Variant Surface Antigens Of Malaria Parasites: Functional And Evolutionary Insights From Comparative Gene Family Classification And Analysis

Background Plasmodium parasites, the causative agents of malaria, express many variant antigens on cell surfaces. Variant surface antigens (VSAs) are typically organized into large subtelomeric gene families that play critical roles in virulence and immune evasion. Many important aspects of VSA function and evolution remain obscure, impeding our understanding of virulence mechanisms and vaccine development. To gain further insights into VSA function and evolution, we comparatively classified and examined known VSA gene families across seven Plasmodium species. Results We identified a set of ultra-conserved orthologs within the largest Plasmodium gene family pir, which should be considered as high-priority targets for experimental functional characterization and vaccine development. Furthermore, we predict a lipid-binding domain in erythrocyte surface-expressed PYST-A proteins, suggesting a role of this second largest rodent parasite gene family in host cholesterol salvage. Additionally, it was found that PfMC-2TM proteins carry a novel and putative functional domain named MC-TYR, which is conserved in other P. falciparum gene families and rodent parasites. Finally, we present new conclusive evidence that the major Plasmodium VSAs PfEMP1, SICAvar, and SURFIN are evolutionarily linked through a modular and structurally conserved intracellular domain. Conclusion Our comparative analysis of Plasmodium VSA gene families revealed important functional and evolutionary insights, which can now serve as starting points for further experimental studies

Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease

Genes underlying important phenotypic differences between Plasmodium species, the causative agents of malaria, are frequently found in only a subset of species and cluster at dynamically evolving subtelomeric regions of chromosomes. We hypothesized that chromosome-internal regions of Plasmodium genomes harbour additional species subset-specific genes that underlie differences in human pathogenicity, human-to-human transmissibility, and human virulence. We combined sequence similarity searches with synteny block analyses to identify species subset-specific genes in chromosome-internal regions of six published Plasmodium genomes, including Plasmodium falciparum, Plasmodium vivax, Plasmodium knowlesi, Plasmodium yoelii, Plasmodium berghei, and Plasmodium chabaudi. To improve comparative analysis, we first revised incorrectly annotated gene models using homology-based gene finders and examined putative subset-specific genes within syntenic contexts. Confirmed subset-specific genes were then analyzed for their role in biological pathways and examined for molecular functions using publicly available databases. We identified 16 genes that are well conserved in the three primate parasites but not found in rodent parasites, including three key enzymes of the thiamine (vitamin B1) biosynthesis pathway. Thirteen genes were found to be present in both human parasites but absent in the monkey parasite P. knowlesi, including genes specifically upregulated in sporozoites or gametocytes that could be linked to parasite transmission success between humans. Furthermore, we propose 15 chromosome-internal P. falciparum-specific genes as new candidate genes underlying increased human virulence and detected a currently uncharacterized cluster of P. vivax-specific genes on chromosome 6 likely involved in erythrocyte invasion. In conclusion, Plasmodium species harbour many chromosome-internal differences in the form of protein-coding genes, some of which are potentially linked to human disease and thus promising leads for future laboratory research

Comparative Genome Analysis of Malaria Parasite Species

With over 200 million infections and up to one million deaths every year, malaria remains one of the most devastating infectious diseases affecting humans. Over the last few years, complete genome sequences of both human and non-human malaria parasite species have become available, adding comparative genomics to the toolbox of molecular biologists to study the genetic basis of human virulence. In this thesis, I computationally compared the published genomes of seven malaria parasite species with the aim to gain new insights into genes underlying human virulence. This comparison was performed using two complementary approaches. In the first approach, I used whole-genome synteny analysis to find genes present in human but not non-human malaria parasites. In the second approach, I first clustered virulence-associated genes into gene families and then examined these gene families for species-specific differences. Both comparisons resulted in interesting gene lists. Synteny analysis identified three key enzymes of the thiamine (vitamin B1) biosynthesis pathway to be present in human but not rodent malaria parasites, indicating that these two groups of parasites differ in their ability to synthesize vitamin B1 de novo. My gene family classification exposed within the largest and highly divergent surface antigen gene family pir a group of unusually well conserved orthologs, which should be considered as high-priority targets for experimental characterization and vaccine development. In conclusion, this thesis highlights genes and pathways that are different between human and non-human malaria parasites and therefore could play important roles in human virulence. Experimental studies can now be initiated to confirm virulence-associated functions and to explore their potential value for drug and vaccine development

Coovar: Co-Occurring Variant Analyzer

Background Evaluating the impact of genomic variations (GV) on protein-coding transcripts is an important step in identifying variants of functional significance. Currently available programs for variant annotation depend on external databases or annotate multiple variants affecting the same transcript independently, which limits program use to organisms available in these databases or results in potentially incorrect or incomplete annotations. Findings We have developed CooVar (Co-occurring Variant Analyzer), a database-independent program for assessing the impact of GVs on protein-coding transcripts. CooVar takes GVs, reference genome sequence, and protein-coding exons as input and provides annotated GVs and transcripts as output. Other than similar programs, CooVar considers the combined impact of all GVs affecting the same transcript, generating biologically more accurate annotations. CooVar is operated from the command-line and supports standard file formats VCF, GFF/GTF, and GVF, which makes it easy to integrate into existing computational pipelines. We have extensively tested CooVar on worm and human data sets and demonstrate that it generates correct annotations in only a short amount of time. Conclusions CooVar is an easy-to-use and lightweight variant annotation tool that considers the combined impact of GVs on protein-coding transcripts. CooVar is freely available at http://genome.sfu.ca/projects/coovar/ webcite

