pp 1221-1222 December 2007
pp 1223-1225 December 2007
pp 1227-1244 December 2007 Perspectives
Datura (Solanaceae) is a small genus of plants that, for long, was thought to occur naturally in both the New and Old Worlds. However, recent studies indicate that all species in the genus originated in the Americas. This finding has prompted the conclusion that no species of Datura could have been present in the Old World prior to its introduction there by Europeans in the early 16th century CE. Further, the textual evidence traditionally cited in support of a pre-Columbian Old World presence of Datura species is suggested to be due to the misreading of classical Greek and Arabic sources. As a result, botanists generally accept the opinion that Datura species were transferred into the Old World in the post-Columbian period. While the taxonomic and geographic evidence for a New World origin for all the Datura species appears to be well supported, the assertion that Datura species were not known in the Old World prior to the 16th century is based on a limited examination of the pre-Columbian non-Anglo sources. We draw on old Arabic and Indic1 texts and southern Indian iconographic representations to show that there is conclusive evidence for the pre-Columbian presence of at least one species of Datura in the Old World. Given the systematic evidence for a New World origin of the genus, the most plausible explanation for this presence is a relatively recent but pre-Columbian (probably first millennium CE) transfer of at least one Datura species, D. metel, into the Old World. Because D. metel is a domesticated species with a disjunct distribution, this might represent an instance of human-mediated transport from the New World to the Old World, as in the case of the sweet potato (Ipomoea batatas).
pp 1245-1250 December 2007 Series
pp 1251-1262 December 2007 Articles
The abundance of an mRNA species depends not only on the transcription rate at which it is produced, but also on its decay rate, which determines how quickly it is degraded. Both transcription rate and decay rate are important factors in regulating gene expression. With the advance of the age of genomics, there are a considerable number of gene expression datasets, in which the expression profiles of tens of thousands of genes are often non-uniformly sampled. Recently, numerous studies have proposed to infer the regulatory networks from expression profiles. Nevertheless, how mRNA decay rates affect the computational prediction of transcription rate profiles from expression profiles has not been well studied. To understand the influences, we present a systematic method based on a gene dynamic regulation model by taking mRNA decay rates, expression profiles and transcription profiles into account. Generally speaking, an expression profile can be regarded as a representation of a biological condition. The rationale behind the concept is that the biological condition is reflected in the changing of gene expression profile. Basically, the biological condition is either associated to the cell cycle or associated to the environmental stresses. The expression profiles of genes that belong to the former, so-called cell cycle data, are characterized by periodicity, whereas the expression profiles of genes that belong to the latter, so-called condition-specific data, are characterized by a steep change after a specific time without periodicity. In this paper, we examine the systematic method on the simulated expression data as well as the real expression data including yeast cell cycle data and condition-specific data (glucose-limitation data). The results indicate that mRNA decay rates do not significantly influence the computational prediction of transcription-rate profiles for cell cycle data. On the contrary, the magnitudes and shapes of transcription-rate profiles for condition specific data are significantly affected by mRNA decay rates. This analysis provides an opportunity for researchers to conduct future research on inferring regulatory networks computationally with available expression profiles under different biological conditions.
pp 1263-1272 December 2007 Articles
Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is one of the principal pre-mRNA-binding proteins found in human cells. The hnRNP L protein is fairly abundant. However, it is not restricted to the nucleus, and instead shuttles between the nucleus and the cytoplasm. It is composed of 558 amino acid residues and harbours four loosely conserved RNP-consensus RNA-binding domains. In an attempt to characterize the interaction occurring between cellular proteins and hnRNP L, yeast two-hybrid screening was conducted using a HeLa cDNA library. Some of the cDNA clones were found to harbour a partial human hnRNP D/AUF1 cDNA (GeneBank accession number NM_031369). In this study, we determined that hnRNP L interacts specifically with the hnRNP D/AUF1 in the yeast two-hybrid system. This interaction was verified via an in vitro pull-down assay.
