110 research outputs found
Citrus Crop production science in horticulture./ L. Gene Albrigo, Lukasz L. Stelinski, Lavern W. Timmer.
No full textTitle from PDF title page (viewed October 9, 2019)Includes bibliographical references and index.This second edition of Citrus, like the original by F.S. Davies and L.G. Albrigo, intends to provide the reader with an updated overview of citriculture from a worldwide perspective. Current theories and technological advances in citriculture are emphasized, citing specific examples of how and where they are used. The text begins with a discussion of major production areas with figures and current trends (Chapter 1). The confusing and controversial taxonomic situation for Citrus and related genera is then discussed, emphasizing molecular biology (biotechnological) advances that are clarifying the genetic relationships between various citrus species. This is followed by a discussion of the major commercially important citrus species and cultivars and traditional and current techniques in citrus breeding (Chapter 2). Chapter 3 covers the importance of rootstocks in citriculture and discusses the major rootstocks, their advantages and disadvantages. In Chapter 4, the role of climatic factors in worldwide citrus production is emphasized, including their effects on citrus yields, growth, economic returns and fruit quality. Plant husbandry, including nursery practices, irrigation, fertilizer application, freeze protection, pruning, growth regulator use and weed control is covered in Chapter 5. In Chapter 6, the major pests and recent changes in their distribution are covered. Diseases of citrus, emphasizing major problems and control measures are the topic of Chapter 7. The final chapter (8) deals with postharvest quality, harvesting and handling of citrus fruits, including the importance of biotic and abiotic problems, as well as packinghouse and processing techniques.History, distribution and uses of citrus fruit -- Taxonomy, cultivars and breeding -- Rootstocks -- Environmental constraints on growth, development and physiology of citrus -- Plant husbandry -- Arthropod pests -- Diseases -- Fruit quality, harvesting and postharvest technology.1 online resource (viii, 314 pages)
Functional genomics analysis of the secretory pathway in Aspergillus niger
No full textFilamentous fungi can be found in the majority of habitats of our planet. The wide-spread presence of filamentous fungi is related to their versatile metabolism, which allows them to grow on simple substrates, such as nitrate, acetate, ethanol, ammonia, or on complex matter such as biopolymers from plant or animal tissues. In order to grow on complex biopolymers such as plant cell wall polysaccharides, fungi must secret hydrolytic and modifying enzymes. These enzymes allow polysaccharide degradation and subsequent internalization of simpler molecules, such as sugar monomers. The filamentous fungus Aspergillus niger has been the subject of intense research in the past decades. This organism is responsible for the largest production of citric acid worldwide. In addition to this, A. niger produces high amounts of enzymes with important applications in the bioindustry, such as enzymes for food and feed processing, or enzymes used for the simultaneous saccharification and fermentation of cellulose for bioethanol production. The secretion of extracellular enzymes in A. niger has been mostly focused on the prediction of gene function based on genome annotation and on the analysis of gene expression. However, there is a gap in the knowledge of all the proteins present in cell, given by proteomics. The aim of the work presented in this thesis was to use a functional genomics approach to identify genes and proteins involved in protein secretion in A. niger and to investigate the dynamic changes of the secretory proteome under high-secretion conditions. For this purpose, we used a combination of gene expression profiling with shotgun proteomics of secretory organelles. Chapter 2 describes a method for gene silencing in filamentous fungi via RNA interference. This method makes use of vectors which express long hairpin RNAs. In A. niger, gene knock-out strategies have been the main method for the determination of gene function. These strategies have proven to be particularly useful when carried out in strains with defective pathways for non-homologous integration, such as the kusA mutant. Nevertheless, a gene knock-down strategy such as the one described in chapter 2 could be relevant for the study of gene function, for two reasons: a) essential genes could be studied as RNAi does not necessarily lead to loss-of-function, and b) multiple gene copies of a gene or paralogous genes could be targeted with a single construct. In our work, the gene coding the transcriptional activator of hemicellulases XlnR was silenced. Gene silencing resulted in various degrees of hemicellulase production depending on the different transformed fungal strains. In chapter 3, the effect of D-xylose on gene expression in A. niger was