@article{AbdaKrysciakKrohnMoltetal.2015,
  author    = {Abda, Ebrahim M. and Krysciak, Dagmar and Krohn-Molt, Ines and Mamat, Uwe and Schmeisser, Christel and F{\"o}rstner, Konrad U. and Schaible, Ulrich E. and Kohi, Thomas A. and Nieman, Stefan and Streit, Wolfgang R.},
  title     = {Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and \(\beta\)-Lactamase Expression},
  series = {Frontiers in Microbiology},
  volume    = {6},
  journal   = {Frontiers in Microbiology},
  number    = {1373},
  doi       = {10.3389/fmicb.2015.01373},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136446},
  year      = {2015},
  abstract  = {Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas rnaltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the Li and L2 beta-lactamases in response to beta-lactam treatment. Here we report that the patient isolate S. rnaltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bleu and bla(L2) were transcriptionally the most strongly upregulated genes. Promoter fusions of b/a(L1) and b/a(L2) genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla(L2) expressing cells as identified by RNA(seq) analysis. Overexpression of cornE in S. maltophilia K279a reduced the level of cells that were in a bla(L2)-ON mode to 1\% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including b/a(L1), b/a(L2), and comE.},
  language  = {en}
}
@article{vonBohlKuehnSimonetal.2015,
  author    = {von Bohl, Andreas and Kuehn, Andrea and Simon, Nina and Nkwouano Ngongang, Vanesa and Spehr, Marc and Baumeister, Stefan and Przyborski, Jude M. and Fischer, Rainer and Pradel, Gabriele},
  title     = {A WD40-repeat protein unique to malaria parasites associates with adhesion protein complexes and is crucial for blood stage progeny},
  series = {Malaria Journal},
  volume    = {14},
  journal   = {Malaria Journal},
  number    = {435},
  doi       = {10.1186/s12936-015-0967-x},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139728},
  year      = {2015},
  abstract  = {Background During development in human erythrocytes, Plasmodium falciparum parasites display a remarkable number of adhesive proteins on their plasma membrane. In the invasive merozoites, these include members of the PfMSP1 and PfAMA1/RON complexes, which facilitate contact between merozoites and red blood cells. In gametocytes, sexual precursor cells mediating parasite transmission to the mosquito vector, plasma membrane-associated proteins primarily belong to the PfCCp and 6-cys families with roles in fertilization. This study describes a newly identified WD40-repeat protein unique to Plasmodium species that associates with adhesion protein complexes of both merozoites and gametocytes. Methods The WD40-repeat protein-like protein PfWLP1 was identified via co-immunoprecipitation assays followed by mass spectrometry and characterized using biochemical and immunohistochemistry methods. Reverse genetics were employed for functional analysis. Results PfWLP1 is expressed both in schizonts and gametocytes. In mature schizonts, the protein localizes underneath the merozoite micronemes and interacts with PfAMA1, while in gametocytes PfWLP1 primarily accumulates underneath the plasma membrane and associates with PfCCp1 and Pfs230. Reverse genetics failed to disrupt the pfwlp1 gene, while haemagglutinin-tagging was feasible, suggesting a crucial function for PfWLP1 during blood stage replication. Conclusions This is the first report on a plasmodial WD40-repeat protein associating with cell adhesion proteins. Since WD40 domains are known to mediate protein-protein contact by serving as a rigid scaffold for protein interactions, the presented data suggest that PfWLP1 supports the stability of adhesion protein complexes of the plasmodial blood stages.},
  language  = {en}
}
@article{SassVanAckerFoerstneretal.2015,
  author    = {Sass, Andrea M. and Van Acker, Heleen and F{\"o}rstner, Konrad U. and Van Nieuwerburgh, Filip and Deforce, Dieter and Vogel, J{\"o}rg and Coenye, Tom},
  title     = {Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315},
  series = {BMC Genomics},
  volume    = {16},
  journal   = {BMC Genomics},
  number    = {775},
  doi       = {10.1186/s12864-015-1993-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139748},
  year      = {2015},
  abstract  = {Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.},
  language  = {en}
}
@article{FanLiChaoetal.2015,
  author    = {Fan, Ben and Li, Lei and Chao, Yanjie and F{\"o}rstner, Konrad and Vogel, J{\"o}rg and Borriss, Rainer and Wu, Xiao-Qin},
  title     = {dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42},
  series = {PLoS One},
  volume    = {10},
  journal   = {PLoS One},
  number    = {11},
  doi       = {10.1371/journal.pone.0142002},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-138369},
  pages     = {e0142002},
  year      = {2015},
  abstract  = {Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizospheremimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.},
  language  = {en}
}
@phdthesis{Frank2015,
  author    = {Frank, Benjamin},
  title     = {Untersuchungen zur Autophagieinduktion in Leishmania major-infizierten Knochenmarksmakrophagen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-137277},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Die von der WHO zu den 17 wichtigsten NTDs gez{\"a}hlte Leishmaniose wird durch intrazellul{\"a}re Parasiten der Gattung Leishmania hervorgerufen. Der Lebenszyklus der Parasiten besteht aus zwei Phasen. Die l{\"a}nglichen und beweglichen Promastigoten kennzeichnen die Phase in der Sandm{\"u}cke - der Vektor der Leishmaniose. Hingegen ist die Phase im S{\"a}ugerwirt durch runde unbewegliche Amastigoten charakterisiert. Aufgrund des Mangels an potenten antileishmanialen Therapien wurde in der vorliegenden Arbeit die Interaktion zwischen L. m. Parasiten und der Hauptwirtszelle, der Makrophage, v. a. in Hinblick auf autophage Prozesse in den infizierten Makrophagen n{\"a}her untersucht, um demgem{\"a}ß neue Erkenntnisse zu gewinnen, welche bei der Herstellung zuk{\"u}nftiger anti-leishmanialer Medikamente helfen k{\"o}nnten. Bei der Autophagie handelt es sich um einen katabolen Prozess, wodurch Zellen bei Nahrungsmangel oder zellul{\"a}rem Stress ihre Hom{\"o}ostase erhalten k{\"o}nnen. Durch diesen Prozess k{\"o}nnen {\"u}berfl{\"u}ssige oder besch{\"a}digte Organellen recycelt werden, um die Funktionen der Zelle aufrechtzuerhalten. Daneben {\"u}bernimmt Autophagie auch eine essenzielle Rolle bei der Abwehr von ins Zytosol eindringenden Pathogenen. Mittels des neu etablierten totalen Autophagiescore konnte festgestellt werden, dass Autophagie in L. m.