Stellar activity as noise in exoplanet detection I. Methods and application to solar-like stars and activity cycles

The detection of exoplanets using any method is prone to confusion due to the intrinsic variability of the host star. We investigate the effect of cool starspots on the detectability of the exoplanets around solar-like stars using the radial velocity method. For investigating this activity-caused "jitter" we calculate synthetic spectra using radiative transfer, known stellar atomic and molecular lines, different surface spot configurations, and an added planetary signal. Here, the methods are described in detail, tested and compared to previously published studies. The methods are also applied to investigate the activity jitter in old and young solar-like stars, and over a solar-like activity cycles. We find that the mean full jitter amplitude obtained from the spot surfaces mimicking the solar activity varies during the cycle approximately between 1 m/s and 9 m/s. With a realistic observing frequency a Neptune mass planet on a one year orbit can be reliably recovered. On the other hand, the recovery of an Earth mass planet on a similar orbit is not feasible with high significance. The methods developed in this study have a great potential for doing statistical studies of planet detectability, and also for investigating the effect of stellar activity on recovered planetary parameters.Comment: Accepted to MNRA

A distinct role for recombination repair factors in an early cellular response to transcription-replication conflicts

Transcription–replication (T–R) conflicts are profound threats to genome integrity. However, whilst much is known about the existence of T–R conflicts, our understanding of the genetic and temporal nature of how cells respond to them is poorly established. Here, we address this by characterizing the early cellular response to transient T–R conflicts (TRe). This response specifically requires the DNA recombination repair proteins BLM and BRCA2 as well as a non-canonical monoubiquitylation-independent function of FANCD2. A hallmark of the TRe response is the rapid co-localization of these three DNA repair factors at sites of T–R collisions. We find that the TRe response relies on basal activity of the ATR kinase, yet it does not lead to hyperactivation of this key checkpoint protein. Furthermore, specific abrogation of the TRe response leads to DNA damage in mitosis, and promotes chromosome instability and cell death. Collectively our findings identify a new role for these well-established tumor suppressor proteins at an early stage of the cellular response to conflicts between DNA transcription and replication

Soil microbial community composition as affected by restoration practices in California grassland

Agricultural practices have strong impacts on soil microbes including both the indices related to biomass and activity as well as those related to community composition. In a grassland restoration project in California, where native perennial bunchgrasses were introduced into non-native annual grassland after a period of intensive tillage, weeding, and herbicide use to reduce the annual seed bank, microbial community composition was investigated. Three treatments were compared: annual grassland, bare soil fallow, and restored perennial grassland. Soil profiles down to 80cm in depth were investigated in four separate layers (0–15, 15–30, 30–60, and 60–80cm) using both phospholipid ester-linked fatty acid (PLFAs) and ergosterol as biomarkers in addition to microbial biomass C by fumigation extraction. PLFA fingerprinting showed much stronger differences between the tilled bare fallow treatment vs. grasslands, compared to fewer differences between restored perennial grassland and annual grassland. The presence or absence of plants over several years clearly distinguished microbial communities. Microbial communities in lower soil layers were little affected by management practices. Regardless of treatment, soil depth caused a strong gradient of changing habitat conditions, which was reflected in Canonical Correspondence Analysis of PLFAs. Fungal organisms were associated with the presence of plants and/or litter since the total amount and the relative proportion of fungal markers were reduced in the tilled bare fallow and in lower layers of the grassland treatments. Total PLFA and soil microbial biomass were highly correlated, and fungal PLFA biomarkers showed strong correlations to ergosterol content. In conclusion, microbial communities are resilient to the grassland restoration process, but do not reflect the change in plant species composition that occurred after planting native bunchgrasses

Time-series Spectroscopy of Pulsating sdB stars III: Line Indices of PG1605+072

We present the detection and analysis of line index variations in the pulsating sdB star PG 1605+072. We have found a strong dependence of line index amplitude on Balmer line order, with high-order Balmer line amplitudes up to 10 times larger than H-beta. Using a simple model, we have found that the line index may not only be dependent on temperature, as is usually assumed for oscillating stars, but also on surface gravity. This information will provide another set of observables that can be used for mode identification of sdBs.Comment: 8 pages, 9 figures, to appear in MNRAS. A high resolution version of Figure 3 can be found at http://www.sternwarte.uni-erlangen.de/~ai25/MC852-fig3.ep

A method for visualizing surface-exposed and internal PfEMP1 adhesion antigens in Plasmodium falciparum infected erythrocytes

<p>Abstract</p> <p>Background</p> <p>The insertion of parasite antigens into the host erythrocyte membrane and the structure and distribution of <it>Plasmodium falciparum </it>adhesion receptors on that membrane are poorly understood. Laser scanning confocal microscopy (LSCM) and a novel labelling and fixation method have been used to obtain high resolution immuno-fluorescent images of erythrocyte surface PfEMP1 and internal antigens which allow analysis of the accumulation of PfEMP1 on the erythrocyte membrane during asexual development.</p> <p>Methods</p> <p>A novel staining technique has been developed which permits distinction between erythrocyte surface PfEMP1 and intracellular PfEMP1, in parasites whose nuclear material is exceptionally well resolved. Primary antibody detection by fluorescence is carried out on the live parasitized erythrocyte. The surface labelled cells are then fixed using paraformaldehyde and permeabilized with a non-ionic detergent to permit access of antibodies to internal parasite antigens. Differentiation between surface and internal antigens is achieved using antibodies labelled with different fluorochromes and confocal microscopy</p> <p>Results</p> <p>Surface exposed PfEMP1 is first detectable by antibodies at the trophozoite stage of intracellular parasite development although the improved detection method indicates that there are differences between different laboratory isolates in the kinetics of accumulation of surface-exposed PfEMP1.</p> <p>Conclusion</p> <p>A sensitive method for labelling surface and internal PfEMP1 with up to three different fluorochromes has been developed for laser scanning confocal optical microscopy and the analysis of the developmental expression of malaria adhesion antigens.</p

