Avianbase: a community resource for bird genomics

Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.Access to complete genome sequences provides the first step towards the understanding of the biology of organisms. It is the template that underpins the phenotypic characteristics of individuals and ultimately separates species due to the accumulation and fixation of mutations over evolutionary timescales. In terms of the available genomic datasets for species, birds, as our more distant relatives, have been historically underrepresented. The high cost of sequencing and annotation in the past led to a bias towards accumulating data for species that are either established model organisms or economically significant (that is, chicken, turkey and duck, representing two sister orders within the Galloanseriformes clade from the large and diverse phylogeny of birds). The recent release of genome assemblies and initial predictions of protein-coding genes [1-4] for 44 bird species, including representatives from all major branches of the bird phylogeny, is, therefore, highly significant.One of the major challenges with the release of this number of newly sequenced genomes and the many more to come [5] is how to make these available to the various research communities in a way that supports basic research. Providing access to the sequences and initial annotations in the format of text files will limit the potential usage of the data as they require significant resources, including bioinformatics personnel and computer infrastructure in place to access and mine - for example, searching for genes belonging to certain protein families or searching for orthologous genes. These overheads pose a serious bottleneck that can hinder research and requires concerted action by the relevant research communities.Once genomes are submitted to public databases, genome-wide annotations are frequently generated and released either via the Ensembl project [6] or by the National Center for Biotechnology Information [7] and sequence and annotation are then made visually available online in integrated views via the Ensembl or the University of California Santa Cruz (UCSC) genome browsers [8]. These systems provide search facilities, sequence alignment tools like BLAT/BLAST and various analysis tools to facilitate subsetting and computational retrieval of the data, including UCSC’s Table Browser or Ensembl’s Perl and REST APIs and BioMart system.While these systems have become almost indispensable for research, not all sequenced genomes are annotated and displayed in genome browsers. Full genome annotation remains time consuming and resource intensive: a full evidence-based Ensembl genebuild takes approximately 4 months. Thus, the list of species represented is currently limited and depends on various factors, including the completeness of the assembled genome sequence and the overall demand in the scientific community for the resources, including whether the species is a model organism (for example, human or mouse), economically important (for example, farmed animals) or of specific phylogenetic interest. Many of the recently sequenced bird genomes do not obviously fall within these categories.     

Polymorphisms of the DNA repair gene MGMT and risk and progression of head and neck cancer

Methylating agents are involved in carcinogenesis, and the DNA repair protein O⁶-methylguanine-DNA methyltransferase (MGMT) removes methyl group from O⁶-methylguanine. Genetic variation in DNA repair genes has been shown to contribute to susceptibility to squamous cell carcinoma of the head and neck (SCCHN). We hypothesize that MGMT polymorphisms are associated with risk of SCCHN. In a hospital-based case–control study of 721 patients with SCCHN and 1234 cancer-free controls frequency-matched by age, sex and ethnicity, we genotyped four MGMT polymorphisms, two in exon 3, 16195C > T and 16286C > T and two in the promoter region, 45996G > T and 46346C > A. We found that none of these polymorphisms alone had a significant effect on risk of SCCHN. However, when these four polymorphisms were evaluated together by the number of putative risk genotypes (i.e. 16195CC, 16286CC, 45996GT + TT, and 46346CA + AA), a statistically significantly increased risk of SCCHN was associated with the combined genotypes with three to four risk genotypes, compared with those with zero to two risk genotypes (adjusted odds ratio (OR) = 1.27; 95% confidence interval (CI) = 1.05–1.53). This increased risk was also more pronounced among young subjects (OR = 1.81; 95% CI = 1.11–2.96), men (OR = 1.24; 95% CI = 1.00–1.55), ever smokers (OR = 1.25; 95% = 1.01–1.56), ever drinkers (OR = 1.29; 95% CI = 1.04–1.60), patients with oropharyngeal cancer (OR = 1.45; 95% CI = 1.12–1.87), and oropharyngeal cancer with regional lymph node metastasis (OR = 1.52; 95% CI = 1.16–1.89). In conclusion, our results suggest that any one of MGMT variants may not have a substantial effect on SCCHN risk, but a joint effect of several MGMT variants may contribute to risk and progression of SCCHN, particularly for oropharyngeal cancer, in non-Hispanic whites.     

