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PubMed2004

Collaborative study for the establishment of erythropoietin BRP batch 2.

The preparation and establishment of the 2nd European Pharmacopoeia (Ph. Eur.) Biological Reference Preparation (BRP) for erythropoietin was the goal of a project run within the framework of the European Biological Standardisation Programme. The project, coded BSP062, was carried out between October 2002 and July 2003. The candidate preparation (cBRP2) was prepared in a similar manner to the first BRP batch (BRP1), as follows: -50:50 (weight/weight) blending of the two erythropoietin preparations currently available on the European market (epoietin-alpha and epoietin-beta), -lyophilisation using a protein-free carrier formulation to allow use of the standard for both biological and physico-chemical assay methods, -each vial contains approximately 250 microg erythropoietin. The cBRP2 was analysed in a collaborative study, carried out with the following aims: -to calibrate cBRP2 by in vivo bioassay in terms of the International Standard for erythropoietin, and assign a unitage, -to demonstrate continuity of unitage with BRP1, -to evaluate the suitability of cBRP2 to serve as a reference material for physico-chemical tests of erythropoietin. The collaborative study involved 14 laboratories both from Europe, and from Australia, Canada, South-Korea and the United States of America. Participants carried out biological and physicochemical assays on the candidate BRP batch 2, using BRP 1 and the 2nd World Health Organization (WHO) International Standard (IS) for recombinant erythropoietin as the reference standards. It was demonstrated that: -an assigned potency of 32,500 U per vial would maintain continuity between BRP1 and BRP2 in terms of the IS for erythropoietin, -the replacement batch was appropriate for use as erythropoietin BRP in the context of the control of erythropoietin concentrated solutions according to the Ph. Eur. monograph 1316. In July 2003, the Ph. Eur. Commission established the proposed standard as 'Erythropoeitin BRP batch 2' for use as a reference preparation for the polycythaemic and normocythaemic mouse bioassay, with an assigned potency of 32,500 U/vial, the identification by capillary zone electrophoresis (CZE), by polyacrylamide gel electrophoresis, immunoblotting and peptide mapping and as a reference for checking the system suitability of size exclusion chromatographic procedures used in the test for 'Dimers and related substances of higher molecular mass'.

Epoetin Alfa↗

PubMed2000

Mapping of the CYP1A1, SSTR1 and TTF1 genes to pig chromosome 7q refines the porcine-human comparative map.

The cytochrome P-450, subfamily I, polypeptide 1 (CYP1A1), somatostatin receptor 1 (SSTR1) and transcription termination factor 1 (TTF1) genes, predicted to reside on SSC7q based on chromosome painting studies, were selected for genetic mapping in the pig. Porcine sequence tagged sites (STSs) spanning 0.9-1.5 kb genomic DNA sequences were generated and all genes were physically assigned to SSC7q12-q23, q26 using a pig-rodent somatic cell hybrid panel. Direct sequencing of PCR products from four different breeds revealed single nucleotide polymorphisms (SNPs) in all genes. SNPs in the SSTR1 and CYP1A1 genes allowed simple genotyping using PCR-restriction fragment length polymorphism (RFLP) analysis and linkage mapping with the PiGMaP reference families. SSTR1 was found to be closely linked to CYP1A1 (0.0 cM; LOD = 11.1) and ANPEP (0.0 cM; LOD = 9.0). This refined the localization of a previously identified breakpoint in the linkage map between regions with orthology to human chromosome 15q (represented by CYP1A1 and ANPEP) and 14q (represented by SSTR1). Moreover, multipoint linkage data suggest inverted segments of orthology between HSA14q11-q13 and SSC7q. The TTF1 SNP was confirmed by allele-specific PCR but was not informative in any of the families used for linkage analysis.

Animals↗

PubMed1993

New markers, D16FC1 and Tp12, differentiate between rat chromosomes 16 and 17.

