bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K‐12
Authors: Link Andrew J. , Robison Keith , Church George M. 
Published: May 2005

AbstractMining the emerging abundance of microbial genome sequences for hypotheses is an exciting prospect of “functional genomics”. At the forefront of this effort, we compared the predictions of the complete Escherichia coli genomic sequence with the observed gene products by assessing 381 proteins for their mature N‐termini, in vivo abundances, isoelectric points, molecular masses, and cellular locations. Two‐dimensional gel electrophoresis (2‐DE) and Edman sequencing were combined to sequence Coomassie‐stained 2‐DE spots representing the abundant proteins of wild‐type E. coli K‐12 strains. Greater than 90% of the abundant proteins in the E. coli proteome lie in a small isoelectric point and molecular mass window of 4–7 and 10–100 kDa, respectively. We identified several highly abundant proteins, YjbJ, YjbP, YggX, HdeA, and AhpC, which would not have been predicted from the genomic sequence alone. Of the 223 uniquely identified loci, 60% of the encoded proteins are proteolytically processed. As previously reported, the initiator methionine was efficiently cleaved when the penultimate amino acid was serine or alanine. In contrast, when the penultimate amino acid was threonine, glycine, or proline, cleavage was variable, and valine did not signal cleavage. Although signal peptide cleavage sites tended to follow predicted rules, the length of the putative signal sequence was occassionally greater than the consensus. For proteins predicted to be in the cytoplasm or inner membrane, the N‐terminal amino acids were highly constrained compared to proteins localized to the periplasm or outer membrane. Although cytoplasmic proteins follow the N‐end rule for protein stability, proteins in the periplasm or outer membrane do not follow this rule; several have N‐terminal amino acids predicted to destabilize the proteins. Surprisingly, 18% of the identified 2‐DE spots represent isoforms in which protein products of the same gene have different observed pI and Mr, suggesting they are post‐translationally processed. Although most of the predicted and observed values for isoelectric point and molecular mass show reasonable concordance, for several proteins the observed values significantly deviate from the expected values. Such discrepancies may represent either highly processed proteins or misinterpretations of the genomic sequence. Our data suggest that AhpC, CspC, and HdeA exist as covalent homomultimers, and that IcdA exists as at least three isoforms even under conditions in which covalent modification is not predicted. We enriched for proteins based on subcellular location and found several proteins in unexpected subcellular locations.
‘Proteomic contigs’ of Mycobacterium tuberculosis and Mycobacterium bovis (BCG) using novel immobilised pH gradients
Authors: Urquhart Brooke L. , Atsalos Thelma E. , Roach Daniel , Basseal David J. , Bjellqvist Bengt , Britton Warwick L. , Humphery‐Smith Ian 
Published: May 2005

AbstractTuberculosis remains a major health problem throughout the world and the failure of the existing bacille Calmette‐Guérin (BCG) vaccine in recent trials has prompted a search for potential replacements. Recent advances in molecular and cell biology have cast doubts on the ability of genetic analysis alone to predict polygenic human diseases and other complex phenotypes and have therefore redirected our attention to proteome studies to complement information obtained from DNA sequencing initiatives. Novel acidic (pH 2.3–5) and basic (pH 6–11) IPG gel gradients were employed in conjunction with commercially available pH 4–7 gradients to significantly increase (fourfold) the number of protein spots previously resolved on two‐dimensional (2‐D) gels of Mycobacterium species. A total of 772 and 638 protein spots were observed for M. bovis BCG and M. tuberculosis H37Rv, respectively, the latter corresponding to only the pH regions 4–7 and 6–11. Of interest was the bimodal distribution observed for proteins separated from M. bovis BCG across both Mr and pH ranges. Some differences in protein expression were observed between these two organisms, contrary to what may have been expected considering the high degree of conservation in gene order and sequence similarity between homologous genes. Further work will be directed towards a more detailed analysis of these differences, so as to allow more accurate diagnosis between vaccination and active tuberculosis. The latter is of major importance to epidemiological studies and for patient management.
The proteome of Salmonella enterica serovar typhimurium: Current progress on its determination and some applications
Authors: O'Connor C. David , Farris Michele , Fowler Richard , Qi Shu‐Yun 
Published: May 2005

