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Search Results: 1 - 10 of 298138 matches for " Bas J. Zwaan "
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Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension
Agnieszka Doroszuk, Martijs J Jonker, Nicolien Pul, Timo M Breit, Bas J Zwaan
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-167
Abstract: We found profound differences between Drosophila lines in their age-related expression. Most of the age-associated changes in normal-lived flies were abrogated in long-lived Drosophila. The stress-related genes, including those involved in proteolysis and cytochrome P450, were generally higher expressed in SR flies and showed a smaller increase in expression with age compared to C flies. The genes involved in reproduction showed a lower expression in middle-aged SR than in C flies and, unlike C flies, a lack of their downregulation with age. Further, we found that malnutrition strongly affected age-associated transcript patterns overriding the differences between the lines. However, under less stressful dietary conditions, line and diet affected age-dependent expression similarly. Finally, we present lists of candidate markers of ageing and lifespan extension.Our study unveils transcriptional changes associated with lifespan extension in SR Drosophila. The results suggest that natural genetic variation for SR and lifespan can operate through similar transcriptional mechanisms as those of dietary restriction and life-extending mutations.
Mitochondrial DNA Signature for Range-Wide Populations of Bicyclus anynana Suggests a Rapid Expansion from Recent Refugia
Maaike A. de Jong, Niklas Wahlberg, Marleen van Eijk, Paul M. Brakefield, Bas J. Zwaan
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021385
Abstract: This study investigates the genetic diversity, population structure and demographic history of the afrotropical butterfly Bicyclus anynana using mitochondrial DNA (mtDNA). Samples from six wild populations covering most of the species range from Uganda to South Africa were compared for the cytochrome c oxidase subunit gene (COI). Molecular diversity indices show overall high mtDNA diversity for the populations, but low nucleotide divergence between haplotypes. Our results indicate relatively little geographic population structure among the southern populations, especially given the extensive distributional range and an expectation of limited gene flow between populations. We implemented neutrality tests to assess signatures of recent historical demographic events. Tajima's D test and Fu's FS test both suggested recent population growth for the populations. The results were only significant for the southernmost populations when applying Tajima's D, but Fu's FS indicated significant deviations from neutrality for all populations except the one closest to the equator. Based on our own findings and those from pollen and vegetation studies, we hypothesize that the species range of B. anynana was reduced to equatorial refugia during the last glacial period, and that the species expanded southwards during the past 10.000 years. These results provide crucial background information for studies of phenotypic and molecular adaptation in wild populations of B. anynana.
Differences in the selection response of serially repeated color pattern characters: Standing variation, development, and evolution
Cerisse E Allen, Patrícia Beldade, Bas J Zwaan, Paul M Brakefield
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-94
Abstract: Here we focus on two ecologically relevant features of butterfly wing color patterns, eyespot size and color composition, which are similarly and strongly correlated across the serially repeated eyespots. Though these two characters show similar patterns of standing variation and covariation within a population, they differ in key features of their underlying development. We targeted pairs of eyespots with artificial selection for coordinated (concerted selection) versus independent (antagonistic selection) change in their color composition and size and compared evolutionary responses of the two color pattern characters.The two characters respond to selection in strikingly different ways despite initially similar patterns of variation in all directions present in the starting population. Size (determined by local properties of a diffusing inductive signal) evolves flexibly in all selected directions. However, color composition (determined by a tissue-level response to the signal concentration gradient) evolves only in the direction of coordinated change. There was no independent evolutionary change in the color composition of two eyespots in response to antagonistic selection. Moreover, these differences in the directions of short-term evolutionary change in eyespot size and color composition within a single species are consistent with the observed wing pattern diversity in the genus.Both characters respond rapidly to selection for coordinated change, but there are striking differences in their response to selection for antagonistic, independent change across eyespots. While many additional factors may contribute to both short- and long-term evolutionary response, we argue that the compartmentalization of developmental processes can influence the diversification of serial repeats such as butterfly eyespots, even under strong selection.Despite the diversity of animal form in nature, a limited range of phenotypes is often observed [1-3]. Stasis, convergence, and limit
Cytogenetic Characterization and AFLP-Based Genetic Linkage Mapping for the Butterfly Bicyclus anynana, Covering All 28 Karyotyped Chromosomes
Arjen E. Van't Hof, Franti?ek Marec, Ilik J. Saccheri, Paul M. Brakefield, Bas J. Zwaan
