Novel transcripts reveal a complex structure of the human TRKA gene and imply the presence of multiple protein isoforms

Publisher Copyright: © 2015 Luberg et al.Background: Tropomyosin-related kinase A (TRKA) is a nerve growth factor (NGF) receptor that belongs to the tyrosine kinase receptor family. It is critical for the correct development of many types of neurons including pain-mediating sensory neurons and also controls proliferation, differentiation and survival of many neuronal and non-neuronal cells. TRKA (also known as NTRK1) gene is a target of alternative splicing which can result in several different protein isoforms. Presently, three human isoforms (TRKAI, TRKAII and TRKAIII) and two rat isoforms (TRKA L0 and TRKA L1) have been described. Results: We show here that human TRKA gene is overlapped by two genes and spans 67 kb-almost three times the size that has been previously described. Numerous transcription initiation sites from eight different 5' exons and a sophisticated splicing pattern among exons encoding the extracellular part of TRKA receptor indicate that there might be a large variety of alternative protein isoforms. TrkA genes in rat and mouse appear to be considerably shorter, are not overlapped by other genes and display more straightforward splicing patterns. We describe the expression profile of alternatively spliced TRKA transcripts in different tissues of human, rat and mouse, as well as analyze putative endogenous TRKA protein isoforms in human SH-SY5Y and rat PC12 cells. We also characterize a selection of novel putative protein isoforms by portraying their phosphorylation, glycosylation and intracellular localization patterns. Our findings show that an isoform comprising mainly of TRKA kinase domain is capable of entering the nucleus. Conclusions: Results obtained in this study refer to the existence of a multitude of TRKA mRNA and protein isoforms, with some putative proteins possessing very distinct properties.publishersversionPeer reviewe

Climate change and freshwater zooplankton: what does it boil down to?

Recently, major advances in the climate–zooplankton interface have been made some of which appeared to receive much attention in a broader audience of ecologists as well. In contrast to the marine realm, however, we still lack a more holistic summary of recent knowledge in freshwater. We discuss climate change-related variation in physical and biological attributes of lakes and running waters, high-order ecological functions, and subsequent alteration in zooplankton abundance, phenology, distribution, body size, community structure, life history parameters, and behavior by focusing on community level responses. The adequacy of large-scale climatic indices in ecology has received considerable support and provided a framework for the interpretation of community and species level responses in freshwater zooplankton. Modeling perspectives deserve particular consideration, since this promising stream of ecology is of particular applicability in climate change research owing to the inherently predictive nature of this field. In the future, ecologists should expand their research on species beyond daphnids, should address questions as to how different intrinsic and extrinsic drivers interact, should move beyond correlative approaches toward more mechanistic explanations, and last but not least, should facilitate transfer of biological data both across space and time

Microbiota profiling of the house fly, Musca Domestica

We share our living spaces with a variety of insects - some of them can be nuisance pests, others can be beneficial, and some insects we do not even notice. These insects carry with them an abundance of microbes, that can be either beneficial (sometimes even crucial) or pathogenic for them, serve as a food source or be part of the transient microbiota. While insects can introduce valuable diversity to the niches they inhabit, they can also transport unwanted microbes to our indoor environments. There have only been a few studies looking at the microbiome of synanthropic insect species (i.e. living in close association with humans), with the most attention given to the vinegar fly Drosophila melanogaster. In this study we chose to focus on the common house fly Musca domestica and characterize its microbiota in detail. Firstly, we set in place the methodology to efficiently analyze both bacteria and fungi in the internal and external compartments of the fly. Subsequently, we collected more than 400 house flies from two distinct geographical locations - Belgium and Rwanda. The sampling was carried out in three different human related habitats, namely in homes, farms and hospitals. The microbes inside and on the outer surface of the collected flies were analyzed using culture-dependent and culture-independent methods. A subset of cultured isolates was identified to the species level and screened for anti-microbial resistance, as it has been proposed that insects can act as environmental reservoirs for anti-microbial resistance genes. Using targeted amplicon sequencing of partial bacterial 16S ribosomal RNA genes and the fungal internal transcribed spacer (ITS) region, we portrayed a detailed picture of house fly microbiota in a variety of habitats. Interestingly, the bacterial communities were more diverse on the outer surface of the flies compared to the internal compartment. This was not the case for fungi, which were equally diverse in both compartments in all habitats. In general, geography and habitat had a stronger influence on the composition of M. domestica external microbial communities than on internal microbiota. The bacterial subset of the internal microbiota, while varying among individuals, was rather stable with similar patterns between flies from different locations. On the other hand, the external bacteria clustered according to the fly's country and habitat of origin, resulting in location specific microbial signatures. For example, Planococcaceae, Ruminococcaceae, Acinetobacter, and Flavobacterium were significantly enriched in fly samples from Belgian farms, whereas Massilia, Carnobacteriaceae and Corynebacterium were enriched in samples from Rwandan farms. Furthermore, the fungal communities were highly dependent on the fly sampling country and less on the habitat. The most abundant bacterial genus detected both with targeted amplicon sequencing and with the culturing method was Staphylococcus. Identification based on β subunit of bacterial RNA polymerase (rpoB) and chaperone DnaJ of isolated strains revealed that at least 17 different Staphylococcus species were present in the house fly samples, among which S. xylosus was most abundant. These isolates were additionally tested for their anti-microbial resistance, which showed high variation between species and slight tendency for more severely resistant strains in flies from Rwandan hospitals. However, for firm conclusions in this regard more isolates from flies from more habitats are needed to be analyzed. Among the cultured isolates we discovered a novel species that we formally described as Apibacter muscae. The genus already included two species that were isolated from bees, suggesting that this is potentially an insect specific genus. Taken together, our study took an in depth look at microbes harbored by one of the most common synanthropic insects, the house fly. We showed that they carry very diverse bacterial and fungal communities that depend on the geographical location and habitat of the flies. However, the internal bacterial communities are more stable compared to the external ones, suggesting that their composition is under a tighter control of the fly physiology. We saw extensive overlap between microbial species found in the flies and the ones reported indoors, but the extent to which house flies influence microbial communities we encounter in our living spaces, remains to be further investigated.status: publishe

