Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Transforming Growth Factor-β1 Downregulates Vascular Endothelial Growth Factor-D Expression in Human Lung Fibroblasts via the Jun NH2-Terminal Kinase Signaling Pathway

Vascular endothelial growth factor (VEGF)-D, a member of the VEGF family, induces both angiogenesis and lymphangiogenesis by activating VEGF receptor-2 (VEGFR-2) and VEGFR-3 on the surface of endothelial cells. Transforming growth factor (TGF)-β1 has been shown to stimulate VEGF-A expression in human lung fibroblast via the Smad3 signaling pathway and to induce VEGF-C in human proximal tubular epithelial cells. However, the effects of TGF-β1 on VEGF-D regulation are unknown. To investigate the regulation of VEGF-D, human lung fibroblasts were studied under pro-fibrotic conditions in vitro and in idiopathic pulmonary fibrosis (IPF) lung tissue. We demonstrate that TGF-β1 downregulates VEGF-D expression in a dose- and time-dependent manner in human lung fibroblasts. This TGF-β1 effect can be abolished by inhibitors of TGF-β type I receptor kinase and Jun NH₂-terminal kinase (JNK), but not by Smad3 knockdown. In addition, VEGF-D knockdown in human lung fibroblasts induces G1/S transition and promotes cell proliferation. Importantly, VEGF-D protein expression is decreased in lung homogenates from IPF patients compared with control lung. In IPF lung sections, fibroblastic foci show very weak VEGF-D immunoreactivity, whereas VEGF-D is abundantly expressed within alveolar interstitial cells in control lung. Taken together, our data identify a novel mechanism for downstream signal transduction induced by TGF-β1 in lung fibroblasts, through which they may mediate tissue remodeling in IPF.     

Molecular characterization and intracellular distribution of the alpha 5 subunit of Trypanosoma cruzi 20S proteasome

Three different monoclonal antibodies were produced against Trypanosona cruzi proteasomes. These antibodies were shown to react with a single 27-kDa band on immunoblots of purified proteasomes. Using a 7E5 monoclonal antibody (IgG1) that recognized the α5 subunit of protozoan protease we have studied the intracellular distribution of the T. cruzi 20S proteasome. Contrary to all cell types described to date, T. cruzi 20S proteasome was found not only in the cytoplasm and nucleus but also in the kinetoplast. As revealed by confocal microscopy, the reactivity of monoclonal antibody 7E5 was highly specific for protozoan proteasome because the antibody recognized only the proteasomes from parasites and not those from the mammalian host in T. cruzi infected cells. These findings were confirmed by immunoblots or immunoprecipitations, followed by chymotrypsin-like activity detection in kinetoplasts isolated by differential centrifugation and sucrose density gradients. Proteasome 20S was present in all T. cruzi stages and only slight differences in terms of relative abundance were found. The potential role of the proteasome in kinetoplast remodeling remains to be determined.     

Disruption of pheromone communication in Tecia solanivora (Lepidoptera: Gelechiidae): flight tunnel and field studies

The moth Tecia (Scrobipalpopsis) solanivora Povolny (Lepidoptera: Gelechiidae) is the most important pest of potato, Solanum spp., in Central America and adjacent South American countries. Insecticide treatments are not sufficiently effective; therefore, we investigated the feasibility of pheromone-mediated mating disruption for control of T. solanivora. Pheromone dispensers were formulated with 70 mg of the three sex pheromone compounds (E)-3-dodecenyl acetate, (Z)-3-dodecenyl acetate, and dodecyl acetate, in a ratio of 100:56:100, respectively. Male attraction to these compounds is optimal at a ratio of 100:1:20, thus the mating disruption dispensers contained an off-blend, which attracted only a few males. Nonetheless, one mating disruption dispenser suppressed male attraction to calling females in a flight tunnel and reduced male activation in response to female pheromone. Communication disruption is accordingly due to camouflage of the female signal and possibly due to a reduction of male responsiveness by sensory imbalance. Only a few males were observed in a 3-ha potato field treated with 84 g pheromone/ha, compared with an untreated control field. During 2 mo, male attraction to traps baited with calling females or synthetic pheromone was strongly reduced. This reduction confirms the potential of mating disruption for management of T. solanivora. The efficacy of the pheromone treatment can be further improved by earlier dispenser application, by increased dispenser load, and by treatment of larger fields to reduce immigration of mated females.     