AbstractSalmonella typhimurium (official designation Salmonella enterica serovar Typhimurium) is an enteric pathogen and a principal cause of gastroenteritis in humans. A comprehensive description of the proteins of Salmonella and their patterns of expression under different environmental conditions would greatly increase our understanding of the virulence of this organism at the molecular level and provide insights into many other aspects of Salmonella biology. While a variety of two‐dimensional studies of Salmonella have been previously carried out to address specific questions, little systematic information is available at the protein level on the numbers of Salmonella polypeptides that have homologues in other organisms, their abundance, and the frequency of post‐translational modifications. To test the feasibility of determining the proteome of Salmonella, the identities of 53 randomly sequenced cell envelope proteins have been determined by N‐terminal sequencing of spots from two‐dimensional gels. In addition to confirming the existence of previously hypothetical proteins predicted from genomic sequencing projects, we found that approximately 20% of the proteins had no matches in sequence databases. The results suggest that proteome anlysis is an efficient way to identify novel proteins from prokaryotes and that the analysis provides a useful approach to the study of Salmonella virulence.
DNA profiling resolves the limited importance of flower colour in defining varieties of Lantana camara
Authors: Scott Leon Jonathan , Graham Glenn Charles , Hannan‐Jones Martin , Yeates David Keith 
Published: May 2005

AbstractRandomly amplified polymorphic DNA (RAPD), successfully used to establish flower colour, is of limited importance in characterising weedy varieties of Lantana camara. Initially the internal transcribed spacer 1 (ITS1) region was sequenced for common pink and common pink‐edged red varieties of L. camara from Australia and L. urticofolia from the neotropics. This proved unhelpful in differentiating varieties due to a lack of variation and the hybrid origin of L. camara, necessitating the utilisation of DNA profiling techniques. Unweighted pair group method arithmethic average (UPGMA) analysis of RAPD data demonstrated that geographical proximity contributes more significantly to genetic relatedness than flower colour. Analysis of molecular variance (AMOVA) likewise demonstrated that geography accounts for a relatively large variance component. These data indicate that the use of flower colour as a primary identification tool needs to be reevaluated. The use of RAPD may prove useful in characterising the weedy varieties of lantana present in Australia and the South Pacific. Since biological control efforts are being hindered by the inadequacy of current morphological taxonomy, it is expected that DNA profiling will underpin continuing studies on the management and control of L. camara.
Genetic diversity at six short tandem repeat loci within the state of Victoria, Australia
Authors: Wilson‐Wilde Linzi M. , van Oorschot Roland A. H. , Mitchell Robert J. 
Published: May 2005

AbstractA new multiplex PCR system, developed by the Forensic Science Service (FSS) in the United Kingdom, permits the coamplification and typing of six short tandem repeat (STR) loci: HUMFGA, D8S1179, HUMTHO1, HUMvWA, D18S51, D21S11 and the sex determining marker Amelogenin. Data are presented on these six STRs for two populations in the state of Victoria, Australia: Caucasian and Asian. Whilst several worldwide databases are already available for the STR loci HUMTHO1 and HUMvWA, only relatively few databases exist for D8S1179, D18S51, D21S11 and HUMFGA. Allele frequencies at each locus displayed some fluctuations between the two populations. This is particularly so for HUMTHO1. Generally, however, the most common allele at each locus was the same in all populations, at all loci. A novel D8S1179 allele was found in Asians, provisionally identified as allele 19 Results for the six loci were compared with similar data from three UK resident populations: Caucasian, Afro‐Caribbean and Asian (Indian/Pakistani) populations. These indicated that ethnically similar populations display similar allele frequencies, while the Australian Asian and UK Afro‐Caribbean were found to be distinct.
A paternity case with apparently conflicting multilocus and single‐locus DNA typing results
Authors: Kühnau Wolfgang , Böhm Ingolf , Krawczak Michael , Schmidtke Jörg 
Published: May 2005