pp 1273-1280 December 2007 Articles
GATA genes are an evolutionarily conserved family, which encode a group of important transcription factors involved in the regulation of diverse processes including the development of the heart, haematopoietic system and sex gonads. However, the evolutionary history of the GATA family has not been completely understood. We constructed a complete phylogenetic tree with functional domain information of the GATA genes of both vertebrates and several invertebrates, and mapped the GATA genes onto relevant chromosomes. Conserved synteny was observed around the GATA loci on the chromosomes. GATAs have a tendency to segregate onto different chromosomes during evolution. The phylogenetic tree is consistent with the relevant functions of GATA members. Analysis of the zinc finger domain showed that the domain tends to be duplicated during evolution from invertebrates to vertebrates. We propose that the balance between duplications of zinc finger domains and GATA members should be maintained to exert their physiological roles in each evolutionary stage. Therefore, evolutionary pressure on the GATAs must exist to maintain the balance during evolution from invertebrates to vertebrates. These results reveal the evolutionary characteristics of the GATA family and contribute to a better understanding of the relationship between evolution and biological functions of the gene family, which will help to uncover the GATAs’ biological roles, evolution and their relationship with associated diseases.
pp 1281-1289 December 2007 Articles
Cyclic AMP (cAMP) is a natural chemoattractant of the social amoeba Dictyostelium discoideum. It is detected by cell surface cAMP receptors. Besides a signalling cascade involving phosphatidylinositol 3,4,5-trisphosphate (PIP3), Ca2+ signalling has been shown to have a major role in chemotaxis. Previously, we have shown that arachidonic acid (AA) induces an increase in the cytosolic Ca2+ concentration by causing the release of Ca2+ from intracellular stores and activating influx of extracellular Ca2+. Here we report that AA is a chemoattractant for D. discoideum cells differentiated for 8–9 h. Motility towards a glass capillary filled with an AA solution was dose-dependent and qualitatively comparable to cAMP-induced chemotaxis. Ca2+ played an important role in AA chemotaxis of wild-type Ax2 as ethyleneglycolbis(b-aminoethyl)-N,N,N′,N′-tetraacetic acid (EGTA) added to the extracellular buffer strongly inhibited motility. In the HM1049 mutant whose iplA gene encoding a putative Ins(1,4,5)P3-receptor had been knocked out, chemotaxis was only slightly affected by EGTA. Chemotaxis in the presence of extracellular Ca2+ was similar in both strains. Unlike cAMP, addition of AA to a cell suspension did not change cAMP or cGMP levels. A model for AA chemotaxis based on the findings in this and previous work is presented.
pp 1291-1298 December 2007 Articles
Embryonic stem (ES) cells are an invaluable model for identifying subtle phenotypes as well as severe outcomes of perturbing gene function that may otherwise result in lethality. However, though ES cells of different origins are regarded as equally pluripotent, their in vitro differentiation potential varies, suggesting that their response to developmental signals is different. The R1 cell line is widely used for gene manipulation due to its good growth characteristics and highly efficient germline transmission. Hence, we analysed the expression of Notch, Wnt and Sonic Hedgehog (Shh) pathway genes during differentiation of R1 cells into early vascular lineages. Notch-, Wnt-and Shh-mediated signalling is important during embryonic development. Regulation of gene expression through these signalling molecules is a frequently used theme, resulting in context-dependent outcomes during development. Perturbing these pathways can result in severe and possibly lethal developmental phenotypes often due to primary cardiovascular defects. We report that during early spontaneous differentiation of R1 cells, Notch-1 and the Wnt target Brachyury are active whereas the Shh receptor is not detected. This expression pattern is similar to that seen in a mouse endothelial cell line. This temporal study of expression of genes representative of all three pathways in ES cell differentiation will aid in further analysis of cell signalling during vascular development.
pp 1299-1305 December 2007 Articles
Natural killer (NK) cells are spontaneously cytotoxic against tumour target cells. Their number was found to be four times more in the spleen of tumour-bearing Swiss albino mice. After activation with recombinant interleukin-2 (rIL-2), NK cells were tested and found to seek out the tumour site when injected intravenously in tumour-bearing mice. Their potential for fighting tumours in vivo was further seen following adoptive transfer of rIL-2 activated NK (A-NK) cells in tumour-bearing mice. After surgical removal of tumour load, adoptive transfer of A-NK cells inhibited tumour recurrence in 92.3% cases, thereby suggesting the use of this protocol for therapeutic purposes to obtain a better outcome.
