Provenance Circuits for Trees and Treelike Instances (Extended Version)

Query evaluation in monadic second-order logic (MSO) is tractable on trees and treelike instances, even though it is hard for arbitrary instances. This tractability result has been extended to several tasks related to query evaluation, such as counting query results [3] or performing query evaluation on probabilistic trees [10]. These are two examples of the more general problem of computing augmented query output, that is referred to as provenance. This article presents a provenance framework for trees and treelike instances, by describing a linear-time construction of a circuit provenance representation for MSO queries. We show how this provenance can be connected to the usual definitions of semiring provenance on relational instances [20], even though we compute it in an unusual way, using tree automata; we do so via intrinsic definitions of provenance for general semirings, independent of the operational details of query evaluation. We show applications of this provenance to capture existing counting and probabilistic results on trees and treelike instances, and give novel consequences for probability evaluation.Comment: 48 pages. Presented at ICALP'1

Versatile toolbox for high throughput biochemical and functional studies with fluorescent fusion proteins

Fluorescent fusion proteins are widely used to study protein localization and interaction dynamics in living cells. However, to fully characterize proteins and to understand their function it is crucial to determine biochemical characteristics such as enzymatic activity and binding specificity. Here we demonstrate an easy, reliable and versatile medium/high-throughput method to study biochemical and functional characteristics of fluorescent fusion proteins. Using a new system based on 96-well micro plates comprising an immobilized GFP-binding protein (GFP-mulitTrap), we performed fast and efficient one-step purification of different GFP- and YFP-fusion proteins from crude cell lysate. After immobilization we determined highly reproducible binding ratios of cellular expressed GFP-fusion proteins to histone-tail peptides, DNA or selected RFP-fusion proteins. In particular, we found Cbx1 preferentially binding to di-and trimethylated H3K9 that is abolished by phosphorylation of the adjacent serine. DNA binding assays showed, that the MBD domain of MeCP2 discriminates between fully methylated over unmethylated DNA and protein-protein interactions studies demonstrate, that the PBD domain of Dnmt1 is essential for binding to PCNA. Moreover, using an ELISA-based approach, we detected endogenous PCNA and histone H3 bound at GFP-fusions. In addition, we quantified the level of H3K4me2 on nucleosomes containing different histone variants. In summary, we present an innovative medium/high-throughput approach to analyse binding specificities of fluroescently labeled fusion proteins and to detect endogenous interacting factors in a fast and reliable manner in vitro

Doped carbon nanotubes as a model system of biased graphene

Albeit difficult to access experimentally, the density of states (DOS) is a key parameter in solid state systems which governs several important phenomena including transport, magnetism, thermal, and thermoelectric properties. We study DOS in an ensemble of potassium intercalated single-wall carbon nanotubes (SWCNT) and show using electron spin resonance spectroscopy that a sizeable number of electron states are present, which gives rise to a Fermi-liquid behavior in this material. A comparison between theoretical and the experimental DOS indicates that it does not display significant correlation effects, even though the pristine nanotube material shows a Luttinger-liquid behavior. We argue that the carbon nanotube ensemble essentially maps out the whole Brillouin zone of graphene thus it acts as a model system of biased graphene

A comparative approach to confirm antibiotic-resistant microbes in the cryosphere

Antibiotic-resistant microbes pose one of the biggest challenges of the current century. While areas with proximity to human impact are closely studied, a lot is yet to learn about antimicrobial resistance in remote regions like the cryosphere. Nowadays, antibiotic (AB) resistance is considered a pollution that has reached the Earth’s most pristine areas. However, monitoring of resistant environmental bacteria therein faces several challenges that inhibit scientific progress in this field. Due to many cultivation-based antibiotic susceptibility tests being optimized for mesophilic pathogenic microorganisms, many researchers opt for expensive molecular biological approaches to detect antibiotic resistance in the cryosphere. However, some disadvantages of these methods prohibit effective comprehensive monitoring of resistant bacteria in pristine areas, hence we suggest established cultivation-based approaches when looking for antimicrobial resistance in the cryosphere. In this study, we compared two common antibiotic susceptibility tests and optimized them to meet the needs of psychrophilic microorganisms. The resulting cultures thereof originated from cryospheric habitats with differing anthropogenic impacts. The results show that these methods are applicable to detect antibiotic resistance in cryospheric habitats and could potentially increase the comparability between studies

Black carbon contributes to organic matter in young soils in the Morteratsch proglacial area (Switzerland)

Most glacier forefields of the European Alps are being progressively exposed since the glaciers reached their maximum expansion in the 1850s. Global warming and climate changes additionally promote the exposure of sediments in previously glaciated areas. In these proglacial areas, initial soils have started to develop so that they may offer a continuous chronosequence from 0 to 150-yr-old soils. The build-up of organic matter is an important factor of soil formation, and not only autochthonous but also distant sources might contribute to its accumulation in young soils and surfaces of glacier forefields. Only little is known about black carbon in soils that develop in glacier forefields, although charred organic matter could be an important component of organic carbon in Alpine soils. The aim of our study was to examine whether black carbon (BC) is present in the initial soils of a proglacial area, and to estimate its relative contribution to soil organic matter. We investigated soil samples from 35 sites distributed over the whole proglacial area of Morteratsch (Upper Engadine, Switzerland), covering a chronosequence from 0 to 150 yr. BC concentrations were determined in fine earth using the benzene polycarboxylic acid (BPCA) marker method. We found that charred organic matter occurred in the whole area, and that it was a main compound of soil organic matter in the youngest soils, where total Corg concentrations were very low. The absolute concentrations of BC in fine earth were generally low but increased in soils that had been exposed for more than 40 yr. Specific initial microbial communities may profit from this additional C source during the first years of soil evolution and potentially promote soil development in its early stage