Problems in differentiating rat chromosomes 16 and 17 cytogenetically can be resolved with unique probes mapped to these chromosomes. Using somatic cell hybridization and nonisotopic in situ hybridization, probes D16FC1 and Tp12 were localized to 16p16-->p15 and 17q12.1-->q12.2, respectively. The locations of these probes can serve as reference points to facilitate mapping of future probes to rat chromosomes 16 and 17.

Animals↗

PubMed2002

Efficient Boolean implementation of universal sequence maps (bUSM).

BACKGROUND: Recently, Almeida and Vinga offered a new approach for the representation of arbitrary discrete sequences, referred to as Universal Sequence Maps (USM), and discussed its applicability to genomic sequence analysis. Their work generalizes and extends Chaos Game Representation (CGR) of DNA for arbitrary discrete sequences. RESULTS: We have considered issues associated with the practical implementation of USMs and offer a variation on the algorithm that: 1) eliminates the overestimation of similar segment lengths, 2) permits the identification of arbitrarily long similar segments in the context of finite word length coordinate representations, 3) uses more computationally efficient operations, and 4) provides a simple conversion for recovering the USM coordinates. Computational performance comparisons and examples are provided. CONCLUSIONS: We have shown that the desirable properties of the USM encoding of nucleotide sequences can be retained in a practical implementation of the algorithm. In addition, the proposed implementation enables determination of local sequence identity at increased speed.

Algorithms↗

PubMed1994

Genetic linkage analysis of the Ak1, Col5a1, Epb7.2, Fpgs, Grp78, Pbx3, and Notch1 genes in the region of mouse chromosome 2 homologous to human chromosome 9q.

The genes for adenylate kinase-1 (AK1), folyl polyglutamate synthetase (FPGS), the collagen pro alpha 1(V) chain (COL5A1), erythrocyte protein band 7.2b (EPB72), and a proto-oncogene homeobox (PBX3) all map to the distal portion of human chromosome 9q (HSA9q) but have not previously been mapped by linking analysis in the mouse. In this study, we have used two interspecific backcrosses to map the mouse homologues of each of these genes to mouse chromosome 2 (MMU2). The Ak1, Col5a1, Epb7.2, Fpgs, and Pbx3 genes were mapped with respect to the genes for Grp78, Rxra, Notch1 (the mouse homologue of TAN1), Spna2, Abl, and Hc (the mouse homologue of C5), all of which have previously been mapped by linkage analysis on MMU2 and have human homologues that map to HSA9q. Two of the reference loci for MMU2, D2Mit1 and Acra, were also mapped in the same cross to facilitate comparisons with existing maps. The consensus gene order deduced by combining data from both crosses is D2Mit1-(Dbh,Notch1)-(Col5a1,Rxra)-Spna2-Ab l-(Ak1,Fpgs)- (Grp78,Pbx3)-(Epb7.2,Hc,Gsn)-Acra. These loci therefore form part of the conserved synteny between HSA9q and MMU2.

Animals↗

PubMed1989

[EEG background activity in patients with dementia of the Alzheimer type--with special reference to analysis by t-statistic significance probability mapping (SPM) in Alzheimer's disease and senile dementia].

EEG power amplitude and power ratio data obtained from 15 (3 men and 12 women) patients with Alzheimer's disease (AD) and 8 (2 men and 6 women) with senile dementia of Alzheimer type (SDAT) were compared with similar data from 40 age- and sex-matched normal controls. Compared with the healthy controls, both patient groups demonstrated increased EEG background slowing, and it indicated more slower in AD than in SDAT. Moreover, both groups showed characteristic findings respectively on EEG topography and t-statistic significance probability mapping (SPM). The differences between AD and their controls indicated high slowing with reductions in alpha 2, beta 1 and beta 2 activity. The SPMs of power ratio in theta and alpha 2 bands showed most prominent significance in the right posterior-temporal region and delta and beta bands did in the frontal region. Severe AD indicated only frontal delta slowing compared to mild AD. The differences between SDAT and their controls indicated only mild slowing in delta and theta bands. The SPM of power amplitude showed occipital slowing, whereas the SPM of power ratio showed the slowing in the frontal region. Judging from both topographic findings, these were considered to denote diffuse slow tendency. In summary, these results presumed that in AD, cortical damages followed by EEG slowing with reductions of alpha 2 and beta bands originated rapidly and thereafter developed subcortical (non-specific area in thalamus) changes with frontal delta activity on SPM. On the other hand, in SDAT, diffuse cortico-subcortical damages with diffuse slowing on EEG topography were caused gradually.

