Simple generation of site-directed point mutations in the Escherichia coli chromosome using Red®/ET® Recombination

Background: Introducing point mutations into bacterial chromosomes is important for further progress in studies relying on functional genomics, systems- and synthetic biology, and for metabolic engineering. For many investigations, chromosomal systems are required rather than artificial plasmid based systems. Results: Here we describe the introduction of a single point mutation into the Escherichia coli chromosome by site-directed mutagenesis without leaving any selection marker. We used Red (R)/ET (R) Recombination in combination with rpsL counter-selection to introduce a single point mutation into the E. coli MG1655 genome, one of the widely used bacterial model strains in systems biology. The method we present is rapid and highly efficient. Since single-stranded synthetic oligonucleotides can be used for recombination, any chromosomal modification can be designed. Conclusion: Chromosomal modifications performed by rpsL counter-selection may also be used for other bacteria that contain an rpsL homologue, since Red (R)/ET (R) Recombination has been applied to several enteric bacteria before

Effective Field Theory: A Modern Approach to Anomalous Couplings

We advocate an effective field theory approach to anomalous couplings. The effective field theory approach is the natural way to extend the standard model such that the gauge symmetries are respected. It is general enough to capture any physics beyond the standard model, yet also provides guidance as to the most likely place to see the effects of new physics. The effective field theory approach also clarifies that one need not be concerned with the violation of unitarity in scattering processes at high energy. We apply these ideas to pair production of electroweak vector bosons.Comment: 16 pages, 1 figur

iGentifier: indexing and large-scale profiling of unknown transcriptomes

Development and refinement of methods to analyse differential gene expression has been essential in the progress of molecular biology. A novel approach called iGentifier is presented for profiling known and unknown transcriptomes, thus bypassing a major limitation in microarray analysis. The iGentifier technology combines elements of fragment display (e.g. Differential Display or RMDD) and tag sequencing (e.g. SAGE, MPSS) and allows for analysis of samples in high throughput using current capillary electrophoresis equipment. Application to epidermal tissue of wild-type and mlo5 barley (Hordeum vulgare) plants, infected with powdery mildew [Blumeria graminis (DC.) E.O. Speer f.sp.hordei], led to the identification of several 100 genes induced or repressed upon infection with many well known for their response to fungal pathogens or other stressors. Ten of these genes are suggested to be classified as marker genes for durable resistance mediated by the mlo5 resistance gene

Marine organic matter in the remote environment of the Cape Verde islands-an introduction and overview to the MarParCloud campaign

The project MarParCloud (Marine biological production, organic aerosol Particles and marine Clouds: a process chain) aims to improve our understanding of the genesis, modification and impact of marine organic matter (OM) from its biological production, to its export to marine aerosol particles and, finally, to its ability to act as ice-nucleating particles (INPs) and cloud condensation nuclei (CCN). A field campaign at the Cape Verde Atmospheric Observatory (CVAO) in the tropics in September-October 2017 formed the core of this project that was jointly performed with the project MARSU (MARine atmospheric Science Unravelled). A suite of chemical, physical, biological and meteorological techniques was applied, and comprehensive measurements of bulk water, the sea surface microlayer (SML), cloud water and ambient aerosol particles collected at a ground-based and a mountain station took place. Key variables comprised the chemical characterization of the atmospherically relevant OM components in the ocean and the atmosphere as well as measurements of INPs and CCN. Moreover, bacterial cell counts, mercury species and trace gases were analyzed. To interpret the results, the measurements were accompanied by various auxiliary parameters such as air mass back-trajectory analysis, vertical atmospheric profile analysis, cloud observations and pigment measurements in seawater. Additional modeling studies supported the experimental analysis. During the campaign, the CVAO exhibited marine air masses with low and partly moderate dust influences. The marine boundary layer was well mixed as indicated by an almost uniform particle number size distribution within the boundary layer. Lipid biomarkers were present in the aerosol particles in typical concentrations of marine background conditions. Accumulation-and coarse-mode particles served as CCN and were efficiently transferred to the cloud water. The ascent of ocean-derived compounds, such as sea salt and sugar-like compounds, to the cloud level, as derived from chemical analysis and atmospheric transfer modeling results, denotes an influence of marine emissions on cloud formation. Organic nitrogen compounds (free amino acids) were enriched by several orders of magnitude in submicron aerosol particles and in cloud water compared to seawater. However, INP measurements also indicated a significant contribution of other non-marine sources to the local INP concentration, as (biologically active) INPs were mainly present in supermicron aerosol particles that are not suggested to undergo strong enrichment during ocean-atmosphere transfer. In addition, the number of CCN at the supersaturation of 0.30 % was about 2.5 times higher during dust periods compared to marine periods. Lipids, sugar-like compounds, UV-absorbing (UV: ultraviolet) humic-like substances and low-molecularweight neutral components were important organic compounds in the seawater, and highly surface-active lipids were enriched within the SML. The selective enrichment of specific organic compounds in the SML needs to be studied in further detail and implemented in an OM source function for emission modeling to better understand transfer patterns, the mechanisms of marine OM transformation in the atmosphere and the role of additional sources. In summary, when looking at particulate mass, we see oceanic compounds transferred to the atmospheric aerosol and to the cloud level, while from a perspective of particle number concentrations, sea spray aerosol (i.e., primary marine aerosol) contributions to both CCN and INPs are rather limited. © Author(s) 2020