Screening for Hydrolytic Enzymes Reveals Ayr1p as a Novel Triacylglycerol Lipase in Saccharomyces cerevisiae

Saccharomyces cerevisiae, as well as other eukaryotes, preserves fatty acids and sterols in a biologically inert form, as triacylglycerols and steryl esters. The major triacylglycerol lipases of the yeast S. cerevisiae identified so far are Tgl3p, Tgl4p, and Tgl5p (Athenstaedt, K., and Daum, G. (2003) YMR313c/TGL3 encodes a novel triacylglycerol lipase located in lipid particles of Saccharomyces cerevisiae. J. Biol. Chem. 278, 23317–23323; Athenstaedt, K., and Daum, G. (2005) Tgl4p and Tgl5p, two triacylglycerol lipases of the yeast Saccharomyces cerevisiae, are localized to lipid particles. J. Biol. Chem. 280, 37301–37309). We observed that upon cultivation on oleic acid, triacylglycerol mobilization did not come to a halt in a yeast strain deficient in all currently known triacylglycerol lipases, indicating the presence of additional not yet characterized lipases/esterases. Functional proteome analysis using lipase and esterase inhibitors revealed a subset of candidate genes for yet unknown hydrolytic enzymes on peroxisomes and lipid droplets. Based on the conserved GXSXG lipase motif, putative functions, and subcellular localizations, a selected number of candidates were characterized by enzyme assays in vitro, gene expression analysis, non-polar lipid analysis, and in vivo triacylglycerol mobilization assays. These investigations led to the identification of Ayr1p as a novel triacylglycerol lipase of yeast lipid droplets and confirmed the hydrolytic potential of the peroxisomal Lpx1p in vivo. Based on these results, we discuss a possible link between lipid storage, lipid mobilization, and peroxisomal utilization of fatty acids as a carbon source.     

Improved high-performance liquid chromatographic separation of peptidoglycan isolated from various Staphylococcus aureus strains for mass spectrometric characterization

Reversed-phase high-performance liquid chromatography (RP-HPLC) of muropeptides, obtained by muramidase digestion of peptidoglycan in combination with amino acid analysis and plasma desorption time-of-flight mass spectrometry is today by far the best tool to analyze the fine structure of the peptidoglycans. Here we report further improvements of the RP-HPLC separation of muropeptides for analyzing the peptidoglycans of various methicillin-resistant strains of Staphylococcus aureus, with emphasis on a more detailed characterization of the interpeptide bridge of the peptidoglycans of this species.     

Differential Activation of Acid Sphingomyelinase and Ceramide Release Determines Invasiveness of Neisseria meningitidis into Brain Endothelial Cells

The interaction with brain endothelial cells is central to the pathogenicity of Neisseria meningitidis infections. Here, we show that N. meningitidis causes transient activation of acid sphingomyelinase (ASM) followed by ceramide release in brain endothelial cells. In response to N. meningitidis infection, ASM and ceramide are displayed at the outer leaflet of the cell membrane and condense into large membrane platforms which also concentrate the ErbB2 receptor. The outer membrane protein Opc and phosphatidylcholine-specific phospholipase C that is activated upon binding of the pathogen to heparan sulfate proteoglycans, are required for N. meningitidis-mediated ASM activation. Pharmacologic or genetic ablation of ASM abrogated meningococcal internalization without affecting bacterial adherence. In accordance, the restricted invasiveness of a defined set of pathogenic isolates of the ST-11/ST-8 clonal complex into brain endothelial cells directly correlated with their restricted ability to induce ASM and ceramide release. In conclusion, ASM activation and ceramide release are essential for internalization of Opc-expressing meningococci into brain endothelial cells, and this segregates with invasiveness of N. meningitidis strains.     

Greenhouse gas fluxes respond to different N fertilizer types due to altered plant-soil-microbe interactions