Dinitrosyl rhenium complexes for ring-opening metathesis polymerization (ROMP)

The treatment of benzene solutions of the cations [Re(NO)2(PR3)2][BArF4] (R = Cy and R = iPr; [BArF4] = tetrakis{3,5-bis(trifluoromethyl)phenyl}borate) with phenyldiazomethane afforded the moderately stable cationic rhenium(I) benzylidene dinitrosyl bis(trialkyl) phosphine complexes as [BArF4]- salts in good yields. The cationic rhenium dinitrosyl bisphosphine complexes catalyze the ring-opening metathesis polymerization (ROMP) of highly strained nonfunctionalized cyclic olefins to give polymers with relatively high polydispersity indices, high molecular weights, and Z configurations of the double bonds in the polymer chain backbones of over 80 %. The benzylidene derivatives are almost inactive in ROMP catalysis with norbornene and in olefin metathesis. NMR experiments gave first hints for the initial formation of carbene complexes when [Re(NO)2(PR3)2][BArF4] was treated with norbornene. The carbene formation is initiated by an unique reaction sequence where the cleavage of the strained olefinic bond starts with phosphine migration forming a cyclic ylid carbene complex. The [2+2] addition of a norbornene molecule to the Re=C bond leads to the rhenacyclobutane complex, which is expected to be converted into an iminate complex by attack of the ylid function onto one of the NNO atoms followed by Wittig-type phosphine oxide elimination. The formation of phosphine oxide was confirmed by NMR spectroscopy. This species is thought to drive the ROMP metathesis with alternating rhenacyclobutane formations and cycloreversions. The proposed mechanism is supported by density functional theory (DFT) calculation

Automated Configuration of Gripper Fingers from a Construction Kit for Robotic Applications

Gripper finger design is a complex process that requires a lot of experience, time, and effort. For this reason, automating this design process is an important area of research that has the potential to improve the efficiency and effectiveness of robotic systems. The current approaches are aimed at the automated design of monolithic gripper fingers, which have to be manufactured additively or by machining. This paper describes a novel approach for the automated design of gripper fingers. The motivation for this work stems from the increasing demand for flexible, adaptable handling systems in various industries in response to the increasing individualization of products as well as the increasing volatility in the markets. Based on the CAD data of the handling objects, the most suitable configuration of gripper fingers can be determined from the existing modules of a construction kit for the respective handling object, which can significantly reduce the provisioning time for new gripper fingers. It can be shown that gripper fingers can be effectively configured for a variety of objects and two different grippers, increasing flexibility in industrial handling processes

The Vibrio Cholerae Type VI Secretion System: Evaluating its Role in the Human Disease Cholera

Vibrio cholerae, the marine bacterium responsible for the diarrheal disease cholera, utilizes a multitude of virulence factors to cause disease. The importance of two of these factors, the toxin co-regulated pilus (TCP) and cholera toxin (CT), has been well documented for pandemic O1 and epidemic O139 serogroups. In contrast, endemic non-O1 and non-O139 serogroups can cause localized outbreaks of cholera-like illness, often in the absence of TCP and CT. One virulence mechanism used by these strains is the type VI secretion system (T6SS) to export toxins across the cell envelope and confer toxicity toward eukaryotic and prokaryotic organisms. The V. cholerae strain V52 (an O37 serogroup strain) possesses a constitutively active T6SS and was responsible for an outbreak of gastroenteritis in Sudan in 1968. To evaluate a potential role of the T6SS in the disease cholera, we compared the T6SS clusters of V. cholerae strains with sequenced genomes. We found that the majority of V. cholerae strains, including one pandemic strain, contain intact T6SS gene clusters; thus, we propose that the T6SS is a conserved mechanism that allows pandemic and endemic V. cholerae to persist both in the host and in the environment

OrthoClusterDB: an online platform for synteny blocks

<p>Abstract</p> <p>Background</p> <p>The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind.</p> <p>Descriptions</p> <p>OrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: <it>Run OrthoCluster </it>and <it>View Synteny</it>. The <it>Run OrthoCluster </it>page serves as web front-end to OrthoCluster, a recently developed program for synteny block detection. <it>Run OrthoCluster </it>offers full control over the functionalities of OrthoCluster, such as specifying synteny block size, considering order and strandedness of genes within synteny blocks, including or excluding nested synteny blocks, handling one-to-many orthologous relationships, and comparing multiple genomes. In contrast, the <it>View Synteny </it>page gives access to perfect and imperfect synteny blocks precomputed for a large number of genomes, without the need for users to retrieve and format input data. Additionally, genes are cross-linked with public databases for effective browsing. For both <it>Run OrthoCluster </it>and <it>View Synteny</it>, identified synteny blocks can be browsed at the whole genome, chromosome, and individual gene level. OrthoClusterDB is freely accessible.</p> <p>Conclusion</p> <p>We have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at <url>http://genome.sfu.ca/orthoclusterdb/</url>.</p

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Background Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. Results Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400&nbsp;bps single reads) and Illumina GA DNA sequencing methods (101&nbsp;bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150&nbsp;bps to 1.2&nbsp;kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains. Conclusions The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains

Whole-Genome Sequencing Of Mesorhizobium huakuii 7653R Provides Molecular Insights into Host Specificity and Symbiosis Island Dynamics

Background Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general. Results In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species. Conclusions Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome