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Insights into extramedullary tumour cell growth revealed by expression profiling of human plasmacytomas and multiple myeloma.

Malignant plasma cells generally grow within the bone marrow microenvironment; however, they can also grow at extramedullary sites. To identify the tumour-specific alterations required for extramedullary growth, we analysed the expression profiles of a series of plasma cell neoplasms including primary multiple myeloma (MM), plasma cell leukaemia (PCL) and extramedullary plasmacytoma (EPC). Hierarchical clustering analysis segregated the EPCs from the remaining samples, and revealed an expression pattern associated with angiogenesis in the EPCs, involving higher expression of the genes TIE2, NOTCH3, CD31 and endoglin. Direct comparison of EPC samples with the MM samples identified 156 genes significantly upregulated and 85 genes significantly downregulated (P < 0.005, t-test) in the EPCs, including several genes involved in angiogenesis and adhesion that were upregulated (including angiopoietin 1, SPARC, Notch3 and fibronectin 1). Immunohistochemical staining demonstrated CD31 and endoglin protein expression in the EPC tumour cells, which are both angiogenesis related and could confer malignant plasma cells with the ability to grow outside the normal bone marrow environment. Defining how malignant plasma cell growth is regulated in the bone marrow versus at extramedullary sites will help to delineate the mechanisms underlying the dependence of tumour cell growth on angiogenesis and cell adhesion.

Cell Division↗

Independent occurrences of multiple repeats in the control region of mitochondrial DNA of white-tailed deer.

Deer in the genera Mazama and Odocoileus generally have two copies of a 75-base-pair (bp) repeat in the left domain of the control region of the mitochondrial DNA (mtDNA). Phylogenetic analyses further suggest an ancient origin for the duplication supporting a previously stated contention that this event occurred before the separation of Mazama and Odocoileus. However, white-tailed deer (Odocoileus virginianus) had three or four copies of a 75-bp repeat in the control region of their mtDNA in 7.8% of the individuals analyzed, and all of these animals were from the coastal plain of the southeastern United States. When copy 3 is present, it is very similar in sequence to copy 2, but variation suggests that copy 3 probably evolved multiple times from copy 2. The pattern of phylogenetic clustering of the haplotypes from across the coastal plain also suggests that phenotypes with three or four copies of the repeat have originated multiple times. The 44 observed haplotypes showed strong spatial subdivision across the area with subpopulations frequently showing complete shifts in haplotype frequencies from others taken from nearby areas. Many of the subpopulations right along the coast or on adjacent barrier islands have a limited number of haplotypes as would occur in populations undergoing drift because of small numbers of breeding females and limited female dispersal.

Animals↗

Development of a ligand knowledge base, part 1: computational descriptors for phosphorus donor ligands.

A prototype collection of knowledge on ligands in metal complexes, termed a ligand knowledge base (LKB), has been developed. This contribution describes the design of DFT-calculated descriptors for monodentate phosphorus(III) donor ligands in a range of representative complexes. Using the resulting data, a ligand space is mapped and predictive models are derived for metal complexes. Important characteristics, including chemical, computational and statistical robustness for the generation and exploitation of such an LKB are described. Chemical robustness ensures transferability of the descriptors, as well as comprehensive sampling of ligand space. To make the calculations amenable to automation in an e-science setting, a reliable, well-defined computational approach has been sought from which the descriptors can be readily extracted. The LKB has been explored with multivariate statistical methods. Principal component analysis (PCA) is used for the mapping of chemical space, projecting multiple descriptors into scatter plots which illustrate the clustering of chemically similar ligands. Interpretation of the resulting principal components in terms of established steric and electronic properties and the importance of its statistical robustness to variations in the ligand set are discussed. Multiple linear regression (MLR) models have been derived, demonstrating the versatility of the descriptors for modeling varied experimentally determined parameters (bond lengths, reaction enthalpies and bond-stretching frequencies). The importance of re-sampling methods for testing the robustness of predictions is highlighted. A strategy for the construction of a robust LKB suitable for the modeling of ligand and complex behavior is outlined based on these observations.

Journal Article↗

How should randomised trials including multiple pregnancies be analysed?

