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The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection
Cindy Martens, Yves Van de Peer
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-353
Abstract: Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora.The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.Oomycetes or water molds form a diverse group of eukaryotic micro-organisms that have originally been classified as Fungi because of their similarity in growth morphology, propagation through spores and weaponry to infect host organisms [1]. Furthermore, they occupy similar ecological niches and share many cell wall degrading enzymes to weaken host tissues [2,3]. However, biochemical and molecular data have shown that oomycetes have little affinity with "
Selection of a set of reliable reference genes for quantitative real-time PCR in normal equine skin and in equine sarcoids
Lies Bogaert, Mario Van Poucke, Cindy De Baere, Luc Peelman, Frank Gasthuys, Ann Martens
BMC Biotechnology , 2006, DOI: 10.1186/1472-6750-6-24
Abstract: In the present study the gene transcription levels of 6 commonly used reference genes (ACTB, B2M, HPRT1, UBB, TUBA1 and RPL32) were determined in normal equine skin and in equine sarcoids. After applying the geNorm applet to this set of genes, TUBA1, ACTB and UBB were found to be most stable in normal skin and B2M, ACTB and UBB in equine sarcoids.Based on these results, TUBA1, ACTB and UBB, respectively B2M, ACTB and UBB can be proposed as reference gene panels for accurate normalisation of quantitative data for normal equine skin, respectively equine sarcoids. When normal skin and equine sarcoids are compared, the use of the geometric mean of UBB, ACTB and B2M can be recommended as a reliable and accurate normalisation factor.Gene expression analysis has become increasingly important in biological research where e.g. gene expression profiles from tissues associated with diseases and disorders have to be compared with each other and with those from normal tissues. One of the most powerful tools in this area is real-time quantitative reverse transcription PCR (qRT-PCR). To account for differences in starting material, RNA preparation, RNA quality and cDNA synthesis, adequate normalisation is frequently performed by comparing expression profiles of the genes of interest with those of constitutively expressed genes (= reference genes). Housekeeping genes are most widely used as reference genes, based on the assumption that they are constitutively expressed in most tissues and under certain circumstances, and that they are more or less resistant to cell cycle fluctuations [1,2]. However, it has been demonstrated that the expression levels of these genes may vary considerably in different tissues, different cell types and different disease stages, particularly in clinical samples associated with malignant disease [3,4]. Housekeeping genes are not only involved in the basal cell metabolism, but appear to participate in other functions too, and therefore are prone to regul
The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina
Aminael Sánchez-Rodríguez, Cindy Martens, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-318
Abstract: In our study we used a selection of recently published genomes of Ascomycetes to analyze how gene family gains, duplications and losses have affected the origin of pathogenic traits. By analyzing the evolutionary history of gene families we found that most gene families with an enlarged size in pathogens were present in an ancestor common to both pathogens and non-pathogens. The majority of these families were selectively maintained in pathogenic lineages, but disappeared in non-pathogens. Non-pathogen-specific losses largely outnumbered pathogen-specific losses.We conclude that most of the proteins for pathogenicity were already present in the ancestor of the Ascomycete lineages we used in our study. Species that did not develop pathogenicity seemed to have reduced their genetic complexity compared to their ancestors. We further show that expansion of gained or already existing families in a species-specific way is important to fine-tune the specificities of the pathogenic host-fungus interaction.The Ascomycetes form the largest phylum in the fungal kingdom. They exhibit a broad range of life styles, ranging from saprophytes to both plant and animal (including human) pathogens. Mycosphaerella fijiensis, for instance, is the causal agent of 'Black Sigatoka', one of the most devastating diseases affecting banana and plantains worldwide [1], while the opportunistic pathogen Aspergillus fumigatus is the cause of allergy in human patients with atopic immune systems [2]. With the increasing number of genomes of Ascomycetes being available, the study of the evolutionary dynamics that give rise to pathogenicity becomes amenable. The phylogeny of the Ascomycetes and more specifically of the Pezizomycotina is of particular interest in this respect as some of the pathogens are more closely related to their non-pathogenic counterparts than to other pathogens, emphasizing the importance of the environment in acquiring the pathogenic phenotype [3,4].Recent studies showed that at
Patient Preferences in the Treatment of Vaginal Candidiasis  [PDF]
Mark G. Martens
Open Journal of Obstetrics and Gynecology (OJOG) , 2018, DOI: 10.4236/ojog.2018.812116
Abstract: Vulvovaginal candidiasis (VVC) is one of the most frequent problems facing women and their healthcare professionals (HCP). It is difficult for providers to understand the prevalence of VVC because effective over the counter treatments (OTC), are available. It is expected that there are a great many more episodes of VVC in our patient population, as the frequency of self-treatment, success and satisfaction for those that use OTC products prior to seeing a women’s health care provider is unknown. In this study; healthcare providers were given OTC miconazole/tioconazole units for free distribution to patients for whom they diagnosed VVC by exam in their offices. Surveys for both HCP and patients were also distributed to determine the initial or recurrent nature of their symptoms and their satisfaction with their treatments. 1265 OBGYNs and 1821 NP/CNM/PAs reported on over 19,000 patients receiving a single complete treatment. Among HCPs, treatment efficacy was the primary reason for recommending miconazole/tioconazole. However, rapid onset of symptom relief, safety vs. fluconazole, patient preference for the less messy ovule, avoidance with drugs metabolized by the liver, and resistance to, or failure on, fluconazole were additional reasons noted for topical preference. Overall, patient satisfaction (n =
