Crucial role for Nox2 and sleep deprivation in aircraft noise-induced vascular and cerebral oxidative stress, inflammation, and gene regulation.

Aims: Aircraft noise causes endothelial dysfunction, oxidative stress, and inflammation. Transportation noise increases the incidence of coronary artery disease, hypertension, and stroke. The underlying mechanisms are not well understood. Herein, we investigated effects of phagocyte-type NADPH oxidase (Nox2) knockout and different noise protocols (around-the-clock, sleep/awake phase noise) on vascular and cerebral complications in mice. Methods and results: C57BL/6j and Nox2-/- (gp91phox-/-) mice were exposed to aircraft noise (maximum sound level of 85 dB(A), average sound pressure level of 72 dB(A)) around-the-clock or during sleep/awake phases for 1, 2, and 4 days. Adverse effects of around-the-clock noise on the vasculature and brain were mostly prevented by Nox2 deficiency. Around-the-clock aircraft noise of the mice caused the most pronounced vascular effects and dysregulation of Foxo3/circadian clock as revealed by next generation sequencing (NGS), suggesting impaired sleep quality in exposed mice. Accordingly, sleep but not awake phase noise caused increased blood pressure, endothelial dysfunction, increased markers of vascular/systemic oxidative stress, and inflammation. Noise also caused cerebral oxidative stress and inflammation, endothelial and neuronal nitric oxide synthase (e/nNOS) uncoupling, nNOS mRNA and protein down-regulation, and Nox2 activation. NGS revealed similarities in adverse gene regulation between around-the-clock and sleep phase noise. In patients with established coronary artery disease, night-time aircraft noise increased oxidative stress, and inflammation biomarkers in serum. Conclusion: Aircraft noise increases vascular and cerebral oxidative stress via Nox2. Sleep deprivation and/or fragmentation caused by noise triggers vascular dysfunction. Thus, preventive measures that reduce night-time aircraft noise are warranted.

Effects of noise on vascular function, oxidative stress, and inflammation: mechanistic insight from studies in mice.

Aims: Epidemiological studies indicate that traffic noise increases the incidence of coronary artery disease, hypertension and stroke. The underlying mechanisms remain largely unknown. Field studies with nighttime noise exposure demonstrate that aircraft noise leads to vascular dysfunction, which is markedly improved by vitamin C, suggesting a key role of oxidative stress in causing this phenomenon. Methods and results: We developed a novel animal model to study the vascular consequences of aircraft noise exposure. Peak sound levels of 85 and mean sound level of 72 dBA applied by loudspeakers for 4 days caused an increase in systolic blood pressure, plasma noradrenaline and angiotensin II levels and induced endothelial dysfunction. Noise increased eNOS expression but reduced vascular NO levels because of eNOS uncoupling. Noise increased circulating levels of nitrotyrosine, interleukine-6 and vascular expression of the NADPH oxidase subunit Nox2, nitrotyrosine-positive proteins and of endothelin-1. FACS analysis demonstrated an increase in infiltrated natural killer-cells and neutrophils into the vasculature. Equal mean sound pressure levels of white noise for 4 days did not induce these changes. Comparative Illumina sequencing of transcriptomes of aortic tissues from aircraft noise-treated animals displayed significant changes of genes in part responsible for the regulation of vascular function, vascular remodelling, and cell death. Conclusion: We established a novel and unique aircraft noise stress model with increased blood pressure and vascular dysfunction associated with oxidative stress. This animal model enables future studies of molecular mechanisms, mitigation strategies, and pharmacological interventions to protect from noise-induced vascular damage.

Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence.

Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually causing population divergence. We investigated differential TE abundance among conspecific populations of the nonbiting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genomewide single-nucleotide polymorphisms (SNPs) and the FST estimated from TEs is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in situ hybridization of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.

The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago.