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003882
Abstract: Background The chromosome characteristics of the butterfly Bicyclus anynana, have received little attention, despite the scientific importance of this species. This study presents the characterization of chromosomes in this species by means of cytogenetic analysis and linkage mapping. Methodology/Principal Findings Physical genomic features in the butterfly B. anynana were examined by karyotype analysis and construction of a linkage map. Lepidoptera possess a female heterogametic W-Z sex chromosome system. The WZ-bivalent in pachytene oocytes of B. anynana consists of an abnormally small, heterochromatic W-chromosome with the Z-chromosome wrapped around it. Accordingly, the W-body in interphase nuclei is much smaller than usual in Lepidoptera. This suggests an intermediate stage in the process of secondary loss of the W-chromosome to a ZZ/Z sex determination system. Two nucleoli are present in the pachytene stage associated with an autosome and the WZ-bivalent respectively. Chromosome counts confirmed a haploid number of n = 28. Linkage mapping had to take account of absence of crossing-over in females, and of our use of a full-sib crossing design. We developed a new method to determine and exclude the non-recombinant uninformative female inherited component in offspring. The linkage map was constructed using a novel approach that uses exclusively JOINMAP-software for Lepidoptera linkage mapping. This approach simplifies the mapping procedure, avoids over-estimation of mapping distance and increases the reliability of relative marker positions. A total of 347 AFLP markers, 9 microsatellites and one single-copy nuclear gene covered all 28 chromosomes, with a mapping distance of 1354 cM. Conserved synteny of Tpi on the Z-chromosome in Lepidoptera was confirmed for B. anynana. The results are discussed in relation to other mapping studies in Lepidoptera. Conclusions/Significance This study adds to the knowledge of chromosome structure and evolution of an intensively studied organism. On a broader scale it provides an insight in Lepidoptera sex chromosome evolution and it proposes a simpler and more reliable method of linkage mapping than used for Lepidoptera to date.
Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R
Willemijn M. Passtoors, Judith M. Boer, Jelle J. Goeman, Erik B. van den Akker, Joris Deelen, Bas J. Zwaan, Ann Scarborough, Ruud van der Breggen, Rolf H. A. M. Vossen, Jeanine J. Houwing-Duistermaat, Gert Jan B. van Ommen, Rudi G. J. Westendorp, Diana van Heemst, Anton J. M. de Craen, Andrew J. White, David A. Gunn, Marian Beekman, P. Eline Slagboom
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0027759
Abstract: The Leiden Longevity Study consists of families that express extended survival across generations, decreased morbidity in middle-age, and beneficial metabolic profiles. To identify which pathways drive this complex phenotype of familial longevity and healthy aging, we performed a genome-wide gene expression study within this cohort to screen for mRNAs whose expression changes with age and associates with longevity. We first compared gene expression profiles from whole blood samples between 50 nonagenarians and 50 middle-aged controls, resulting in identification of 2,953 probes that associated with age. Next, we determined which of these probes associated with longevity by comparing the offspring of the nonagenarians (50 subjects) and the middle-aged controls. The expression of 360 probes was found to change differentially with age in members of the long-lived families. In a RT-qPCR replication experiment utilizing 312 controls, 332 offspring and 79 nonagenarians, we confirmed a nonagenarian specific expression profile for 21 genes out of 25 tested. Since only some of the offspring will have inherited the beneficial longevity profile from their long-lived parents, the contrast between offspring and controls is expected to be weak. Despite this dilution of the longevity effects, reduced expression levels of two genes, ASF1A and IL7R, involved in maintenance of chromatin structure and the immune system, associated with familial longevity already in middle-age. The size of this association increased when controls were compared to a subfraction of the offspring that had the highest probability to age healthily and become long-lived according to beneficial metabolic parameters. In conclusion, an “aging-signature” formed of 21 genes was identified, of which reduced expression of ASF1A and IL7R marked familial longevity already in middle-age. This indicates that expression changes of genes involved in metabolism, epigenetic control and immune function occur as a function of age, and some of these, like ASF1A and IL7R, represent early features of familial longevity and healthy ageing.
Response to Grisedale and Van Daal: comparison of STR profiling from low template DNA extracts with and without the consensus profiling method
Kokshoorn Bas,Blankers Bart J
Investigative Genetics , 2013, DOI: 10.1186/2041-2223-4-1
Abstract: In a recent contribution to this journal Grisedale and Van Daal concluded that a single STR analysis of all available template DNA is to be preferred over replicate analyses and a consensus approach when analyzing low template DNA samples. A single STR analysis approach does not allow for an assessment of the validity of the resulting DNA profile. We argue that the use of replicate amplifications is the best way to objectively quantify the extent of the stochastic variation in the data. By applying consensus methodology and/or a probabilistic model, the interpretation of the data will therefore be more objective and reliable.
