Genome sequence analysis: scientific objectives and practical strategies

A comprehensive comparative analysis of the occurrence of developmental sequences in fungal, plant and animal genomes

We report a fully comprehensive data-mining exercise, involving an estimated total of 590,000 similarity searches, using agents available on the Internet to search for homologies to polypeptide sequences assigned to the category 'development' in the Gene Ontology Consortium AmiGO database (www.godatabase.org). The results indicate that of 552 such developmental sequences only 78 are shared between all three kingdoms, 72 are shared only between fungi and animals, 58 sequences are shared between plants and fungi, and four sequences were common only to Dictyostelium and fungi. No sequences were strictly fungus specific, but 68 occurred only in plants (Viridiplantae) and 239 occurred only in animals (Metazoa). Although some homology was indicated for a total of 219 fungal sequences, 143 (65%) of the matches returned were assigned E-values of 0.05 and must be categorised as weak similarities at best. The majority of the highly similar matches found in this survey proved to be between sequences involved in basic cell metabolism or essential eukaryotic cell processes (enzymes in common metabolic pathways, transcription regulators, binding proteins, receptors and membrane proteins). What is lacking is cross-kingdom similarity in the management processes that regulate multicellular development. The crown group of eukaryotic kingdoms control and regulate their developmental processes in very different ways. Unfortunately, we know nothing about molecular control of multicellular fungal developmental biology.

Congenital and idiopathic scoliosis: clinical and genetic aspects

OBJECTIVE

Genetic and environmental factors influencing spinal development in lower vertebrates are likely to play a role in the abnormalities associated with human congenital scoliosis (CS) and idiopathic scoliosis (IS). An overview of the molecular embryology of spinal development and the clinical and genetic aspects of CS and IS are presented. Utilizing synteny analysis of the mouse and human genetic databases, likely candidate genes for human CS and IS were identified.

DESIGN

Review and synteny analysis.

METHODS

A search of the Mouse Genome Database was performed for "genes," "markers" and "phenotypes" in the categories Neurological and neuromuscular, Skeleton, and Tail and other appendages. The Online Mendelian Inheritance in Man was used to determine whether each mouse locus had a known human homologue. If so, the human homologue was assigned candidate gene status. Linkage maps of the chromosomes carrying loci with possibly relevant phenotypes, but without known human homologues, were examined and regions of documented synteny between the mouse and human genomes were identified.

RESULTS

Searching the Mouse Genome Database by phenotypic category yielded 100 mutants of which 66 had been mapped. The descriptions of each of these 66 loci were retrieved to determine which among these included phenotypes of scoliosis, kinky or bent tails, other vertebral abnormalities, or disturbances of axial skeletal development. Forty-five loci of interest remained, and for 27 of these the comparative linkage maps of mouse and human were used to identify human syntenic regions to which plausible candidate genes had been mapped.

CONCLUSION

Synteny analysis of mouse candidate genes for CS and IS holds promise due to the close evolutionary relationship between mice and human beings. With the identification of additional genes in animal model systems that contribute to different stages of spine development, the list of candidate genes for CS and IS will continue to grow.

Surface-grafted molecularly imprinted polymers for protein recognition

A technique for coating microplate wells with molecularly imprinted polymers (MIPs) specific for proteins is presented. 3-Aminophenylboronic acid was polymerized in the presence of the following templates: microperoxidase, horseradish peroxidase, lactoperoxidase, and hemoglobin, via oxidation of the monomer by ammonium persulfate. This process resulted in the grafting of a thin polymer layer to the polystyrene surface of the microplates. Imprinting resulted in an increased affinity of the polymer toward the corresponding templates. The influence of the washing procedure, template concentration, and buffer pH on the polymer affinity was analyzed. It was shown that the stabilizing function of the support and spatial orientation of the polymer chains and template functional groups are the major factors affecting the imprint formation and template recognition. Easy preparation of the MIPs, their high stability, and their ability to recognize small and large proteins, as well as to discriminate molecules with small variations in charge, make this approach attractive and broadly applicable in biotechnology, assays and sensors.

Patenting genes. J. Craig Venter and the Human Genome Project

He often begins to answer before you have finished asking your question, but his replies are to the point. He speaks with emotion about the people he hopes to help, particularly children with fatal genetic diseases. 'I prefer to do something: the outcome of doing nothing is perfectly clear', he says. He began sequencing human genes while others were discussing how and when to do so. His methods have been called inelegant, redundant, wasteful, and too 'industrial'. Will his method fail to detect some infrequently transcribed genes? That's all right with him. He is not concerned with finding all the human genes, but rather with the fastest possible route to a useful catalog of most human genes.