Susceptibility of Pancreatic Beta Cells to Fatty Acids Is Regulated by LXR/PPARα-Dependent Stearoyl-Coenzyme A Desaturase
Karine H. Hellemans, Jean-Claude Hannaert, Bart Denys, Knut R. Steffensen, Cindy Raemdonck, Geert A. Martens, Paul P. Van Veldhoven, Jan-?ke Gustafsson, Daniel Pipeleers
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0007266
Abstract: Chronically elevated levels of fatty acids-FA can cause beta cell death in vitro. Beta cells vary in their individual susceptibility to FA-toxicity. Rat beta cells were previously shown to better resist FA-toxicity in conditions that increased triglyceride formation or mitochondrial and peroxisomal FA-oxidation, possibly reducing cytoplasmic levels of toxic FA-moieties. We now show that stearoyl-CoA desaturase-SCD is involved in this cytoprotective mechanism through its ability to transfer saturated FA into monounsaturated FA that are incorporated in lipids. In purified beta cells, SCD expression was induced by LXR- and PPARα-agonists, which were found to protect rat, mouse and human beta cells against palmitate toxicity. When their SCD was inhibited or silenced, the agonist-induced protection was also suppressed. A correlation between beta cell-SCD expression and susceptibility to palmitate was also found in beta cell preparations isolated from different rodent models. In mice with LXR-deletion (LXRβ-/- and LXRαβ-/-), beta cells presented a reduced SCD-expression as well as an increased susceptibility to palmitate-toxicity, which could not be counteracted by LXR or PPARα agonists. In Zucker fatty rats and in rats treated with the LXR-agonist TO1317, beta cells show an increased SCD-expression and lower palmitate-toxicity. In the normal rat beta cell population, the subpopulation with lower metabolic responsiveness to glucose exhibits a lower SCD1 expression and a higher susceptibility to palmitate toxicity. These data demonstrate that the beta cell susceptibility to saturated fatty acids can be reduced by stearoyl-coA desaturase, which upon stimulation by LXR and PPARα agonists favors their desaturation and subsequent incorporation in neutral lipids.
Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling
Marie JJ Huysman, Cindy Martens, Klaas Vandepoele, Jeroen Gillard, Edda Rayko, Marc Heijde, Chris Bowler, Dirk Inzé, Yves Peer, Lieven De Veylder, Wim Vyverman
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-2-r17
Abstract: By profile-based annotation of cell cycle genes, counterparts of conserved as well as new regulators were identified in T. pseudonana and P. tricornutum. In particular, the cyclin gene family was found to be expanded extensively compared to that of other eukaryotes and a novel type of cyclins was discovered, the diatom-specific cyclins. We established a synchronization method for P. tricornutum that enabled assignment of the different annotated genes to specific cell cycle phase transitions. The diatom-specific cyclins are predominantly expressed at the G1-to-S transition and some respond to phosphate availability, hinting at a role in connecting cell division to environmental stimuli.The discovery of highly conserved and new cell cycle regulators suggests the evolution of unique control mechanisms for diatom cell division, probably contributing to their ability to adapt and survive under highly fluctuating environmental conditions.Diatoms (Bacillariophyceae) are unicellular photosynthetic eukaryotes responsible for approximately 20% of the global carbon fixation [1,2]. They belong to the Stramenopile algae (chromists) that most probably arose from a secondary endosymbiotic process in which a red eukaryotic alga was engulfed by a heterotrophic eukaryotic host approximately 1.3 billion years ago [3,4]. This event led to an unusual combination of conserved features with novel metabolism and regulatory elements, as recently confirmed by whole-genome analysis of Thalassiosira pseudonana and Phaeodactylum tricornutum [5-7], which are representatives of the two major architectural diatom types, the centrics and the pennates, respectively.Besides their huge ecological importance, diatoms are interesting from a biotechnological perspective as producers of a variety of metabolites (including oils, fatty acids, and pigments) [8,9], and because of their highly structured mesoporous cell wall, made of amorphous silica [10]. Thus, understanding the basic mechanisms controlling t
Abstinence Education Changes Perceptions of Middle School Students  [PDF]
Tary J. Tobin, Cindy Bankston
Creative Education (CE) , 2017, DOI: 10.4236/ce.2017.815164
Abstract: Abstinence education lessons were designed to address teen pregnancy and sexually transmitted infection (STI) among adolescent youth. A community nonprofit organization with extensive experience in abstinence education trained youth leaders and high school students to collaborate with public school health education teachers. The lessons were based on Promoting Health Among Teens! [PHAT] Abstinence-Only, School Edition(Jemmott, Jemmott, & McCaffree, 2014). Originally developed for use in schools with a high proportion of African Americans, they were adapted for use in schools with a high proportion of Latinos. Over 1000 students from nine middle schools in the northwest part of the United States participated. Responses to pre- and post-intervention survey items were compared and indicated improvements in knowledge of the benefits of sexual abstinence and changes in attitudes toward abstinence. The outcomes of the It’s Legit II: Promoting Health Among Teens! Project indicated?that it was implemented well, received well, and had a beneficial effect.