Marine organic matter in the remote environment of the Cape Verde islands – an introduction and overview to the MarParCloud campaign

The project MarParCloud (Marine biological production, organic aerosol Particles and marine Clouds: a process chain) aims to improve our understanding of the genesis, modification and impact of marine organic matter (OM) from its biological production, to its export to marine aerosol particles and, finally, to its ability to act as ice-nucleating particles (INPs) and cloud condensation nuclei (CCN). A field campaign at the Cape Verde Atmospheric Observatory (CVAO) in the tropics in September–October 2017 formed the core of this project that was jointly performed with the project MARSU (MARine atmospheric Science Unravelled). A suite of chemical, physical, biological and meteorological techniques was applied, and comprehensive measurements of bulk water, the sea surface microlayer (SML), cloud water and ambient aerosol particles collected at a ground-based and a mountain station took place. Key variables comprised the chemical characterization of the atmospherically relevant OM components in the ocean and the atmosphere as well as measurements of INPs and CCN. Moreover, bacterial cell counts, mercury species and trace gases were analyzed. To interpret the results, the measurements were accompanied by various auxiliary parameters such as air mass back-trajectory analysis, vertical atmospheric profile analysis, cloud observations and pigment measurements in seawater. Additional modeling studies supported the experimental analysis. During the campaign, the CVAO exhibited marine air masses with low and partly moderate dust influences. The marine boundary layer was well mixed as indicated by an almost uniform particle number size distribution within the boundary layer. Lipid biomarkers were present in the aerosol particles in typical concentrations of marine background conditions. Accumulation- and coarse-mode particles served as CCN and were efficiently transferred to the cloud water. The ascent of ocean-derived compounds, such as sea salt and sugar-like compounds, to the cloud level, as derived from chemical analysis and atmospheric transfer modeling results, denotes an influence of marine emissions on cloud formation. Organic nitrogen compounds (free amino acids) were enriched by several orders of magnitude in submicron aerosol particles and in cloud water compared to seawater. However, INP measurements also indicated a significant contribution of other non-marine sources to the local INP concentration, as (biologically active) INPs were mainly present in supermicron aerosol particles that are not suggested to undergo strong enrichment during ocean–atmosphere transfer. In addition, the number of CCN at the supersaturation of 0.30 % was about 2.5 times higher during dust periods compared to marine periods. Lipids, sugar-like compounds, UV-absorbing (UV: ultraviolet) humic-like substances and low-molecular-weight neutral components were important organic compounds in the seawater, and highly surface-active lipids were enriched within the SML. The selective enrichment of specific organic compounds in the SML needs to be studied in further detail and implemented in an OM source function for emission modeling to better understand transfer patterns, the mechanisms of marine OM transformation in the atmosphere and the role of additional sources. In summary, when looking at particulate mass, we see oceanic compounds transferred to the atmospheric aerosol and to the cloud level, while from a perspective of particle number concentrations, sea spray aerosol (i.e., primary marine aerosol) contributions to both CCN and INPs are rather limited

Physics searches at the LHC

With the LHC up and running, the focus of experimental and theoretical high energy physics will soon turn to an interpretation of LHC data in terms of the physics of electroweak symmetry breaking and the TeV scale. We present here a broad review of models for new TeV-scale physics and their LHC signatures. In addition, we discuss possible new physics signatures and describe how they can be linked to specific models of physics beyond the Standard Model. Finally, we illustrate how the LHC era could culminate in a detailed understanding of the underlying principles of TeV-scale physics.Comment: 184 pages, 55 figures, 14 tables, hundreds of references; scientific feedback is welcome and encouraged. v2: text, references and Overview Table added; feedback still welcom

Simple generation of site-directed point mutations in the <it>Escherichia coli </it>chromosome using Red^®/ET^®Recombination

Abstract Background Introducing point mutations into bacterial chromosomes is important for further progress in studies relying on functional genomics, systems- and synthetic biology, and for metabolic engineering. For many investigations, chromosomal systems are required rather than artificial plasmid based systems. Results Here we describe the introduction of a single point mutation into the Escherichia coli chromosome by site-directed mutagenesis without leaving any selection marker. We used Red®/ET® Recombination in combination with rpsL counter-selection to introduce a single point mutation into the E. coli MG1655 genome, one of the widely used bacterial model strains in systems biology. The method we present is rapid and highly efficient. Since single-stranded synthetic oligonucleotides can be used for recombination, any chromosomal modification can be designed. Conclusion Chromosomal modifications performed by rpsL counter-selection may also be used for other bacteria that contain an rpsL homologue, since Red®/ET® Recombination has been applied to several enteric bacteria before.</p