235 Works

Data from: Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa

Roderich Roemhild, Camilo Barbosa, Robert E. Beardmore, Gunther Jansen & Hinrich Schulenburg
Antibiotic resistance is a growing concern to public health. New treatment strategies may alleviate the situation by slowing down the evolution of resistance. Here, we evaluated sequential treatment protocols using two fully independent laboratory-controlled evolution experiments with the human pathogen Pseudomonas aeruginosa PA14 and two pairs of clinically relevant antibiotics (doripenem/ciprofloxacin and cefsulodin/gentamicin). Our results consistently show that the sequential application of two antibiotics decelerates resistance evolution relative to monotherapy. Sequential treatment enhanced population extinction...

Data from: Association mapping of morphological traits in wild and captive zebra finches: reliable within but not between populations

Ulrich Knief, Holger Schielzeth, Niclas Backstrom, Georg Hemmrich-Stanisak, Michael Wittig, Andre Franke, Simon C. Griffith, Hans Ellegren, Bart Kempenaers & Wolfgang Forstmeier
Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single...

Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva

Marian Hu, Marian Hu, Inga Petersen, William Chang, Christine Blurton & Meike Stumpp
The sea urchin embryo develops a calcitic endoskeleton through intracellular formation of amorphous calcium carbonate (ACC). Intracellular precipitation of ACC, requires HCO3-/CO32- concentrating as well as proton export mechanisms to promote calcification. These processes are of fundamental importance in biological mineralization, but remain largely unexplored. Here we demonstrate that the calcifying primary mesenchyme cells (PMCs) utilize Na+/H+- exchange (NHE) mechanisms to control cellular pH homeostasis during maintenance of the skeleton. During skeleton re-calcification, pHi of...

Uwagi o plenerowych rekonstrukcjach pradziejowych i średniowiecznych przepraw mostowych w Europie Środkowej. Mosty drewniane

Gerard Wilke
The article presents remarks on outdoor reconstructions of primeval and medieval bridge crossings in Central Europe on the example of the selected constructions with a wooden structure. The presented bridges were the subject of archaeological research on terrestrialised lake and river reservoirs or the subject of underwater prospection. Firstly the article presents the construction of primeval bridges, by showing the bridge of the defensive settlement of the Lusatian culture from the 8th century BC in...

ADCP current measurements (75 kHz) during Maria S. Merian cruise MSM96

Timm Schoening, Robert Kopte, Jochen Mohrmann & Iason-Zois Gazis
Upper-ocean velocities along the cruise track of Maria S. Merian cruise MSM96 were continuously collected by a vessel-mounted Teledyne RD Instruments 75 kHz Ocean Surveyor ADCP. The transducer was located at 6.5 m below the water line. The instrument was operated in narrowband mode with 8 m bins and a blanking distance of 4.0 m, while 100 bins were recorded using a pulse of 1.43 s. The ship's velocity was calculated from position fixes obtained...

ADCP current measurements (38 kHz) during Maria S. Merian cruise MSM88/1

Colin W Devey & Robert Kopte
Upper-ocean velocities along the cruise track of Maria S. Merian cruise MSM88/1 were continuously collected by a vessel-mounted Teledyne RD Instruments 38 kHz Ocean Surveyor ADCP. The transducer was located at 6.5 m below the water line. The instrument was operated in narrowband mode with 32 m bins and a blanking distance of 16.0 m, while 50 bins were recorded using a pulse of 2.90 s. The ship's velocity was calculated from position fixes obtained...

Riesen in der Literatur des Mittelalters

Lena van Beek
1000 Worte Forschung: Germanistisch-mediävistische Dissertation in der Älteren deutschen Literatur, Institut für Germanistik, Universität Hamburg, verteidigt im Februar 2020, publiziert im März 2021 im Archivum Medii Aevi Digitale (AMAD) unter DOI: 10.25716/amad-85226 in der Reihe Archivum Medii Aevi Digitale – Studies: Theses.

Data from: Multiple sequence alignment averaging improves phylogeny reconstruction

Haim Ashkenazy, Itamar Sela, Eli Levy Karin, Giddy Landan & Tal Pupko
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this...

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

Dilan Sarange Rajapaksha Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra Schmöckel, Mark Tester & Christian Jung
Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively....