-infizierten BMDM induziert wird. Die intrazellul{\"a}ren Amastigoten werden durch Autophagie in den BMDM verdaut. Die erh{\"o}hte autophage Aktivit{\"a}t konnte zudem durch Western-Blot-Analysen der autophagierelevanten Proteine ATG5, LC3B und UB best{\"a}tigt werden. Die molekulargenetischen Untersuchungen von L. m.-infizier-ten BMDM mithilfe von Affymetrix Microarrays f{\"u}hrten zu einem Netzwerk aus autophagierelevanten und infektionsspezifischen Genen, welches als LISA bezeichnet worden ist. Hier hat sich ebenfalls eine starke Verkn{\"u}pfung von autophagierelevanten Genen und den Genen der Glykolyse, einem zweiten katabolen Prozess, gezeigt. Zudem konnten zwei weitere autophagierelevante und infektionsspezifische Gene außerhalb von LISA identifiziert werden, n{\"a}mlich Bnip3 und Ctse, welche im Anschluss genauer untersucht worden sind. Bei beiden Genen konnte auf Proteinebene gezeigt werden, dass sie in L. m.-infizierten BMDM signifikant erh{\"o}ht sind. Durch siRNA-Analysen konnte {\"u}berdies beobachtet werden, dass beide f{\"u}r die erfolgreiche Elimination der Amastigoten essenziell sind. Somit konnte mit den Proteinen BNIP3 und CTSE zwei potenzielle neue Ansatzpunkte f{\"u}r m{\"o}gliche zuk{\"u}nftige antileishmaniale Therapien gefunden werden. Auch die in LISA enthaltenen Gene stellen prinzipiell vielversprechende Ziele f{\"u}r k{\"u}nftige Medikamente gegen Leishmaniose dar. Durch all diese Untersuchungen kommt man dem Ziel einer neuen, gezielten und nebenwirkungs{\"a}rmeren Behandlung der Leishmaniose einen Schritt n{\"a}her.},
  subject      = {Autophagie},
  language  = {de}
}
@article{BeissSpiegelBoesetal.2015,
  author    = {Beiss, Veronique and Spiegel, Holger and Boes, Alexander and Scheuermayer, Matthias and Reimann, Andreas and Schillberg, Stefan and Fischer, Rainer},
  title     = {Plant expression and characterization of the transmission-blocking vaccine candidate PfGAP50},
  series = {BMC Biotechnology},
  volume    = {15},
  journal   = {BMC Biotechnology},
  number    = {108},
  doi       = {10.1186/s12896-015-0225-x},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-137327},
  year      = {2015},
  abstract  = {Background: Despite the limited success after decades of intensive research and development efforts, vaccination still represents the most promising strategy to significantly reduce the disease burden in malaria endemic regions. Besides the ultimate goal of inducing sterile protection in vaccinated individuals, the prevention of transmission by so-called transmission blocking vaccines (TBVs) is being regarded as an important feature of an efficient malaria eradication strategy. Recently, Plasmodium falciparum GAP50 (PfGAP50), a 44.6 kDa transmembrane protein that forms an essential part of the invasion machinery (glideosome) multi-protein complex, has been proposed as novel potential transmission-blocking candidate. Plant-based expression systems combine the advantages of eukaryotic expression with a up-scaling potential and a good product safety profile suitable for vaccine production. In this study we investigated the feasibility to use the transient plant expression to produce PfGAP50 suitable for the induction of parasite specific inhibitory antibodies. Results: We performed the transient expression of recombinant PfGAP50 in Nicotiana benthamiana leaves using endoplasmatic reticulum (ER) and plastid targeting. After IMAC-purification the protein yield and integrity was investigated by SDS-PAGE and Western Blot. Rabbit immune IgG derived by the immunization with the plastidtargeted variant of PfGAP50 was analyzed by immune fluorescence assay (IFA) and zygote inhibition assay (ZIA). PfGAP50 could be produced in both subcellular compartments at different yields IMAC (Immobilized Metal Affinity Chromatography) purification from extract yielded up to 4.1 mu g/g recombinant protein per fresh leaf material for ER-retarded and 16.2 mu g/g recombinant protein per fresh leave material for plasmid targeted PfGAP50, respectively. IgG from rabbit sera generated by immunization with the recombinant protein specifically recognized different parasite stages in immunofluorescence assay. Furthermore up to 55 \% inhibition in an in vitro zygote inhibition assay could be achieved using PfGAP50-specific rabbit immune IgG. Conclusions: The results of this study demonstrate that the plant-produced PfGAP50 is functional regarding the presentation of inhibitory epitopes and could be considered as component of a transmission-blocking malaria vaccine formulation.},
  language  = {en}
}
@article{OkoroBarquistConnoretal.2015,
  author    = {Okoro, Chinyere K. and Barquist, Lars and Connor, Thomas R. and Harris, Simon R. and Clare, Simon and Stevens, Mark P. and Arends, Mark J. and Hale, Christine and Kane, Leanne and Pickard, Derek J. and Hill, Jennifer and Harcourt, Katherine and Parkhill, Julian and Dougan, Gordon and Kingsley, Robert A.},
  title     = {Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa},
  series = {PLoS Neglected Tropical Diseases},
  volume    = {9},
  journal   = {PLoS Neglected Tropical Diseases},
  number    = {3},
  doi       = {10.1371/journal.pntd.0003611},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143779},
  pages     = {e0003611},
  year      = {2015},