Adult↗

PubMed1989

The importance of alignment in blind subjects' use of tactual maps.

An experiment was conducted to test for the presence of alignment effects (previously found in sighted map users) in blind and visually impaired subjects using tactual maps. The term 'alignment effects' refers to the fact that when points represented as further up on a map do not correspond to points forward from the user in the environment, errors in the directional judgments made by subjects are greatly increased. The results show that alignment effects do exist in blind and visually impaired map users. Blind subjects encoded maps using the 'up equals forward' rule, and demonstrated some similarity to sighted subjects in the types of errors made. There was also some indication of improved performance over repeated trials. Differences between blind and sighted subjects were also found and were tentatively attributed to visual experience with object transformations and/or representational variables. Subject background variables were also investigated and some relationships between background of the subject and performance were drawn.

Adult↗

PubMed1999

Standard G-, Q-, and R-banded ideograms of the domestic sheep (Ovis aries): homology with cattle (Bos taurus). Report of the committee for the standardization of the sheep karyotype.

Revised G-, Q- and R-banded karyotypes and ideograms for sheep chromosomes at the 420-band level of resolution are presented. The positions of landmark bands on the sheep chromosomes are defined by their distance relative to the centromere to facilitate comparison with equivalent cattle chromosomes. Chromosome-specific (reference) molecular markers that have been mapped to sheep chromosomes and their equivalent cattle chromosomes are proposed. Reference markers will facilitate genome comparisons between sheep and cattle and minimise confusion due to chromosome nomenclature. Numbering of the Robertsonian translocation chromosomes remains as previously reported.

Animals↗

PubMed1999

Standard G-, Q-, and R-banded ideograms of the domestic sheep (Ovis aries): homology with cattle (Bos taurus). Report of the committee for the standardization of the sheep karyotype.

Animals↗

PubMed2006

Cytoarchitectonic identification and probabilistic mapping of two distinct areas within the anterior ventral bank of the human intraparietal sulcus.

Anatomical studies in the macaque cortex and functional imaging studies in humans have demonstrated the existence of different cortical areas within the intraparietal sulcus (IPS). Such functional segregation, however, does not correlate with presently available architectonic maps of the human brain. This is particularly true for the classical Brodmann map, which is still widely used as an anatomical reference in functional imaging studies. The aim of this cytoarchitectonic mapping study was to use previously defined algorithms to determine whether consistent regions and borders can be found within the cortex of the anterior IPS in a population of 10 post-mortem human brains. Two areas, the human intraparietal area 1 (hIP1) and the human intraparietal area 2 (hIP2), were delineated in serial histological sections of the anterior, lateral bank of the human IPS. The region hIP1 is located posterior and medial to hIP2, and the former is always within the depths of the IPS. The latter, on the other hand, sometimes reaches the free surface of the superior parietal lobule. The delineations were registered to standard reference space, and probabilistic maps were calculated, thereby quantifying the intersubject variability in location and extent of both areas. In the future, they can be a tool for analyzing structure-function relationships and a basis for determining degrees of homology in the IPS among anthropoid primates. We conclude that the human IPS has a more finely grained parcellation than shown in Brodmann's map.

Adult↗

PubMed1993

The positions of 12 simple sequence repeat markers relative to reference loci on mouse chromosome 16.

