Microtraps for neutral atoms using superconducting structures in the critical state

Recently demonstrated superconducting atom-chips provide a platform for trapping atoms and coupling them to solid-state quantum systems. Controlling these devices requires a full understanding of the supercurrent distribution in the trapping structures. For type-II superconductors, this distribution is hysteretic in the critical state due to the partial penetration of the magnetic field in the thin superconducting film through pinned vortices. We report here an experimental observation of this memory effect. Our results are in good agreement with the redictions of the Bean model of the critical state without adjustable parameters. The memory effect allows to write and store permanent currents in micron-sized superconducting structures and paves the way towards new types of engineered trapping potentials.Comment: accepted in Phys. Rev.

Loss of control in pattern-directed nucleation: a theoretical study

The properties of template-directed nucleation are studied close to the transition where full nucleation control is lost and additional nucleation occurs beyond the pre-patterned regions. First, kinetic Monte Carlo simulations are performed to obtain information on a microscopic level. Here the experimentally relevant cases of 1D stripe patterns and 2D square lattice symmetry are considered. The nucleation properties in the transition region depend in a complex way on the parameters of the system, i.e. the flux, the surface diffusion constant, the geometric properties of the pattern and the desorption rate. Second, the properties of the stationary concentration field in the fully controlled case are studied to derive the remaining nucleation probability and thus to characterize the loss of nucleation control. Using the analytically accessible solution of a model system with purely radial symmetry, some of the observed properties can be rationalized. A detailed comparison to the Monte Carlo data is included

Cytokine profiles of cord and adult blood leukocytes: differences in expression are due to differences in expression and activation of transcription factors

<p>Abstract</p> <p>Background</p> <p>Stem cell transplantation as therapy for hematological disorders is often hampered by severe graft-versus-host-disease. This may be reduced by umbilical cord blood transplantation, an effect that has been attributed to qualitative differences between neonatal and adult T cells. We compared levels of secreted proteins and cytokine mRNA induced in cord blood leukocytes (CBL) and adult blood leukocytes (ABL) by various stimuli.</p> <p>Results</p> <p>While interleukin-2 (IL-2) levels were similar in CBL and ABL, there was less induction of the Th1 cytokine interferon-γ in CBL. Production of the Th2 cytokines IL-4, IL-5, and IL-13 and the hematopoietic cytokine IL-3 was much lower in CBL versus ABL after T-cell receptor-mediated stimulation, whereas production of GM-CSF was comparable in the 2 cell types. The lower levels of Th1 and Th2 cytokines were maintained in CBL during a 4-day time-course study, while after 12 hours IL-3 and GM-CSF reached in CBL levels similar to those in ABL. For all cytokines except IFNγ, the IC₅₀values for inhibition by cyclosporin A were similar in ABL and CBL. In contrast, there was less expression and activation of transcription factors in CBL. Activation of NF-κB by TPA/ionomycin was detected in ABL but not CBL. Furthermore, there was less expression of the Th subset-specific transcription factors T-bet and c-maf in CBL versus ABL, whereas GATA-3 expression was similar. Expression of T-bet and c-maf correlated with expression of the Th1 and Th2 cytokines, respectively. Time course experiments revealed that T-bet expression was stimulated in both cell types, whereas c-maf and GATA-3 were induced only in ABL.</p> <p>Conclusion</p> <p>The diminished capability of CBL to synthesize cytokines is probably due to decreased activation of NF-κB, whereas differences in Th subsets are due to differences in regulation of Th lineage-specific transcriptions factors. We propose that the reduced incidence and severity of GvHD after allogeneic transplantation of umbilical CB cells is due to lesser activation of specific transcription factors and a subsequent reduction in production of certain cytokines.</p

