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PubMed2005

Mean arterial pressure in concordant and discordant triplets during the first week of life.

OBJECTIVE: To retrospectively determine mean arterial pressure (MAP) for stable concordant and discordant triplets during the first 7 days of life. BACKGROUND: Morbidity and mortality for prematurely born triplets is high, therefore, MAP monitoring during the first day of life is important for their clinical management. MAP reference values for special populations such as triplets have not been published. Recently, we reported that in stable discordant twins MAP values during the first day of life were significantly lower in the smaller than in their larger siblings. Comparable information for triplets is not available. DESIGN: Retrospective cohort study. METHODS: We studied 30 sets of concordant and 29 sets of discordant (birth weight difference > or =20%) consecutively born triplets. Stable patients were defined as those having umbilical cord hemoglobin > or =13 g/dl, normal blood gases, who were never treated for hypotension, and survived at least 7 days. MAP (torr) were measured by oscillometry in 3410, and by transducer via an umbilical arterial catheter in 1251 instances. RESULTS: Concordant and discordant triplets were similar in demographics, history of preterm labor (63 and 63%), chorioamnionitis (10 and 10%), pre-eclampsia (53 and 48%), cesarean delivery (100 and 100%), antenatal steroids (77 and 73%), cord hemoglobin (16 and 16 g/dl), combined triplets birth weight (4922 and 4732 g), gestational age (32 and 33 weeks), normal head ultrasounds or Grade I intracranial hemorrhage (96 and 100%) and neonatal mortality (2 and 1%), but were different in the number of infants requiring mechanical ventilation (57 and 31%). A total of 80 (89%) concordant triplets and 77 (88%) discordant triplets were stable according to our definition. Concordant stable triplets, whether small, medium or large, had similar MAP at birth. Their MAP values increased noticeably from birth to 24 hours and more subtlely to 7 days. Triplets of < or =32 weeks GA had lower MAP throughout than those of > or =33 weeks GA. Discordant stable triplets were divided into 27 small (1382 g), 26 medium (1683 g) and 27 large (1969 g); during the first 24 hours, medium and smaller triplets had MAP values that were lower than those of their larger siblings. From the second to the seventh day of life, all MAP values and trends were similar. Among discordant triplets, 86% of the smallest, 13% of the medium and 13% of the largest infants had asymmetrical intrauterine growth restriction. CONCLUSION: In stable concordant and stable discordant triplets, MAP correlates with birth weight, gestational age and postnatal age. MAP values increase noticeably during the first 24 hours and more subtlely during the next 7 days. Concordant or discordant, small, medium, and large triplets have similar MAP values and trends to that of their siblings. Small and medium discordant triplets have lower MAP values during the first day of life than their larger siblings but by the second day there MAP trends and values were no longer different.

Age Factors↗
PubMed2001

Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9.

Comparative mapping of chicken and human genomes is described, primarily of regions corresponding to human chromosomes 1, 4 and 9. Segments of chicken orthologues of selected human genes were amplified from parental DNA of the East Lansing backcross reference mapping population, and the two parental alleles were sequenced. In about 80% of the genes tested, sequence polymorphism was identified between reference population parental DNAs. The polymorphism was used to design allele-specific primers with which to genotype the backcross panel and place genes on the chicken linkage map. Thirty-seven genes were mapped which confirmed the surprisingly high level of conserved synteny between orthologous chicken and human genes. In several cases the order of genes in conserved syntenic groups differs between the two genomes, suggesting that there may have been more frequent intrachromosomal inversions as compared with interchromosomal translocations during the separate evolution of avian and mammalian genomes.

Alleles↗
PubMed2003

Mapping the proteome of barrel medic (Medicago truncatula).