OBJECTIVE: To compare the effects of four methods of analysis on the results of randomised controlled trials that recruit women with multiple pregnancies and measure outcomes on their babies. DESIGN: Analysis of one real and two simulated data sets. SETTING: Secondary analysis of perinatal randomised controlled trials. POPULATION: Randomised controlled trials including women with multiple pregnancies. METHODS: The analytical methods compared were (a) assuming independence among babies, (b) analysing outcomes per women, counting a woman as having an outcome if any of her babies had it (equivalent to selecting the worst outcome among any of a woman's babies), (c) randomly selecting one baby from each set of multiples for inclusion in the analysis, (d) adjustment of the analysis to take account of non-independence of babies from multiple pregnancies, using methods developed for analysis of cluster randomised trials. MAIN OUTCOME MEASURES: Odds ratios for trials' main outcomes. RESULTS: Results from application of cluster trial methods were similar to those from assuming independence among babies, but with slightly wider confidence intervals, reflecting the reduced effective sample size caused by non-independence between babies from the same pregnancy. Results were more variable using the other two methods, and in some cases, departed markedly from the results of the cluster trial methods. CONCLUSIONS: Cluster trial methods provide a simple way of adjusting the analysis to take account of non-independence between babies from the same pregnancy. Random selection and analysis by pregnancy (methods (b) and (c)) have disadvantages and do not report outcomes for all of the babies in the trial. This may cause problems with incorporating trials analysed using these methods into systematic reviews.

Cluster Analysis↗

Molecular epidemiology of Neisseria gonorrhoeae in Amsterdam, The Netherlands, shows distinct heterosexual and homosexual networks.

Molecular typing, added to epidemiological data, can better identify transmission patterns of gonorrhea in Western countries, where the incidence has recently been rising. From September 2002 to September 2003, patients with a laboratory-confirmed diagnosis of gonorrhea at the Clinic for Sexually Transmitted Infections in Amsterdam, The Netherlands, were subjected to a questionnaire pertaining to sexual risk behavior and sexual partners in the 6 months prior to the diagnosis. The Neisseria gonorrhoeae isolates were all genotyped using PCR-restriction fragment length polymorphism of the porin and opacity genes. All patients with a completed questionnaire and genotyped isolates were included in the study. We obtained 885 N. gonorrhoeae isolates from 696 patients that revealed 88 clusters and 46 unique genotypes. Patients infected at multiple anatomical sites with one or more strains and patients infected several times during the study period were shown to pursue high-risk sexual behavior and were considered core groups. There were 11 clusters of > or =20 patients; in seven clusters, 81% to 100% of patients were men who have sex with men (MSM), three clusters contained 87 to 100% heterosexual men and women, and one cluster was formed by equal proportions of MSM and heterosexual male and female patients. However, the various clusters differed in characteristics such as types of coinfections, numbers of sexual partners, Internet use to seek sexual partners, and locations of sexual encounters. Molecular epidemiology of gonococcal isolates in Amsterdam revealed core groups and clusters of MSM and heterosexual patients that probably indicate distinct transmission networks.

Adult↗

A phosphorylation cluster in the chromatin-binding region regulates chromosome association of LAP2alpha.

LAP2alpha is a LEM family protein associated with nucleoplasmic A-type lamins and chromatin in interphase. Like lamins and other lamina proteins LAP2alpha is cytoplasmic in metaphase, but it associates with chromosomes prior to nuclear envelope formation in late anaphase to telophase. In vitro phosphorylation analysis and mass spectrometry identified a cluster of at least three mitotic cyclin-dependent kinase 1 phosphorylation sites in the C-terminal chromatin-binding region of LAP2alpha as well as four additional potential sites in the cluster, some of which were targeted alternatively in LAP2alpha mutated at the major sites. LAP2alpha mutants containing serine --> alanine mutations at all seven sites revealed a clear phenotype. Mutated LAP2alpha remained associated with chromosomes throughout mitosis, but the dissociation of lamins into the cytoplasm and nuclear envelope disassembly were not affected. These data demonstrate the in vivo significance of mitotic phosphorylation for the dynamic behavior of LAP2alpha in the cell cycle and show that, unlike the interaction with lamins, the chromatin association of LAP2alpha is regulated by multiple mitosis-specific phosphorylation at sites clustered within a defined region in the C terminus of the protein.