The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences

BACKGROUND: The genus Corynebacterium includes Gram-positive microorganisms of great biotechnologically importance, such as Corynebacterium glutamicum and Corynebacterium efficiens, as well as serious human pathogens, such as Corynebacterium diphtheriae and Corynebacterium jeikeium. Although genome sequences of the respective species have been determined recently, the knowledge about the repertoire of transcriptional regulators and the architecture of global regulatory networks is scarce. Here, we apply a combination of bioinformatic tools and a comparative genomic approach to identify and characterize a set of conserved DNA-binding transcriptional regulators in the four corynebacterial genomes. RESULTS: A collection of 127 DNA-binding transcriptional regulators was identified in the C. glutamicum ATCC 13032 genome, whereas 103 regulators were detected in C. efficiens YS-314, 63 in C. diphtheriae NCTC 13129 and 55 in C. jeikeium K411. According to amino acid sequence similarities and protein structure predictions, the DNA-binding transcriptional regulators were grouped into 25 regulatory protein families. The common set of DNA-binding transcriptional regulators present in the four corynebacterial genomes consists of 28 proteins that are apparently involved in the regulation of cell division and septation, SOS and stress response, carbohydrate metabolism and macroelement and metal homeostasis. CONCLUSION: This work describes characteristic features of a set of conserved DNA-binding transcriptional regulators present within the corynebacterial core genome. The knowledge on the physiological function of these proteins should not only contribute to our understanding of the regulation of gene expression but will also provide the basis for comprehensive modeling of transcriptional regulatory networks of these species

The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences

Brune I, Brinkrolf K, Kalinowski J, Pühler A, Tauch A. The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics. 2005;6(1): 86.Background: The genus Corynebacterium includes Gram-positive microorganisms of great biotechnologically importance, such as Corynebacterium glutamicum and Corynebacterium efficiens, as well as serious human pathogens, such as Corynebacterium diphtheriae and Corynebacterium jeikeium. Although genome sequences of the respective species have been determined recently, the knowledge about the repertoire of transcriptional regulators and the architecture of global regulatory networks is scarce. Here, we apply a combination of bioinformatic tools and a comparative genomic approach to identify and characterize a set of conserved DNA-binding transcriptional regulators in the four corynebacterial genomes. Results: A collection of 127 DNA-binding transcriptional regulators was identified in the C. glutamicum ATCC 13032 genome, whereas 103 regulators were detected in C. efficiens YS-314, 63 in C. diphtheriae NCTC 13129 and 55 in C. jeikeium K411. According to amino acid sequence similarities and protein structure predictions, the DNA-binding transcriptional regulators were grouped into 25 regulatory protein families. The common set of DNA-binding transcriptional regulators present in the four corynebacterial genomes consists of 28 proteins that are apparently involved in the regulation of cell division and septation, SOS and stress response, carbohydrate metabolism and macroelement and metal homeostasis. Conclusion: This work describes characteristic features of a set of conserved DNA-binding transcriptional regulators present within the corynebacterial core genome. The knowledge on the physiological function of these proteins should not only contribute to our understanding of the regulation of gene expression but will also provide the basis for comprehensive modeling of transcriptional regulatory networks of these species

Initialization and Ensemble Generation for Decadal Climate Predictions: A Comparison of Different Methods

Five initialization and ensemble generation methods are investigated with respect to their impact on the prediction skill of the German decadal prediction system “Mittelfristige Klimaprognose” (MiKlip). Among the tested methods, three tackle aspects of model‐consistent initialization using the ensemble Kalman filter, the filtered anomaly initialization, and the initialization method by partially coupled spin‐up (MODINI). The remaining two methods alter the ensemble generation: the ensemble dispersion filter corrects each ensemble member with the ensemble mean during model integration. And the bred vectors perturb the climate state using the fastest growing modes. The new methods are compared against the latest MiKlip system in the low‐resolution configuration (Preop‐LR), which uses lagging the climate state by a few days for ensemble generation and nudging toward ocean and atmosphere reanalyses for initialization. Results show that the tested methods provide an added value for the prediction skill as compared to Preop‐LR in that they improve prediction skill over the eastern and central Pacific and different regions in the North Atlantic Ocean. In this respect, the ensemble Kalman filter and filtered anomaly initialization show the most distinct improvements over Preop‐LR for surface temperatures and upper ocean heat content, followed by the bred vectors, the ensemble dispersion filter, and MODINI. However, no single method exists that is superior to the others with respect to all metrics considered. In particular, all methods affect the Atlantic Meridional Overturning Circulation in different ways, both with respect to the basin‐wide long‐term mean and variability and with respect to the temporal evolution at the 26° N latitude

Условия формирования и перспективы обнаружения россыпных месторождений пылевидного золота в Украине