investigated. The inducer of (hemi)cellulases D-xylose was added to cultures of A. niger growing on the non-inducer sorbitol. Genes differentially expressed on D-xylose were identified as candidate genes involved in the response to this sugar. This study confirmed that D-xylose activates enzymes involved in xylan degradation and D-xylose utilisation, but also enzymes responsible for the removal of other monomers that occurr on arabinoxylan and cellulases. Statistical analysis of variance components was used to assess the contribution of each external factors affecting the measured gene expression. Such analysis of variance components is important for reproducible sample processing for microarray analysis. Chapter 4 describes the A. niger secretory pathway proteins that are involved in the production of (hemi)cellulases, via induction by D-xylose. For this, A. niger was grown under the same conditions as the ones described in chapter 3. After the isolation of microsomes, the corresponding proteins were analysed by shotgun proteomics. Induction by D-xylose was correlated with an increase in proteins related to protein secretion, namely small GTPases for vesicle transport and polarised growth. Most importantly, under induction by D-xylose, the complex for protein degradation 20S proteasome was associated with microsomes. These results indicate a novel mode of regulation in which the proteasome is recruited to secretory organelles upon the induction of extracellular enzymes. In chapter 5, the analysis of secretory proteins described in chapter 4 is now applied to a system in which D-maltose is an inducer of starch-degrading enzymes. This chapter also includes the study of the proteins secreted after D-maltose or D-xylose. After D-maltose addition, three starch-degrading enzymes were found more abundant and after D-xylose addition, several enzymes were more abundant and these enzymes were mostly related to arabinoxylan and cellulose degradation. The effects of D-maltose on the microsomal proteome are similar to the effects of D-xylose. Both the induction by D-maltose and by D-xylose resulted in increased amounts of mitochondrial proteins. Moreover, the 20S proteasome assembly is an ATP-dependent process. For this reason, it is hypothesised that the assembly and association of 20S proteasome upon induction is related to an increased ATP production in the vicinity of secretory organelles. <br/
Identification of novel genetic and prognostic markers in hereditary and sporadic cancer: "two sides of the same coin"
No full textThis thesis has focused on the discovery and characterization of novel diagnostic and prognostic markers in various cancer entities, with a special emphasis on colorectal cancer (CRC).
In Switzerland the incidence of colorectal cancer ranks third in males and second in females, with about 4000 new patients diagnosed each year. Incidence trends over the last decades have remained constant in both sexes, whereas mortality rates have been decreasing. Decreasing mortality is thought to be related to improved treatment during the past years as well as generalisation of colorectal cancer screening in the Swiss population. About 80% of colorectal cancers are thought to have occurred by chance (sporadic) with the remainder displaying either familial aggregation (about 15%) or mendelian inheritance (about 5%).
In the first part of this work we identify and characterize a novel target gene locus for microsatellite instability (MSI) consisting of a mononucleotide (T/U)16 tract, EWS16T, located in the 3’ UTR of the Ewing sarcoma break point region 1 (EWSR1) gene in 319 patients with hereditary and sporadic CRC. We show that the EWS16T locus discriminates MMR proficient from deficient cancers with high diagnostic sensitivity (100%) and specificity (100%). It could thus substantially improve and facilitate MSI analysis in routine daily practice. In addition, biochemical analyses indicate that EWS16T contractions alter poly(A) site selection by promoting SFPQ-mediated distal poly(A) site usage in EWSR1 pre-mRNAs and result in decreased mRNA as well as EWS protein expression. Our findings thus directly implicate the RNA-/DNA-binding Ewing sarcoma protein in MSI-associated colorectal tumorigenesis.
In the second part we characterize a new tumour suppressor gene designated SH2D4A located on the short arm of chromosome 8. We demonstrate that SH2D4A physically interacts with the EGFR/STAT3 pathway and controls cell proliferation. Upon EGF signaling, SH2D4A recruits the serine/threonine phosphatase PP1β to the receptor complex and represses activated STAT3 via dephosphorylation. SH2D4A expression reduces anchorage-independent tumour cell growth and its loss promotes the expression of c-Myc, Cyclin D1 and Jun B. In addition we show that SH2D4A expression is partially lost in human colorectal cancers as a result of chromosomal instability, mutations and epigenetic changes. Finally, diminished SH2D4A protein expression was found to correlate with advanced disease stages and was associated with poor prognosis.
In the third part we investigate HGMA1/HGM2 protein expression 210 and 1202 patients with pancreatic and breast cancers, respectively. HMGA1 and HMGA2 over-expression was found in a significant number of breast and pancreatic carcinoma samples, and its over-expression positively correlated with grade and stage of the disease. Conversely, no HMGA1 and HMGA2 expression was observed in cancer-free breast and pancreas tissues. Taken together, our findings show that high expression levels of HMGA1 and HMGA2 are related to an unfavorable histological type and a poor prognosis in both, pancreatic and breast cancer. Moreover, these findings further support the notion that these proteins represent appropriate targets for the therapy of human cancer, as suggested by numerous in vitro and in vivo studies.
In the fourth part of the thesis we evaluate the potential role of the cancer stem cell (CSC) proteins EpCAM, CD44s, CD166 and CD133 in tumors of the ampulla of Vater. CSC expression was determined in 175 carcinoma, 111 adenoma and 152 cancer free-mucosa specimens arranged on a tissue microarray format. The expression of all evaluated marker proteins differed significantly between cancer-free mucosa, adenoma and carcinoma samples. EpCAM expression was significantly correlated with better patient survival. In contrast, increased expression of CD44s, CD166 and CD133 from normal mucosa samples to adenoma and carcinoma was linked to tumor progression but no statistically significant correlation with survival observed. Our findings therefore indicate that in ampullary carcinomas loss of EpCAM expression may be associated with a more aggressive tumor phenotype.
In the fifth part we develop a specific monoclonal antibody for the highly immunogenic member of the MAGE-A family of cancer/testis tumor-associated antigens (C/T TAAs). The antibody was used to stain a multi-tumor tissue microarray comprising more than 2,500 paraffin-embedded specimens of different histological origin. C/T TAA appears to be expressed in a high percentage (>50%) of cancer cells from different tumor types such as lung, skin, gynecological, stomach and gall bladder cancers. The future characterization of MAGE-A10-specific antibodies might set the stage for the development of targeted active immunotherapy by clarifying potential indications and by allowing the selection of patients eligible for treatment and monitoring of its effectiveness
Current methodological Issues in Candidate Gene Association Studies in Psychiatric Disorders
No full textOne of the most rapidly emerging areas of neuroscience research is the study of genetic approaches to complex psychiatric disorders. The author discusses potential benefits and pitfalls of candidate gene association studies. Association studies search for correlations in the population between a DNA marker and a disorder. The so-called candidate gene approach is frequently used in association studies. Candidate gene studies are usually based on hypotheses about relationships between specific known loci and particular phenotypes. The aim of molecular genetic studies of behavioral disorders includes the development of predictive and diagnostic testing for psychiatric disorders that can help to establish the accurate diagnosis and the identification of target for therapeutic drugs. To date, case-control association studies investigating polymorphisms of candidate genes in psychiatric disorders have produced a lot of positive and negative findings with few consistent replications. The false positive and false negative findings in candidate gene association studies are due to population stratification, heterogeneity of psychiatric disorders, multiple tests, low prior odds of association, and small sample size. A researcher planning a genetic association study for a psychiatric disorder needs to have the following: 1) suitable phenotypes; 2) a good rationale for studying not only the gene in question, but the specific polymorphism; 3) enough subjects and control for meaningful analyses; and 4) use of ethnically homogenous case-control data sets or family based association designs
Phylogeography and conservation genomics of the African lion (Panthera leo) at a continental and local scale based on mitochondrial and nuclear molecular markers
No full textPresented at the 9th international wildlife ranching symposium: wildlife - the key to prosperity for rural communities, held on 12-16 September 2016 at Hotel Safari & the Safari Court, Windhoek, Namibia.The African lion (Panthera leo) is listed as "vulnerable" by the IUCN Red List, mainly threatened by indiscriminate killing, primarily as a result of retaliatory or pre-emptive killing to protect human life and livestock, and prey base depletion. Habitat loss and conversion has led to a number of subpopulations becoming small and isolated. With the weakened connectivity between the main strongholds, genetic drift and loss of genetic diversity could affect the genetic health of the species. In the present study, we investigated the evolutionary history of the species at different scales of time and space. A total of 182 samples were used, including a larger number of 77 samples from Tanzanian protected areas. The mitochondrial cytochrome b gene was sequenced and the specimens were genotyped for 11 microsatellites and more