Complexity of diatom response to Lateglacial and Holocene climate and environmental change in ancient, deep and oligotrophic Lake Ohrid (Macedonia and Albania)

© Author(s) 2016. Lake Ohrid (Macedonia and Albania) is a rare example of a deep, ancient Mediterranean lake and is a key site for palaeoclimate research in the northeastern Mediterranean region. This study conducts the analysis of diatoms as a proxy for Lateglacial and Holocene climate and environmental change in Lake Ohrid at a higher resolution than in previous studies. While Lake Ohrid has the potential to be sensitive to water temperature change, the data demonstrate a highly complex diatom response, probably comprising a direct response to temperature-induced lake productivity in some phases and an indirect response to temperaturerelated lake stratification or mixing and epilimnetic nutrient availability in others. The data also demonstrate the possible influence of physical limnological (e.g. the influence of wind stress on stratification or mixing) and chemical processes (e.g. the influence of catchment dynamics on nutrient input) in mediating the complex response of diatoms. During the Lateglacial (ca. 12 300-11 800 cal yr BP), the low-diversity dominance of hypolimnetic Cyclotella fottii indicates low lake productivity, linked to low water temperature. Although the subsequent slight increase in small, epilimnetic C. minuscula during the earliest Holocene (ca. 11 800-10 600 cal yr BP) suggests climate warming and enhanced stratification, diatom concentration remains as low as during the Lateglacial, suggesting that water temperature increase was muted across this major transition. The early Holocene (ca. 10 600-8200 cal yr BP) is characterised by a sustained increase in epilimnetic taxa, with mesotrophic C. ocellata indicating high water-temperature-induced productivity between ca. 10 600-10 200 cal yr BP and between ca. 9500-8200 cal yr BP and with C. minuscula in response to low nutrient availability in the epilimnion between ca. 10 200-9500 cal yr BP. During the middle Holocene (ca. 8200-2600 cal yr BP), when sedimentological and geochemical proxies provide evidence for maximum Holocene water temperature, anomalously low C. ocellata abundance is probably a response to epilimnetic nutrient limitation, almost mimicking the Lateglacial flora apart from the occurrence of mesotrophic Stephanodiscus transylvanicus in the hypolimnion. During the late Holocene (ca. 2600 cal yr BP-present), high abundance and fluctuating composition of epilimnetic taxa are probably a response more to enhanced anthropogenic nutrient input, particularly nitrogen enrichment, than to climate. Overall, the data indicate that previous assumptions concerning the linearity of diatom response in this deep, ancient lake are invalid, and multi-proxy analysis is essential to improve understanding of palaeolimnological dynamics in future research on the long, Quaternary sequence

The Development and Study of High-Position Resolution (50 micron) RPCs for Imaging X-rays and UV photons

Nowadays, commonly used Resistive Plate Chambers (RPCs) have counting rate capabilities of ~10E4Hz/cm2 and position resolutions of ~1cm. We have developed small prototypes of RPCs (5x5 and 10x10cm2) having rate capabilities of up to 10E7Hz/cm2 and position resolutions of 50 micron("on line" without application of any treatment method like "center of gravity"). The breakthrough in achieving extraordinary rate and position resolutions was only possible after solving several serious problems: RPC cleaning and assembling technology, aging, spurious pulses and afterpulses, discharges in the amplification gap and along the spacers. High-rate, high-position resolution RPCs can find a wide range of applications in many different fields, for example in medical imaging. RPCs with the cathodes coated by CsI photosensitive layer can detect ultraviolet photons with a position resolution that is better than ~30 micron. Such detectors can also be used in many applications, for example in the focal plane of high resolution vacuum spectrographs or as image scanners.Comment: 6 pages, 5 figures, other comment

Clustering of Intermediate Luminosity X-ray selected AGN at z~3

We present the first clustering results of X-ray selected AGN at z~3. Using Chandra X-ray imaging and UVR optical colors from MUSYC photometry in the ECDF-S field, we selected a sample of 58 z~3 AGN candidates. From the optical data we also selected 1385 LBG at 2.8<z< 3.8 with R<25.5. We performed auto-correlation and cross-correlation analyses, and here we present results for the clustering amplitudes and dark matter halo masses of each sample. For the LBG we find a correlation length of r_0,LBG = 6.7 +/- 0.5 Mpc, implying a bias value of 3.5 +/- 0.3 and dark matter (DM) halo masses of log(Mmin/Msun) = 11.8 +/- 0.1. The AGN-LBG cross-correlation yields r_0,AGN-LBG = 8.7 +/- 1.9 Mpc, implying for AGN at 2.8<z<3.8 a bias value of 5.5 +/- 2.0 and DM halo masses of log(Mmin/Msun) = 12.6 +0.5/-0.8. Evolution of dark matter halos in the Lambda CDM cosmology implies that today these z~3 AGN are found in high mass galaxies with a typical luminosity of 7+4/-2 L*.Comment: Accepted for publication in ApJ Letters. 4 pages, 4 figures (1 in color

LocateP: Genome-scale subcellular-location predictor for bacterial proteins

Contains fulltext : 69477.pdf ( ) (Open Access)BACKGROUND: In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a few SCLs, whereas others such as CELLO and Psortb.v.2.0 aim at a broader classification. Although these tools and pipelines can achieve a high precision in the accurate prediction of signal peptides and transmembrane helices, they have a much lower accuracy when other sequence characteristics are concerned. For instance, it proved notoriously difficult to identify the fate of proteins carrying a putative type I signal peptidase (SPIase) cleavage site, as many of those proteins are retained in the cell membrane as N-terminally anchored membrane proteins. Moreover, most of the SCL classifiers are based on the classification of the Swiss-Prot database and consequently inherited the inconsistency of that SCL classification. As accurate and detailed SCL prediction on a genome scale is highly desired by experimental researchers, we decided to construct a new SCL prediction pipeline: LocateP. RESULTS: LocateP combines many of the existing high-precision SCL identifiers with our own newly developed identifiers for specific SCLs. The LocateP pipeline was designed such that it mimics protein targeting and secretion processes. It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. Moreover, it distinguishes pathways for Sec- or Tat-dependent secretion and alternative secretion of bacteriocin-like proteins. The pipeline was tested on data sets extracted from literature, including experimental proteomics studies. The tests showed that LocateP performs as well as, or even slightly better than other SCL predictors for some locations and outperforms current tools especially where the N-terminally anchored and the SPIase-cleaved secreted proteins are concerned. Overall, the accuracy of LocateP was always higher than 90%. LocateP was then used to predict the SCLs of all proteins encoded by completed Gram-positive bacterial genomes. The results are stored in the database LocateP-DB http://www.cmbi.ru.nl/locatep-db1. CONCLUSION: LocateP is by far the most accurate and detailed protein SCL predictor for Gram-positive bacteria currently available

Pollen-based temperature and precipitation changes in the Ohrid Basin (western Balkans) between 160 and 70 ka