Correlation between precolonization of trigeminal ganglia by attenuated strains of pseudorabies virus and resistance to wild-type virus latency.

We compared the levels of latent pseudorabies virus (PRV) DNA in trigeminal ganglia (TG) of pigs after intranasal inoculation of different PRV strains by using quantitative DNA PCR. The extent of colonization attained in each case varied significantly according to the type of strain and inoculum dose, wild-type (WT) PRV being the most efficient strain in colonizing TG. When groups of pigs representing different levels of precolonization of TG with an attenuated PRV strain were challenged with WT PRV, it became evident that there is a statistically significant inverse correlation between the extent of precolonization attained by an attenuated PRV strain in TG and the level of establishment of latency by superinfecting WT PRV. The protection against WT PRV latency did not correlate with the extent of WT PRV replication at the portal of entry.     

Identification of DNA sequence variation in Campylobacter jejuni strains associated with the Guillain-Barré syndrome by high-throughput AFLP analysis

Background  

Campylobacter jejuni is the predominant cause of antecedent infection in post-infectious neuropathies such as the Guillain-Barré (GBS) and Miller Fisher syndromes (MFS). GBS and MFS are probably induced by molecular mimicry between human gangliosides and bacterial lipo-oligosaccharides (LOS). This study describes a new C. jejuni-specific high-throughput AFLP (htAFLP) approach for detection and identification of DNA polymorphism, in general, and of putative GBS/MFS-markers, in particular.     

Relationships between pupil working range and habitat luminance in flies and butterflies

The luminance range over which the pupil mechanism operates was measured with pupil reflectometry in 11 species of butterflies and 13 species of dipteran flies. The different species were selected to be as different as possible regarding the range of ambient luminances in which they are active. Habitat luminance ranges were also measured and correlated to luminances in the experimental situation. The pupil mechanism in butterflies operates in the centre of the luminance range in which the different species are active. Three distinct groups of butterflies with pupil sensitivities matched to their specific types of activity pattern were identified: species active only in direct sunlight, species active also in shaded places and species extending their activity into dawn and dusk. Quite differently, the pupil mechanisms of dipteran flies operate in the upper end of the ambient luminances, and in some species well above the luminances normally encountered by the animal. All fly pupils start to close roughly at the same luminance, irrespective of the luminances in which the species are active. The results suggest that the most important role for the pupil mechanism in many of the butterfly species is to maximize acuity over a wide range of luminances, whereas in flies it is to avoid saturation of transduction units and thereby maximize the photoreceptor's signal-to-noise ratio at high light intensities. Accepted: 1 July 1997     

Enzymatic lysis of sulfated glycosaminoglycans reduces the electrophoretic mobility of vascular endothelial cells

The main purpose of this work was to identify the macromolecules carrying the surface charge of endothelial cells. This was done by measuring changes in cell electrophoretic mobility caused by enzymatic removal of glycocalyx components. Endothelial cells were removed from the bovine pulmonary artery using nonenzymatic procedures, plated, and identified by immunocytochemical methods and electron microscopy. Cultured cells were suspended in saline and placed in the lumen of a capillary in a Rank Brothers electrophoresis instrument. Voltage was applied between the ends of the capillary, and the velocity acquired by the cells was measured with a microscope. Preincubating the cells in protein-free saline for 1 h reduced the mobility by 25%. This reflects the loss of proteoheparan sulfate from the cell surface. Cell mobility was totally suppressed by exposing the entire cell surface to chondroitin sulfate lyase, but it was only slightly diminished when the enzyme was applied only to the cell side facing the culture medium. A partial decrease in mobility was obtained after enzymatic removal of either heparin, heparan sulfate, or collagen. The results indicate that sulfated glycosaminoglycans are the main carriers of the surface change in vascular endothelial cells. The asymmetrical effect of chondroitinase on the two sides of the cell indicates a distribution polarization for glycosaminoglycans in endothelial cells.