pp 1307-1316 December 2007 Articles
Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties
Delvardine and its structural derivatives are important non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs). In this work, 15 delvardine analogues were studied. A free energy-of-binding (FEB) expression was developed in the form of an optimized linear combination of van der Waal (vdW), electrostatic, solvation and solvent-accessible surface area (SASA) energy terms. The solvation energy terms estimated by generalized born/surface area (GB/SA) play an important role in predicting the binding affinity of delvardine analogues. Out of 15 derivatives, substitution of CH3 with H at the Y and R positions, as well as substitution of SO2CH3 with only CH2 at the Z position in S2, S8 and S12 analogues, were found to be the most potent (glide score = –7.60, –8.06 and –7.44; pIC50 = 7.28, 7.37 and 7.64) in comparison with the template delvardine (which is used currently as the drug candidate). All the three analogues also passed the absorption, distribution, metabolism and excretion (ADME) screening and Lipinski’s rule of 5, and have the potential to be used for second-generation drug development. The work demonstrates that dock molecular mechanics-generalized born/surface area (MM–GB/SA–ADME) is a promising approach to predict the binding activity of ligands to the receptor and further screen for a successful candidate drug in a computer-aided rational drug design.
pp 1317-1324 December 2007 Articles
The genetic basis of the transmission disequilibrium test (TDT) for two-marker loci is explored from first principles. In this case, parents doubly heterozygous for a given haplotype at the pair of marker loci that are each in linkage disequilibrium with the disease gene with the further possibility of a second-order linkage disequilibrium are considered. The number of times such parents transmit the given haplotype to their affected offspring is counted and compared with the frequencies of haplotypes that are not transmitted. This is done separately for the coupling and repulsion phases of doubly heterozygous genotypes. Expectations of the counts for each of the sixteen cells possible with four-marker gametic types (transmitted vs not transmitted) are derived. Based on a test of symmetry in a square 4 × 4 contingency table, chi-square tests are proposed for the null hypothesis of no linkage between the markers and the disease gene. The power of the tests is discussed in terms of the corresponding non-centrality parameters for the alternative hypothesis that both the markers are linked with the disease locus. The results indicate that the power increases with the decrease in recombination probability and that it is higher for a lower frequency of the disease gene. Taking a pair of markers in an interval for exploring the linkage with the disease gene seems to be more informative than the single-marker case since the values of the non-centrality parameters tend to be consistently higher than their counterparts in the single-marker case. Limitations of the proposed test are also discussed.
pp 1325-1330 December 2007 Review
The formation of diverse cell types from an invariant set of genes is governed by biochemical and molecular processes that regulate gene activity. A complete understanding of the regulatory mechanisms of gene expression is the major function of genomics. Computational genomics is a rapidly emerging area for deciphering the regulation of metazoan genes as well as interpreting the results of high-throughput screening. The integration of computer science with biology has expedited molecular modelling and processing of large-scale data inputs such as microarrays, analysis of genomes, transcriptomes and proteomes. Many bioinformaticians have developed various algorithms for predicting transcriptional regulatory mechanisms from the sequence, gene expression and interaction data. This review contains compiled information of various computational methods adopted to dissect gene expression pathways.
pp 1331-1344 December 2007 Review
Edwardsiellosis is one of the most important bacterial diseases in fish. Scientific work on this disease started more than forty years ago and numerous workers around the world are continually adding to the knowledge of the disease. In spite of this, not a single article that reviews the enormous scientific data thus generated is available in the English language. This article briefly discusses some of the recent research on edwardsiellosis, describing the pathogen’s interaction with the host and environment, its pathogenesis and pathology as well as diagnostic, preventive and control measures.
pp 1345-1345 December 2007 Erratum
Green auto-fluorescence (GAF) of different age groups of mouse blood erythrocytes was determined by using a double in vivo biotinylation (DIB) technique that enables delineation of circulating erythrocytes of different age groups. A significant increase in GAF was seen for erythrocytes of old age group (age in circulation > 40 days) as compared to young erythrocytes (age < 15 days). Erythrocytes are removed from blood circulation by macrophages in the reticulo-endothelial system and depletion of macrophages results in an increased proportion of aged erythrocytes in the blood. When mice were depleted of macrophages for 7 days by administration of clodronate loaded liposomes, the overall GAF of erythrocytes increased significantly and this increase could be ascribed to an increase in GAF of the oldest population of erythrocytes. Using the DIB technique, the GAF of a cohort of blood erythrocyte generated during a 5 day window was tracked in vivo. GAF of the defined cohort of erythrocytes remained low till 40 days of age in circulation and then increased steeply till the end of the life span of erythrocytes. Taken together our results provide evidence for an age dependent increase in the GAF of blood erythrocytes that is accentuated by depletion of macrophages. Kinetics of changes in GAF of circulating erythrocytes with age has also been defined.
pp 1347-1363 December 2007
pp 1363-1372 December 2007
pp 1373-1375 December 2007