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PubMed2001

Distribution of Indel lengths.

Protein sequence alignment has become a widely used method in the study of newly sequenced proteins. Most sequence alignment methods use an affine gap penalty to assign scores to insertions and deletions. Although affine gap penalties represent the relative ease of extending a gap compared with initializing a gap, it is still an obvious oversimplification of the real processes that occur during sequence evolution. To improve the efficiency of sequence alignment methods and to obtain a better understanding of the process of sequence evolution, we wanted to find a more accurate model of insertions and deletions in homologous proteins. In this work, we extract the probability of a gap occurrence and the resulting gap length distribution in distantly related proteins (sequence identity < 25%) using alignments based on their common structures. We observe a distribution of gaps that can be fitted with a multiexponential with four distinct components. The results suggest new approaches to modeling insertions and deletions in sequence alignments.

Amino Acid Sequence↗
PubMed2005

The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and Therians.

Morphological data supports monotremes as the sister group of Theria (extant marsupials + eutherians), but phylogenetic analyses of 12 mitochondrial protein-coding genes have strongly supported the grouping of monotremes with marsupials: the Marsupionta hypothesis. Various nuclear genes tend to support Theria, but a comprehensive study of long concatenated sequences and broad taxon sampling is lacking. We therefore determined sequences from six nuclear genes and obtained additional sequences from the databases to create two large and independent nuclear data sets. One (data set I) emphasized taxon sampling and comprised five genes, with a concatenated length of 2,793 bp, from 21 species (two monotremes, six marsupials, nine placentals, and four outgroups). The other (data set II) emphasized gene sampling and comprised eight genes and three proteins, with a concatenated length of 10,773 bp or 3,669 amino acids, from five taxa (a monotreme, a marsupial, a rodent, human, and chicken). Both data sets were analyzed by parsimony, minimum evolution, maximum likelihood, and Bayesian methods using various models and data partitions. Data set I gave bootstrap support values for Theria between 55% and 100%, while support for Marsupionta was at most 12.3%. Taking base compositional bias into account generally increased the support for Theria. Data set II exclusively supported Theria, with the highest possible values and significantly rejected Marsupionta. Independent phylogenetic evidence in support of Theria was obtained from two single amino acid deletions and one insertion, while no supporting insertions and deletions were found for Marsupionta. On the basis of our data sets, the time of divergence between Monotremata and Theria was estimated at 231-217 MYA and between Marsupialia and Eutheria at 193-186 MYA. The morphological evidence for a basal position of Monotremata, well separated from Theria, is thus fully supported by the available molecular data from nuclear genes.

Amino Acid Sequence↗
PubMed2006

Selective targeting of indel-inferred differences in spatial structures of homologous proteins.

The eukaryotic pathogen Leishmania donovani possesses a housekeeping protein Elongation-Factor-1alpha (EF-1alpha) which has been found to be unexpectedly involved in the pathogen's virulence. Because it is associated with virulence and essential for cell survival, this protein is an attractive choice for drug targeting; however, its sequence is highly similar (> 80% sequence identity) to that of its human homolog, rendering it a risky choice for a drug target. The chief difference between these two proteins has been found to be a 12 amino acid sequence present in human EF-1alpha but absent from leishmania EF-1alpha. Furthermore, it has been shown that this 12 amino acid insert in the human sequence corresponds to a hairpin loop on the surface of the protein. In this study, we searched for those spatial features in leishmania EF-1alpha that are impacted or obscured by the extra hairpin loop in the human counterpart. We have also conducted a large-scale in silico screening for small molecules that could plausibly bind to these protein features. While experimental evidence is required to verify our results, our findings thus far appear to support this approach as a new strategy for the development of antagonists against pathogenic targets having close human homologs.

Amino Acid Sequence↗
PubMed1992

Indelible bond location marks: an avoidable aesthetic hazard.

An increasingly popular method of aiding the precise placement of bonded brackets is to identify the long axis and centre of the crown with small pencil marks. A case is reported where marks placed with a soft pencil in the centre of the etched enamel have led to the inclusion of pigment deep in the enamel surface which has proved impossible to remove.

Adolescent↗
PubMed1996

An indelible lineage marker for Xenopus using a mutated green fluorescent protein.

We describe the use of a DNA construct (named GFP.RN3) encoding green fluorescent protein as a lineage marker for Xenopus embryos. This offers the following advantages over other lineage markers so far used in Xenopus. When injected as synthetic mRNA, its protein emits intense fluorescence in living embryos. It is non-toxic, and the fluorescence does not bleach when viewed under 480 nm light. It is surprisingly stable, being strongly visible up to the feeding tadpole stage (5 days), and in some tissues for several weeks after mRNA injection. We also describe a construct that encodes a blue fluorescent protein. We exemplify the use of this GFP.RN3 construct for marking the lineage of individual blastomeres at the 32- to 64-cell stage, and as a marker for single transplanted blastula cells. Both procedures have revealed that the descendants of one embryonic cell can contribute single muscle cells to nearly all segmental myotomes rather than predominantly to any one myotome. An independent aim of our work has been to follow the fate of cells in which an early regulatory gene has been temporarily overexpressed. For this purpose, we co-injected GFP.RN3 mRNA and mRNA for the early Xenopus gene Eomes, and found that a high concentration of Eomes results in ectopic muscle gene activation in only the injected cells. This marker may therefore be of general value in providing long term identification of those cells in which an early gene with ephemeral expression has been overexpressed.

Animals↗