BACKGROUND: Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In this study we analyzed the genomic locus and expression of stk33 in the class Aves, using a combination of large scale next generation sequencing data analysis and traditional PCR. RESULTS: Within the subclass Palaeognathae we analyzed the white-throated tinamou (Tinamus guttatus), the African ostrich (Struthio camelus) and the emu (Dromaius novaehollandiae). For the African ostrich we were able to generate a 62,778 bp long genomic contig and an mRNA sequence that encodes a protein showing highly significant similarity to STK33 proteins from other vertebrates. The emu has been shown to encode and transcribe a functional STK33 as well. For the white-throated tinamou we were able to identify 13 exons by sequence comparison encoding a protein similar to STK33 as well. In contrast, in all 28 neognath birds analyzed, we could not find evidence for the existence of a functional copy of stk33 or its expression. In the genomes of these 28 bird species, we found only remnants of the stk33 locus carrying several large genomic deletions, leading to the loss of multiple exons. The remaining exons have acquired various indels and premature stop codons. CONCLUSIONS: We were able to elucidate and describe the genomic structure and the transcription of a functional stk33 gene within the subclass Palaeognathae, but we could only find degenerate remnants of stk33 in all neognath birds analyzed. This led us to the conclusion that stk33 became a unitary pseudogene in the evolutionary history of the class Aves at the paleognath-neognath branch point during the late cretaceous period about 100 million years ago. We hypothesize that the pseudogenization of stk33 might have become fixed in neognaths due to either genetic redundancy or a non-orthologous gene displacement and present potential candidate genes for such an incident.

Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis.

BACKGROUND: Primary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. Few studies have analyzed primary roots at a molecular level, and were mostly limited to Arabidopsis. Here we study the primary root transcriptomes of standard type, heterozygous columnar and homozygous columnar apple (Malus x domestica) by RNA-Seq and quantitative real-time PCR. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches. This compact growth possesses economic potential because it allows high density planting and mechanical harvesting of the trees. Its molecular basis has been identified as a nested Gypsy-44 retrotransposon insertion; however the link between the insertion and the phenotype as well as the timing of the phenotype emergence are as yet unclear. We extend the transcriptomic studies of columnar tissues to the radicles, which are the earliest developmental stage and investigate whether homozygous columnar seedlings are viable. RESULTS: Radicles mainly express genes associated with primary metabolism, growth and development. About 200 genes show differential regulation in a comparison of heterozygous columnar radicles with non-columnar radicles, whereas the comparison of homozygous columnar radicles with non-columnar radicles yields about 300 differentially regulated genes. Genes involved in cellulose and phenylpropanoid biosynthesis, cell wall modification, transcription and translation, ethylene and jasmonate biosynthesis are upregulated in columnar radicles. Genes in the vicinity of the columnar-specific Gypsy-44 insertion experience an especially strong differential regulation: the direct downstream neighbor, dmr6-like, is downregulated in heterozygous columnar radicles, but strongly upregulated in columnar shoot apical meristems. CONCLUSIONS: The transcriptomic profile of primary roots reflects their pivotal role in growth and development. Homozygous columnar embryos are viable and form normal radicles under natural conditions, and selection towards heterozygous plants most likely occurs due to breeders' preferences. Cell wall and phytohormone biosynthesis and metabolism experience differential regulation in columnar radicles. Presumably the first step of the differential regulation most likely happens within the region of the retrotransposon insertion and its tissue-specificity suggests involvement of one (or several) tissue-specific regulator(s).

Co-localization of serine/threonine kinase 33 (Stk33) and vimentin in the hypothalamus.

We investigate the immunoreactivity of serine/threonine kinase 33 (Stk33) and of vimentin in the brain of mouse, rat and hamster. Using a Stk33-specific polyclonal antibody, we show by immunofluorescence staining that Stk33 is present in a variety of brain regions. We found a strong staining in the ependymal lining of all cerebral ventricles and the central canal of the spinal cord as well as in hypothalamic tanycytes. Stk33 immunoreactivity was also found in circumventricular organs such as the area postrema, subfornical organ and pituitary and pineal glands. Double-immunostaining experiments with antibodies against Stk33 and vimentin showed a striking colocalization of Stk33 and vimentin. As shown previously, Stk33 phosphorylates recombinant vimentin in vitro. Co-immunoprecipitation experiments and co-sedimentation assays indicate that Stk33 and vimentin are associated in vivo and that this association does not depend on further interacting partners (Brauksiepe et al. in BMC Biochem 9:25, 2008). This indicates that Stk33 is involved in the dynamics of vimentin polymerization/depolymerization. Since in tanycytes the vimentin expression is regulated by the photoperiod (Kameda et al. in Cell Tissue Res 314:251-262, 2003), we determine whether this also holds true for Stk33. We study hypothalamic sections from adult Djungarian hamsters (Phodopus sungorus) held under either long photoperiods (L:D 16:8 h) or short photoperiods (L:D 8:16 h) for 2 months. In addition, we examine whether age-dependent changes in Stk33 protein content exist. Our results show that Stk33 in tanycytes is regulated by the photoperiod as is the case for vimentin. Stk33 may participate in photoperiodic regulation of the endocrine system.

Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies.

The columnar phenotype of apple trees (Malus x domestica) is characterized by a compact growth habit with fruit spurs instead of lateral branches. These properties provide significant economic advantages by enabling high density plantings. The columnar growth results from the presence of a dominant allele of the gene Columnar (Co) located on chromosome 10 which can appear in a heterozygous (Co/co) or homozygous (Co/Co) state. Although two deep sequencing approaches could shed some light on the transcriptome of columnar shoot apical meristems (SAMs), the molecular mechanisms of columnar growth are not yet elaborated. Since the influence of phytohormones is believed to have a pivotal role in the establishment of the phenotype, we performed RNA-Seq experiments to study genes associated with hormone homeostasis and clearly affected by the presence of Co. Our results provide a molecular explanation for earlier findings on the hormonal state of columnar apple trees. Additionally, they allow hypotheses on how the columnar phenotype might develop. Furthermore, we show a statistically approved enrichment of differentially regulated genes on chromosome 10 in the course of validating RNA-Seq results using additional gene expression studies.

Somatic breakpoints, distribution of repetitive DNA and non-LTR retrotransposon insertion sites in the chromosomes of Chironomus piger Strenzke (Diptera, Chironomidae).

Structural aberrations, their frequency and distribution as well as distribution of the tandem repetitive minisatellite DNA clusters of Alu and Hinf elements and two retroelements, the LINE NLRCth1 and the SINE CTRT1, were analyzed in the genome of the chironomid C. piger Strenzke larvae from a Bulgarian population. A consistent somatic variability in the structure of the polytene chromosomes was detected, showing that the C. piger genome is more actively rearranging than supposed before. Breakpoints were concentrated in proximal parts of chromosomes significantly more often than in distal parts. By FISH analysis we could detect only one locus containing Alu elements and 38 Hinf cluster loci which appear to be dispersed equally all over the chromosomes. The retrotransposons NLRCth1 and CTRT1 are present only in a few loci, but highly variant among different individuals. The mean number of NLRCth1 sites per individual was 18.4 +/- 2.09 and of CTRT1 was 54.8 +/- 8.42. A third of breakpoint locations were close to or coincide with a locus occupied by a retroelement (either NLRCth1 or CTRT1). Nineteen percent of breakpoints coincided with Hinf repetitive DNA elements. Some breakpoints were identical in the two sibling species C. piger and C. riparius Meigen (syn.: C. thummi thummi) and are considered as conserved hot spots of chromosome breakage.

The Serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein Vimentin.

BACKGROUND: Colocalization of Stk33 with vimentin by double immunofluorescence in certain cells indicated that vimentin might be a target for phosphorylation by the novel kinase Stk33. We therefore tested in vitro the ability of Stk33 to phosphorylate recombinant full length vimentin and amino-terminal truncated versions thereof. In order to prove that Stk33 and vimentin are also in vivo associated proteins co-immunoprecipitation experiments were carried out. For testing the enzymatic activity of immunoprecipitated Stk33 we incubated precipitated Stk33 with recombinant vimentin proteins. To investigate whether Stk33 binds directly to vimentin, an in vitro co-sedimentation assay was performed. RESULTS: The results of the kinase assays demonstrate that Stk33 is able to specifically phosphorylate the non-alpha-helical amino-terminal domain of vimentin in vitro. Furthermore, co-immunoprecipitation experiments employing cultured cell extracts indicate that Stk33 and vimentin are associated in vivo. Immunoprecipitated Stk33 has enzymatic activity as shown by successful phosphorylation of recombinant vimentin proteins. The results of the co-sedimentation assay suggest that vimentin binds directly to Stk33 and that no additional protein mediates the association. CONCLUSION: We hypothesize that Stk33 is involved in the in vivo dynamics of the intermediate filament cytoskeleton by phosphorylating vimentin.