Animals↗

Relationship between terminal ileal pressure waves and propagating proximal colonic pressure waves.

The relationship between propagating distal ileal and proximal colonic motor patterns has not been systematically examined in humans. Our aim was to define the relationships, if any, between prolonged propagating contractions or discrete clustered contractions and cecal propagating sequences using multiple manometric recording sites spanning the distal ileum and unprepared colon. In 14 healthy volunteers, a 17-lumen-perfused silicon catheter was positioned pernasally such that at least three recording sites lay in the ileum and the remainder in the colon. Intersidehole distance was 7.5 cm. In 271 h of recording, 30% of the terminal ileal propagating events was temporally associated with cecal propagating sequences. Significantly more prolonged propagating contractions (11 of 24, 46%; P = 0.02) were associated with cecal propagating sequences than were associated with ileal discrete clustered contractions (4 of 26, 15%). This trend was more pronounced at night. Of 159 cecal propagating sequences, 15 (9%) were preceded by an ileal propagating event. The remaining 91% was preceded by increased nonpropagating activity commencing 2 min before the cecal propagating sequence (P = 0.0002). We conclude that distal ileal propagating motor patterns are one stimulus for cecal propagating sequences, with the association being stronger for prolonged propagating contractions than for discrete clustered contractions.

Adult↗

Cluster ions derived from sodium and potassium tetrafluoroborate and their collision induced dissociation in an ion trap mass spectrometer.

Electrospray ionization was used to produce distributions of gas-phase cluster ions from solutions of sodium and potassium tetrafluoroborate. The majority of the cluster species followed the trend (MBF(4))(n)M(+), where M=Na and K. The values of n, for both salts, ranged from 1-15. Collision induced dissociation (MS/MS and MS(n)) in an ion trap mass spectrometer was used to determine the dissociation pathways for the cluster ions. The (NaBF(4))(n)Na(+) cluster ions fragmented via two pathways: (a) the loss of one or multiple neutral BF(3) molecules and (b) the loss of one or more NaBF(4) units. Of the two, the product ions corresponding to the loss of BF(3) units were more prominent. Unlike the Na salt, the (KBF(4))(n)K(+) cluster ions decomposed primarily by the loss of one or multiple KBF(4) units. Similar differences in dissociation behavior were observed when the heated transfer capillary, normally used to desolvate ions, was used to investigate cluster ion stability to thermal degradation and dissociation. The dissociation profiles (decrease in ion abundance with increasing activation amplitude) for several (NaF)(n)Na(+) and (KF)(n)K(+) cluster ions were measured and compared to probe the influence of the relative stability of the alkali fluorides (NaF and KF) on the dissociation behavior exhibited by the tetrafluoroborate cluster distributions. We found that the (NaF)(n)Na(+) cluster ions required higher activation amplitudes to induce fragmentation than the corresponding (KF)(n)K(+) species, indicative of stronger ionic bonding and higher gas-phase stability for the former. This in turn indicates that the reaction pathway involving only the loss of one or multiple units of BF(3), favored for the (NaBF(4))(n)Na(+) cluster series, but not for the analogous (KBF(4))(n)K(+) series, may be due to the high gas-phase stability of NaF, and relatively lower stability of KF, towards dissociation.

Journal Article↗

Analysis of circulation of neuronal activity in the waking cortex.

It is well known that the rhythmic activity of the cerebral cortex is closely associated with a highly organized circulation of neuronal impulses through the networks in which the activity develops. The present study has attempted to determine by quantitative methods, the consistency of this circulation and of its association with the cortical waves, over relatively long periods. Cortical gross waves and neuronal activity have been recorded by means of arrays of extracellular microelectrodes, in freely moving cats as well as in cats immobilized with flaxedil. Autocorrelations have been performed on trains of rhythmic waves and on associated clusters of action potentials; cross-correlations and multiple correlations have been performed between waves and action potentials and between action potentials generated by different groups of neurons. It has been found that the rhythmicity of the waves, the rhythmicity of the associated clusters of action potentials, the time and phase relations between them, and the circulation of neuronal activity through the networks, remain highly consistent over periods as long as two hours.

Action Potentials↗

The nigrotectal projection and tectospinal neurons in the rat. A light and electron microscopic study demonstrating a monosynaptic nigral input to identified tectospinal neurons.