The genetic map positions of 12 simple sequence repeat (SSR) markers spanning mouse Chromosome (Chr) 16 were determined relative to reference markers on that chromosome. Interval mapping data were obtained with a panel of DNAs from two intersubspecific backcrosses. All but one of the markers were typed by us of nonradioactive polymerase chain reaction (PCR) products analyzed on agarose gels. The marker order was determined to be Prm-1, D16Mit9, Igl-1, D16Mit29, D16Mit1/D16Mit2, Smst, D16Mit4, D16Mit11, Gap43, D16Mit14, D16Mit30, D16Mit5, Pit-1, D16Mit27, D16H21S16 (formerly D21S16h), D16Mit19, App, D16Mit7, Sod-1. Two of these markers mapped to the known human Chr 21 (HSA21)/Chr 16 conserved linkage group. Nine additional SSR markers could not be typed because they were not polymorphic (four markers), did not amplify MOLD/Rk DNA (three markers), or failed to give PCR products under a range of conditions (two markers). A subset of the most robust SSRs provide a useful marker set for the analysis of previously unmapped crosses.

Animals↗

PubMed2003

Redox signaling and the MAP kinase pathways.

The mitogen-activated protein (MAP) kinases are a large family of proline-directed, serine/threonine kinases that require tyrosine and threonine phosphorylation of a TxY motif in the activation loop for activation through a phosphorylation cascade involving a MAPKKK, MAPKK and MAPK, often referred to as the MAP kinase module. Three separate such modules have been identified, based on the TxY motif of the MAP kinase and the dual-specificity kinases that strictly phosphorylate their specific TxY sequence. They are the extracellular signal regulated kinases (ERKs), c-jun N-terminal kinases (JNKs) and p38 MAPKs. The ERKs are mainly associated with proliferation and differentiation while the JNKs and p38MAP kinases regulate responses to cellular stresses. Redox homeostasis is critical for proper cellular function. While reactive oxygen species (ROS) and oxidative stress have been implicated in injury, a rapidly growing literature suggests that a transient increase in ROS levels is an important mediator of proliferation and results in activation of various signaling molecules and pathways, among which the MAP kinases. This review will summarize the role of ROS in MAP kinase activation in various systems, including in macrophages, cells of myeloid origin that play an essential role in inflammation and express a multi-component NADPH oxidase that catalyzes the receptor-regulated production of ROS.

Animals↗

PubMed2026

nf-core/magmap: Map metatranscriptomes to large collections of genomes.

SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes. AVAILABILITY AND IMPLEMENTATION: The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

Software↗

PubMed2004

Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat.

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to related large-genome species has revolutionized molecular genetics and breeding strategies for improving those crops. Comparative sequence analysis methods can be used to cross-reference genes between species maps, enhance the resolution of comparative maps, study patterns of gene evolution, identify conserved regions of the genomes, and facilitate interspecies gene cloning. In this study, 5,780 Triticeae ESTs that have been physically mapped using wheat ( Triticum aestivum L.) deletion lines and segregating populations were compared using NCBI BLASTN to the first draft of the public rice ( Oryza sativa L.) genome sequence data from 3,280 ordered BAC/PAC clones. A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP. For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes. The physical locations of non-conserved regions were not consistent across rice chromosomes. Some wheat ESTs with multiple wheat genome locations are associated with the non-conserved regions of similarity between rice and wheat. The inverse view, showing the relationship between the wheat deletion map and rice genomic sequence, revealed the breakdown of gene content and order at the resolution conferred by the physical chromosome deletions in the wheat genome. An average of 35% of the putative single copy genes that were mapped to the most conserved bins matched rice chromosomes other than the one that was most similar. This suggests that there has been an abundance of rearrangements, insertions, deletions, and duplications eroding the wheat-rice genome relationship that may complicate the use of rice as a model for cross-species transfer of information in non-conserved regions.

Chromosome Mapping↗

PubMedDate not supplied

Learning proper and common names in inferential versus ostensive contexts.