A Targeted Survey for HI Clouds in Galaxy Groups
Martin Zwaan
Physics , 2001, DOI: 10.1046/j.1365-8711.2001.04514.x
Abstract: Five galaxy groups with properties similar to those of the Local Group have been surveyed for HI clouds with the Arecibo Telescope. In total 300 pointings have been observed on grids of approximately 2.5 x 1.5 Mpc centred on the groups. The 4.5 sigma detection limit on the minimal detectable HI masses is approximately 7 x 10^6 M_sun (H_0=65). All detections could be attributed to optical galaxies; no significant detections of HI clouds have been made. This null result leads to the conclusion that the total HI mass of intragroup clouds must be less than 10 per cent of the total HI mass of galaxy groups and less than 0.05 per cent of the dynamical mass. The recent hypothesis that Galactic high velocity clouds are Local Group satellite galaxies is highly inconsistent with these observations.
The Local HI Mass Function
Martin Zwaan
Physics , 1998,
Abstract: The local HI mass function (HIMF), like the optical luminosity function, is an important observational input into models of cosmology and galaxy evolution. It is a helpful framework for assessing the number density of gas rich dwarf galaxies, which are easily missed in optically selected galaxy samples, as well as for determining the cosmological density of neutral gas at the present epoch. For HI masses larger than 10^8 M_solar the HIMF is determined with reasonable accuracy and the same function is obtained from both optical and HI selected samples of galaxies. However, the faint tail below M_HI = 10^7 M_solar is still ill-constrained and leaves room for a population of gas rich dwarfs or free floating HI clouds which hypothetically could contribute significantly to the local gas density. Determining the faint tail far below HI masses of 10^7 M_solar will be a great challenge for the future.
Optimality Principles in the Regulation of Metabolic Networks
Jan Berkhout,Frank J. Bruggeman,Bas Teusink
Metabolites , 2012, DOI: 10.3390/metabo2030529
Abstract: One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterisation of the molecular components and interactions. Then, the cellular “task” of the network—its function—should be identified. A network contributes to organismal fitness through its function. The premise is that the same functions are often implemented in different organisms by the same type of network; hence, the concept of design principles. In biology, due to the strong forces of selective pressure and natural selection, network functions can often be understood as the outcome of fitness optimisation. The hypothesis of fitness optimisation to understand the design of a network has proven to be a powerful strategy. Here, we outline the use of several optimisation principles applied to biological networks, with an emphasis on metabolic regulatory networks. We discuss the different objective functions and constraints that are considered and the kind of understanding that they provide.
Are triple-negative tumours and basal-like breast cancer synonymous? Authors' response
Bas Kreike, Marc J van de Vijver
Breast Cancer Research , 2007, DOI: 10.1186/bcr1832
Abstract: It is important to realize that, as we have also pointed out in our article [2], the basal-like breast cancer subtype was initially defined based on the gene expression pattern of the so-called 'intrinsic gene list' in only six breast tumours [3]. Since this initial report, the intrinsic gene list that is used to identify basal-like breast tumours has been updated multiple times [3-5]. This shows that a gene-expression-based definition of basal-like breast cancer has its limitations.There are two reasons for Rakha and colleagues [1] to dispute our results. First, there are nine triple-negative tumours that have a gene expression pattern that is not strongly correlated to the basal-like centroid. However, when we do not set the threshold for the correlation coefficient to the molecular subtype centroids at 0.1, but simply look at the closest centroid, all our unclassifiable samples will be allocated to the basal-like subtype. This leaves only the four samples that are allocated to the normal epithelial-like subtype. This is a problematic group, as it was originally defined on the basis of samples that did not contain tumour cells after neoadjuvant chemotherapy treatment and there are many similarities between this subtype and the basal-like subtype [3].Second, Rakha and colleagues [1] state that '18.6% of non-TNP cancers cluster together with TNP cancers in the "basal-like" cluster'. This argument is based on an incorrect understanding of our findings. These 18.6% are not part of a series of tumours that were all negative for a TNP, but 18.6% of a series of tumours not selected for TNP. These tumours include both TNP and non-TNP samples. In Additional file 1 [2], it is shown that some of these tumours have the gene expression pattern of triple-negative tumours – these are in fact the TNP tumours from this unselected series of tumours. This lends even greater support to the notion that triple-negative tumours are synonymous with basal-like tumours.We therefore stand b
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