  abstract  = {Two lineages of Salmonella enterica serovar Typhimurium (S. Typhimurium) of multi-locus sequence type ST313 have been linked with the emergence of invasive Salmonella disease across sub-Saharan Africa. The expansion of these lineages has a temporal association with the HIV pandemic and antibiotic usage. We analysed the whole genome sequence of 129 ST313 isolates representative of the two lineages and found evidence of lineage-specific genome degradation, with some similarities to that observed in S. Typhi. Individual ST313 S. Typhimurium isolates exhibit a distinct metabolic signature and modified enteropathogenesis in both a murine and cattle model of colitis, compared to S. Typhimurium outside of the ST313 lineages. These data define phenotypes that distinguish ST313 isolates from other S. Typhimurium and may represent adaptation to a distinct pathogenesis and lifestyle linked to an-immuno-compromised human population.},
  language  = {en}
}
@article{BergSchellingHailuetal.2015,
  author    = {Berg, Stefan and Schelling, Esther and Hailu, Elena and Firdessa, Rebuma and Gumi, Balako and Erenso, Girume and Gadisa, Endalamaw and Mengistu, Araya and Habtamu, Meseret and Hussein, Jemal and Kiros, Teklu and Bekele, Shiferaw and Mekonnen, Wondale and Derese, Yohannes and Zinsstag, Jakob and Ameni, Gobena and Gagneux, Sebastien and Robertson, Brian D and Tschopp, Rea and Hewinson, Glyn and Yamuah, Lawrence and Gordon, Stephen V and Aseffa, Abraham},
  title     = {Investigation of the high rates of extrapulmonary tuberculosis in Ethiopia reveals no single driving factor and minimal evidence for zoonotic transmission of Mycobacterium bovis infection},
  series = {BMC Infectious Diseases},
  volume    = {15},
  journal   = {BMC Infectious Diseases},
  number    = {112},
  doi       = {10.1186/s12879-015-0846-7},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143935},
  year      = {2015},
  abstract  = {Background: Ethiopia, a high tuberculosis (TB) burden country, reports one of the highest incidence rates of extra-pulmonary TB dominated by cervical lymphadenitis (TBLN). Infection with Mycobacterium bovis has previously been excluded as the main reason for the high rate of extra-pulmonary TB in Ethiopia. Methods: Here we examined demographic and clinical characteristics of 953 pulmonary (PTB) and 1198 TBLN patients visiting 11 health facilities in distinct geographic areas of Ethiopia. Clinical characteristics were also correlated with genotypes of the causative agent, Mycobacterium tuberculosis. Results: No major patient or bacterial strain factor could be identified as being responsible for the high rate of TBLN, and there was no association with HIV infection. However, analysis of the demographic data of involved patients showed that having regular and direct contact with live animals was more associated with TBLN than with PTB, although no M. bovis was isolated from patients with TBLN. Among PTB patients, those infected with Lineage 4 reported "contact with other TB patient" more often than patients infected with Lineage 3 did (OR = 1.6, CI 95\% 1.0-2.7; p = 0.064). High fever, in contrast to low and moderate fever, was significantly associated with Lineage 4 (OR = 2.3; p = 0.024). On the other hand, TBLN cases infected with Lineage 4 tended to get milder symptoms overall for the constitutional symptoms than those infected with Lineage 3. Conclusions: The study suggests a complex role for multiple interacting factors in the epidemiology of extra-pulmonary TB in Ethiopia, including factors that can only be derived from population-based studies, which may prove to be significant for TB control in Ethiopia.},
  language  = {en}
}
@article{RodriguezRicoYepesetal.2015,
  author    = {Rodriguez, H{\´e}ctor and Rico, Sergio and Yepes, Ana and Franco-Echevarr{\´i}a, Elsa and Antoraz, Sergio and Santamar{\´i}a, Ram{\´o}n I. and D{\´i}az, Margerita},
  title     = {The two kinases, AbrC1 and AbrC2, of the atypical two-component system AbrC are needed to regulate antibiotic production and differentiation in Streptomyces coelicolor},
  series = {Frontiers in Microbiology},
  volume    = {6},
  journal   = {Frontiers in Microbiology},
  number    = {450},
  doi       = {10.3389/fmicb.2015.00450},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143048},
  year      = {2015},
  abstract  = {Two-component systems (TCSs) are the most important sensing mechanisms in bacteria. In Streptomyces, TCSs-mediated responses to environmental stimuli are involved in the regulation of antibiotic production. This study examines the individual role of two histidine kinases (HKs), AbrC1 and AbrC2, which form part of an atypical TCS in Streptomyces coelicolor. gRT-PCR analysis of the expression of both kinases demonstrated that both are expressed at similar levels in NB and NMMP media. Single deletion of abrC1 elicited a significant increase in antibiotic production, while deletion of abrC2 did not have any clear effect. The origin of this phenotype, probably related to the differential phosphorylation ability of the two kinases, was also explored indirectly, analyzing the toxic phenotypes associated with high levels of phosphorylated RR. The higher the AbrC3 regulator phosphorylation rate, the greater the cell toxicity. For the first time, the present work shows in Streptomyces the combined involvement of two different HKs in the response of a regulator to environmental signals. Regarding the possible applications of this research, the fact that an abrC1 deletion mutant overproduces three of the S. coelicolor antibiotics makes this strain an excellent candidate as a host for the heterologous production of secondary metabolites.},
  language  = {en}
}
@article{AfonsoGrunzHoffmeierMuelleretal.2015,
  author    = {Afonso-Grunz, Fabian and Hoffmeier, Klaus and M{\"u}ller, S{\"o}ren and Westermann, Alexander J. and Rotter, Bj{\"o}rn and Vogel, J{\"o}rg and Winter, Peter and Kahl, G{\"u}nter},
  title     = {Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells},
