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Several versions of the rice genome were published in 2002, providing a first overview of the genome content of this model monocot. At the same time, the genome of the model dicot, Arabidopsis thaliana, reached a new level of annotation as thousands of full-length cDNA sequences were integrated with the genome sequence.
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Despite the recent decline in the incidence of cancer, long-term mortality rates remain unchanged. One of the most important factors in the survival of cancer is detection at an early stage. Clinical assays that detect the early events of cancer offer an opportunity to intervene and prevent cancer progression. Biomarkers are important molecular signatures of the phenotype of a cell that aid in early cancer detection and risk assessment. Although new information and technologies are clearly important for new biomarker discovery, we face major hurdles in translating new findings into clinical application. Here, we discuss examples of recent advances and limitations in cancer biomarker identification and validation, and the implications for cancer prevention.
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We have identified microRNAs (miRNAs) in undifferentiated and differentiated mouse embryonic stem (ES) cells. Some of these appear to be ES cell specific, have related sequences, and are encoded by genomic loci clustered within 2.2 kb of each other. Their expression is repressed as ES cells differentiate into embryoid bodies and is undetectable in adult mouse organs. In contrast, the levels of many previously described miRNAs remain constant or increase upon differentiation. Our results suggest that miRNAs may have a role in the maintenance of the pluripotent cell state and in the regulation of early mammalian development.
Recent studies of Echinococcus granulosus molecular strain typing have enabled a better understanding of the transmission cycle of cystic echinococcosis. There have been many publications in this area but there is a need for the evaluation of these tools. We have attempted to respond to this need in our study, which assessed 8 DNA fragments of 40 E. granulosus cysts from North Africa. Parasitological material was collected from 5 types of intermediate hosts, in 5 different countries. The primers chosen to amplify DNA targets were defined either in nuclear DNA, or in mitochondrial DNA. After amplification, PCR products were sequenced. The sequences obtained were aligned and comparisons were made within the group and with GenBank sequences. Whether the target was nuclear or mitochondrial, the same 2 main groups of genotypes were found. The first one, the 'sheep' strain, was found in the human, sheep and cattle samples collected in North Africa. The second one, the 'camel' strain, was found in the camel cysts and cattle and human cysts from Mauritania. These findings further confirm the congruence of the data given by the nuclear and the mitochondrial genome.
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Phanerochaete is a genus of resupinate homobasidiomycetes that are saprophytic on woody debris and logs. Morphological studies in the past indicated that Phanerochaete is a heterogeneous assemblage of species. In this study the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA was used to test the monophyly of the genus Phanerocthaete and to infer phylogenetic relationships of the 24 taxa studied. Maximum parsimony, maximum likelihood, and Bayesian analyses do not support the monophyly of the genus. However, a core group of species represented by Phanerochaete velutina, P. chrysosporium, P. sordida, P. sanguinea and others are closely related and group together in a clade. Other common Phanerochaete species including Phanerochaete rimosa, P. chrysorhiza, P. omnivora, P. avellanea, P. tiberculata, P. flava, and P. allantospora, however, do not cluster with the core Phanerochaete group.
Homobasidiomycetes display a variety of fruit body morphologies. Examples include gilled mushrooms, coral fungi, polypores and puffballs but also species with simple crust-like basidiomata, usually called corticioid fungi. The latter group has largely been neglected in recent studies of homobasidiomycete evolution. The major goal of the present study was to explore the impact that the addition of a wide selection of species with crust-like basidiomata would have on homobasidiomycete phylogeny. Two genes, 5.8S and 28S in the nuclear rDNA repeats, were sequenced and a data set with 178 taxa analysed using neighbour-joining and maximum parsimony methods. Support for clades was evaluated by bootstrap. Basal nodes generally received weak support and branching order for major clades remained largely unresolved. Twelve major groups were recovered and corticioid fungi make up a major or important constituent in most of them. Nine groups are strongly supported but support for euagarics and polyporoid clades is poor. Phlebioid fungi were in earlier studies merged with the polyporoid clade but are here identified as a separate clade. Athelia is allied with ectomycorrhizal genera, inter alia Piloderma and Amphinema, in a separate clade forming a sister group to the boletes. We conclude that corticioid fungi hold a considerable share of the phylogenetic diversity displayed by homobasidiomycetes, and should always be considered when phylogenetic studies of larger basidiomycetes are designed.
The last couple of years an overwhelming amount of data has emerged in the field of biomolecular structure determination. To explore information hidden in these structure databases, clustering techniques can be used. The outcome of the clustering experiments largely depends, among others, on the way the data is represented; therefore, the choice how to represent the molecular structure information is extremely important. This article describes what the influence of the different representations on the clustering is and how it can be analyzed by means of a dendrogram comparison method. All experiments are performed using a data set consisting of RNA trinucleotides. Besides the most basic structure representation, the Cartesian coordinates representation, several other structure representations are used.
Multidimensional separations combined with mass spectrometry are used to study the proteins that are present in two states of Drosophila melanogaster: the whole embryo and the adult head. The approach includes the incorporation of a gas-phase separation dimension in which ions are dispersed according to differences in their mobilities and is described as a means of providing a detailed analytical map of the proteins that are present. Overall, we find evidence for 1133 unique proteins. In total, 780 are identified in the head, and 660 are identified in the embryo. Only 307 proteins are in common to both developmental stages, indicating that there are significant differences in these proteomes. A comparison of the proteome to a database of mRNAs that are found from analysis by cDNA approaches (i.e., transcriptome) also shows little overlap. All of this information is discussed in terms of the relationship between the predicted genome, and measured transcriptomes and proteomes. Additionally, the merits and weaknesses of current technologies are assessed in some detail.
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Haemoglobin genes have been found in a number of plant species, but the number of genes known has been too small to allow effective evolutionary inferences. We present nine new non-symbiotic haemoglobin sequences from a range of plants, including class 1 haemoglobins from cotton, Citrus and tomato, class 2 haemoglobins from cotton, tomato, sugar beet and canola and two haemoglobins from the non-vascular plants, Marchantia polymorpha (a liverwort) and Physcomitrella patens (a moss). Our molecular phylogenetic analysis of all currently known non-symbiotic haemoglobin genes and a selection of symbiotic haemoglobins have confirmed the existence of two distinct classes of haemoglobin genes in the dicots. It is likely that all dicots have both class 1 and class 2 non-symbiotic haemoglobin genes whereas in monocots we have detected only class 1 genes. The symbiotic haemoglobins from legumes and Casuarina are related to the class 2 non-symbiotic haemoglobins, whilst the symbiotic haemoglobin from Parasponia groups with the class 1 non-symbiotic genes. Probably, there have been two independent recruitments of symbiotic haemoglobins. Although the functions of the two non-symbiotic haemoglobins remain unknown, their patterns of expression within plants suggest different functions. We examined the expression in transgenic plants of the two non-symbiotic haemoglobins from Arabidopsis using promoter fusions to a GUS reporter gene. The Arabidopsis GLB1 and GLB2 genes are likely to be functionally distinct. The class 2 haemoglobin gene (GLB2) is expressed in the roots, leaves and inflorescence and can be induced in young plants by cytokinin treatment in contrast to the class 1 gene (GLB1) which is active in germinating seedlings and can be induced by hypoxia and increased sucrose supply, but not by cytokinin treatment.
Finding genes by the positional candidate approach requires abundant cDNAs mapped to chromosomes. To provide such important information, we computationally mapped 19032 of our mouse cDNAs to mouse chromosomes by using data from public databases. We used 2 approaches. In the first, we integrated the mapping data of cDNAs on the human genome, known gene-related data, and comparative mapping data. From this, we calculated map positions on the mouse chromosomes. For this first approach, we developed a simple and powerful criterion to choose the correct map position from candidate positions in sequence homology searches. In the second approach, we related cDNAs to expressed sequence tags (EST) previously mapped in radiation hybrid experiments. We discuss improving the mapping by combining the 2 methods.
Most chloroplastic proteins are nuclear-encoded and must be transported into the organelle post-translationally. Proteinaceous components in the outer and inner envelope membranes of chloroplasts responsible for this import process were originally identified from pea seedlings. We sought to determine whether these proteins are conserved among different plant species other than pea and among different plastid types. We analyzed plant EST databases and found the presence of homologues to pea chloroplastic protein translocation components, Tic110 and Toc75, in both monocot and dicot species. Because these clones were obtained from various tissues, their presence in different types of plastids is proposed. Protein extracts were prepared from several plant species and from different plant tissues, and then probed with antisera raised against pea Tic110 and Toc75. The results support the idea that translocation components originally found in pea chloroplasts are conserved among different plant species and are present in various plastid types.
We have investigated the somatic activity of the maize Activator (Ac) element in aspen with the objective of developing an efficient transposon-based system for gene isolation in a model tree species. The analysis of the new insertion sites revealed the exact reconstitution of the Ac, however, aberrant transposition events were also found. Characterization of the genomic sequences flanking the Ac insertions showed that about one third (22/75) of the sequences were significantly similar to sequences represented in public databases and might correspond to genes. The frequency of Ac landing into coding regions was about two-fold higher when compared to the frequency of T-DNA hitting the predicted genes (5/32) in the aspen genome. Thus, Ac is demonstrated to be a potentially useful heterologous transposon tag in a tree species. This is the first report on transposon-based gene tagging in a tree species describing the excision and reinsertion of transposable element into new genomic positions. We also suggest a heterologous transposon tagging strategy that can be used in aspen somatic cells to obtain dominant gain-of-function mutants and recessive loss-of-function mutants overcoming the regeneration time barrier of a long-lived tree species.
Whole genome shotgun assemblies have proven remarkably successful in reconstructing the bulk of euchromatic genes, with the only limit appearing to be determined by the sequencing depth. For genes imbedded in heterochromatin, however, the low cloning efficiency of repetitive sequences, combined with the computational challenges, demand that additional clues be used to annotate the sequences. One approach that has proven very successful in identifying protein coding genes in Y-linked heterochromatin of Drosophila melanogaster has been to make a BLASTable database of the small, unmapped contigs and fragments leftover at the end of a shotgun assembly, and to attempt to capture these by blasting with an appropriate query sequence. This approach often yields a staggered alignment of contigs from the unmapped set to the query sequence, as though the disjoint contigs represent small portions of the gene. Further inspection frequently shows that the contigs are broken by very large, heterochromatic introns. Methods of this sort are being expanded to make best use of all available clues to determine which unmapped contigs are associated with genes. These include use of EST libraries, and, in the case of the Y chromosome, testing of male specific genes and reduced shotgun depth of relevant contigs. It appears much more hopeful than anyone would have imagined that whole genome shotgun assemblies can recover the great bulk of even heterochromatic genes.