A survey of six organ-/tissue-specific proteomes of the model legume barrel medic (Medicago truncatula) was performed. Two-dimensional polyacrylamide gel electrophoresis reference maps of protein extracts from leaves, stems, roots, flowers, seed pods, and cell suspension cultures were obtained. Five hundred fifty-one proteins were excised and 304 proteins identified using peptide mass fingerprinting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Nanoscale high-performance liquid chromatography coupled with tandem quadrupole time-of-flight mass spectrometry was used to validate marginal matrix-assisted laser desorption ionization time-of-flight mass spectrometry protein identifications. This dataset represents one of the most comprehensive plant proteome projects to date and provides a basis for future proteome comparison of genetic mutants, biotically and abiotically challenged plants, and/or environmentally challenged plants. Technical details concerning peptide mass fingerprinting, database queries, and protein identification success rates in the absence of a sequenced genome are reported and discussed. A summary of the identified proteins and their putative functions are presented. The tissue-specific expression of proteins and the levels of identified proteins are compared with their related transcript abundance as quantified through EST counting. It is estimated that approximately 50% of the proteins appear to be correlated with their corresponding mRNA levels.

Amino Acid Sequence↗
PubMed2004

Functionally associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.).

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important biological processes was used to detect polymorphic EST-RFLP loci in the F(1)(NA(6) x AU(6)) population. A comprehensive set of EST-SSR markers was developed from the analysis of 14,767 unigenes, with 310 primer pairs showing efficient amplification and detecting 113 polymorphic loci. Two parental genetic maps were produced: the NA(6) genetic map contains 88 EST-RFLP and 71 EST-SSR loci with a total map length of 963 cM, while the AU(6) genetic map contains 67 EST-RFLP and 58 EST-SSR loci with a total map length of 757 cM. Bridging loci permitted the alignment of homologous chromosomes between the parental maps, and a sub-set of genomic DNA-derived SSRs was used to relate linkage groups to the perennial ryegrass reference map. Regions of segregation distortion were identified, in some instances in common with other perennial ryegrass maps. The EST-derived marker-based map provides the basis for in silico comparative genetic mapping, as well as the evaluation of co-location between QTLs and functionally associated genetic loci.

Base Sequence↗
PubMed1997

The analysis of registry data in relation to various different types of hypothesis regarding the geographical distribution of disease.

Disease registries will often contain the addresses of cases included in the registry. If the registry includes information on all cases, or deaths, occurring in a defined geographical area and time period and if there is a postcode/zip code or map reference for each case it is possible to carry out a variety of different types of geographical analysis that may give clues to the aetiology of the disease. For such analyses it will usually also be necessary to have population data for the region covered by the registry and for separate sub-regions within it. In this paper we review types of analysis that may be applied to such data and give references to examples of applications and the statistical methods used. These include, first, methods of presenting incidence rates, and particularly the use of maps; of particular concern is the development of methods for presenting data that take into account the problems of rates calculated for small populations and which may therefore happen to be high or low simply by chance. Secondly, we consider, the analysis of "clustering" and "clusters" of cases of disease. These problems have been the subject of considerable methodological development in recent years. Analyses of clustering address the question of whether there is a general tendency for there to be aggregations of cases or areas of high incidence the analysis of clusters is concerned with problems of detecting specific locations where there are unusual aggregations of cases. The third type of problem considered here is whether there are, within the registry region, aetiological factors that vary geographically with consequent variations in disease incidence in different sub-regions. Where there is geographical variation it may be possible to use regression analysis to relate such variation to factors such as socio-economic status or levels of some environmental hazard. Finally we consider the problem of determining whether disease rates in certain areas may be related to distance from the source of some potential causative agent.

Cluster Analysis↗
PubMedDate not supplied

Cerebral cartography--a method for visualizing cortical structures.

We present a method for visualizing the human cortex on one planar map. The data are taken from a 3D MRI study. Ray tracing with non-parallel rays is used to project the cortical relief onto a non-planar projection surface, which is in turn mapped onto the plane by cartographical projection. Two modifications of the method are proposed: the spherical mapping uses a sphere as the projection surface; the model-based mapping uses an analytically defined model of the scalp to generate the normal vectors. The cerebral cartography can be used for example for producing anatomical reference maps on which EEG measurement data can be superimposed.