AbstractA paternity case is presented in which DNA typing with thirteen variable number of tandem repeat (VNTR) systems was in apparent conflict with an initial multilocus DNA analysis using oligonucleotide probe (CAC)5. A dual approach was necessary, because the multilocus analysis yielded a proportion of aberrant nonmaternal offspring bands far too small and level of band‐sharing too high for non‐paternity. The case could finally be solved by reference to the joint likelihood ratio combining both approaches. Arguments are presented that summation of log likelihoods is indeed valid even if no information is available regarding linkage between the VNTR loci and the loci contributing to a multilocus DNA fingerprint.
High microvariation sequence polymorphism at short tandem repeat loci: Human beta‐actin related pseudogene as an example
Authors: Miścicka‐Śliwka Danuta , Grzybowski Tomasz 
Published: May 2005

AbstractThe human beta‐actin related pseudogene (HUMACTBP2) seems to be one of the most informative microsatellite markers known because of the high number of length and sequence variants. A total of 50 alleles found in white Caucasians from the Pomerania‐Kujawy region of Poland were analyzed by automated sequencing. In addition to STR length polymorphism, seven different types of sequence variation were observed. Alleles ranging in size between 233 and 273 bp showed regular sequence structure with tetranucleotide repeats AAAG. In the alleles ranging in size from 275 to 323 bp, hexamer units AAAAAG or AGAAAG occurred in the repeat region in addition to AAAG repeats. Two alleles (317 and 321 bp) contained two hexamers in the repeat region. There was considerable polymorphism of the hexamer position leading to allelic variants of the same size but different sequence structures. A large amount of variation in both 5′ and 3′ flanking regions was also observed. Allelic designation based on the number of all types of units within the repeat region (including the hexamer unit) is proposed. An allelic ladder composed of 21 sequenced alleles was constructed to add precision and accuracy to the identification of alleles at ACTBP2 locus.
Variation at three short tandem repeat (STR) loci in Australians: Forensic and ethnic considerations
Authors: Kaska Danuta E. , van Oorschot Roland A. H. , Mitchell Robert J. 
Published: May 2005

AbstractWe report the results of typing three short tandem repeat (STR) polymorphisms by a multiplex system in three forensically relevant populations of Australia; (i) a general Australian, (ii) a Caucasian, and (iii) an Asian sample. The STRs are tetranucleotide repeats in the following autosomal genes; CSF1PO, TPOX and THO1, and collectively comprise the CTT multiplex (Promega). In all three population samples, each of the loci exhibited genotype frequencies consistent with those expected under Hardy‐Weinberg equilibrium, and, further, there was no significant deviation from random association of alleles across separate loci. These two characteristics, plus the high discrimination power values, demonstrate that the CTT multiplex system is a powerful tool for DNA profiling in Australian jurisdictions. Australian Asians and Caucasians exhibit frequencies of alleles at these three STR loci very similar to those in other Asian and Caucasian samples. While most of the variation exists within any single population, there are still considerable differences between Asians and Caucasians. This difference between the two groups is minimal with respect to TPOX and greatest for THO1 alleles.
DNA analysis in disputed parentage: The occurrence of two apparently false exclusions of paternity, both at short tandem repeat (STR) loci, in the one child
Authors: Gunn Peter R. , Trueman Katherine , Stapleton Patricia , Klarkowski Derryck B. 
Published: May 2005