than 9,000 SNPs. The preliminary results indicate that the lion is structured into two lineages at the continental scale (West-Central vs South-Eastern), a pattern observed within many other large African savanna species displaying large distribution ranges. Pleistocene climatic oscillations and biogeographical barriers were proposed as the main factors to have driven the lineage sorting. The first results based on microsatellites highlighted that the Tanzanian population displayed good level of genetic diversities with no signs of inbreeding. Indication of isolation-by-distance nevertheless highlighted a potential future impact of fragmentation on the population genetic health. SNPs allowed to identify 3 populations of lions in Tanzania, geographically structured. Using various molecular markers, the present work will further explore the taxonomy and the evolutionary history of the African lion for bringing insights in its conservation requirements
Making a Network Orchard by Adding Leaves
No full textPhylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here, we study the minimum number of additional leaves needed to make a network orchard. We demonstrate that computing this proximity measure for a given network is NP-hard and describe a tight upper bound. We also give an equivalent measure based on vertex labellings to construct a mixed integer linear programming formulation. Our experimental results, which include both real-world and synthetic data, illustrate the efficiency of our implementation
Identification of Haemobartonella felis (Mycoplasma haemofelis) in captive nondomestic cats
No full textThis study was undertaken to determine whether Haemobartonella felis (Mycoplasma haemofelis), the causative bacterial agent of feline infectious anemia, infects nondomestic cats. Routine complete blood count and polymerase chain reaction (PCR) were performed to detect the gene for 16S ribosomal RNA for the organism. Sixty-four blood samples were collected from 54 nondomestic cats, including tigers (Panthera tigris), cheetahs (Acinonyx jubatus), lions (P. leo), mountain lions (Felis concolor), snow leopards (P. unica), and a jaguar (P. onca). Some cats were sampled on two or three different dates. Two tigers were positive for H. felis by PCR analysis. As previously described in domestic cats, the parasitemia appears to be intermittent in nondomestic cats.PUBM: Print; JID: 8915208; 0 (DNA, Bacterial); 0 (RNA, Ribosomal, 16S); ppublishSource type: Electronic(1
Polynomial-Time Algorithms for Phylogenetic Inference Problems
No full textA common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model of speciation and duplication where duplications are clustered in duplication episodes. The goal is to minimize the number of such episodes. The second variant, Parental Hybridization, aims at inferring a species network based on a model of speciation and reticulation. The goal is to minimize the number of reticulation events. It is a variant of the well-studied Hybridization Number problem with a more generous view on which gene trees are consistent with a given species network. We show that these seemingly different problems are in fact closely related and can, surprisingly, both be solved in polynomial time, using a structure we call “beaded trees”. However, we also show that methods based on these problems have to be used with care because the optimal species phylogenies always have some restricted form. We discuss several possibilities to overcome this problem.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Discrete Mathematics and Optimizatio
The rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs
No full textThe process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments
Expression of the Leo1-like domain of replicative senescence down-regulated Leo1-like (RDL) protein promotes senescence of 2BS fibroblasts
No full textReplicative senescence is thought to relate to aging in vivo and tumor suppression. In this report, we isolated a gene and designated it as RDL (replicative senescence down-regulated Leo1-like gene). RDL’s expression decreased upon replicative senescence of human diploid 2BS fibroblasts. Overexpression of RDL slightly delayed 2BS fibroblast senescence, whereas suppression of RDL expression imposed no obvious effects on senescence. However, introduction of cDNA fragment encoding the Leo1-like domain of RDLp (Leo) alone shortened the replicative life span of 2BS fibroblasts and promoted several senescent features; the introduction of truncated RDL cDNA fragment resulting from deletion of Leo (RDL-Leo–) significantly prolonged 2BS life span and caused a noticeable delay of these senescent features. We demonstrated that introduction of Leo obviously increased the expression of p16INK4a, p21WAF1, and PTEN, whereas introduction of RDL-Leo– distinctly decreased p16INK4a expression. Taken together, our results suggest that the Leo1-like domain of RDLp is a senescence-associated domain that accelerates the senescence of 2BS fibroblasts and that there should be another counteractive domain in the remaining part of RDLp.—Zhao, L., Tong, T., Zhang, Z. Expression of the Leo1-like domain of replicative senescence down-regulated Leo1-like (RDL) protein promotes senescence of 2BS fibroblasts
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