The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary

Fluorescencein situ hybridization (FISH) of microlibraries established from distinct chromosome subregions can test the evolutionary conservation of chromosome bands as well as chromosomal rearrangements that occurred during primate evolution and will help to clarify phylogenetic relationships. We used a DNA library established by microdissection and microcloning from the entire long arm of human chromosome 2 for fluorescencein situ hybridization and comparative mapping of the chromosomes of human, great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus) and Old World monkeys (Macaca fuscata andCercopithecus aethiops). Inversions were found in the pericentric region of the primate chromosome 2p homologs in great apes, and the hybridization pattern demonstrates the known phylogenetically derived telomere fusion in the line that leads to human chromosome 2. The hybridization of the 2q microlibrary to chromosomes of Old World monkeys gave a different pattern from that in the gorilla and the orang-utan, but a pattern similar to that of chimpanzees. This suggests convergence of chromosomal rearrangements in different phylogenetic lines

A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics

Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components

Evolution of human chromosome 7: new information from the mapping of Williams- Beuren locus on non-human primates chromosomes

Human chromosome 7 (HSA7) derives, by a pericentric inversion and a paracentric inversion, from an ancestral chromosome homologous to chromosome 10 of Pongo pygmaeus (the Asiatic Orang-Utan). Nevertheless the genesis of this autosome during primates evolution is not clear. Even if chromosome painting shows that HAS 7 synteny is highly conserved, GTG-banding comparison in Hominoidea and Cercopithecoidea indicates the probable occurrence of complex rearrangements during the evolution. In this study we used a single locus FISH approach, a powerful tool to detect fine rearrangements, in order to investigate the evolution of HAS 7. We report the chromosome mapping of Williams-Beuren syndrome locus (WS - HSA 7q11.23) on Macaca fascicularis (MFA), Cercopithecus (Chlorocebus) aethiops (CAE) and Trachypithecus cristatus (TCR) (Cercopithecoidea, Primates). The probe hybridises on all species tested and demonstrates the occurrence of rearrangements like fusion, fission and pericentric plus paracentric inversions respectively in MFA, CAE and TCR. Together with the first chromosome mapping of WS locus in Cercopithecoidea, this study confirms that single locus mapping is a very efficacious tool for the analysis of chromosomal rearrangements as it gave the opportunity to have a fine molecular confirmation to proposed banding patterns homologies

Examining the uses of shared data

Background
 Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose.

 Materials and Methods
 We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with reused data.

 Results
 Studies on humans, mice, chordata, and invertebrates were equally likely to be conducted using original or shared microarray data, whereas shared data was used in a relatively high proportion of studies involving fungi (odds ratio (OR)=2.4), and a relatively low proportion involving rats, bacteria, viruses, plants, or genetically-altered or inbred animals (OR<0.05). Unsurprisingly, when we looked at Major MeSH terms to represent the primary purpose of the studies, statistical and computational methods clearly dominated. The only biomedical topics with a relatively high proportion of data reuse Major MeSH terms were Promoter Regions, Evolution, and Protein Interaction Mapping.

 Discussion
 Identifying areas of particularly successful microarray data reuse—such as Saccharomyces cerevisiae datasets and studies of promoter regions and evolution—can highlight best practices to be used when developing research agendas, tools, standards, repositories, and communities in areas which have yet to receive major benefits from shared data.
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