The Adverse Effects of Environmental Noise Exposure on Oxidative Stress and Cardiovascular Risk.

Epidemiological studies have provided evidence that traffic noise exposure is linked to cardiovascular diseases such as arterial hypertension, myocardial infarction, and stroke. Noise is a nonspecific stressor that activates the autonomous nervous system and endocrine signaling. According to the noise reaction model introduced by Babisch and colleagues, chronic low levels of noise can cause so-called nonauditory effects, such as disturbances of activity, sleep, and communication, which can trigger a number of emotional responses, including annoyance and subsequent stress. Chronic stress in turn is associated with cardiovascular risk factors, comprising increased blood pressure and dyslipidemia, increased blood viscosity and blood glucose, and activation of blood clotting factors, in animal models and humans. Persistent chronic noise exposure increases the risk of cardiometabolic diseases, including arterial hypertension, coronary artery disease, diabetes mellitus type 2, and stroke. Recently, we demonstrated that aircraft noise exposure during nighttime can induce endothelial dysfunction in healthy subjects and is even more pronounced in coronary artery disease patients. Importantly, impaired endothelial function was ameliorated by acute oral treatment with the antioxidant vitamin C, suggesting that excessive production of reactive oxygen species contributes to this phenomenon. More recently, we introduced a novel animal model of aircraft noise exposure characterizing the underlying molecular mechanisms leading to noise-dependent adverse oxidative stress-related effects on the vasculature. With the present review, we want to provide an overview of epidemiological, translational clinical, and preclinical noise research addressing the nonauditory, adverse effects of noise exposure with focus on oxidative stress. Antioxid. Redox Signal. 28, 873-908.

ESTAnnotator: A tool for high throughput EST annotation.

In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information. ESTAnnotator is a tool for the high throughput annotation of expressed sequence tags (ESTs) by automatically running a collection of bioinformatics applications. In the first step, a quality check is performed and repeats, vector parts and low quality sequences are masked. Then successive steps of database searching and EST clustering are performed. Already known transcripts present within mRNA and genomic DNA reference databases are identified. Subsequently, tools for the clustering of anonymous ESTs, and for further database searches at the protein level, are applied. Finally, the outputs of each individual tool are gathered and the relevant results presented in a descriptive summary. ESTAnnotator was already successfully applied for the systematic identification and characterisation of novel human genes involved in cartilage/bone formation, growth, differentiation and homeostasis. ESTAnnotator is available at http://genome.dkfz-heidelberg.de, contact: genome@dkfz.de.

Expression profiling of human fetal growth plate cartilage by EST sequencing.

The differentiation of mesenchymal stem cells into hypertrophic chondrocytes is an integral and multistep process important in pattern formation, endochondral ossification, and postnatal growth of the skeleton. In recent years, novel genes involved in these processes have been identified, but still only little is known about the large-scale gene expression profile during skeletal development. We initiated an expressed sequence tag (EST) project aiming at the identification of genes and pathways involved in this complex process. Candidate genes are expected to be of value for diagnosis and treatment of monogenic and multigenic heritable disorders of the skeleton. Here, we describe the sequences of 4,748 clones from a human growth plate cartilage cDNA library generated from 20 weeks prenatal-2 years postnatal specimens. In silico analysis of these sequences revealed 1,688 individual transcription units, corresponding to known (1,274) and to novel, yet uncharacterised potential genes (414). The tissue specificity of the library was reflected by its corresponding EST profile representing a total of approximately 10% proteins already shown to be involved in cartilage/bone development or homeostasis. The EST profile also reflects the developmental stage of the tissue with significant differences in the expression of matrix proteins compared to corresponding EST profiles from 8-12 and 12-20 week human fetal cartilage. Calculation of the relative frequency of transcripts in our cDNA library, as compared to their abundance in other EST datasets, revealed a set of approximately 200 genes, including 81 novel, yet uncharacterised genes, showing increased expression. These genes represent candidates for the large number of osteochondrodysplasias for which the causative gene defects have not yet been identified.

Differential expression pattern of the novel serine/threonine kinase, STK33, in mice and men.