In order to investigate the nigro-tecto-spinal pathway in the rat, the pattern of termination of nigrotectal fibres and the distribution of tectospinal neurons have been investigated in a light and electron microscopic study of the superior colliculus. In addition, the pattern of termination of nigrotectal fibres was compared to the pattern of acetylcholinesterase staining. The light microscopic studies showed that the nigrotectal fibres, which had been identified by anterograde transport of horseradish peroxidase from the substantia nigra, terminated in a distinctive clustered pattern throughout the rostrocaudal extent of the stratum griseum intermedium, stratum album intermedium and adjacent dorsal portion of the stratum griseum profundum of the ipsilateral superior colliculus. The clusters of nigrotectal terminals formed a series of branching, interconnected longitudinal columns which largely corresponded with the pattern of acetylcholinesterase staining. The tectospinal neurons, which had been identified by retrograde transport of horseradish peroxidase from the spinal cord, had mainly large-sized somata, were stellate in shape with multiple long dendrites, and formed variable-sized clusters of 4-15 neurons within lateral regions of the ventral stratum album intermedium and dorsal stratum griseum profundum. In experiments where both the nigrotectal terminals and the tectospinal neurons were labelled by the transport of horseradish peroxidase, the clusters of tectospinal neurons largely corresponded with the regions of densest nigrotectal fibre termination in the lateral regions of the superior colliculus. In addition, a small contralateral nigrotectal projection was localized in the rostrolateral region of the superior colliculus where the crossed fibres terminated in a clustered pattern in alignment with clusters of tectospinal neurons in this region. Electron microscopic examination of the superior colliculus following ibotenic acid lesions in the substantia nigra and horseradish peroxidase injections in the spinal cord showed multiple degenerating nigrotectal boutons in synaptic contact with the soma and the mainstem and secondary dendrites of labelled tectospinal neurons in the lateral regions of the stratum album intermedium and stratum griseum profundum of the superior colliculus. The majority of the degenerating nigrotectal boutons showed electron-lucent degenerative changes and were in axodendritic contact. All of the identified nigrotectal synapses were of the symmetrical type.(ABSTRACT TRUNCATED AT 400 WORDS)

Acetylcholinesterase↗

Precise placement of multiple electrodes into functionally predefined cortical locations.

Current research on topics such as effective connectivity, neuronal coding strategy or signal propagation in the central nervous system requires simultaneous recordings from multiple sites within functionally grouped but topologically distributed neuronal clusters. We have addressed this issue by characterization of the cortical functional architecture using optical imaging of intrinsic signals (OI) and subsequent placement of multiple, individually adjustable electrodes into pre-selected domains. In order to achieve maximum precision and flexibility for the positioning of electrodes, a plastic cylinder containing channels of an extremely high aspect ratio (density >20 channels/mm(2)) was fixed above the cortex and individual channel positions were superimposed onto the functional maps of orientation columns obtained previously with OI. Subsequently, channels corresponding to the desired locations in the functional map were used as guide tubes for electrode insertion. The spatial precision of this approach was in the range of 100 microm and experiments in cat primary visual cortex revealed a close correlation between the desired and the actually recorded orientation preferences of the targeted columns. The method is applicable to all cortical areas in which OI is feasible and offers a high degree of flexibility with respect to the number and geometry of applicable probes. It is, thus, an excellent tool for studying distributed codes and interactions between multiple predefined recording sites.

Animals↗

Organization of the human skeletal myosin heavy chain gene cluster.

Myosin is an important structural and enzymatic component of skeletal muscle. Multiple myosin isoforms are encoded by a multigene family and are expressed in different developmental stages and fiber types. In humans and mice, skeletal myosin heavy chain (MYH) genes are clustered on a single chromosome (17p and 11, respectively). Since the structural organization of the gene cluster may affect its expression as well as shed light on MYH genetic alterations, a physical map of the human MYH gene cluster was constructed. Nine yeast artificial chromosomes containing MYH genes were isolated and used to construct a contiguous set (contig) of overlapping yeast artificial chromosomes. This contig encompasses a genetic marker mapped to 17p13.1. Six MYH genes were located within a 500-kilobase segment of human DNA. The order of the genes within this cluster does not correspond to the developmental pattern of expression of individual members.