Изложены тезисы новой гипотезы гравитационной дифференциации мельчайших твердых частиц в жидкой и твердой, но дезинтегрированной средах. На этой основе прогнозируется образование россыпей пылевидного золота в дельтах Дона, Днепра, Днестра и Дуная, а также на прилегающих к ним частям шельфа Азово-Черноморского бассейна. Приведены доказательства биогенного и хемогенного генезиса некоторой части пылевидного золота. Приведен подсчет результата прогнозных ресурсов самородного мельчайшего золота по трем открытым автором россыпям на шельфе Черного моря, равный в сумме 25 т металла. Они были открыты только благодаря применению устройства “Говерла”.Викладено тези нової гіпотези гравітаційної диференціації дрібних твердих часток у твердому, але дезінтегрированому середовищі. На цій основі прогнозується утворення розсипів пилеподібного золота в дельтах Дону, Дніпра, Дністра й Дунаю, а також на прилеглих до них частинах шельфу Азово-Чорпоморського басейну. Наведено докази біогенного й хемогенного генезису деякої частини пилеподібного золота. Наведено результат підрахунку прогнозних ресурсів самородного найдрібні-шого золота по трьох відкритих автором розсипах на шельфі Чорного моря, які дорівнюють 25т металу. Розсипи були відкриті тільки завдяки використанню пристрою “Говерла”.It is expounded thesises for the new theory about gravitational differentiation of title rocky particles inside rocky environment. On this basis it is forecasted formation of gold flour placers in the deltas of Don, Dnieper, Dniester and Danube, and also on the adjoining part of the Azov-Black Sea shelf. There are introduced the evidence of biogenetical and chemogenetical genesis of some part of the gold flour. It is represented the prognosical resources of three gold placers which was discovered by author on the Black Sea shelf only due to using his device “Goverla”. They are amount to 25 ton of gold flour

The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum

BACKGROUND: The knowledge about complete bacterial genome sequences opens the way to reconstruct the qualitative topology and global connectivity of transcriptional regulatory networks. Since iron is essential for a variety of cellular processes but also poses problems in biological systems due to its high toxicity, bacteria have evolved complex transcriptional regulatory networks to achieve an effective iron homeostasis. Here, we apply a combination of transcriptomics, bioinformatics, in vitro assays, and comparative genomics to decipher the regulatory network of the iron-dependent transcriptional regulator DtxR of Corynebacterium glutamicum. RESULTS: A deletion of the dtxR gene of C. glutamicum ATCC 13032 led to the mutant strain C. glutamicum IB2103 that was able to grow in minimal medium only under low-iron conditions. By performing genome-wide DNA microarray hybridizations, differentially expressed genes involved in iron metabolism of C. glutamicum were detected in the dtxR mutant. Bioinformatics analysis of the genome sequence identified a common 19-bp motif within the upstream region of 31 genes, whose differential expression in C. glutamicum IB2103 was verified by real-time reverse transcription PCR. Binding of a His-tagged DtxR protein to oligonucleotides containing the 19-bp motifs was demonstrated in vitro by DNA band shift assays. At least 64 genes encoding a variety of physiological functions in iron transport and utilization, in central carbohydrate metabolism and in transcriptional regulation are controlled directly by the DtxR protein. A comparison with the bioinformatically predicted networks of C. efficiens, C. diphtheriae and C. jeikeium identified evolutionary conserved elements of the DtxR network. CONCLUSION: This work adds considerably to our currrent understanding of the transcriptional regulatory network of C. glutamicum genes that are controlled by DtxR. The DtxR protein has a major role in controlling the expression of genes involved in iron metabolism and exerts a dual regulatory function as repressor of genes participating in iron uptake and utilization and as activator of genes responsible for iron storage and DNA protection. The data suggest that the DtxR protein acts as global regulator by controlling the expression of other regulatory proteins that might take care of an iron-dependent regulation of a broader transcriptional network of C. glutamicum genes

Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota and a potential to switch between hosts

Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores. Nephridiophagids are poor in morphological characteristics, and although they have been tentatively identified as early-branching fungi based on the SSU rRNA gene sequences of three species, their exact position within the fungal tree of live remained unclear. In this study, we describe two new species of nephridiophagids (Nephridiophaga postici and Nephridiophaga javanicae) from cockroaches. Using long-read sequencing of the nearly complete rDNA operon of numerous further species obtained from cockroaches and earwigs to improve the resolution of the phylogenetic analysis, we found a robust affiliation of nephridiophagids with the Chytridiomycota—a group of zoosporic fungi that comprises parasites of diverse host taxa, such as microphytes, plants, and amphibians. The presence of the same nephridiophagid species in two only distantly related cockroaches indicates that their host specificity is not as strict as generally assumed