A Supercooled Spin Liquid State in the Frustrated Pyrochlore Dy2Ti2O7

A "supercooled" liquid develops when a fluid does not crystallize upon cooling below its ordering temperature. Instead, the microscopic relaxation times diverge so rapidly that, upon further cooling, equilibration eventually becomes impossible and glass formation occurs. Classic supercooled liquids exhibit specific identifiers including microscopic relaxation times diverging on a Vogel-Tammann-Fulcher (VTF) trajectory, a Havriliak-Negami (HN) form for the dielectric function, and a general Kohlrausch-Williams-Watts (KWW) form for time-domain relaxation. Recently, the pyrochlore Dy2Ti2O7 has become of interest because its frustrated magnetic interactions may, in theory, lead to highly exotic magnetic fluids. However, its true magnetic state at low temperatures has proven very difficult to identify unambiguously. Here we introduce high-precision, boundary-free magnetization transport techniques based upon toroidal geometries and gain a fundamentally new understanding of the time- and frequency-dependent magnetization dynamics of Dy2Ti2O7. We demonstrate a virtually universal HN form for the magnetic susceptibility, a general KWW form for the real-time magnetic relaxation, and a divergence of the microscopic magnetic relaxation rates with precisely the VTF trajectory. Low temperature Dy2Ti2O7 therefore exhibits the characteristics of a supercooled magnetic liquid; the consequent implication is that this translationally invariant lattice of strongly correlated spins is evolving towards an unprecedented magnetic glass state, perhaps due to many-body localization of spin.Comment: Version 2 updates: added legend for data in Figures 4A and 4B; corrected equation reference in caption for Figure 4

Fine-tuning the functional properties of carbon nanotubes via the interconversion of encapsulated molecules

Tweaking the properties of carbon nanotubes is a prerequisite for their practical applications. Here we demonstrate fine-tuning the electronic properties of single-wall carbon nanotubes via filling with ferrocene molecules. The evolution of the bonding and charge transfer within the tube is demonstrated via chemical reaction of the ferrocene filler ending up as secondary inner tube. The charge transfer nature is interpreted well within density functional theory. This work gives the first direct observation of a fine-tuned continuous amphoteric doping of single-wall carbon nanotubes

Highly specific PCR-RFLP assays for karyotyping the widespread 2Rb inversion in malaria vectors of the Anopheles gambiae complex

Background: Chromosomal inversion polymorphisms play a role in adaptation to heterogeneous environments. Inversion polymorphisms are implicated in the very high ecological flexibility of the three main malaria vector species of the Afrotropical Anopheles gambiae complex, facilitating the exploitation of anthropogenic environmental modifications and promoting a strong association with humans. In addition to extending the species' spatial and temporal distribution, inversions are associated with epidemiologically relevant mosquito behavior and physiology, underscoring their medical importance. We here present novel PCR-RFLP based assays strongly predictive of genotype for the cosmopolitan 2Rb inversion in An. coluzzii and An. gambiae, a development which overcomes the numerous constraints inherent to traditional cytological karyotyping. Methods: We designed PCR-RFLP genotyping assays based on tag SNPs previously computationally identified as strongly predictive (> 95%) of 2Rb genotype. We targeted those tags whose alternative allelic states destroyed or created the recognition site of a commercially available restriction enzyme, and designed assays with distinctive cleavage profiles for each inversion genotype. The assays were validated on 251 An. coluzzii and 451 An. gambiae cytologically karyotyped specimens from nine countries across Africa and one An. coluzzii laboratory colony. Results: For three tag SNPs, PCR-RFLP assays (denoted DraIII, MspAI, and TatI) reliably produced robust amplicons and clearly distinguishable electrophoretic profiles for all three inversion genotypes. Results obtained with the DraIII assay are ≥ 95% concordant with cytogenetic assignments in both species, while MspAI and TatI assays produce patterns highly concordant with cytogenetic assignments only in An. coluzzii or An. gambiae, respectively. Joint application of species-appropriate pairs of assays increased the concordance levels to > 99% in An. coluzzii and 98% in An. gambiae. Potential sources of discordance (e.g. imperfect association between tag and inversion, allelic dropout, additional polymorphisms in the restriction target site, incomplete or failed restriction digestion) are discussed. Conclusions: The availability of highly specific, cost effective and accessible molecular assays for genotyping 2Rb in An. gambiae and An. coluzzii allows karyotyping of both sexes and all developmental stages. These novel tools will accelerate deeper investigations into the role of this ecologically and epidemiologically important chromosomal inversion in vector biology.[Figure not available: see fulltext.