Base Sequence↗

In Vitro Analysis of Light-Induced Transcription in the Wheat psbD/C Gene Cluster Using Plastid Extracts from Dark-Grown and Short-Term-Illuminated Seedlings.

We describe a plastid in vitro transcription system that reflects characteristic features of the light-regulated transcription observed in vivo. Multiple transcripts of the wheat (Triticum aestivum) psbD/C gene cluster comprise six distinct 5[prime] ends including four transcription initiation sites designated as D/C-1 through D/C-4. Transcripts from one particular site, D/C-3, were found to be conspicuously enhanced in abundance after 4 h of illumination in vivo. The plastid extract prepared from 5-d-old dark-grown wheat seedlings was capable of transcribing from the D/C-2 and D/C-4 sites in vitro but had almost no transcription activity from the light-responsive D/C-3 site (the D/C-1 site was not examined). The plastid extract from 4-h-illuminated seedlings initiated transcription from the light-responsive site (D/C-3). Transcription from the D/C-2 and D/C-4 sites was not enhanced by using the extract from 4-h-illuminated seedlings, indicative of specific activation of the light-responsive promoter on the D/C-3 site by the extract from 4-h-illuminated seedlings. The plastid extract from 4-h-illuminated seedlings was divided into two fractions on a heparin-Sepharose column, into which the light-induced component(s) responsible for activation of the D/C-3 promoter and RNA polymerase were separated. The fraction containing the component(s) activating the D/C-3 promoter induced the transcription activity from the D/C-3 site in the plastid extract from dark-grown seedlings. It is concluded that the plastid extract from 4-h-illuminated seedlings contains some light-regulatory component(s) that activate specifically the light-responsive promoter.

Journal Article↗

Clustered somatic mutations in and around first exon of non-rearranged c-myc in Burkitt lymphoma with t(8;22) translocation.

We have examined the restriction map of the c-myc gene in 15 BL cell lines carrying the variant t(8;22) translocation in which c-myc is known to remain on chromosome 8. Using 3 restriction enzymes cutting outside the c-myc domain (EcoRI, BamHI, HindIII), we found no evidence for a c-myc/Ig lambda rearrangement in 14 BL cell lines. In the last one, BL 37, the 3' flanking region was rearranged corresponding to the already identified breakpoint located 400 pb downstream from the c-myc gene (9). Using 4 restriction enzymes cutting inside the c-myc gene (PvuII, PstI, SacI, HincII) we looked for discrete abnormalities within the gene limits, and we found in 9 BL cell lines several abolished and created sites, compatible with multiple independent somatic mutations. They are significantly clustered in the 5' non coding region, with a striking prevalence at the end of exon 1. The role of mutations in the non-coding first exon region for the deregulation of c-myc expression is discussed.

Burkitt Lymphoma↗

Gene structure and expression of the mouse APOBEC-1 complementation factor: multiple transcriptional initiation sites and a spliced variant with a premature stop translation codon.

Editing of apolipoprotein (apo) B mRNA is mediated by an enzyme-complex that consists of the catalytic cytidine deaminase APOBEC-1 and the mRNA binding protein APOBEC-1 complementation factor or APOBEC-1 stimulating protein (ACF/ASP). Here we describe the detailed characterization of the structure, expression and splicing pattern of the mouse ACF/ASP gene. ACF/ASP mRNA is mainly expressed in mouse liver, small intestine and kidney. The deduced protein sequences of ACF/ASP from mouse and man share an identity of 93%. The mouse ACF/ASP gene consists of 12 exons and gives rise predominantly to full-length transcripts. To a minor extent (<10%) ACF/ASP mRNA with unspliced exon 8 is generated in liver, kidney and small intestine that encodes a truncated protein with a predicted molecular weight of 43 kDa. The promoter of the mouse ACF/ASP gene lacks a canonical TATA-box, but contains a cluster of Sp1 binding sites and uses multiple transcriptional initiation sites. Transfection studies demonstrated a preference of this promoter for cell lines derived from the gastrointestinal tract and proved the location of the promoter core region. The high sequence identity between man and mouse-much higher as observed for APOBEC-1-indicates a strong evolutionary constraint on the structure-function relationship of ACF/ASP, most probably due to a central role in editing and processing of apo B mRNA.

