Two types of metal–organic frameworks (MOFs) have been synthesized and evaluated in the separation of C2 and C3 olefins and paraffins. Whereas Co2(dhtp) (=Co–CPO-27 = Co–MOF-74) and Mg2(dhtp) show an ...adsorption selectivity for the olefins ethene and propene over the paraffins ethane and propane, the zeolitic imidazolate framework ZIF-8 behaves in the opposite way and preferentially adsorbs the alkane. Consequently, in breakthrough experiments, the olefins or paraffins, respectively, can be separated.
The microporous zeolitic imidazolate framework ZIF-4 has been synthesized, and its ethylene/ethane and propylene/propane separation potentials have been evaluated by single-component adsorption ...isotherms and breakthrough experiments of the respective binary mixtures. In all experiments, a higher selectivity for the paraffin is observed that is manifested by a steeper equilibrium isotherm as well as a later breakthrough in the fixed-bed adsorber experiments. Microporous adsorbents with paraffin selectivity are rare but highly interesting for cyclic adsorption processes such as pressure-swing adsorption (PSA).
Plasmodium vivax gene regulation remains difficult to study due to the lack of a robust in vitro culture method, low parasite densities in peripheral circulation and asynchronous parasite ...development. We adapted an RNA-seq protocol "DAFT-seq" to sequence the transcriptome of four P. vivax field isolates that were cultured for a short period ex vivo before using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5' and 3' untranslated regions, some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity between P. vivax schizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lack Plasmodium falciparum homologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity within P. vivax transcriptomes will be essential for the prioritisation of novel vaccine targets.
Many variant proteins encoded by Plasmodium-specific multigene families are exported into red blood cells (RBC). P. falciparum-specific variant proteins encoded by the var, stevor and rifin multigene ...families are exported onto the surface of infected red blood cells (iRBC) and mediate interactions between iRBC and host cells resulting in tissue sequestration and rosetting. However, the precise function of most other Plasmodium multigene families encoding exported proteins is unknown. To understand the role of RBC-exported proteins of rodent malaria parasites (RMP) we analysed the expression and cellular location by fluorescent-tagging of members of the pir, fam-a and fam-b multigene families. Furthermore, we performed phylogenetic analyses of the fam-a and fam-b multigene families, which indicate that both families have a history of functional differentiation unique to RMP. We demonstrate for all three families that expression of family members in iRBC is not mutually exclusive. Most tagged proteins were transported into the iRBC cytoplasm but not onto the iRBC plasma membrane, indicating that they are unlikely to play a direct role in iRBC-host cell interactions. Unexpectedly, most family members are also expressed during the liver stage, where they are transported into the parasitophorous vacuole. This suggests that these protein families promote parasite development in both the liver and blood, either by supporting parasite development within hepatocytes and erythrocytes and/or by manipulating the host immune response. Indeed, in the case of Fam-A, which have a steroidogenic acute regulatory-related lipid transfer (START) domain, we found that several family members can transfer phosphatidylcholine in vitro. These observations indicate that these proteins may transport (host) phosphatidylcholine for membrane synthesis. This is the first demonstration of a biological function of any exported variant protein family of rodent malaria parasites.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Two zeolitic imidazolate frameworks, ZIF‐9 and ZIF‐71, are evaluated by adsorption experiments and molecular simulations with respect to their potential towards olefin/paraffin separation. Pure ...component adsorption isotherms are measured and compared to grand‐canonical Monte–Carlo (GCMC) simulations. The experiments show that the adsorption of the paraffin is favorable over the olefin in both structures. Whereas the isotherms are predicted well by simulations for ZIF‐71, in case of ZIF‐9 only the saturation loading could be computed accurately because the latter material seems to undergo a so‐called gate‐opening effect upon adsorption of guest molecules; ZIF‐71 does not show this effect. Both structures show promising results with respect to olefin/paraffin separation.
Experimental adsorption isotherms of ethane, ethene, propane, and propene on the metal‐organic frameworks ZIF‐71 and ZIF‐9 have been compared to simulated isotherms, showing the potential of predicting the separation behavior of rigid and flexible adsorbents by grand canonical Monte–Carlo simulation.
Genome of the African Trypanosome Trypanosoma brucei Berriman, Matthew; Ghedin, Elodie; Hertz-Fowler, Christiane ...
Science (American Association for the Advancement of Science),
07/2005, Letnik:
309, Številka:
5733
Journal Article
Recenzirano
African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma ...brucei. The 26-megabase genome contains 9068 predicted genes, including approximately900 pseudogenes and approximately1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.
BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. It supports the BAM (Binary ...Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. Availability: BamView and Artemis are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at: http://bamview.sourceforge.net/ Contact: artemis@sanger.ac.uk
Here we describe the ways in which the sequence and annotation of the
reference genome has changed since its publication in 2002. As the malaria species responsible for the most deaths worldwide, the ...richness of annotation and accuracy of the sequence are important resources for the
research community as well as the basis for interpreting the genomes of subsequently sequenced species. At the time of publication in 2002 over 60% of predicted genes had unknown functions. As of March 2019, this number has been significantly decreased to 33%. The reduction is due to the inclusion of genes that were subsequently characterised experimentally and genes with significant similarity to others with known functions. In addition, the structural annotation of genes has been significantly refined; 27% of gene structures have been changed since 2002, comprising changes in exon-intron boundaries, addition or deletion of exons and the addition or deletion of genes. The sequence has also undergone significant improvements. In addition to the correction of a large number of single-base and insertion or deletion errors, a major miss-assembly between the subtelomeres of chromosome 7 and 8 has been corrected. As the number of sequenced isolates continues to grow rapidly, a single reference genome will not be an adequate basis for interpreting intra-species sequence diversity. We therefore describe in this publication a population reference genome of
, called Pfref1. This reference will enable the community to map to regions that are not present in the current assembly.
3D7 will continue to be maintained, with ongoing curation ensuring continual improvements in annotation quality.
is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in ...continuous
culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of
have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds. Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. An extensive repertoire of over 1200
interspersed repeat (
) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.
: Although thousands of clinical isolates of
are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain ...polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions.
: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15
isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal
genes clusters.
: The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates. We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa.
: These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.
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