To clone or not to clone plant QTLs: present and future challenges

Recent technical advancements and refinement of analytical methods have enabled the loci (quantitative trait loci, QTLs) responsible for the genetic control of quantitative traits to be dissected molecularly. To date, most plant QTLs have been cloned using a positional cloning approach following identification in experimental crosses. In some cases, an association between sequence variation at a candidate gene and a phenotype has been established by analysing existing genetic accessions. These strategies can be refined using appropriate genetic materials and the latest developments in genomics platforms. We foresee that although QTL analysis and cloning addressing naturally occurring genetic variation should shed light on mechanisms of plant adaptation, a greater emphasis on approaches relying on mutagenesis and candidate gene validation is likely to accelerate the pace of discovering the genes underlying QTLs.     

To die or not to die: DNA repair in neurons

One of the critical emerging problems in modern pathobiology is how cells govern the decision to live or die, and the cost of making such a decision. Nowhere are these questions more poignant than in deciphering the tissue-specific responses to DNA damage. Mutations in DNA repair enzymes, malfunctions in cell cycle regulation, and genetic instability are associated with most somatic cancers. However, in many hereditary diseases arising from mutations in DNA repair proteins, the same dominant mutations that cause cancer in dividing cells are often associated with cell death in terminally differentiated neurons. Context dependent differences in the response to DNA damage are used to make fundamental choices as to cell fate, and are likely to shed light on the mechanisms underlying human disease.     

To skip or not to skip: choosing repriming to tolerate DNA damage

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A clustering method for repeat analysis in DNA sequences

Background

A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.

Results

The resulting software tool collects all repeat classes and outputs summary statistics as well as a file containing multiple sequences (multi fasta), that can be used as the target of searches. Its use is demonstrated here on several complete microbial genomes, the entire Arabidopsis thaliana genome, and a large collection of rice bacterial artificial chromosome end sequences.

Conclusions

We propose a new clustering method for analysis of the repeat data captured in suffix trees. This method has been incorporated into a system that can find repeats in individual genome sequences or sets of sequences, and that can organize those repeats into classes. It quickly and accurately creates repeat databases from small and large genomes. The associated software (RepeatFinder), should prove helpful in the analysis of repeat structure for both complete and partial genome sequences.     

Novel strategies to clone identical and distinct DNA sequences for several complex genomes

In this minireview I briefly describe the new methods suggested for cloning sequences identical by descent, homo-or hemizygously deleted, amplified or polymorphic, and compare them with the most efficient techniques developed earlier. The new methods include cloning of identical sequences (CIS), cloning of polymorphic sequences (COP), and cloning of deleted sequences (CODE). Although these methods are based on the same combination of biochemical techniques, their aims are different. These methods are fully complementary, and they may be combined to analyze a given object. If one aims to clone a disease gene responsible for familial cancer syndrome, these methods may be applied as follows. CIS can be used to identify the sequences identical by descent comparing the DNA obtained from affected or unaffected family members. COP can be used to find sequences that are different between affected and unaffected members, and CODE would be useful to compare tumor and normal (control) samples to isolate, deleted sequences (putative candidate tumor suppressor genes) and amplified sequences (putative oncogenes). The COP and CODE procedures can be applied to analyze the CpG islands, thus allowing direct candidate gene identification.     

Pattern recognition in DNA sequences and its application to consensus foot-printing

We consider the problem of comparing several nucleic acid sequencesto identify words occurring imperfectly (patterns with no gap)with unusual frequency. Methods for computing, representing,and inspecting interactively the structure of such repeatingmotifs in nucleic acids and more generally any text are described.Multiple sequences are treated as one large concatenate. Ina preprocessing step, a lexical index is created to providerapid string matching for the enumeration of the words matchinga pattern. For given word features (word length, minimal frequency),a sequence profile is displayed. The profile can be inspectedinteractively with on-line algorithms. Applications to the identificationof regulatory elements in DNA regions involved in the controlof gene expression are presented. Our program (‘DNA-Lexemics’)runs on the Macintosh.     

To age or not to age

According to the antagonistic pleiotropy theory of ageing, natural selection has favoured genes conferring short-term benefits to the organism at the cost of deterioration in later life. The 'disposable soma' theory expresses this as a life-history strategy in which somatic maintenance is below the level required to prevent ageing, thus enabling higher immediate fertility. It has been argued that a non-ageing strategy will always be bettered by a low but non-zero rate of ageing, because the costs of such ageing will be felt only in the distant future when they are of negligible importance. Here, we examine this argument critically. We find that a non-ageing strategy will be locally optimal if, in the presence of ageing, the onset of deterioration is sufficiently rapid or early. Conversely, ageing will be optimal if deterioration is sufficiently slow or late. As the temporal profile of ageing changes from one of steady deterioration to one involving a sudden loss of vitality after a period of little or no decline, the conditions for a non-ageing strategy to be locally optimal become progressively more stringent. But for all forms of profile considered, conditions can be found for which a strategy involving no ageing is locally optimal.     

To adhere or not to adhere

The modulation of cell adhesion is fundamental to the morphogenesis that accompanies proper embryonic development. Cadherins are a large family of calcium-dependent cell adhesion molecules whose spatial and temporal expression is critical to the formation of the neural crest, a unique, multipotent cell type that contributes to the patterning of the vertebrate body plan. Neural crest cells arise from the embryonic ectoderm through inductive interactions and reside in the dorsal aspect of the neural tube. These cells under go an epithelial-to-mesenchymal transition and migrate to precise destinations in the embryo, where they go on to differentiate into such diverse structures as melanocytes, elements of the peripheral nervous system, and the craniofacial skeleton. Distinct cadherins are expressed during the induction, migration and differentiation of the neural crest. With the advent of genomic sequencing, assembly and annotation for various model organisms, it has become possible to elucidate the molecular mechanisms underlying cadherin expression, and how these cadherins function, during neural crest development. This review explores the known roles of cadherins and details, where relevant, how different cadherins are regulated during the formation of the neural crest.     

To model or not to model

Summary Self-improving control systems may belong to either of two categories, according to whether or not they embody an explicit model of the part of their environment with which they interact. The two forms of operation are discussed and compared, and it is shown that the two may be mathematically equivalent. The treatment also gives theoretical justification for a particular mode of operation for nonmodel-forming controllers.     

To tree or not to tree

The practice of tracking geographical divergence along a phylogenetic tree has added an evolutionary perspective to biogeographic analysis within single species. In spite of the popularity of phylogeography, there is an emerging problem. Recurrent mutation and recombination both create homoplasy, multiple evolutionary occurrences of the same character that are identical in state but not identical by descent. Homoplasic molecular data are phylogenetically ambiguous. Converting homoplasic molecular data into a tree represents an extrapolation, and there can be myriad candidate trees among which to choose. Derivative biogeographic analyses of 'the tree' are analyses of that extrapolation, and the results depend on the tree chosen. I explore the informational aspects of converting a multicharacter data set into a phylogenetic tree, and then explore what happens when that tree is used for population analysis. Three conclusions follow: (i) some trees are better than others; good trees are true to the data, whereas bad trees are not; (ii) for biogeographic analysis, we should use only good trees, which yield the same biogeographic inference as the phenetic data, but little more; and (iii) the reliable biogeographic inference is inherent in the phenetic data, not the trees.     

To permute or not to permute

Permutation test is a popular technique for testing a hypothesis of no effect, when the distribution of the test statistic is unknown. To test the equality of two means, a permutation test might use a test statistic which is the difference of the two sample means in the univariate case. In the multivariate case, it might use a test statistic which is the maximum of the univariate test statistics. A permutation test then estimates the null distribution of the test statistic by permuting the observations between the two samples. We will show that, for such tests, if the two distributions are not identical (as for example when they have unequal variances, correlations or skewness), then a permutation test for equality of means based on difference of sample means can have an inflated Type I error rate even when the means are equal. Our results illustrate permutation testing should be confined to testing for non-identical distributions. CONTACT: calian@raunvis.hi.is.