Algorithms↗
PubMed1994

Chromosomal localization of the human retinoid X receptors.

The recently described retinoid X receptors (RXRs) respond to the novel retinoid 9-cis-retinoic acid and also serve as heterodimeric partners for the vitamin D, thyroid hormone, and retinoic acid receptors (VDR, TR, and RAR, respectively). In this work, we report high-resolution localization of the human RXR genes within cytogenetic bands and also within a standard reference map of cosmid DNA markers on human chromosomes. We have determined the location of the human RXR genes by pairwise hybridization of the RXR cosmids and reference markers, using fluorescence in situ hybridization. We localized (i) RXR alpha (RXRA) to chromosome 9 band q34.3; (ii) RXR beta (RXRB) to chromosome 6 band 21.3; and (iii) RXR gamma (RXRG) to chromosome 1 band q22-q23. Six retinoid-responsive transcription factors have been identified so far, including three retinoic acid receptors in addition to the three RXRs. Interestingly, each of these receptors in human and mouse is encoded by genes located at distinct chromosomal loci and on separate chromosomes. The proximity of RXR genes to loci known to be associated with genetic disorders suggests that their location may be useful in establishing a link between RXRs and certain human diseases.

Animals↗
PubMed2005

Proteome mapping of mature pollen of Arabidopsis thaliana.

The male gametophyte of Arabidopsis is a three-celled pollen grain that is thought to contain almost all the mRNAs needed for germination and rapid pollen tube growth. We generated a reference map of the Arabidopsis mature pollen proteome by using multiple protein extraction techniques followed by 2-DE and ESI-MS/MS. We identified 135 distinct proteins from a total of 179 protein spots. We found that half of the identified proteins are involved in metabolism (20%), energy generation (17%), or cell structure (12%); these percentages are similar to those determined for the pollen transcriptome and this similarity is consistent with the idea that in addition to the mRNAs, the mature pollen grain contains proteins necessary for germination and rapid pollen tube growth. We identified ten proteins of unknown function, three of which are flower- or pollen-specific, and we identified nine proteins whose RNAs were absent from the transcriptome, seven of which are involved in metabolism, energy generation, or cell wall structure. Our work complements and extends recent analyses of the pollen transcriptome.

Amino Acid Sequence↗
PubMed2006

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes.

BACKGROUND: Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the proposed recent polyploidy event, was also utilized in our analysis to further elucidate the evolutionary relationship. RESULTS: We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing 475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was calculated using simulated Arabidopsis genome. CONCLUSION: We report here the result of the first extensive analysis of the conserved microsynteny using DNA sequences across the Prunus genome and their Arabidopsis homologs. Our study also illustrates that both the ancestral and present Arabidopsis genomes can provide a useful resource for marker saturation and candidate gene search, as well as elucidating evolutionary relationships between species.

Arabidopsis↗
PubMed2006

Mapping and comprehensive analysis of the extracellular and cell surface proteome of the human pathogen Corynebacterium diphtheriae.

Secreted proteins of the human pathogen Corynebacterium diphtheriae might be involved in important pathogen-host cell interactions. Here, we present the first systematic reference map of the extracellular and cell surface proteome fractions of the type strain C. diphtheriae C7s(-)tox-. The analysis window of 2-DE covered the pI range from 3 to 10 along with a MW range from 8 to 150 kDa. Computational analysis of the 2-D gels detected almost 150 protein spots in the extracellular proteome fraction and about 80 protein spots of the cell surface proteome. MALDI-TOF-MS and PMF with trypsin unambiguously identified 107 extracellular protein spots and 53 protein spots of the cell surface, representing in total 85 different proteins of C. diphtheriae C7s(-)tox-. Several of the identified proteins are encoded by pathogenicity islands and might represent virulence factors of C. diphtheriae. Additionally, four solute-binding proteins (HmuT, Irp6A, CiuA, and FrgD) of different iron ABC transporters were identified, with the hitherto uncharacterized FrgD protein being the most abundant one of the cell surface proteome of C. diphtheriae C7s(-)tox-.