Serine/threonine kinase 33 (STK33/Stk33) is a recently discovered gene whose inferred amino acid sequence translation displays characters typical for a calcium/calmodulin dependent kinase (CAMK). In this study we analysed the STK33/Stk33 RNA and protein distribution and the localization of the protein. The STK33/Stk33 expression pattern resembles those of some related members of the CAMK group. STK33/Stk33 displays a nonubiquitous and, in most tissues, low level of expression. It is highly expressed in testis, particularly in cells from the spermatogenic epithelia. Moreover, significant expression is detected in lung epithelia, alveolar macrophages, horizontal cells in the retina and in embryonic organs such as heart, brain and spinal cord. A possible role of STK33/Stk33 in spermatogenesis and organ ontogenesis is discussed.

The transcriptomes of columnar and standard type apple trees (Malus x domestica) - a comparative study.

Columnar apple trees (Malus x domestica) provide several economic advantages due to their specific growth habit. The columnar phenotype is the result of the dominant allele of the gene Co and is characterized by thick stems with short internodes and reduced lateral branching. Co is located on chromosome 10 and often appears in a heterozygous state (Co/co). The molecular explanation of columnar growth is not well established. Therefore, we studied the transcriptomes of columnar and standard type apple trees using 454 and Illumina next generation sequencing (NGS) technologies. We analyzed the transcriptomes of shoot apical meristems (SAMs) because we expect that these organs are involved in forming the columnar growth phenotype. The results of the comparative transcriptome analysis show significant differences in expression levels of hundreds of genes. Many of the differentially expressed genes are associated with membrane and cell wall growth or modification and can be brought in line with the columnar phenotype. Additionally, earlier findings on the hormonal state of shoots of columnar apples could be affirmed. Our study resulted in a large number of genes differentially expressed in columnar vs. standard type apple tree SAMs. Although we have not unraveled the nature of the Co gene, we could show that the modified expression of these genes, most likely due to the presence of Co, can determine the columnar phenotype. Furthermore, the usefulness of NGS for the analysis of the molecular basis of complex phenotypes is discussed.

Chromatophore development and cell interactions in the skin of xiphophorine fish.

Regeneration-induced development of chromatophores in the skin of fish was used to study cell interactions affecting cell differentiation and cell destruction. The typical differentiation process of chromatophores in the regenerating fish skin is described with special interest in the differentiation of macro- and micromelanophores. Between micro- and macromelanophores two types of cell interactions were found: 1. The macromelanophores inhibit the differentiation of melanocytes and micromelanophores 2. the macromelanophores induce the destruction of micromelanophores in their vicinity. These cell interactions are very specific to cell type, that means they are strictly limited to macro- and micromelanophores. On the other hand, the effectiveness of these cell interactions isnot limited to one genotype or one species of Xiphophorine fish. The inhibiting and the destruction-inducing influence of macromelanophores upon micromelanophores is shown for three different species of Xiphophorine fish. The role of cell interaction in chromatophore development is discussed.

Nonrandom chromosomal distribution of spontaneous breakpoints and satellite DNA clusters in two geographically distant populations of Chironomus riparius (Diptera: Chironomidae).

Two geographically distant populations of Chimnomus riparius (syn. C. thummi) from two environmentally polluted sites (Santena, Italy and Varna, Bulgaria) show numerous somatic and inherited chromosomal aberrations (inversions, deletions and deficiencies). Fifty-five percent of the observed breakpoints occurred in at least two larvae from both populations. Breakpoints occurring twice or more were considered as 'common' structural chromosomal breakpoints. We tested whether such common breakpoints in larvae of the two polluted populations had a random chromosomal distribution or occurred preferentially in specific heterochromatic regions. Distribution of common breakpoints was not random, and proximal regions of first and third chromosome had significantly more common breakpoints than distal ones. By FISH we identified and mapped 56 chromosomal sections containing clusters of two tandem-repetitive satellite DNA families called Hinf and Alu elements. Like the common breakpoints, these repetitive DNA clusters appeared to be significantly more abundant in regions of constitutive heterochromatin such as the pericentromeric regions, while in distal sections of chromosomal arms they were rare or absent. Twenty-four out of 45 common breakpoints (i.e., 53.3%) occurred in cytogenetic sections where Alu and Hinf satellite DNA probes hybridized. The frequency of co-localization between common breakpoints and repetitive DNA hybridization signals was significantly higher than expected by chance. We hypothesize that spontaneous or induced breaks occur more frequently in sections containing blocks of repetitive DNA.