Our study aims to reconstruct climate changes that occurred at Lake Ohrid (south-western Balkan Peninsula), the oldest extant lake in Europe, between 160 and 70&thinsp;ka (covering part of marine isotope stage 6, MIS 6; all of MIS 5; and the beginning of MIS 4). A multi-method approach, including the “Modern Analog Technique” and the “Weighted Averaging Partial Least-Squares Regression”, is applied to the high-resolution pollen sequence of the DEEP site, collected from the central part of Lake Ohrid, to provide quantitative estimates of climate and bioclimate parameters. This allows us to document climatic change during the key periods of MIS 6 and MIS 5 in southern Europe, a region where accurate climate reconstructions are still lacking for this time interval. Our results for the penultimate glacial show cold and dry conditions, while the onset of the “last interglacial” is characterized by wet and warm conditions, with temperatures higher than today (by ca. 2&thinsp;∘C). The Eemian also shows the well-known climatic tri-partition in the Balkans, with an initial pre-temperate phase of abrupt warming (128–121&thinsp;ka), a central temperate phase with decreasing temperatures associated with wet conditions (121–118&thinsp;ka), followed by a post-temperate phase of progressive change towards cold and dry conditions (118–112&thinsp;ka). After the Eemian, an alternation of four warm/wet periods with cold/dry ones, likely related to the succession of Greenland stadials and cold events known from the North Atlantic, occurred. The observed pattern is also consistent with hydrological and isotopic data from the central Mediterranean. The Lake Ohrid climate reconstruction shows greater similarity with climate patterns inferred from northern European pollen records than with southern European ones, which is probably due to its intermediate position and the mountainous setting. However, this hypothesis needs further testing as very few climate reconstructions are available for southern Europe for this key time period.</p

Study of capillary-based gaseous detectors

We have studied gain vs. voltage characteristics and position resolutions of multistep capillary plates (two or three capillary plates operating in a cascade), as well as capillary plates operating in a mode when the main amplification occurs between plates or between the capillary plate and the readout plate (parallel plate amplification mode). Results of these studies demonstrated that in the parallel-plate amplification mode one can reach both high gains (>100000) and good position resolutions (~100 micro meter) even with a single step arrangement. It offers a compact amplification structure, which can be used in many applications. For example, in preliminary tests we succeeded to combine it with a photocathode and use it as a position sensitive gaseous photomultiplier. CsI coated capillary plates could also be used as a high position resolution and high rate X-ray converter.Comment: Presented at the NSS IEEE 2003 conference in Portland, submitted to TN

Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups

Cis-acting elements in Lactobacillus plantarum were predicted by comparative analysis of the upstream regions of conserved genes and predicted transcriptional units (TUs) in different bacterial genomes. TUs were predicted for two species sets, with different evolutionary distances to L.plantarum. TUs were designated ‘cluster of orthologous transcriptional units’ (COT) when >50% of the genes were orthologous in different species. Conserved DNA sequences were detected in the upstream regions of different COTs. Subsequently, conserved motifs were used to scan upstream regions of all TUs. This method revealed 18 regulatory motifs only present in lactic acid bacteria (LAB). The 18 LAB-specific candidate regulatory motifs included 13 that were not described previously. These LAB-specific different motifs were found in front of genes encoding functions varying from cold shock proteins to RNA and DNA polymerases, and many unknown functions. The best-described LAB-specific motif found was the CopR-binding site, regulating expression of copper transport ATPases. Finally, all detected motifs were used to predict co-regulated TUs (regulons) for L.plantarum, and transcriptome profiling data were analyzed to provide regulon prediction validation. It is demonstrated that phylogenetic footprinting using different species sets can identify and distinguish between general regulatory motifs and LAB-specific regulatory motifs

Spectroscopic characterization of reaction centers of the (M)Y210W mutant of the photosynthetic bacterium Rhodobacter sphaeroides

The tyrosine-(M)210 of the reaction center of Rhodobacter sphaeroides 2.4.1 has been changed to a tryptophan using site-directed mutagenesis. The reaction center of this mutant has been characterized by low-temperature absorption and fluorescence spectroscopy, time-resolved sub-picosecond spectroscopy, and magnetic resonance spectroscopy. The charge separation process showed bi-exponential kinetics at room temperature, with a main time constant of 36 ps and an additional fast time constant of 5.1 ps. Temperature dependent fluorescence measurements predict that the lifetime of P* becomes 4–5 times slower at cryogenic temperatures. From EPR and absorbance-detected magnetic resonance (ADMR, LD-ADMR) we conclude that the dimeric structure of P is not significantly changed upon mutation. In contrast, the interaction of the accessory bacteriochlorophyll BA with its environment appears to be altered, possibly because of a change in its position