Transport and Noise Characteristics of Submicron High-Temperature Superconductor Grain-Boundary Junctions

We have investigated the transport and noise properties of submicron YBCO bicrystal grain-boundary junctions prepared using electron beam lithography. The junctions show an increased conductance for low voltages reminiscent of Josephson junctions having a barrier with high transmissivity. The voltage noise spectra are dominated by a few Lorentzian components. At low temperatures clear two-level random telegraph switching (RTS) signals are observable in the voltage vs time traces. We have investigated the temperature and voltage dependence of individual fluctuators both from statistical analysis of voltage vs time traces and from fits to noise spectra. A transition from tunneling to thermally activated behavior of individual fluctuators was clearly observed. The experimental results support the model of charge carrier traps in the barrier region.Comment: 4 pages, 4 figures, to be published in Appl. Phys. Let

Andreev Bound States in High Temperature Superconductors

Andreev bound states (ABS) at the surface of superconductors are expected for any pair potential showing a sign change in different k-directions with their spectral weight depending on the relative orientation of the surface and the pair potential. We report on the observation of ABS in HTS employing tunneling spectroscopy on bicrystal grain boundary Josephson junctions (GBJs). The tunneling spectra were studied as a function of temperature and applied magnetic field. The tunneling spectra of GBJ formed by YBCO, BSCCO, and LSCO show a pronounced zero bias conductance peak that can be interpreted in terms of Andreev bound states at zero energy that are expected at the surface of HTS having a d-wave symmetry of the order parameter. In contrast, for the most likely s-wave HTS NCCO no zero bias conductance peak was observed. Applying a magnetic field results in a shift of spectral weight from zero to finite energy. This shift is found to depend nonlinearly on the applied magnetic field. Further consequences of the Andreev bound states are discussed and experimental evidence for anomalous Meissner currents is presented.Comment: 17 pages, 10 figures, to appear in Eur. Phys. J.

Obligate Biotroph Pathogens of the Genus Albugo Are Better Adapted to Active Host Defense Compared to Niche Competitors

Recent research suggested that plants behave differently under combined versus single abiotic and biotic stress conditions in controlled environments. While this work has provided a glimpse into how plants might behave under complex natural conditions, it also highlights the need for field experiments using established model systems. In nature, diverse microbes colonize the phyllosphere of Arabidopsis thaliana, including the obligate biotroph oomycete genus Albugo, causal agent of the common disease white rust. Biotrophic, as well as hemibiotrophic plant pathogens are characterized by efficient suppression of host defense responses. Lab experiments have even shown that Albugo sp. can suppress non-host resistance, thereby enabling otherwise avirulent pathogen growth. We asked how a pathogen that is vitally dependent on a living host can compete in nature for limited niche space while paradoxically enabling colonization of its host plant for competitors? To address this question, we used a proteomics approach to identify differences and similarities between lab and field samples of Albugo sp.-infected and -uninfected A. thaliana plants. We could identify highly similar apoplastic proteomic profiles in both infected and uninfected plants. In wild plants, however, a broad range of defense-related proteins were detected in the apoplast regardless of infection status, while no or low levels of defense-related proteins were detected in lab samples. These results indicate that Albugo sp. do not strongly affect immune responses and leave distinct branches of the immune signaling network intact. To validate our findings and to get mechanistic insights, we tested a panel of A. thaliana mutant plants with induced or compromised immunity for susceptibility to different biotrophic pathogens. Our findings suggest that the biotroph pathogen Albugo selectively interferes with host defense under different environmental and competitive pressures to maintain its ecological niche dominance. Adaptation to host immune responses while maintaining a partially active host immunity seems advantageous against competitors. We suggest a model for future research that considers not only host–microbe but in addition microbe–microbe and microbe–host environment factors

Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing

Abstract Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce “blocking oligos”, a low‐cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A . thaliana ‐specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots ( Bromus erectus , Plantago lanceolata , Lotus corniculatus , Amaranth sp., Arabidopsis thaliana ). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant‐derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A . thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems‐based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics

Background: Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10–20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5’ ends of mRNA or use of RNA ligations.  Results: We have developed EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) that employs acoustic waves to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3′ end of each mRNA. Implementation of the method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations. EXPRSS is highly reproducible, is high-throughput and it also reveals alternative polyadenylation and polyadenylated antisense transcripts. It is cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing.  Conclusions: EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis

Low frequency 1/f noise in doped manganite grain-boundary junctions

We have performed a systematic analysis of the low frequency 1/f-noise in single grain boundary junctions in the colossal magnetoresistance material La_{2/3}Ca_{1/3}MnO_{3-delta}. The grain boundary junctions were formed in epitaxial La_{2/3}Ca_{1/3}MnO_{3-delta} films deposited on SrTiO_3 bicrystal substrates and show a large tunneling magnetoresistance of up to 300% at 4.2 K as well as ideal, rectangular shaped resistance versus applied magnetic field curves. Below the Curie temperature T_C the measured 1/f noise is dominated by the grain boundary. The dependence of the noise on bias current, temperature and applied magnetic field gives clear evidence that the large amount of low frequency noise is caused by localized sites with fluctuating magnetic moments in a heavily disordered grain boundary region. At 4.2 K additional temporally unstable Lorentzian components show up in the noise spectra that are most likely caused by fluctuating clusters of interacting magnetic moments. Noise due to fluctuating domains in the junction electrodes is found to play no significant role.Comment: 9 pages, 7 figure

Surgery and transplantation – Guidelines on Parenteral Nutrition, Chapter 18

In surgery, indications for artificial nutrition comprise prevention and treatment of catabolism and malnutrition. Thus in general, food intake should not be interrupted postoperatively and the re-establishing of oral (e.g. after anastomosis of the colon and rectum, kidney transplantation) or enteral food intake (e.g. after an anastomosis in the upper gastrointestinal tract, liver transplantation) is recommended within 24 h post surgery. To avoid increased mortality an indication for an immediate postoperatively artificial nutrition (enteral or parenteral nutrition (PN)) also exists in patients with no signs of malnutrition, but who will not receive oral food intake for more than 7 days perioperatively or whose oral food intake does not meet their needs (e.g. less than 60–80%) for more than 14 days. In cases of absolute contraindication for enteral nutrition, there is an indication for total PN (TPN) such as in chronic intestinal obstruction with a relevant passage obstruction e.g. a peritoneal carcinoma. If energy and nutrient requirements cannot be met by oral and enteral intake alone, a combination of enteral and parenteral nutrition is indicated. Delaying surgery for a systematic nutrition therapy (enteral and parenteral) is only indicated if severe malnutrition is present. Preoperative nutrition therapy should preferably be conducted prior to hospital admission to lower the risk of nosocomial infections. The recommendations of early postoperative re-establishing oral feeding, generally apply also to paediatric patients. Standardised operative procedures should be established in order to guarantee an effective nutrition therapy