Data from: Conservation genetics of the pond bat (Myotis dasycneme) with special focus on the populations in northwestern Germany and Jutland, Denmark

Liselotte Wesley Andersen, Ronja Dirksen, Elena A. Nikulina, Hans J. Baagøe, Gunars Petersons, Péter Estók, Oleg L. Orlov, Maria V. Orlova, Florian Gloza-Rausch, Matthias Göttsche, Esben Fjederholt, Frauke Krüger & Morten Elmeros
Conservation genetics is important in the management of endangered species, helping to understand their connectivity and long-term viability, thus identifying populations of importance for conservation. The pond bat (Myotis dasycneme) is a rare species classified as ‘Near threatened’ with a wide but patchy Palearctic distribution. A total of 277 samples representing populations in Denmark, Germany, Latvia, Hungary and Russia were used in the genetic analyses; 224 samples representing Denmark, Germany and Russia were analysed at...

Experimental data for Pseudomonas aeruginosa from experimental evolution under different bottleneck sizes and antibiotic selection pressures

Hinrich Schulenburg
We here combined evolution experiments with genomic and genetic analyses to assess whether bottleneck size and antibiotic-induced selection influences the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Two sets of evolution experiments were performed across 16 transfers, in which either the aminoglycoside gentamicin or the fluoroquinolone ciprofloxacin were used as antibiotic. The evolutionary response was studied using counts of bacterial cells at the end of each...

ADCP current measurements (75 kHz) during RV MARIA S. MERIAN cruise MSM101

Felix Gross, Robert Kopte & Ralph R Schneider
Upper-ocean velocities along the cruise track of Maria S. Merian cruise MSM101 were continuously collected by a vessel-mounted Teledyne RD Instruments 75 kHz Ocean Surveyor ADCP. The transducer was located at 6.5 m below the water line. The instrument was operated in narrowband mode with 8 m bins and a blanking distance of 8.0 m, while 100 bins were recorded using a pulse of 1.43 s. The ship's velocity was calculated from position fixes obtained...

GEOWiki@LMU – an online platform for university and school education in geosciences

Magdalena Luise Plitz , Katrin Mühlberg , Donja Aßbichler , Laurin Lidl , Malte Junge & Eileen Eckmeier
GEOWiki@LMU is a constantly growing open platform for the promotion of practical and research-oriented knowledge acquisition elaborated by and for students of earth sciences. The contents are developed by students in courses or on their own initiative in interdisciplinary teams. All topics are discussed in weekly editorial online-meetings and revised in close collaboration with lecturers. One of the main goals is to provide information on methods relevant to geosciences. Focus is on field, preparation and...

IODP/ICDP Kolloquium 2022, Abstract Volume

Markus Schwab, Jens Kallmeyer, Sebastian Krastel & André Bornemann

ADCP current measurements (75 kHz working area dataset) during RV MARIA S. MERIAN cruise MSM105

Volker Mohrholz, Robert Kopte & Toralf Heene
Upper-ocean velocities along the cruise track of RV MARIA S. MERIAN cruise MSM105 were continuously collected by a vessel-mounted Teledyne RD Instruments 75 kHz Ocean Surveyor ADCP. The transducer was located at 6.0 m below the water line. The instrument was operated in broadband mode with 8 m bins and a blanking distance of 8.0 m, while 100 bins were recorded using a pulse of 0.82 s. The ship's velocity was calculated from position fixes...

The pteropod species Heliconoides inflatus as an archive of late Pleistocene to Holocene environmental conditions on the Northwest Shelf of Australia

Maximilian Hallenberger, Lars Reuning, Hideko Takayanagi, Yasufumi Iryu, Nina Keul, Takeshige Ishiwa & Yusuke Yokoyama
Abstract There is growing interest in the use of pteropods as potential archives of past changes in ocean chemistry. However, pteropods have rarely been used in studies of millennial-scale sedimentary records, especially in shallow-marine environments. This study obtained core data for the last 16 kyr from the Northwest Shelf of Australia (NWS). Changes in the carbonate saturation state were assessed based on the carbon isotope ratios (δ13C) of shells and the Limacina dissolution index (LDX)...

Additional file 1 of The pteropod species Heliconoides inflatus as an archive of late Pleistocene to Holocene environmental conditions on the Northwest Shelf of Australia

Maximilian Hallenberger, Lars Reuning, Hideko Takayanagi, Yasufumi Iryu, Nina Keul, Takeshige Ishiwa & Yusuke Yokoyama
Additional file 1: Table S1. Limacina dissolution index and carbon and oxygen isotope data for pteropods (Heliconoides inflatus) from IODP Site U1461. Table S2. Limacina dissolution index and carbon and oxygen isotope data for pteropods (Heliconoides inflatus) and benthic foraminifera (Uvigerina spp.) from IODP Site U1463. Table S3. Calculated water temperatures and carbonate ion concentrations based on the δ13C and δ18O values of pteropods (Heliconoides inflatus) from IODP Site U1461. Water temperatures were calculated based...