AbstractIn cases of disputed paternity investigated by DNA analysis, it is generally accepted that at least two independent exclusions be observed before concluding that a putative father is not the biological father of the child. We report here a case in which two apparent exclusions of paternity were obtained (at the loci FESFPS and TPOX), from a total of nineteen loci examined (short tandem repeats, AMFLPs, DQA1, Polymarkers). The combined paternity index of the other seventeen loci, and of two multilocus probes (33.15 and 33.6) would exceed twenty‐eight trillion to one. In the absence of any alternative putative father (including close relatives of the man tested), we concluded that the most likely explanation for these results was that the putative father was indeed the biological father, but that two independent mutations had occurred in either the ovum and/or spermatozoon. We have altered our internal laboratory criterion for exclusion of paternity to require exclusions in three independent loci.
Repetitive DNA sequences as an insight into Aeglidae (Crustacea, Anomura) evolution
Authors: D'Amato María Eugenia , Corach Daniel 
Published: May 2005

AbstractThe evolutionary relationships of five Atlantic Aeglidae species (Aegla neuquensis affinis, A. humahuaca, A. jujuyana, A. platensis, and A. uruguayana) were studied by (i) satellite DNA analysis using a restriction enzyme digestion and hybridization pattern approach and (ii) genome screening by using randomly amplified polymorphic DNA (RAPD) typing. The identical restriction patterns and intense interspecific hybridization patterns obtained in this study strongly suggest a recent cladogenetic event for the Aeglidae. The species‐specific amplification products which were detected using RAPD markers allowed species characterization. A total of 49 amplification products were used to construct trees by cluster analysis. The new scheme agrees in part with previous proposals based on biogeography and morphology. We considered that the subdivision northwestern‐platensis species was probably due to the rising of the Andes, which started in the Middle Miocene. Divergence due to altitude is suggested by the different altitudinal distribution of three northwestern species along the same river. The possible role of selection by ecological factor/s was observed at the population level in A. jujuyana, which has a wider altitudinal range distribution. RAPD markers revealed a high level of intraspecific diversity and important genetic flow among populations. However, a few markers showed significant differences in frequency or H between the lowermost population and the other populations, located in a different biogeographical region. The differences were not in relation to geographical distance, and we interpreted them as being due to selection. Repetitive sequences constitute an important reservoir of genetic variation, and these results show their usefulness in testing and proposing evolutionary hypothesis in crabs. These sequences seem to have played an important role in aeglid evolution. Ecological factors related to altitude have probably influenced macro‐ and microevolutionary processes, at least in northwestern species.
Assessment of genetic diversity by DNA profiling and its significance in silkworm, Bombyx mori
Authors: Nagaraju Javare Gowda , Singh Lalji 
Published: May 2005

AbstractSilkworm genetic resources that are being maintained in different countries are yet to be adequately tapped to develop elite varieties that are suited to different agro‐eco‐climatic conditions of countries like India. This is mostly due to unavailability of efficient protocols that could uncover usable genetic variability in silkworms. Molecular markers are known to provide unambiguous estimates of genetic variability of populations since they are independent of confounding effects of environment. The DNA fingerprinting assays, based on random amplified polymorphic DNA (RAPD) and banded krait minor satellite DNA (Bkm) 2(8) multilocus probes, which successfully characterise the diverse silkworm genotypes at their DNA level, are described. The use of these two DNA fingerprinting assays in estimation of within‐ and between‐population genetic diversity is discussed.
Informative enzyme/probe combinations for the multilocus DNA fingerprinting of marsupials
Authors: Lambert Kim , Jones Michelle , Shimmin Glenn , Sofronidis George , Bowden Don , Taggart David , Temple‐Smith Peter 
Published: May 2005