The application of inorganic nitrogen (N) fertilizers strongly influences the contribution of agriculture to the greenhouse effect, especially by potentially increasing emissions of nitrous oxide (N₂O), carbon dioxide (CO₂) and methane (CH₄) from soils. The present microcosm-study investigates the effect of different forms of inorganic N fertilizers on greenhouse gas (GHG) emissions from two different agricultural soils. The relationship between greenhouse gas emissions and soil microbial communities, N transformation rates and plant (Hordeum vulgare L. cv. Morex) growth were investigated. Repeated N fertilization led to increased N₂O emissions. In a parallel survey of functional microbial population dynamics we observed a stimulation of bacterial and archaeal ammonia oxidisers accompanied with these N₂O emissions. The ratio of archaeal to bacterial ammonium monooxygenase subunit A (amoA) gene copies (data obtained from Inselsbacher et al., 2010) correlated positively with N₂O fluxes, which suggests a direct or indirect involvement of archaea in N₂O fluxes. Repeated N fertilization also stimulated methane oxidation, which may also be related to a stimulation of ammonia oxidizers. The fertilizer effects differed between soil types: In the more organic Niederschleinz soil N-turnover rates increased more strongly after fertilization, while in the sandy Purkersdorf soil plant growth and soil respiration were accelerated depending on fertilizer N type. Compared to addition of NH ₄ ⁺ and NO ₃ ^? , addition of NH₄NO₃ fertilizer resulted in the largest increase in global warming potential as a summary indicator of all GHG related effects. This effect resulted from the strongest increase of both N₂O and CO₂ emission while plant growth was not equally stimulated, compared to e.g. KNO₃ fertilization. In order to decrease N losses from agricultural ecosystems and in order to minimize soil derived global warming potential, this study points to the need for interdisciplinary investigations of the highly complex interactions within plant-soil-microbe-atmosphere systems. By understanding the microbial processes underlying fertilizer effects on GHG emissions the N use efficiency of crops could be refined.     

Physiologische Untersuchungen an einer ungewöhnlich säureresistenten Chlorella

Summary The influence of the hydrogen-ion concentration on the growth and metabolism of a highly acid-resistant green alga, Chlorella ellipsoidea (strain Marburg St), was studied. Chlorella pyrenoidosa (Emerson strain) served as a normal control organism. Growth of Chlorella ellipsoidea occurs in the entire range from Ph 2.0 to Ph 10, whereas for Chlorella pyrenoidosa the limits were found to be Ph 3.5 and Ph 10. Respiration is much less sensitive to hydrogen-ion concentration in the acid-resistant as compared to the normal strain. Thus an increase in acidity from Ph 4.0 to Ph 2.0 increases the respiratory oxygen uptake by 120% in Chlorella pyrenoidosa and by 25% in Chlorella ellipsoidea. In addition, only the less resistant Chlorella pyrenoidosa shows an accumulation of nitrite in the dark in acid culture media, indicating a disturbance of the normal course of nitrate reduction under these conditions. On the other hand, the rate of photosynthesis of both organisms was found to be almost independent of acidity between Ph 4.0 and Ph 2.0. At the acid and alkaline limits of growth in both algae, an inhibition of cell division leads to an increase of cell size and dry weight per cell, frequently connected with the occurrence of bizarre giant cells. — In addition, adaptation phenomena were found to play a role in determining the acid limit of growth. Cells of Chlorella ellipsoidea, after inoculation from normal medium (Ph about 6) into a solution of Ph 2.0, begin growth at a high rate only after a lag of about two weeks. Cells grown previously in an acid medium, however, immediately resume growth upon inoculation into a medium of Ph 2.0. This adaptation involves a considerable reduction of cell size.     

Breeding system of tristylous Eichhornia azurea (Pontederiaceae) in the southern Pantanal, Brazil

The breeding system of Eichhornia azurea (Pontederiaceae) has been described as being both self- and heteromorphic incompatible based on crossing experiments performed on plants grown in an experimental garden. We studied the breeding system of tristylous E. azurea population under natural conditions in the Pantanal wetlands, Brazil. Controlled pollinations were conducted using 35 individuals of each floral morph. Legitimate pollinations produced more fruits than self- and illegitimate pollinations, except for the mid-styled morph which was highly self- and heteromorphic compatible. The number of seeds per fruit was higher under legitimate pollinations than in the other treatments, but self- and illegitimate pollinations produced more fruits and seeds in the Pantanal than for individuals of E. azurea in other populations. The higher fruit and seed production resulting from legitimate pollinations corroborate previous studies, but self-compatibility of mid-styled plants was not previously reported. Overall results indicate a partially self- and heteromorphic compatible system for this species in the Pantanal.     

The gene fimU affects expression of Salmonella typhimurium type 1 fimbriae and is related to the Escherichia coli tRNA gene argU

The gene fimU, located on a recombinant plasmid carrying the Salmonella typhimurium type 1 fimbrial gene cluster is closely related to the Escherichia coli tRNA gene argU. The fimU gene complements an E. coli argU mutant that is a P2 lysogen, thereby allowing the phage P4 to grow in this strain but preventing the growth of phage lambda. In addition, fimU was shown to be involved in fimbrial expression since transformants of the E. coli argU mutant could produce fimbriae only in the presence of fimU but not in its absence, whereas in an E. coli argU ⁺ strain fimbriation did not require the fimU gene.     

