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Current
Genomics
ISSN: 1389-2029
Current Genomics
Volume 7, Number 2, April 2006
Contents
Comparison of DNA Isolation Kits to Extract DNA from
Whole Blood Samples Pp. 73-78
R.A.M. Op den Buijsch, J.E. de Vries, J. ten Kate, P.A.H.M.
Wijnen, S. Rothkrantz-Kos, M.P. van Dieijen-Visser and O.
Bekers
[Abstract]
The Use of Phylogenetic Profiles for Gene Predictions
Revisited Pp. 79-86
Å. Björklund, A. Thorén, G. von Heijne and
A. Elofsson
[Abstract]
Predicting Type-I (Rate-Shift) Functional Divergence
of Protein Sequences and Applications in Functional Genomics
Pp. 87-96
X. Gu, Y. Wang, J. Gu, K.V. Velden and D. Xu
[Abstract]
Building Biological Complexity with Limited Genes
Pp. 97-114
R. Singh, M.D. Robida and S. Karimpour
[Abstract]
Gene Expression Profiling of Epithelial Ovarian Cancer
Pp. 115-135
A. Sommer, F. Hilpert and N. Arnold
[Abstract]
EXTraordinary Bones: Functional and Genetic Analysis
of the EXT Gene Family Pp. 137-148
C.A. Wise
[Abstract]
Abstracts
[Back to top]
Comparison of DNA Isolation Kits to Extract DNA from
Whole Blood Samples
R.A.M. Op den Buijsch, J.E. de Vries, J. ten Kate, P.A.H.M.
Wijnen, S. Rothkrantz-Kos, M.P. van Dieijen-Visser and O.
Bekers
Genomic DNA from WBCs is widely often used for PCR. Although
kits for DNA isolation are in common use, there is scarce
information about their performance and about the PCR quality
of the genomic DNA obtained. Hence, three different kits,
QIAamp blood mini kit, High Pure PCR Template Preparation
Kit and the Puregene DNA isolation kit were evaluated on these
aspects. Genomic DNA was isolated from whole blood samples
with WBC counts ranging from 0.5 to 20*109 WBC/L.
The WBC count was used to calculate the amount of genomic
DNA. The actual amount of genomic DNA isolated, was determined
spectrophotometrically. The DNA extraction efficiency was
obtained by dividing the actual amount of DNA by the calculated
amount yielded. PCR quality was analysed by measuring Cycle
threshold (Ct)
values with a quantitative real-time PCR β-globin
assay. The extraction efficiency of the three DNA isolation
kits was 20% to 40%. Spectrophotometrically determined DNA
concentrations correlated inversely with Ct
values, regardless of the DNA isolation kit applied, whereas
the strongest correlation was obtained for the Puregene DNA
isolation kit. WBC counts also correlated inversely with Ct
values and here the strongest correlation was found for the
QIAamp blood mini kit. In conclusion, the overall performance
of the DNA isolation kits was quite comparable (DNA recoveries
of 20-40%), albeit the QIAamp blood mini kit yielded the most
reproducible extraction efficiencies and lowest Ct
values within every WBC count category.
[Back to top]
The Use of Phylogenetic Profiles for Gene Predictions
Revisited
Å. Björklund, A. Thorén, G. von Heijne and
A. Elofsson
Determining gene functions from genomic sequences is
a central goal of bioinformatics. Traditionally computational
approaches to this problem are based on the detection of genes
with homologous sequences. With the completion of fully sequenced
genomes alternative approaches have become feasible. One such
method is that of phylogenetic profiles. In this method a
gene is described by its phylogenetic profile, i.e. a string
that encodes the presence or absence of a homologous gene
in other genomes. This string is then used to search for other
genes with similar profiles. In this paper we briefly review
the field, including extensions to the original method. We
also discuss variations on this theme including inverse phylogenetic
profiles and non-exact profiles using phylogenetic trees.
In conclusion our work indicates that phylogenetic profiles
might be useful for some, but not all functional annotations.
Functional annotation of genomes remains an important problem
in genomics when no close homologs exist.