Alternative Splicing↗

Genetic and physical mapping in Brassica diploid species of a gene cluster defined in Arabidopsis thaliana.

We report the genetic and physical analysis by pulse field gel electrophoresis (PFGE) in three Brassica diploid genomes for a cluster of five genes characterized in a selected segment of 15 kb on chromosome 3 of Arabidopsis thaliana, encoding a Bradyrhizobium CycJ homologue (At1), a rat p67 translation factor homologue (At2), an Em-like (early methionine) protein (At3), chlorophyll synthase (At4) and a yeast Sac1 homologue (A5). The Arabidopsis gene array was found to be conserved on a single linkage group in each of the Brassica genomes. However, partial complexes were found to be duplicated in other chromosome segments on the same or other linkage groups. Some of the At genes, which could not be genetically mapped because of lack of polymorphism, were assigned to their respective linkage groups by physical mapping. The presence of multiple copies of the A. thaliana gene cluster in the three Brassica genomes further establishes their complex nature, which results from extensive duplication and chromosomal rearrangement. In general, genetic distances between the At genes agreed with values expected for the physical distances determined in Brassica.

Aminopeptidases↗

Multiple chemical sensitivity (MCS)--differential diagnosis in clinical neurotoxicology: a German perspective.

The multiple chemical sensitivity syndrome (MCS) is a new cluster of environmental symptoms which have been described and commented on for more than 15 years now in the USA. In the meantime it has also been observed in European countries. The main features of this syndrome are: multiple symptoms in multiple organ systems, precipitated by a variety of chemical substances with relapses and exacerbation under certain conditions when exposed to very low levels which do not affect the population at large. There are no lab markers or specific investigative findings. In our view, MCS is not a separate clinical syndrome but a collective term. A very small part of the patients in question may actually exhibit a somatic or psychosomatic response to low levels of a variety of chemicals in the environment. For another part, even if the MCS symptoms are induced by chemical substances in the environment, the basic hypersensitivity is a psychological stress reaction. In the third and largest group, the patients have been misdiagnosed, i.e. a somatic or psychiatric disease has been overlooked. There is a fourth group of patients in whom there is no evidence of any exposure at all but instead a belief system installed by certain physicians, the media and other groups in society. This paper tries to describe the neurological and neurotoxic aspects of MCS problems and to illustrate it with examples of an alleged outbreak of chronic neurotoxic disease caused by pyrethroids in Germany. Research strategy should establish clearly determined diagnostic criteria, agreement on the use of specific questionnaires as well as clinical and technical diagnostic procedures, prospective clinical studies of MCS patients and comparative groups as well as experimental approaches.

Adolescent↗

Clusters of biochemical markers are associated with radiographic subtypes of osteoarthritis (OA) in subject with familial OA at multiple sites. The GARP study.

OBJECTIVE: To assess the relationship of biochemical markers and radiographic signs of osteoarthritis (ROA) in the subjects with symptomatic osteoarthritis (OA) at multiple sites of the Genetics osteoARthritis and Progression (GARP) study. METHODS: We have measured eight biochemical markers, representing tissue turnover of cartilage, bone, synovium, and inflammation. ROA was assessed in the knees, hips, hands, vertebral facet joints and spinal disc degeneration (DD) by using the Kellgren score. A proportionate score was subsequently made for each joint location based on the number of joints with ROA. Principal component and linear mixed model analyses were applied to analyze the data. RESULTS: Three different clusters of markers were identified that may reflect different pathophysiological processes of OA. The first component appeared to be reflected by structural markers of cartilage and bone turnover and associated especially in subjects with hip ROA. The second component was reflected by a marker of inflammation and was associated with knee ROA, high Western Ontario and McMaster Universities (WOMAC) scores and body mass index (BMI). The third component included markers of cartilage turnover and was associated with ROA at hands, spine as well as age. High familial aggregation was observed for serum cartilage oligomeric matrix protein (S-COMP) (70%) and serum N-propeptide of collagen type IIA (S-PIIANP) (62%). CONCLUSION: Using a large well-characterized study and eight biochemical markers, we were able to observe three components that may reflect different molecular mechanisms (bone, cartilage, synovium turnover and inflammation). Our data suggested that these components contribute differently to ROA at different joint sites.

Adult↗