  series = {BMC Genomics},
  volume    = {16},
  journal   = {BMC Genomics},
  number    = {323},
  doi       = {10.1186/s12864-015-1489-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143230},
  year      = {2015},
  abstract  = {Background: The interaction of eukaryotic host and prokaryotic pathogen cells is linked to specific changes in the cellular proteome, and consequently to infection-related gene expression patterns of the involved cells. To simultaneously assess the transcriptomes of both organisms during their interaction we developed dual 3'Seq, a tag-based sequencing protocol that allows for exact quantification of differentially expressed transcripts in interacting pro-and eukaryotic cells without prior fixation or physical disruption of the interaction. Results: Human epithelial cells were infected with Salmonella enterica Typhimurium as a model system for invasion of the intestinal epithelium, and the transcriptional response of the infected host cells together with the differential expression of invading and intracellular pathogen cells was determined by dual 3'Seq coupled with the next-generation sequencing-based transcriptome profiling technique deepSuperSAGE (deep Serial Analysis of Gene Expression). Annotation to reference transcriptomes comprising the operon structure of the employed S. enterica Typhimurium strain allowed for in silico separation of the interacting cells including quantification of polycistronic RNAs. Eighty-nine percent of the known loci are found to be transcribed in prokaryotic cells prior or subsequent to infection of the host, while 75\% of all protein-coding loci are represented in the polyadenylated transcriptomes of human host cells. Conclusions: Dual 3'Seq was alternatively coupled to MACE (Massive Analysis of cDNA ends) to assess the advantages and drawbacks of a library preparation procedure that allows for sequencing of longer fragments. Additionally, the identified expression patterns of both organisms were validated by qRT-PCR using three independent biological replicates, which confirmed that RELB along with NFKB1 and NFKB2 are involved in the initial immune response of epithelial cells after infection with S. enterica Typhimurium.},
  language  = {en}
}
@article{BoesSpiegelVoepeletal.2015,
  author    = {Boes, Alexander and Spiegel, Holger and Voepel, Nadja and Edgue, Gueven and Beiss, Veronique and Kapelski, Stephanie and Fendel, Rolf and Scheuermayer, Matthias and Pradel, Gabriele and Bolscher, Judith M. and Behet, Marije C. and Dechering, Koen J. and Hermsen, Cornelus C. and Sauerwein, Robert W. and Schillberg, Stefan and Reimann, Andreas and Fischer, Rainer},
  title     = {Analysis of a multi-component multi-stage malaria vaccine candidate—tackling the cocktail challenge},
  series = {PLoS ONE},
  volume    = {10},
  journal   = {PLoS ONE},
  number    = {7},
  doi       = {10.1371/journal.pone.0131456},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173092},
  pages     = {e0131456},
  year      = {2015},
  abstract  = {Combining key antigens from the different stages of the P. falciparum life cycle in the context of a multi-stage-specific cocktail offers a promising approach towards the development of a malaria vaccine ideally capable of preventing initial infection, the clinical manifestation as well as the transmission of the disease. To investigate the potential of such an approach we combined proteins and domains (11 in total) from the pre-erythrocytic, blood and sexual stages of P. falciparum into a cocktail of four different components recombinantly produced in plants. After immunization of rabbits we determined the domain-specific antibody titers as well as component-specific antibody concentrations and correlated them with stage specific in vitro efficacy. Using purified rabbit immune IgG we observed strong inhibition in functional in vitro assays addressing the pre-erythrocytic (up to 80\%), blood (up to 90\%) and sexual parasite stages (100\%). Based on the component-specific antibody concentrations we calculated the IC50 values for the pre-erythrocytic stage (17-25 μg/ml), the blood stage (40-60 μg/ml) and the sexual stage (1.75 μg/ml). While the results underline the feasibility of a multi-stage vaccine cocktail, the analysis of component-specific efficacy indicates significant differences in IC50 requirements for stage-specific antibody concentrations providing valuable insights into this complex scenario and will thereby improve future approaches towards malaria vaccine cocktail development regarding the selection of suitable antigens and the ratios of components, to fine tune overall and stage-specific efficacy.},
  language  = {en}
}
@article{NguyenKraftYuetal.2015,
  author    = {Nguyen, Minh Thu and Kraft, Beatrice and Yu, Wenqi and Demicrioglu, Dogan Doruk and Hertlein, Tobias and Burian, Marc and Schmaler, Mathias and Boller, Klaus and Bekeredjian-Ding, Isabelle and Ohlsen, Knut and Schittek, Birgit and G{\"o}tz, Friedrich},
  title     = {The vSa\(\alpha\) Specific Lipoprotein Like Cluster (lpl) of S. aureus USA300 Contributes to Immune Stimulation and Invasion in Human Cells},
  series = {PLoS Pathogens},
  volume    = {11},
  journal   = {PLoS Pathogens},
  number    = {6},
  doi       = {10.1371/journal.ppat.1004984},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151856},
  pages     = {e1004984},
  year      = {2015},
