a high level at the onset of sporulation. The ypfD gene, which encodes the ribosomal protein S1 homologue, was also found to be expressed significantly during the early sporulation stage. In order to demonstrate the significance of these genes for sporulation, mutants were constructed using the pMutinT3 disruption vector. We detected an impaired sporulation in the mutants of rpmA (gene for the ribosomal protein L27), efp (elongation factor P), frr (ribosome recycling factor), and ypfD. The effect was especially pronounced in the efp mutant, sporulation of which was entirely abolished without affecting growth. The reduced expression of rpmGB (ribosomal protein L33) resulted in an impaired sporulation only at a high temperature (47 degrees C). Only the rplI mutant, which encodes the ribosomal protein L9, could not be obtained, implying that its function is essential for viability. Thus, we successfully demonstrated the significance of several translation-associated genes in sporulation by using the results of the gene expression profiling.

Bacillus subtilis↗

Genotypic and phenotypic studies of murine intestinal lactobacilli: species differences in mice with and without colitis.

Lactobacilli represent components of the commensal mammalian gastrointestinal microbiota and are useful as probiotics, functional foods, and dairy products. This study includes systematic polyphasic analyses of murine intestinal Lactobacillus isolates and correlation of taxonomic findings with data from cytokine production assays. Lactobacilli were recovered from mice with microbiota-dependent colitis (interleukin-10 [IL-10]-deficient C57BL/6 mice) and from mice without colitis (Swiss Webster and inducible nitric oxide synthetase-deficient C57BL/6 mice). Polyphasic analyses were performed to elucidate taxonomic relationships among 88 reference and murine gastrointestinal lactobacilli. Genotypic tests included single-locus analyses (16S ribosomal DNA sequencing and 16S-23S rRNA intergenic spacer region PCR) and genomic DNA profiling (repetitive DNA element-based PCR), and phenotypic analyses encompassed more than 50 tests for carbohydrate utilization, enzyme production, and antimicrobial resistance. From 20 mice without colitis, six Lactobacillus species were recovered; the majority of the mice were colonized with L. reuteri or L. murinus (72% of isolates). In contrast, only, L. johnsonii was isolated from 14 IL-10-deficient mice. Using an in vitro assay, we screened murine isolates for their ability to inhibit tumor necrosis factor alpha (TNF-alpha) secretion by lipopolysaccharide-activated macrophages. Interestingly, a subpopulation of lactobacilli recovered from mice without colitis displayed TNF-alpha inhibitory properties, whereas none of the L. johnsonii isolates from IL-10-deficient mice exhibited this effect. We propose that differences among intestinal Lactobacillus populations in mammals, combined with host genetic susceptibilities, may account partly for variations in host mucosal responses.

Animals↗

Thermo-tolerant Campylobacter fetus bacteraemia identified by 16S ribosomal RNA gene sequencing: an emerging pathogen in immunocompromised patients.

Eight Campylobacter isolates that were able to grow at 25 degrees C and 42 degrees C and had the same biochemical profile were isolated from the blood of eight immunocompromised patients. Conventional biochemical tests were unable to determine whether they were isolates of thermo-tolerant C. fetus, H2S-negative C hyointestinalis, or a new Campylobacter species. Sequencing of the 16S ribosomal RNA genes showed that all eight isolates had the same nucleotide sequence and this was identical to that of C. fetus (GenBank accession no. AF219233). All eight patients had underlying disease and two died despite antibiotic treatment. Because of the ability of C fetus to grow over a wide range of temperatures and a higher incidence of bacteraemia by this organism than C. jejuni in the past 5 years in Hong Kong, thermo-tolerant C fetus may be an emerging pathogen in immunocompromised patients in the years to come.

Aged↗