A single, indirect exposure to a novel word provides information that could be used to make a fast mapping between the word and its referent, but it is not known how well this initial mapping specifies the function of the new word. The four studies reported here compare preschoolers' (N = 64) fast mapping of new proper and common names following an indirect exposure requiring inference with their learning of new names following ostension. In Study 1, 3-year-olds were shown an animate-inanimate pair of objects and asked to select, for example, Dax, a dax, or one. Children spontaneously selected an animate over an inanimate object as the referent for a novel proper name, but had no animacy preference in common name or baseline conditions. Next, the children were asked to perform actions on, for example, Dax or a dax, when presented with an array of three objects: the one they had just selected, another member of like kind, and a distracter. An indirectly learned proper name was treated as a marker for the originally selected object only, whereas a new common name was generalized to include the other category member. Study 2 showed that mappings made by inference were as robust as those made by ostension. Studies 3 and 4 demonstrated that even 2-year-olds can learn as much about the function of a new word from an indirect exposure as from ostension.

Child, Preschool↗

PubMed2006

Central sensitization in patients with non-cardiac chest pain: a clinical experimental study.

OBJECTIVE: Patients with non-cardiac chest pain (NNCP) suffer from unexplained and often intractable pain which can pose a major clinical problem. The aim of this study was to investigate nociceptive processing in NNCP patients and their response to experimentally acid-induced oesophageal hyperalgesia using a multimodal stimulation protocol. MATERIAL AND METHODS: Ten highly selected patients with NCCP (mean age 43 years, 1 M) were compared with an age- and gender-matched group of 20 healthy subjects. After preconditioning, the distal oesophagus was painfully distended with a balloon using "impedance planimetry". This method assesses the luminal cross-sectional area of the oesophagus based on the electrical impedance of the fluid inside the balloon. The baseline distensions were done before and after pharmacological relaxation of the smooth muscle with 20 mg butylscopolamine. After baseline distensions, a series of up to 10 mechanical stimuli was performed (temporal summation). The stimulations were repeated after sensitization of the oesophagus induced by acid perfusion. The sensory intensities were assessed during the stimulations and the referred pain area was mapped. RESULTS: At baseline distensions, no differences were seen between patients and controls before and after relaxation of the smooth muscles. The patients tolerated fewer repeated distensions than controls (4.8+/-0.5 versus 9.1+/-0.9; p=0.04) and had an increased size of the referred pain areas to the mechanical stimulations (32.9+/-6.2 versus 64.9+/-18.3 cm2; p=0.01). After sensitization with acid, the patients developed hyperalgesia (p<0.001), whereas no significant changes were seen in controls. CONCLUSIONS: NCCP patients showed facilitated central pain mechanisms (temporal summation and visceral hyperalgesia after sensitization). This could be used in the diagnosis and understanding of the symptoms in these patients.

Acids↗

PubMed2004

Comparative analysis and development of microsatellite markers on swine (Sus scrofa) chromosome 1qter.

Several quantitative trait loci (QTL) have been detected on SSC1qter (Sus scrofa chromosome 1qter), including QTL for the number of vertebrae, as reported in our previous study. To provide the tools for analysis of QTLs on SSC1qter, we constructed a comparative map of swine and human. In addition, we identified 26 swine STSs and mapped 16 of them on SSC1qter using the INRA - University of Minnesota porcine radiation hybrid (IMpRH) panel. We screened a BAC library using these swine STSs and developed 35 new polymorphic microsatellite markers from the BAC clones, of which 26 were informative in our reference family. We also mapped nine microsatellite markers we had isolated previously. Consequently a total of 44 new polymorphic microsatellite markers were located within a 60-cM region of SSC1qter, spanning from SW1092 to the telomere.

Animals↗

PubMedDate not supplied

An evaluation of FASTMAP with emphasis on fine-mapping.

We present an evaluation of the FASTMAP method with special reference to the issue of fine-mapping, using both 'real-life' and constructed data, and demonstrate some of the shortcomings of the method. Since the advantages of FASTMAP in terms of savings in computer resources compared to LINK-MAP are enormous, further improvements of the FASTMAP method would be highly desirable.

Chromosome Mapping↗