Untersuchungen zur Inkompatibilitt imCulex pipiens-Komplex

Zusammenfassung Bei Kreuzungen zwischenCulex pipiens-Popalationen verschiedener geographischer Herkunft werden drei Kreuzungstypen festgestellt: normale Kreuzbarkeit, reduzierte Kreuzbarkeit und Inkompatibilitt (Nichtkreuzbarkeit). Die drei Kreuzungstypen sind mit Hilfe der Embryonierungsrate, der Schlüpfrate und der entstehenden Nachkommenschaft gegeneinander abgrenzbar. Bei Inkompatibilitt sind 99,9% der Embryonen letal, und etwa 0,1% der Tiere schlüpfen und sind fertile, diploide Weibchen.Die Aktivierung des Eies und der Entwicklungsansto\ erfolgt durch das Spermium. Das Spermium gelangt nicht zur Karyogamie mit dem Pronucleus. Es liegt induzierte, meiotische Parthenogenese vor.Die diploiden, parthenogenetischen Weibchen gehen aus einer Oocyte 2. Ordnung oder aus Teilungsprodukten einer Oocyte 2. Ordnung hervor. Die letalen Embryonen sind haploid. Das Spermium beteiligt sich nicht am Aufbau des Embryos. Nach Aktivierung des Eies wird das Spermium im Eiplasma resorbiert, whrend der haploide Pronucleus einen rein haploiden Embryo aufbaut.Bei einigen Kreuzungen entwickeln sich bis zu 75% der Embryonen bis zum Stadium der histologischen Differenzierung der Organe. Die Embryonen zeigen noch einige Stunden nach dem normalen Schlüpftermin Muskelkontraktionen, vermögen die Eihülle jedoch nicht zu sprengen.Die DNS-Verteilungen von Interphasekernen der letalen Embryonen liegen zwischen den Werten C und 2C für haploide Zellen. ltere Embryonen besitzen in geringem Ma\e höhere DNS-Werte als 2C. Whrend der histologischen Differenzierung der Organe liegen in diploiden Kontrollembryonen und in letalen Embryonen die Ploidiestufen C, 2C, 4C, 8C and 16C vor. Bei inkompatiblen Kreuzungen wird das in das Ei eindringende Spermium cytophotometrisch nachgewiesen. Die Wanderung des Spermiums im Ei wird untersucht.In Normalkreuzungen wird nur ein geringer Grad von Polyspermie festgestellt. Monound Dispermie sind am hufigsten. Es werden die Möglichkeiten diskutiert die zur Blockierung der Karyogamie in inkompatiblen Kreuzungen führen können.

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Investigations on the incompatibility in theCulex pipiens-complex

Summary In crosses between populations of the mosquitoCulex pipiens of different geographical origin three crossing types have been found (1) crosses with normal offspring (2) crosses with reduced offspring and (3) crosses that show almost total incompatibility. In the case of incompatible crosses 99.9% of the embryos are lethal and only about 0.1% of the embryos hatch and develop to fertile diploid females. Based on genetical and cytological data it is argued that induced meiotic parthenogenesis takes place. The sperm does not play any part in the production of the diploid females and the lethal embryos. After the activation of the egg the sperm moves to the center of the egg but it does not succeed in fusing with the pronucleus. As a result the pronucleus starts to develop into a haploid embryo in about 99.9% and only in a few cases the diploidy is restored by a change in the meiotic process in the egg. Up to 75% of the haploid embryos develop to the stage of histological differentiation. The frequency distribution of the DNA in interphase nuclei of these embryos shows a maximum at C and 2 C characteristic for haploid cells. The absence of ploidy classes higher than 2 C in the early embryos is in agreement with the assumption of pure haploidy. After histological differentiation ploidy classes C to 16 C can be found in tissues that show endomitotic growth. The development of the haploid embryos is described. It has been shown through cytophotometric methods that in incompatible crosses entrance of the sperm into the egg takes place. In normal crosses polyspermy is rather rare, monospermy and dispermy are most common. The blocking of the sperm in incompatible crosses is discussed.

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Teil einer Dissertation der Math.-Nat. Fakultt der Universitt Mainz. Herrn Prof. Dr. H. Laven danke ich für die Bereitstellung des Untersuchungsmaterials sowie für die Anregungen bei der Durchführung der Arbeit.