  abstract  = {All Staphylococcus aureus genomes contain a genomic island, which is termed vSa\(\alpha\) and characterized by two clusters of tandem repeat sequences, i.e. the exotoxin (set) and 'lipoprotein-like' genes (lpl). Based on their structural similarities the vSa\(\alpha\) islands have been classified as type I to IV. The genomes of highly pathogenic and particularly epidemic S. aureus strains (USA300, N315, Mu50, NCTC8325, Newman, COL, JH1 or JH9) belonging to the clonal complexes CC5 and CC8 bear a type I vSa\(\alpha\) island. Since the contribution of the lpl gene cluster encoded in the vSa\(\alpha\) island to virulence is unclear to date, we deleted the entire lpl gene cluster in S. aureus USA300. The results showed that the mutant was deficient in the stimulation of pro-inflammatory cytokines in human monocytes, macrophages and keratinocytes. Purified lipoprotein Lpl1 was further shown to elicit a TLR2-dependent response. Furthermore, heterologous expression of the USA300 lpl cluster in other S. aureus strains enhanced their immune stimulatory activity. Most importantly, the lpl cluster contributed to invasion of S. aureus into human keratinocytes and mouse skin and the non-invasive S. carnosus expressing the lpl gene cluster became invasive. Additionally, in a murine kidney abscess model the bacterial burden in the kidneys was higher in wild type than in mutant mice. In this infection model the lpl cluster, thus, contributes to virulence. The present report is one of the first studies addressing the role of the vSa\(\alpha\) encoded lpl gene cluster in staphylococcal virulence. The finding that the lpl gene cluster contributes to internalization into non-professional antigen presenting cells such as keratinocytes high-lights the lpl as a new cell surface component that triggers host cell invasion by S. aureus. Increased invasion in murine skin and an increased bacterial burden in a murine kidney abscess model suggest that the lpl gene cluster serves as an important virulence factor.},
  language  = {en}
}
@article{PapenfortVogel2014,
  author    = {Papenfort, Kai and Vogel, J{\"o}rg},
  title     = {Small RNA functions in carbon metabolism and virulence of enteric pathogens},
  series = {Frontiers in Cellular and Infection Microbiology},
  volume    = {4},
  journal   = {Frontiers in Cellular and Infection Microbiology},
  number    = {91},
  issn      = {2235-2988},
  doi       = {10.3389/fcimb.2014.00091},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197520},
  year      = {2014},
  abstract  = {Enteric pathogens often cycle between virulent and saprophytic lifestyles. To endure these frequent changes in nutrient availability and composition bacteria possess an arsenal of regulatory and metabolic genes allowing rapid adaptation and high flexibility. While numerous proteins have been characterized with regard to metabolic control in pathogenic bacteria, small non-coding RNAs have emerged as additional regulators of metabolism. Recent advances in sequencing technology have vastly increased the number of candidate regulatory RNAs and several of them have been found to act at the interface of bacterial metabolism and virulence factor expression. Importantly, studying these riboregulators has not only provided insight into their metabolic control functions but also revealed new mechanisms of post-transcriptional gene control. This review will focus on the recent advances in this area of host-microbe interaction and discuss how regulatory small RNAs may help coordinate metabolism and virulence of enteric pathogens.},
  language  = {en}
}
@article{CullLimaPradoGodinhoFernandesRodriguesetal.2014,
  author    = {Cull, Benjamin and Lima Prado Godinho, Joseane and Fernandes Rodrigues, Juliany Cola and Frank, Benjamin and Schurigt, Uta and Williams, Roderick AM and Coombs, Graham H and Mottram, Jeremy C},
  title     = {Glycosome turnover in Leishmania major is mediated by autophagy},
  series = {Autophagy},
  volume    = {10},
  journal   = {Autophagy},
  number    = {12},
  doi       = {10.4161/auto.36438},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150277},
  pages     = {2143-2157},
  year      = {2014},
  abstract  = {Autophagy is a central process behind the cellular remodeling that occurs during differentiation of Leishmania, yet the cargo of the protozoan parasite's autophagosome is unknown. We have identified glycosomes, peroxisome-like organelles that uniquely compartmentalize glycolytic and other metabolic enzymes in Leishmania and other kinetoplastid parasitic protozoa, as autophagosome cargo. It has been proposed that the number of glycosomes and their content change during the Leishmania life cycle as a key adaptation to the different environments encountered. Quantification of RFP-SQL-labeled glycosomes showed that promastigotes of L. major possess ~20 glycosomes per cell, whereas amastigotes contain ~10. Glycosome numbers were significantly greater in promastigotes and amastigotes of autophagy-defective L. major Δatg5 mutants, implicating autophagy in glycosome homeostasis and providing a partial explanation for the previously observed growth and virulence defects of these mutants. Use of GFP-ATG8 to label autophagosomes showed glycosomes to be cargo in ~15\% of them; glycosome-containing autophagosomes were trafficked to the lysosome for degradation. The number of autophagosomes increased 10-fold during differentiation, yet the percentage of glycosome-containing autophagosomes remained constant. This indicates that increased turnover of glycosomes was due to an overall increase in autophagy, rather than an upregulation of autophagosomes containing this cargo. Mitophagy of the single mitochondrion was not observed in L. major during normal growth or differentiation; however, mitochondrial remnants resulting from stress-induced fragmentation colocalized with autophagosomes and lysosomes, indicating that autophagy is used to recycle these damaged organelles. These data show that autophagy in Leishmania has a central role not only in maintaining cellular homeostasis and recycling damaged organelles but crucially in the adaptation to environmental change through the turnover of glycosomes.},
  language  = {en}
}
@phdthesis{Schiller2014,
  author    = {Schiller, Roswitha Dorothee},