Optimierte Bestimmung der unterirdischen Pflanzenbiomasse in Theorie und Praxis

Will man den C oder N Eintrag von Pflanzen ermitteln, muss die unterirdische Pflanzenbiomasse möglichst exakt bestimmt werden. Diese besteht aus der Rhizodeposition und dem Wurzelsystem einer Pflanze. Als Rhizodeposition wird die Abgabe von organischen und anorganischen Verbindungen bezeichnet. Sie setzt sich unter anderem aus Wurzelfragmenten, Wurzelrandzellen, Wurzelexudaten und Lysaten zusammen. Auf Grund einer fehlenden Wurzelraumbegrenzung, ist die Erfassung des vollständigen Wurzelsystems einer Pflanze im Freiland problematisch. Zur Quantifizierung von Wurzelsystemen sind jedoch Freilandversuche stets Gefäßversuchen vorzuziehen, da nur so ein ungestörtes Wurzelwachstum erreicht werden kann. Als Konsequenz lassen sich unterschiedliche Wurzel-Spross-Verhältnisse in Gefäß- und Freilandversuchen feststellen. Verlagerungsprozesse innerhalb der Pflanze können zusätzlich die Berechnung der Rhizodeposition beeinflussen und so zur Über- oder Unterschätzung der unterirdischen Pflanzenbiomasse führen. Ziel war daher ein Beprobungsschema zu entwickeln, welches es ermöglicht die Wurzelbiomasse im Freiland zu erfassen und unterschiedliche Berechnungsmethoden der Rhizodeposition zu vergleichen. Hierfür wurden sowohl im Gefäß als auch im Freiland Erbsen mittels Dochtmethode mit multiplen 13C und 15N-Pulsen markiert, wodurch eine annähernd kontinuierliche Markierung simuliert wurde. Die Wurzelbiomasse der Erbse wurde im Freiland bestimmt, indem Unterproben mit einem definierten Volumen in 3 festgelegten Positionen im Bestand genommen wurden (direkt auf einer Pflanze; zwischen 2 Pflanzen in der Reihe; in der Mitte von 4 Pflanzen zwischen 2 Reihen). Durch die unterschiedliche Gewichtung der Positionen, die sich aus dem Beprobungsdurchmesser und dem Pflanze-/Reihenabstand ergaben, konnte die vollständige Wurzelbiomasse bestimmt werden. Die Rhizodeposition wurde mit einer Massenbilanz (1) und mit der Janzen und Bruinsma Methode (2) ermittelt. Zum Zeitpunkt der Blüte waren die Wurzelbiomasse und das Wurzel-Spross-Verhältnis im Feld um ein vielfaches Größer verglichen mit dem Gefäß. Bei der Berechnung nach Janzen und Bruinsma können Verlagerungsprozesse während der Blüte zur Überschätzung der Rhizodeposition führen. Erfolgt eine kontinuierliche Markierung über den gesamten Vegetationsverlauf, so kann die Rhizodeposition am Kulturende sowohl nach Janzen und Bruinsma als auch mit der Massenbilanz berechnet werden

Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes

<p>Abstract</p> <p>Background</p> <p>The PFD1235w <it>Plasmodium falciparum </it>erythrocyte membrane protein 1 (PfEMP1) antigen is associated with severe malaria in children and can be expressed on the surface of infected erythrocytes (IE) adhering to ICAM1. However, the exact three-dimensional structure of this PfEMP1 and its surface-exposed epitopes are unknown. An insect cell and <it>Escherichia coli </it>based system was used to express single and double domains encoded by the <it>pfd1235w var </it>gene. The resulting recombinant proteins have been evaluated for yield and purity and their ability to induce rat antibodies, which react with the native PFD1235w PfEMP1 antigen expressed on 3D7_PFD1235w-IE. Their recognition by human anti-malaria antibodies from previously infected Tanzanian donors was also analysed.</p> <p>Methods</p> <p>The recombinant proteins were run on SDS-PAGE and Western blots for quantification and size estimation. Insect cell and <it>E. coli</it>-produced recombinant proteins were coupled to a bead-based Luminex assay to measure the plasma antibody reactivity of 180 samples collected from Tanzanian individuals. The recombinant proteins used for immunization of rats and antisera were also tested by flow cytometry for their ability to surface label 3D7_PFD1235w-IE.</p> <p>Results</p> <p>All seven pAcGP67A constructs were successfully expressed as recombinant protein in baculovirus-infected insect cells and subsequently produced to a purity of 60-97% and a yield of 2-15 mg/L. By comparison, only three of seven pET101/D-TOPO constructs expressed in the <it>E. coli </it>system could be produced at all with purity and yield ranging from 3-95% and 6-11 mg/L. All seven insect cell, but only two of the <it>E. coli </it>produced proteins induced antibodies reactive with native PFD1235w expressed on 3D7_PFD1235w-IE. The recombinant proteins were recognized in an age- and transmission intensity-dependent manner by antibodies from 180 Tanzanian individuals in a bead-based Luminex assay.</p> <p>Conclusions</p> <p>The baculovirus based insect cell system was distinctly superior to the <it>E. coli </it>expression system in producing a larger number of different recombinant PFD1235w protein domains and these were significantly easier to purify at a useful yield. However, proteins produced in both systems were able to induce antibodies in rats, which can recognize the native PFD1235w on the surface of IE.</p