[Back to top]
Predicting Type-I (Rate-Shift) Functional Divergence
of Protein Sequences and Applications in Functional Genomics
X. Gu, Y. Wang, J. Gu, K.V. Velden and D. Xu
Functional divergence after gene duplications is a fundamental
issue for functional innovations in many organisms. As gene
family proliferation (gene duplication) may have provided
the raw materials for the origin of new genes, the details
of how duplicate genes have preserved through functional divergence
remain largely unknown. In this review paper, we discuss some
recent developments about this important issue, with special
references to the implication for functional genomics. With
a combination of large-scale genome sequencing and powerful
computational analysis, we show a great deal of functional
information can be obtained from the evolutionary perspective,
which can in turn be used to facilitate high throughput functional
assays. The software DIVERGE can be obtained form http://xgu.gdcb.iastate.edu.
[Back to top]
Building Biological Complexity with Limited Genes
R. Singh, M.D. Robida and S. Karimpour
How organismal complexity is achieved is a fundamental
biological issue. The surprising revelation that complex eukaryotes
have fewer than expected genes presents an important challenge
for deciphering how organisms achieve complexity. The genome
size and the gene number do not necessarily correlate in a
consistent manner with the perceived organismal complexity.
In this review, we focus on known molecular mechanisms that
increase genetic complexity at the molecular and functional
levels, and discuss features that have likely contributed
to organismal complexity.
[Back to top]
Gene Expression Profiling of Epithelial Ovarian Cancer
A. Sommer, F. Hilpert and N. Arnold
Gene expression profiling using microarrays and SAGE
is a widely used technology to elucidate important aspects
of epithelial ovarian cancer (EOC) in order to improve the
clinical management of this disease: Despite the high degree
of morphological heterogeneity, epithelial ovarian cancer
gene expression profiling reflects morphology and biological
behaviour. Based on multiple studies, gene expression profiling
results can be used to stratify the four different subtypes
of EOC, namely serous papillary, mucinous, endometrioid, and
clear cell carcinoma, but some overlapping gene expression
was also noted. An aneuploid DNA content is a frequent phenomenon
in EOC as well as in other solid tumours. However, when differential
RNA expression and the DNA copy number as measured by comparative
genomic hybridisation (CGH) were compared, the level of concordance
was not significant in most studies. The reason for this will
mostly lie in the low resolving power of currently used CGH
methods and might improve with a wider access to arrayCGH.
Several novel candidate markers for the early detection of
EOC have been identified by gene expression profiling and
examples that have been validated by ELISA on the protein
level in serum from EOC patients and healthy controls are
discussed. The information from gene expression profiling
experiments is now being overlaid with additional information
from Gene Ontology, protein-protein interaction and signal
transduction pathway databases in order to discover novel
therapeutic pathways and targets. Genes involved in cell cycle
regulation, the extracellular matrix, and in immunological
responses are relevant to epithelial ovarian cancer biology
and particular genes might have the potential to be exploited
as therapeutic targets for small molecules, biologicals, and
immunologicals. We hope to accomplish that the scope of the
review which includes a discussion of the recently published
papers and the implications of the results for the clinical
management of EOC is of help to researchers and clinicians
in the field.
[Back to top]
EXTraordinary Bones: Functional and Genetic Analysis
of the EXT Gene Family
C.A. Wise
Far from serving as an inert skeletal scaffold,
bone is a dynamic tissue that cycles through tightly coordinated
cycles of developmental growth and regeneration. Bone growth,
which determines the overall growth of vertebrates, is well-characterized
histologically and increasingly understood at the molecular
level. Positional cloning strategies applied to diseases of
simple Mendelian inheritance have revealed genes important
in the proper formation of bone. Functional studies of these
genes, aided considerably by insights provided by studies
of orthologs in various model systems, have led to significant
advances in our understanding of the pathways of mammalian
bone morphogenesis. One such disorder, hereditary multiple
exostoses, is caused by members of the EXT tumor suppressor
gene family. Progress on the molecular dissection of this
disorder, with emphasis on the interplay of genomic, model
system, and clinical studies, is reviewed herein. We are now
challenged to re-direct the biochemical pathway of chondrogenesis/osteogenesis
defined by the EXT genes toward therapeutic control of bone
growth and malignancy.
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