Amino Acid Sequence↗
PubMed2003

Spot overlapping in two-dimensional polyacrylamide gel electrophoresis maps: relevance to proteomics.

Proteomics requires a large-scale, simultaneous separation of proteins from a mixture, assessment of the relative abundance of these molecules, and identification and characterization of each component. In 2-D PAGE separations, the best method of choice for protein analysis, separation of all the proteins present in the sample is still far to be achieved and comigrating proteins in the same spot are in general present. A statistical estimation of the degree of spot overlapping present in a 2-D PAGE separation is here described: for different conditions of spot overcrowding in the map, the degree of overlapping can be quantified in terms of purity degree of each spot or percentage of proteins that will appear in the map as a single spot. A computer simulation approach is described: it is based on the protein separation pattern present in the experimental maps. The results thus obtained are compared to a theoretical model (statistical degree of peak overlapping model) based on random spot position. The described procedures were applied to an experimental reference map of human plasma. The severity of spot overlapping in 2-D PAGE maps is estimated and the influence of different experimental conditions (strip dimension, detector system performance, pI range) is discussed. These informations are useful to quantitatively estimate the degree of error associated with identification and quantitation of each protein and to set-up experimental conditions which will increase resolution and greatly decrease the probability of spot overlapping.

Computer Simulation↗
PubMed2004

SWISS-2DPAGE, ten years later.

The SWISS-2DPAGE database was established in 1993 and is maintained collaboratively by the Swiss Institute of Bioinformatics (SIB) and the Biomedical Proteomics Research Group (BPRG) of the Geneva University Hospital. During these years, SWISS-2DPAGE underwent constant modification and improvement. Current content includes about 4000 identified spots corresponding to 1200 different protein entries in 36 reference maps from human, mouse, Arabidopsis thaliana, Dictyostelium discoideum, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus origins. With a high level of annotation and integration with other relevant databases, SWISS-2DPAGE is a reference source in the proteomics world. Queries to SWISS-2DPAGE database currently reach 1000 hits per day.

Animals↗
PubMed2005

Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins.

The marine bacterium Rhodopirellula baltica, a member of the phylum Planctomycetes, has distinct morphological properties and contributes to remineralization of biomass in the natural environment. On the basis of its recently determined complete genome we investigated its proteome by 2-DE and established a reference 2-DE gel for the soluble protein fraction. Approximately 1000 protein spots were excised from a colloidal Coomassie-stained gel (pH 4-7), analyzed by MALDI-MS and identified by PMF. The non-redundant data set contained 626 distinct protein spots, corresponding to 558 different genes. The identified proteins were classified into role categories according to their predicted functions. The experimentally determined and the theoretically predicted proteomes were compared. Proteins, which were most abundant in 2-DE gels and the coding genes of which were also predicted to be highly expressed, could be linked mainly to housekeeping functions in glycolysis, tricarboxic acid cycle, amino acid biosynthesis, protein quality control and translation. Absence of predictable signal peptides indicated a localization of these proteins in the intracellular compartment, the pirellulosome. Among the identified proteins, 146 contained a predicted signal peptide suggesting their translocation. Some proteins were detected in more than one spot on the gel, indicating post-translational modification. In addition to identifying proteins present in the published sequence database for R. baltica, an alternative approach was used, in which the mass spectrometric data was searched against a maximal ORF set, allowing the identification of four previously unpredicted ORFs. The 2-DE reference map presented here will serve as framework for further experiments to study differential gene expression of R. baltica in response to external stimuli or cellular development and compartmentalization.