  title     = {Studien zu Virulenzeigenschaften typischer und atypischer uropathogener Escherichia coli},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-103907},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {Die Forschungsergebnisse der letzten Jahre liefern immer mehr Hinweise darauf, dass eine klare Unterscheidung von Fitness- und Virulenzfaktoren in vielen F{\"a}llen, insbesondere bei extraintestinal pathogenen Escherichia coli, nicht m{\"o}glich ist. So l{\"a}sst sich auch bei Harnwegsinfektionen verursachenden E. coli den bakteriellen und teils stammspezifischen Faktoren oftmals nicht eindeutig eine typische Virulenz- oder Fitness-assoziierte Funktion zuordnen. Zudem werden in neueren Studien immer h{\"a}ufiger atypische uropathogene Isolate von E. coli beschrieben, die in ihrem „Virulenzrepertoire" deutlich von typischen uropathogenen E. coli (UPEC) abweichen, da sie keine klassischen UPEC-Virulenzfaktoren aufweisen. In dieser Arbeit wurden daher Virulenzeigenschaften typischer als auch atypischer UPEC untersucht. Der Effekt eines bestimmten bakteriellen Faktors auf den Wirtsorganismus wird teilweise indirekt durch sekund{\"a}re Modifikation bedingt. Dies offenbart sich beispielsweise am Autotransporterprotein AIDA-I, dessen Konformation durch posttranslationale Glykosylierung stabilisiert wird, wodurch es seine Funktionalit{\"a}t als Adh{\"a}sin erh{\"a}lt. Da bisherige Studien zum AIDA-I homologen Autotransporterprotein Antigen 43 (Ag43) auf der Analyse von k{\"u}nstlich glykosyliertem Protein basieren, lag ein Schwerpunkt dieser Arbeit auf der Untersuchung der nat{\"u}rlichen Glykosylierung von Ag43 in UPEC Stamm 536. Es zeigte sich, dass beide Ag43-Varianten von E. coli Stamm 536 nat{\"u}rlicherweise glykosyliert vorliegen, der Grad der Glykosylierung jedoch wesentlich geringer ausf{\"a}llt als bei nat{\"u}rlich glykosyliertem AIDA-I. Inwieweit die nat{\"u}rliche Glykosylierung von Ag43 zu dessen Funktionalit{\"a}t beitr{\"a}gt, kann erst durch die Identifizierung der f{\"u}r die Ag43-Glykosylierung verantwortlichen Glykosyltransferase gekl{\"a}rt werden. Die in silico-Analyse des Genoms von UPEC Stamm 536 f{\"u}r potentielle Glykosyltransferasen von Ag43 lieferte neun Kandidatengene. Die Gene wurde teils im Wildtyp-Hintergrund, teils im rfaH-negativen Hintergrund von E. coli Stamm 536 deletiert und die Mutanten im Anschluss ph{\"a}notypisch charakterisiert. Die Deletion der Kandidatengene waaF, waaG und waaQ, die f{\"u}r Glykosyltransferasen des LPS-Biosynthesesystems kodieren, f{\"u}hrte zu den deutlichsten Unterschieden in Bezug auf Motilit{\"a}t, Curli/Zellulose-Produktion, H{\"a}molyseaktivit{\"a}t und Expression von Typ 1 Fimbrien. Der Einfluss des „knock-out" der Kandidatengene auf die Glykosylierung von Ag43 muss in weiterf{\"u}hrenden Studien untersucht werden. Zur Charakterisierung des uropathogenen Virulenzpotentials verschiedener E. coli St{\"a}mme in vivo hat sich in den letzten Jahren das murine Modell der aufsteigenden Harnwegsinfektion etabliert. Mit Hilfe dieses Modells wurden in der vorliegenden Arbeit sowohl spezifische Deletionsmutanten prototypischer UPEC als auch atypische E. coli Harnwegsisolate bez{\"u}glich ihrer Urovirulenz getestet und verglichen. Bei der Untersuchung der klassischen UPEC lag der Fokus auf der m{\"o}glichen Urovirulenzmodulation durch die folgenden spezifischen Faktoren: dem Autotransporterprotein Ag43, dem „Response regulator" UvrY, dem Polyketid Colibactin sowie dem Exopolysaccharid poly-β-1,6-N-Acetylglucosamin (PGA). F{\"u}r Ag43 war bei der Etablierung einer Harnwegsinfektion keine eindeutige Funktion feststellbar. Es ist jedoch denkbar, dass Ag43 zur Langzeitpersistenz im Harnwegstrakt beitragen kann, was in weiteren Studien belegt werden sollte. Die Expression von UvrY in der nat{\"u}rlichen uvrY-Deletionsmutante UPEC Stamm 536 ließ keine Erh{\"o}hung des Urovirulenzpotentials im Mausmodell erkennen. In diesem Zusammenhang konnte allerdings gezeigt werden, dass die Expression des Genotoxins Colibactin in UPEC Stamm 536 dessen Virulenz signifikant herabsetzte. Die Untersuchungen zur Relevanz des Exopolysaccharids PGA belegen deutlich, dass PGA f{\"u}r die Langzeitpersistenz von E. coli im murinen Harnwegstrakt ben{\"o}tigt wird. F{\"u}r die initiale Kolonisierung scheint PGA hingegen keine Bedeutung zu haben. F{\"u}r atypische UPEC Isolate, die Charakteristika von STEC und EAEC zeigen und sich in ihrem Virulenzmuster deutlich von prototypischen UPEC unterscheiden, ließ sich im murinen Modell der aufsteigenden Harnwegsinfektion, verglichen mit dem UPEC Modellorganismus 536, ein {\"a}hnliches, teils sogar erh{\"o}htes uropathogenes Virulenzpotential nachweisen. Die Ergebnisse der Arbeit untermauern somit die heutige Vorstellung bez{\"u}glich der Entwicklung und Etablierung einer Harnwegsinfektion, dass verschiedene E. coli St{\"a}mme unterschiedliche (Kontroll-) Mechanismen entwickelt haben, um erfolgreich den Harnwegstrakt kolonisieren und eine Infektion ausl{\"o}sen zu k{\"o}nnen. Zudem weisen sie darauf hin, dass diese F{\"a}higkeit nicht auf Isolate typischer phylogenetischer UPEC Entwicklungslinien beschr{\"a}nkt und auf das Vorhandensein charakteristischer UPEC Virulenzfaktoren angewiesen ist.},
  subject      = {Escherichia coli},
  language  = {de}
}
@phdthesis{Westermann2014,
  author    = {Westermann, Alexander J.},
