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At least 991 records · Page 55Linked to original sources
PubMed1996

Sorting signals and targeting of infectious agents through axons: an annotation to the 100 years' birth of the name "axon".

A brief review is given on mechanisms by which axons may be initiated during development and by which the polarity of neurons is maintained by selective sorting and delivery of molecules to axons and dendrites. The use of viruses as tools to study targeting of newly synthesized proteins to axons is described. Emphasis is then given to the hazards that are presented to the individual by the retrograde transport of infectious agents in axons to the brain. Borna disease virus, prions, and Listeria monocytogenes are examined briefly as examples of these mechanisms. These agents have attracted interest previously in veterinary medicine for the most part, but they may present potential and substantial threats to human health. Such infectious agents also represent a new type of virus, a new principle for disease transmission, and a new mechanism for intracellular transport, respectively.

Animals↗
PubMed2001

The cytochrome P450 gene superfamily in Drosophila melanogaster: annotation, intron-exon organization and phylogeny.

The cytochrome P450 gene superfamily is represented by 90 sequences in the Drosophila melanogaster genome. Of these 90 P450 sequences, 83 code for apparently functional genes whereas seven are apparent pseudogenes. More than half of the genes belong to only two families, CYP4 and CYP6. The CYP6 family is insect specific whereas the CYP4 family includes sequences from vertebrates. There are eight genes coding for mitochondrial P450s as deduced from their homology to CYP12A1 from the house fly. The genetic map of the distribution of D. melanogaster P450 genes shows (a) the absence of P450 genes on the chromosome 4 and Y, (b) more than half of the P450 genes are found on chromosome 2, and (c) the largest cluster contains nine genes. Sequence alignments were used to draw phylogenetic trees and to analyze the intron-exon organization of each functional P450 gene. Only five P450 genes are intronless. We found 57 unique intron positions, of which 23 were phase zero, 19 were phase one and 15 were phase two. There was a relatively good correlation between intron conservation and phylogenetic relationship between members of the P450 subfamilies. Although the function of many P450 proteins from vertebrates, fungi, plants and bacteria is known, only a single P450 from D. melanogaster, CYP6A2, has been functionally characterized. Gene organization appears to be a useful tool in the study of the regulation, the physiological role and the function of these P450s.

Alternative Splicing↗
PubMed2002

The odorant-binding proteins of Drosophila melanogaster: annotation and characterization of a divergent gene family.

Insect odorant-binding proteins (OBPs) are thought to facilitate the delivery of hydrophobic odorants, such as sex pheromones or food odors, to receptors on sensory neurons. Increasingly, OBP family members are also being found in non-sensory tissues where they might carry other types of small hydrophobic molecules. They are identifiable by four or six conserved Cys residues and contain six alpha-helices which enclose a hydrophobic ligand-binding pocket. Through exhaustive BLAST searches we have increased the total number of OBPs identified in Drosophila melanogaster to 38, and have amplified the DNA complementary to RNA corresponding to 21 of these by reverse transcriptase polymerase chain reaction. Isoforms frequently share less than 30% amino acid identity and appear to have radically changed since the separation of the major insect orders. However, their sequences are consistent with known OBP structures. Most are located in clusters of between four and 14 genes and several were unusual in that they contained additions, deletions, or fusions. These hexa-helical insect OBPs are structurally unrelated to the functionally analogous lipocalin-like beta-barrel OBPs of vertebrates. As only two lipocalin-like proteins have been found in D. melanogaster, these helical proteins appear to be the dominant carrier of small hydrophobic molecules in insects.

Amino Acid Sequence↗
PubMed2001

Computational methods for gene annotation: the Arabidopsis genome.

Since the structure of the DNA molecule was identified half a century ago, the complete genome sequence has been determined for 37 prokaryotes and several eukaryotes. With the exponential growth of genetic information, bioinformatics has attempted to predict gene locations and functions in cyberspace prior to experimental confirmation at the bench.

Arabidopsis↗
PubMed2000

Biological function made crystal clear - annotation of hypothetical proteins via structural genomics.

Many of the gene products of completely sequenced organisms are 'hypothetical' - they cannot be related to any previously characterized proteins - and so are of completely unknown function. Structural studies provide one means of obtaining functional information in these cases. A 'structural genomics' project has been initiated aimed at determining the structures of 50 hypothetical proteins from Haemophilus influenzae to gain an understanding of their function. Each stage of the project - target selection, protein production, crystallization, structure determination, and structure analysis - makes use of recent advances to streamline procedures. Early results from this and similar projects are encouraging in that some level of functional understanding can be deduced from experimentally solved structures.

Bacterial Proteins↗
PubMed1997

Mycoplasma genes: a case for reflective annotation.

Although function can be assigned to genome sequence by homology at a macroscopic level, this can be misleading in the absence of data on enzyme activities. Together, such data can reveal whether open reading frames are expressed, identify multienzyme function and point to 'orphan' function. Because of their small size and small genomes, the genome sequences of some Mycoplasma spp. are very amenable to detailed analyses.

Genes, Bacterial↗
PubMed2001

An integrated Arabidopsis annotation database for Affymetrix Genechip data analysis, and tools for regulatory motif searches.

Genome-scale sequencing projects have provided the essential information required for the construction of entire genome chips or microarrays for RNA expression studies. The Arabidopsis and rice genomes have been sequenced and whole-genome oligonucleotide arrays are being manufactured. These should soon become available to researchers. Expression studies using genomic-scale expression arrays are providing us with a vast quantity of information at a rapid pace. The rate-limiting step in this type of experiments is not the data generation step but rather the data analysis component of experiments. We report improvements that should facilitate the analysis of Affymetrix Genechip expression data.

Arabidopsis↗