Neutral processes related to regional bee commonness and dispersal distances are important predictors of plant-pollinator networks along gradients of climate and landscape conditions

Markus Arne Sydenham, Zander Venter, Stein Moe, Katrine Eldegard, Michael Kuhlmann, Trond Reitan, Claus Rasmussen, Robert Paxton, Yoko Dupont, Astrid Skrindo, Megan Nowell, Stein Hegland, Anders Nielsen, Jens Olesen & Graciela Rusch
Understanding how niche-based and neutral processes contribute to the spatial variation in plant-pollinator interactions is central to designing effective pollination conservation schemes. Such schemes are needed to reverse declines of wild bees and other pollinating insects and to promote pollination services to wild and cultivated plants. We used data on wild bee interactions with plants belonging to the four tribes Loteae, Trifolieae, Anthemideae, and either spring- or summer-flowering Cichorieae, sampled systematically along a 682km latitudinal...

Continuous thermosalinograph oceanography along RV MARIA S. MERIAN cruise track MSM102

Sebastian Krastel & Michael Schlundt
Underway temperature and salinity data was collected along the cruise track with two autonomous measurement systems. Usually, the systems are changed after 6 hours. While temperature is taken at the water inlet in about 6.5 m depth, salinity is estimated within the interior measurement container from conductivity and interior temperature. Salinity was calibrated independently for both measurement containers (MCs). No correction was done for temperature. For details to all processing steps see Data Processing Report.

Additional file 10 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 10: Fig. S6. Expression correlation between BCL11B & C14ORF64 (LINC01550). Expression correlation between BCL11B & C14ORF64 (LINC01550) in 426 human datasets with 42563 samples from R2: Genomics analysis and visualization platform (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi).

Holocene palaeoenvironmental conditions in the Baltic: Reconstructions based on palynological and biogeochemical data from IODP Expedition 347, Site M0063 (Landsort Deep)

Ulrich Kotthoff & Thorsten Bauersachs
Restricted basins, such as the Baltic Sea, are particularly affected by global warming, which leads to intensifying stratification, severe oxygen depletion and increasing water temperatures. This, in turn, results in significant and lasting ecosystem alterations. Sediment cores recovered during IODP Expedition 347 allow reconstructing such changes. We analysed Holocene sediments from the Landsort Deep (IODP Site M0063) using combined palynological and biogeochemical approaches to reconstruct palaeoclimate variations as well as ecosystem changes and to identify...

Comparison of combustion duration and end-gas autoignition in inwardly and outwardly propagating flames induced by different ignition configurations

Linlin Yang, Yiqing Wang & Zheng Chen
Recently, multiple spark ignition has received great attention since it helps to increase thermal efficiency and to reduce misfire in engines. Multiple spark ignition also affects the combustion duration and thereby it can be used for knock control. However, previous studies reported opposite trends in terms of how multiple spark ignition affects engine knock. This work aims to assess and interpret the influence of flame propagation direction induced by different ignition configurations on combustion duration...

Additional file 1 of A correlation map of genome-wide DNA methylation patterns between paired human brain and buccal samples

Yasmine Sommerer, Olena Ohlei, Valerija Dobricic, Derek H. Oakley, Tanja Wesse, Sanaz Sedghpour Sabet, Ilja Demuth, Andre Franke, Bradley T. Hyman, Christina M. Lill & Lars Bertram
Additional file 1. Supplementary Tables.

A correlation map of genome-wide DNA methylation patterns between paired human brain and buccal samples

Yasmine Sommerer, Olena Ohlei, Valerija Dobricic, Derek H. Oakley, Tanja Wesse, Sanaz Sedghpour Sabet, Ilja Demuth, Andre Franke, Bradley T. Hyman, Christina M. Lill & Lars Bertram
Abstract Epigenome-wide association studies (EWAS) assessing the link between DNA methylation (DNAm) and phenotypes related to structural brain measures, cognitive function, and neurodegenerative diseases are becoming increasingly more popular. Due to the inaccessibility of brain tissue in humans, several studies use peripheral tissues such as blood, buccal swabs, and saliva as surrogates. To aid the functional interpretation of EWAS findings in such settings, there is a need to assess the correlation of DNAm variability across...

Measurement of Diffuse Submarine Groundwater Discharge at intertidal puddles at the Königshafen - Sylt

Sebastian Janßen , Alexandra Nozik , Ulf Mallast & Nils Moosdorf
Coastal regions represent a transition between land and sea. From the hydro(geo)logical point of view freshwater and saltwater are coming together here. The groundwater discharge which discharges directly into the sea is called submarine groundwater discharge (SGD). At the regional scale, SGD is often measured indirectly based on tracers. At the local scale, SGD flux over time can be measured directly, e.g. using seepage meters. However, this method only represents the punctual source of discharge....

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