Bacteria↗
PubMed2005

Proteomics meets microbiology: technical advances in the global mapping of protein expression and function.

The availability of complete genome sequences for a large number of pathogenic organisms has opened the door for large-scale proteomic studies to dissect both protein expression/regulation and function. This review highlights key proteomic methods including two-dimensional gel electrophoresis, reference mapping, protein expression profiling and recent advances in gel-free separation techniques that have made a significant impact on the resolution of complex proteomes. In addition, we highlight recent developments in the field of chemical proteomics, a branch of proteomics aimed at functionally profiling a proteome. These techniques include the development of activity-based probes and activity-based protein profiling methods as well as the use of synthetic small molecule libraries to screen for pharmacological tools to perturb basic biological processes. This review will focus on the applications of these technologies to the field of microbiology.

Bacterial Proteins↗
PubMed1998

Two-dimensional polyacrylamide gel electrophoresis map of bull seminal plasma proteins.

A two-dimensional polyacrylamide gel electrophoresis map of bull seminal plasma proteins has been established. About 250 spots were detected after silver staining and polypeptides from 24 spots have been N-terminally sequenced. Major proteins already described in bull seminal plasma, like PDC-109 and aSFP, have been located on the map; proteins not yet reported in male reproductive tracts have been evidenced; for some polypeptides showing a previously unknown N-terminal sequence, structural similarities with proteins described in other organisms have been found. A reference map of seminal plasma proteins could be useful in relating protein pattern changes to physiopathological events influencing the reproductive sphere.

Amino Acid Sequence↗
PubMed2006

Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome.

The root-knot nematode (Meloidogyne spp.) is a major plant pathogen, affecting several solanaceous crops worldwide. In Capsicum annuum, resistance to this pathogen is controlled by several independent dominant genes--the Me genes. Six Me genes have previously been shown to be stable at high temperature in three highly resistant and genetically distant accessions: PI 322719, PI 201234, and CM334 (Criollo de Morelos 334). Some genes (Me4, Mech1, and Mech2) are specific to certain Meloidogyne species or populations, whereas others (Me1, Me3, and Me7) are effective against a wide range of Meloidogyne species, including M. arenaria, M. javanica, and M. incognita, the most common species in Mediterranean and tropical areas. These genes direct different response patterns in root cells depending on the pepper line and nematode species. Allelism tests and fine mapping using the BSA-AFLP approach showed these genes to be different but linked, with a recombination frequency of 0.02-0.18. Three of the PCR-based markers identified in several genetic backgrounds were common to the six Me genes. Comparative mapping with CarthaGene software indicated that these six genes clustered in a single genomic region within a 28 cM interval. Four markers were used to anchor this cluster on the P9 chromosome on an intraspecific reference map for peppers. Other disease resistance factors have earlier been mapped in the vicinity of this cluster. This genomic area is colinear to chromosome T12 of tomato and chromosome XII of potato. Four other nematode resistance genes have earlier been identified in this area, suggesting that these nematode resistance genes are located in orthologous genomic regions in Solanaceae.

Alleles↗
PubMed1998

Development of mini-gel technology in two-dimensional electrophoresis for mass-screening of samples: application to tears.

Despite the extensive literature available on tear proteins and lipids, very little has been reported on the tear fluid as a whole and it's changes in contact lens wear or ocular diseased patients. Initially a human reflex tear two-dimensional map was created by Molloy et al. (Electrophoresis 1997, 18, 2811-2815), using this information a process for mass-screening was established. The large format two-dimensional technique was evaluated, using a basal tear reference map, and modified to describe a fast, efficient and cost effective method of protein separation. The use of one pH 3-10 18 cm nonlinear immobilised pH gradient (IPG) strip and two mini-gels for the second-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) results in an effective separation of tear proteins which will be applied in diagnostic studies of tear samples.

Acrylic Resins↗