The many layers of immunity
Sascha Martens
Genome Biology , 2002, DOI: 10.1186/gb-2002-3-8-reports4025
Abstract: The Cologne Spring Meeting organized by the Institute for Genetics in Cologne covers a different topic each year. This year's meeting on the theme 'Immunity' consisted of 22 talks over two and a half days. The meeting dealt with all aspects of immunity, ranging from cell-autonomous immunity, which functions in all nucleated cells, to the adaptive immune system that depends on B and T cells. It is becoming increasingly clear that the immune system has many layers, all of which are essential and highly interconnected. Here, I summarize some representative talks on different aspects of immunity.Antonio Lanzavecchia (Institute of Biomedicine, Bellinzona, Switzerland) addressed the question of how memory is maintained in the adaptive immune system. In particular, he focused on the role of cytokines derived from dendritic cells (DCs) - tumor necrosis factor (TNF) α, interleukin (IL)-6, IL-10 and IL-12 - in promoting the proliferation of CD4+ T cells in response to γc cytokines, which bind to receptors that share the γ common (γc) signaling chain, namely IL-2, IL-4, IL-7 and IL-15. Lanzavecchia reported that sensitivity to cytokines, and expression of cytokine receptors, vary with the differentiation stage of T cells. Naive human CD4+ T cells progressively acquire responsiveness to IL-7 and IL-15 and upregulate the IL-2/IL-15 receptor β chain while differentiating to central memory T (TCM) cells or effector memory T (TEM) cells. In addition, IL-7 and IL-15 act synergistically on all T-cell sub-populations but only TEM can directly proliferate in response to these cytokines. In contrast, na?ve and TCM cells also need DCs or DC-derived cytokines in order to upregulate their relevant receptors. Lanzavecchia emphasized the striking difference in the response of na?ve T cells and TCM to cytokine stimulation. Cytokine-expanded na?ve T cells maintain a lymph-node homing phenotype (CD45RA+, CCR7+) and undergo only limited differentiation. In contrast, TCM cells acquire a phenotype
The Impact of High-Stakes Assessments on Beliefs about Reading, Perceptions of Self-as-Reader, and Reading Proficiency of Two Urban Students Retained in Third Grade
Prisca Martens
Journal of Curriculum and Instruction , 2007,
Abstract: This yearlong study explores the perceptions of self-as-reader, beliefs about reading, and reading proficiency of two urban students retained in third grade on the basis of high-stakes assessment scores. The data presented focus on four individual reading and retrospective miscue analysis (RMA) sessions each student had with the researcher across one school year. When the study began, the students were less focused on reading for meaning and did not perceive themselves as good readers. In RMA sessions the students read and retold stories and then analyzed high quality miscues with the researcher facilitating their revaluation of reading as a process of constructing meaning and themselves as capable readers. Findings show that while the students grew in their understanding of the reading process and in their reading proficiency, they did not fully change their perceptions of themselves as readers. Thus the impact of the high-stakes assessment superseded the understanding the students gained while participating in more authentic reading experiences.
Community Essay: Sustainability: science or fiction?
Pim Martens
Sustainability : Science, Practice and Policy , 2006,
Abstract: It is clear that in making the concept of sustainable development concrete, one has to take into account a number of practical elements and obstacles. There is little doubt that integrated approaches are required to support sustainable development. Therefore, a new research paradigm is needed that is better able to reflect the complexity and the multidimensional character of sustainable development. The new paradigm, referred to as sustainability science, must be able to encompass different magnitudes of scales (of time, space, and function), multiple balances (dynamics), multiple actors (interests) and multiple failures (systemic faults). I also think that sustainability science has to play a major role in the integration of different styles of knowledge creation in order to bridge the gulf between science, practice, and politics—which is central to successfully moving the new paradigm forward.
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