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A cytogenetic examination of eight species of Tribolium (Coleoptera: Tenebrionidae)
Comparative genomics of vertebrate Fox cluster loci.
Published onlineComparative StudyJournal ArticleResearch Support, Non-U.S. Gov'tThis is the final version of the article. Available from BioMed Central via the DOI in this record.BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication.We thank Peter Holland and Dave Ferrier for their discussions on this project and John Mulley for supplying the Amia calva genomic DNA, and for comments on the manuscript. This work was supported by the BBSRC
Eucalyptus spp. pollen transport across Liawenee Moor, on the Central Plateau of Tasmania
Investigation of Eucalyptus spp. pollen transport modes on Liawenee Moor in Tasmania revealed that it is possible to separate woodland areas from areas of moor and heath vegetation. While most Eucalyptus spp. pollen is deposited locally, a relatively small component is distributed across treeless areas, where it behaves in a manner similar to the long-distance transported (LOT) pollen of rainforest and alpine conifer taxa. When deposited into lakes, the Eucalyptus spp. component of the terrestrial pollen is increased compared with local pollen.
Knowledge of the percentage Eucalyptus spp. pollen values from extant vegetation communities and the LOT components ofEucalyptus
spp. and rainforest-alpine conifer taxa is useful for palaeoecological interpretation of vegetation history from lake sediment cores.
Applied to the 8000-year-Iong Camerons Lagoon record, the study confirms the treeless character of Liawenee Moor during the
Holocene. The evidence indicates that the moorland has altered from grassy to heath, due to the impacts ofgrazing and burning associated with European pastoral practices, but that the boundaries between the moor and adjacent woodlands have remained stable
Evolution of developmental mechanisms
A report on the joint Spring meeting of the British Society of Developmental Biology and the Genetics Society, York, UK, 20-23 March 2002
Comparative genomics of vertebrate Fox cluster loci
BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication
A microfluidic chip for immobilization and imaging of Ciona intestinalis larvae
Sea squirts (Tunicata) are chordates and develop a swimming larva with a small and defined number of individually identifiable cells. This offers the prospect of connecting specific stimuli to behavioral output and characterizing the neural activity that links these together. Here, we describe the development of a microfluidic chip that allows live larvae of the sea squirt Ciona intestinalis to be immobilized and recorded. By generating transgenic larvae expressing GCaAMP6m in defined cells, we show that calcium ion levels can be recorded from immobilized larvae, while microfluidic control allows larvae to be exposed to specific waterborne stimuli. We trial this on sea water carrying increased levels of carbon dioxide, providing evidence that larvae can sense this gas
Data report: logging while drilling data analysis of Leg 171A, a multivariate statistical approach
In the northern Barbados accretionary wedge, several Deep Sea Drilling
Project (DSDP) and Ocean Drilling Program (ODP) legs (DSDP Leg
78 and ODP Legs 110, 156, and 171A) targeted the décollement and the
seaward extension of the décollement, the proto-décollement. During
Leg 171A, the logging while drilling (LWD) technique was used to determine
the physical properties variations along a profile across the deformation
front. Because of the unstable borehole conditions in
accretionary wedges, LWD is the most effective method for the measurements
of physical properties in these poorly consolidated sediments.
LWD data are acquired just above the drill bit a few minutes
after the formation has been drilled, yielding measurements as close to
in situ conditions as possible.
The large amount of LWD data and the demand for a quick, objective,
and reliable evaluation calls for the application of multivariate statistical
methods. The multivariate factor analysis is a method of
reducing the amount of logging data while giving them a new integrated
meaning with no loss of important information, resulting in factor
logs that are helpful tools for further interpretation. The cluster
analysis of the two or three most significant factors proved to be a useful
and objective method to identify and confirm significant logging
units. The main objective of the application of multivariate statistical
methods in this study is twofold. First, Leg 171A was a stand-alone logging
leg, where no cores were retrieved. The factor analysis was used as
an objective tool for a classification of the drilled sequences based on
their physical and chemical properties. The new factor logs mirror the
basic processes behind the measured geophysical properties and make
them easier to interpret. Second, in the succeeding cluster analysis, similar
geophysical properties are grouped into one cluster, reflecting one
logging unit. These objectively defined logging units can be compared
to statistical electrofacies, which are helpful in differentiating lithologic
characterizations. In particular for LWD measurements, the multivariate
statistical methods of factor and cluster analysis are helpful tools for
a fast, reliable, and objective definition of logging units, which should
be considered for future legs
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