AbstractDNA fingerprinting has become an invaluable tool in the study of population genetics, paternity success, and individual identification; however, the species specificity of some methods has made the wide‐range screening of many different species very time‐consuming. In this study we describe the development and application of reliable and informative DNA fingerprinting techniques in a range of marsupial species using three different restriction enzyme and two oligonucleotide probe combinations. Six species from four marsupial families, the koala (Phascolarctidae), tammar wallaby (Macropodidae), southern hairynosed wombat (Vombatidae), kowari, and dusky and brown marsupial mice (Dasyuridae) were examined. Restriction enzymes HinfI AluI and HaeIII were used in combination with the digoxygenin (DIG)‐labelled oligonucleotide probes (CAC)5 and (GGAT)4. The combinations of HinfI/(GGAT)4, AluI/(CAC)5 and AluI/(GGAT)4 were the most informative, providing highly resolved bands, low background, and the lowest band sharing between individuals. The genetic diversity evident within the different species showed a clear relationship between the level of band sharing and population size. The greatest levels of band sharing were found in the kowaris (80%), which were part of a long‐term captive colony originating from a few founders, and the lowest levels of band sharing were found in the marsupial mice (30–35%) and tammar wallaby (45%), which were caught from large outbred wild populations.
Microsatellite‐based cancer detection using capillary array electrophoresis and energy‐transfer fluorescent primers
Authors: Wang Yiwen , Hung Su‐Chun , Linn Jürgen F. , Steiner Gabriel , Glazer Alexander N. , Sidransky David , Mathies Richard A. 
Published: May 2005

AbstractThe development of sensitive, rapid, and accurate methods and apparatus for high‐throughput short tandem repeat (STR) analysis will be critical for the use of microsatellite alteration in cancer screening. Here we show that STR‐based bladder cancer diagnosis can be performed using capillary array electrophoresis and two‐color labeling with energy‐transfer (ET) fluorescent primers. Rapid (≤35 min) separations are achieved on capillary arrays using replaceable separation matrices and the allelic ratios are quantitatively determined with a precision of ± 10%. With this precision, a variation of 20% was considered diagnostically significant. These methods provide a significant improvement in the speed, ease, and precision of STR analyses compared to slab gel electrophoresis.
Capillary electrophoresis for diagnosis of metabolic disease
Authors: Elgstoen Katja B. Presto , Jellum Egil 
Published: May 2005

AbstractCapillary electrophoresis (CE) equipped with a diode‐array detector have been used to determine diagnostic metabolites occurring in urine of patients with various diseases. The urine samples were injected directly onto the CE instrument without any pretreatment. Identification of abnormal metabolites was based on relative migration times and characteristic diode‐array spectra. The CE‐method readily diagnosed alkaptonuria, neuroblastoma and liver failure due to galactosemia. The simple and automated CE method appears to be suitable for implementation as a screening test in analytical systems aimed at diagnosis of metabolic disorders.
Enhancement of resolution of low molecular weight RNA profiles by staircase electrophoresis
Authors: Cruz‐Sánchez José M. , Velázquez Encarna , Mateos Pedro F. , Velázquez Enrique , Martínez‐Molina Eustoquio 
Published: May 2005

AbstractStable low molecular weight (LMW) RNA comprises molecules used in the taxonomy of microorganisms and in studies on the microbial diversity of populations. However, the use of electrophoretic techniques has been hampered due to the low resolution obtained with techniques used for the separation of this kind of molecule. In this work we develop an electrophoretic method (staircase electrophoresis) that increases the resolution of the technique. This improvement in the resolution adequately resolves the three zones that integrate the profiles of LMW RNA: ribosomic 5S RNA (5S rRNA), class 2 transfer RNA (tRNA), and class 1 transfer RNA, allowing the technique to be applied to taxonomic studies (diagnostic, the identification of the individuals), phylogenetic studies and studies on naturally occurring microbial populations.
Reorientation of large DNA molecules in concentrated polyacrylamide solution during crossed‐field electrophoresis
Authors: Oana Hidehiro , Doi Masao , Ueda Masanori , Yoshikawa Kenichi 
Published: May 2005

AbstractRecently, we found that, in concentrated neutral solutions, DNA molecules migrate in linear conformation under steady electric field. In this paper, we report the conformational change of DNA during 120° crossed‐field electrophoresis in the same polymer solution. We found that, in concentrated polyacrylamide solutions, the reorientation process of DNAs becomes simple: the DNA goes back along the previous track and the reorientation time is longer motion for the separation of DNA fragments in pulsed field gel electrophoresis. We expect that this phenomenon is useful for a more efficient separation technique of large DNAs than the current pulsed field gel electrophoresis.