  title     = {Dual RNA-seq of pathogen and host},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-112462},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {The infection of a eukaryotic host cell by a bacterial pathogen is one of the most intimate examples of cross-kingdom interactions in biology. Infection processes are highly relevant from both a basic research as well as a clinical point of view. Sophisticated mechanisms have evolved in the pathogen to manipulate the host response and vice versa host cells have developed a wide range of anti-microbial defense strategies to combat bacterial invasion and clear infections. However, it is this diversity and complexity that makes infection research so challenging to technically address as common approaches have either been optimized for bacterial or eukaryotic organisms. Instead, methods are required that are able to deal with the often dramatic discrepancy between host and pathogen with respect to various cellular properties and processes. One class of cellular macromolecules that exemplify this host-pathogen heterogeneity is given by their transcriptomes: Bacterial transcripts differ from their eukaryotic counterparts in many aspects that involve both quantitative and qualitative traits. The entity of RNA transcripts present in a cell is of paramount interest as it reflects the cell's physiological state under the given condition. Genome-wide transcriptomic techniques such as RNA-seq have therefore been used for single-organism analyses for several years, but their applicability has been limited for infection studies. The present work describes the establishment of a novel transcriptomic approach for infection biology which we have termed "Dual RNA-seq". Using this technology, it was intended to shed light particularly on the contribution of non-protein-encoding transcripts to virulence, as these classes have mostly evaded previous infection studies due to the lack of suitable methods. The performance of Dual RNA-seq was evaluated in an in vitro infection model based on the important facultative intracellular pathogen Salmonella enterica serovar Typhimurium and different human cell lines. Dual RNA-seq was found to be capable of capturing all major bacterial and human transcript classes and proved reproducible. During the course of these experiments, a previously largely uncharacterized bacterial small non-coding RNA (sRNA), referred to as STnc440, was identified as one of the most strongly induced genes in intracellular Salmonella. Interestingly, while inhibition of STnc440 expression has been previously shown to cause a virulence defect in different animal models of Salmonellosis, the underlying molecular mechanisms have remained obscure. Here, classical genetics, transcriptomics and biochemical assays proposed a complex model of Salmonella gene expression control that is orchestrated by this sRNA. In particular, STnc440 was found to be involved in the regulation of multiple bacterial target mRNAs by direct base pair interaction with consequences for Salmonella virulence and implications for the host's immune response. These findings exemplify the scope of Dual RNA-seq for the identification and characterization of novel bacterial virulence factors during host infection.},
  subject      = {Transkriptomanalyse},
  language  = {en}
}
@article{VembarScherfSiegel2014,
  author    = {Vembar, Shruti S. and Scherf, Artur and Siegel, T. Nicolai},
  title     = {Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression},
  series = {Current Opinion in Microbiology},
  volume    = {20},
  journal   = {Current Opinion in Microbiology},
  number    = {100},
  issn      = {1369-5274},
  doi       = {10.1016/j.mib.2014.06.013},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121416},
  pages     = {153-61},
  year      = {2014},
  abstract  = {The eukaryotic unicellular pathogen Plasmodium falciparum tightly regulates gene expression, both during development and in adaptation to dynamic host environments. This regulation is evident in the mutually exclusive expression of members of clonally variant virulence multigene families. While epigenetic regulators have been selectively identified at active or repressed virulence genes, their specific recruitment remains a mystery. In recent years, noncoding RNAs (ncRNAs) have emerged as lynchpins of eukaryotic gene regulation; by binding to epigenetic regulators, they provide target specificity to otherwise non-specific enzyme complexes. Not surprisingly, there is great interest in understanding the role of ncRNA in P. falciparum, in particular, their contribution to the mutually exclusive expression of virulence genes. The current repertoire of P. falciparum ncRNAs includes, but is not limited to, subtelomeric ncRNAs, virulence gene-associated ncRNAs and natural antisense RNA transcripts. Continued improvement in high-throughput sequencing methods is sure to expand this repertoire. Here, we summarize recent advances in P. falciparum ncRNA biology, with an emphasis on ncRNA-mediated epigenetic modes of gene regulation.},
  language  = {en}
}
@article{JaegerFoerstnerSharmaetal.2014,
  author    = {J{\"a}ger, Dominik and F{\"o}rstner, Konrad U. and Sharma, Cynthia M. and Santangelo, Thomas J. and Reeve, John N.},
  title     = {Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis},
  series = {BMC Genomics},
  volume    = {15},
  journal   = {BMC Genomics},
  number    = {684},
  issn      = {1471-2164},
  doi       = {10.1186/1471-2164-15-684},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-120966},
  year      = {2014},
  abstract  = {Background Prokaryotes have relatively small genomes, densely-packed with protein-encoding sequences. RNA sequencing has, however, revealed surprisingly complex transcriptomes and here we report the transcripts present in the model hyperthermophilic Archaeon, Thermococcus kodakarensis, under different physiological conditions. Results Sequencing cDNA libraries, generated from RNA isolated from cells under different growth and metabolic conditions has identified >2,700 sites of transcription initiation, established a genome-wide map of transcripts, and consensus sequences for transcription initiation and post-transcription regulatory elements. The primary transcription start sites (TSS) upstream of 1,254 annotated genes, plus 644 primary TSS and their promoters within genes, are identified. Most mRNAs have a 5'-untranslated region (5'-UTR) 10 to 50 nt long (median = 16 nt), but ~20\% have 5'-UTRs from 50 to 300 nt long and ~14\% are leaderless. Approximately 50\% of mRNAs contain a consensus ribosome binding sequence. The results identify TSS for 1,018 antisense transcripts, most with sequences complementary to either the 5'- or 3'-region of a sense mRNA, and confirm the presence of transcripts from all three CRISPR loci, the RNase P and 7S RNAs, all