Physiology, ecology and industrial applications of aroma formation in yeast

Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.status: publishe

Apibacter muscae sp. nov., a novel bacterial species isolated from house flies

We describe the isolation and characterization of three bacterial isolates from the common house fly, Musca domestica, caught in Londerzeel, Belgium and Huye District, Rwanda. Although isolated from distinct geographical locations, the strains show >99 % identical 16S rRNA gene sequences and are <95 % identical to type strains of Apibacter species. Whole-genome sequences were obtained for all three strains. The genomes are 2.4-2.5 Mb with a G+C content of ~30.3 mol%. Bacteriological and biochemical analysis of the strains demonstrate distinctly different characteristics compared to known Apibacter species. Particularly, the three strains investigated in this study can be distinguished from the known Apibacter species (Apibacter mensalisand Apibacter adventoris) through urease and β-glucosidase activities. Whole-cell fatty acid methyl ester analysis shows that the fatty acid composition of the novel strains is also unique. On the basis of phylogenetic, genotypic and phenotypic data, we propose to classify these isolates as representatives of a novel species of the genus Apibacter, Apibacter muscae sp. nov., in reference to its prevalence in house flies, with strain G8T (=LMG 30898T=DSM 107922T) as the type strain.status: publishe

MOESM2 of Novel transcripts reveal a complex structure of the human TRKA gene and imply the presence of multiple protein isoforms

Additional file 2: Primers and cycling conditions used in this study

Germline variation of Ribonuclease H2 genes in ovarian cancer patients

Abstract Epithelial ovarian carcinoma (EOC) is a genetically heterogeneous disease that is partly driven by molecular defects in mismatch repair (MMR) or homology-directed DNA repair (HDR). Ribonuclease H2 serves to remove mis-incorporated ribonucleotides from DNA which alleviates HDR mechanisms and guides the MMR machinery. Although Ribonuclease H2 has been implicated in cancer, the role of germline variants for ovarian cancer is unknown. In the present case-control study, we sequenced the coding and flanking untranslated regions of the RNASEH2A, RNASEH2B and RNASEH2C genes, encoding all three subunits of Ribonuclease H2, in a total of 602 German patients with EOC and of 940 healthy females from the same population. We identified one patient with a truncating variant in RNASEH2B, p.C44X, resulting in a premature stop codon. This patient had high-grade serous EOC with an 8 years survival after platinum/taxane-based therapy. Subsequent analysis of TCGA data similarly showed a significantly longer progression-free survival in ovarian cancer patients with low RNASEH2B or RNASEH2C expression levels. In conclusion, loss-of-function variants in Ribonuclease H2 genes are not common predisposing factors in ovarian cancer but the possibility that they modulate therapeutic platinum response deserves further investigation

Germline variation of Ribonuclease H2 genes in ovarian cancer patients.

Epithelial ovarian carcinoma (EOC) is a genetically heterogeneous disease that is partly driven by molecular defects in mismatch repair (MMR) or homology-directed DNA repair (HDR). Ribonuclease H2 serves to remove mis-incorporated ribonucleotides from DNA which alleviates HDR mechanisms and guides the MMR machinery. Although Ribonuclease H2 has been implicated in cancer, the role of germline variants for ovarian cancer is unknown. In the present case-control study, we sequenced the coding and flanking untranslated regions of the RNASEH2A, RNASEH2B and RNASEH2C genes, encoding all three subunits of Ribonuclease H2, in a total of 602 German patients with EOC and of 940 healthy females from the same population. We identified one patient with a truncating variant in RNASEH2B, p.C44X, resulting in a premature stop codon. This patient had high-grade serous EOC with an 8 years survival after platinum/taxane-based therapy. Subsequent analysis of TCGA data similarly showed a significantly longer progression-free survival in ovarian cancer patients with low RNASEH2B or RNASEH2C expression levels. In conclusion, loss-of-function variants in Ribonuclease H2 genes are not common predisposing factors in ovarian cancer but the possibility that they modulate therapeutic platinum response deserves further investigation