tRNAs and rRNAs and 69 predicted snoRNAs. Two putative riboswitch RNAs were present in growing but not in stationary phase cells. The procedure used is designed to identify TSS but, assuming that the number of cDNA reads correlates with transcript abundance, the results also provide a semi-quantitative documentation of the differences in T. kodakarensis genome expression under different growth conditions and confirm previous observations of substrate-dependent specific gene expression. Many previously unanticipated small RNAs have been identified, some with relative low GC contents (≤50\%) and sequences that do not fold readily into base-paired secondary structures, contrary to the classical expectations for non-coding RNAs in a hyperthermophile. Conclusion The results identify >2,700 TSS, including almost all of the primary sites of transcription initiation upstream of annotated genes, plus many secondary sites, sites within genes and sites resulting in antisense transcripts. The T. kodakarensis genome is small (~2.1 Mbp) and tightly packed with protein-encoding genes, but the transcriptomes established also contain many non-coding RNAs and predict extensive RNA-based regulation in this model Archaeon.},
  language  = {en}
}
@article{AdelfingerGentschevdeGuibertetal.2014,
  author    = {Adelfinger, Marion and Gentschev, Ivaylo and de Guibert, Julio Grimm and Weibel, Stephanie and Langbein-Laugwitz, Johanna and H{\"a}rtl, Barbara and Escobar, Hugo Murua and Nolte, Ingo and Chen, Nanhai G. and Aguilar, Richard J. and Yu, Yong A. and Zhang, Qian and Frentzen, Alexa and Szalay, Aladar A.},
  title     = {Evaluation of a New Recombinant Oncolytic Vaccinia Virus Strain GLV-5b451 for Feline Mammary Carcinoma Therapy},
  series = {PLoS ONE},
  volume    = {9},
  journal   = {PLoS ONE},
  number    = {8},
  doi       = {10.1371/journal.pone.0104337},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-119387},
  pages     = {e104337},
  year      = {2014},
  abstract  = {Virotherapy on the basis of oncolytic vaccinia virus (VACV) infection is a promising approach for cancer therapy. In this study we describe the establishment of a new preclinical model of feline mammary carcinoma (FMC) using a recently established cancer cell line, DT09/06. In addition, we evaluated a recombinant vaccinia virus strain, GLV-5b451, expressing the anti-vascular endothelial growth factor (VEGF) single-chain antibody (scAb) GLAF-2 as an oncolytic agent against FMC. Cell culture data demonstrate that GLV-5b451 virus efficiently infected, replicated in and destroyed DT09/06 cancer cells. In the selected xenografts of FMC, a single systemic administration of GLV-5b451 led to significant inhibition of tumor growth in comparison to untreated tumor-bearing mice. Furthermore, tumor-specific virus infection led to overproduction of functional scAb GLAF-2, which caused drastic reduction of intratumoral VEGF levels and inhibition of angiogenesis. In summary, here we have shown, for the first time, that the vaccinia virus strains and especially GLV-5b451 have great potential for effective treatment of FMC in animal model.},
  language  = {en}
}
@article{SiegelHonZhangetal.2014,
  author    = {Siegel, T. Nicolai and Hon, Chung-Chau and Zhang, Qinfeng and Lopez-Rubio, Jose-Juan and Scheidig-Benatar, Christine and Martins, Rafeal M. and Sismeiro, Odile and Copp{\´e}e, Jean-Yves},
  title     = {Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum},
  series = {BMC Genomics},
  volume    = {15},
  journal   = {BMC Genomics},
  doi       = {10.1186/1471-2164-15-150},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-119892},
  pages     = {150},
  year      = {2014},
  abstract  = {Background Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of organisms, where these transcripts have been shown to play important roles in the regulation of gene expression. Likewise, the existence of NATs has been observed in Plasmodium but our understanding towards their genome-wide distribution remains incomplete due to the limited depth and uncertainties in the level of strand specificity of previous datasets. Results To gain insights into the genome-wide distribution of NATs in P. falciparum, we performed RNA-ligation based strand-specific RNA sequencing at unprecedented depth. Our data indicate that 78.3\% of the genome is transcribed during blood-stage development. Moreover, our analysis reveals significant levels of antisense transcription from at least 24\% of protein-coding genes and that while expression levels of NATs change during the intraerythrocytic developmental cycle (IDC), they do not correlate with the corresponding mRNA levels. Interestingly, antisense transcription is not evenly distributed across coding regions (CDSs) but strongly clustered towards the 3′-end of CDSs. Furthermore, for a significant subset of NATs, transcript levels correlate with mRNA levels of neighboring genes. Finally, we were able to identify the polyadenylation sites (PASs) for a subset of NATs, demonstrating that at least some NATs are polyadenylated. We also mapped the PASs of 3443 coding genes, yielding an average 3′ untranslated region length of 523 bp. Conclusions Our strand-specific analysis of the P. falciparum transcriptome expands and strengthens the existing body of evidence that antisense transcription is a substantial phenomenon in P. falciparum. For a subset of neighboring genes we find that sense and antisense transcript levels are intricately linked while other NATs appear to be regulated independently of mRNA transcription. Our deep strand-specific dataset will provide a valuable resource for the precise determination of expression levels as it separates sense from antisense transcript levels, which we find to often significantly differ. In addition, the extensive novel data on 3′ UTR length will allow others to perform searches for regulatory motifs in the UTRs and help understand post-translational regulation in P. falciparum.},
  language  = {en}
}