The CTP-binding domain is disengaged from the DNA-binding domain in a cocrystal structure of Bacillus subtilis Noc–DNA complex

In Bacillus subtilis, a ParB-like nucleoid occlusion protein (Noc) binds specifically to Noc-binding sites (NBSs) on the chromosome to help coordinate chromosome segregation and cell division. Noc does so by binding to CTP to form large membrane-associated nucleoprotein complexes to physically inhibit the assembly of the cell division machinery. The site-specific binding of Noc to NBS DNA is a prerequisite for CTP-binding and the subsequent formation of a membrane-active DNA-entrapped protein complex. Here, we solve the structure of a C-terminally truncated B. subtilis Noc bound to NBS DNA to reveal the conformation of Noc at this crucial step. Our structure reveals the disengagement between the N-terminal CTP-binding domain and the NBS-binding domain of each DNA-bound Noc subunit; this is driven, in part, by the swapping of helices 4 and 5 at the interface of the two domains. Site-specific crosslinking data suggest that this conformation of Noc-NBS exists in solution. Overall, our results lend support to the recent proposal that parS/NBS binding catalyzes CTP binding and DNA entrapment by preventing the reengagement of the CTP-binding domain and the DNA-binding domain from the same ParB/Noc subunit

Universal Resistances of the Quantum RC circuit

We examine the concept of universal quantized resistance in the AC regime through the fully coherent quantum RC circuit comprising a cavity (dot) capacitively coupled to a gate and connected via a single spin-polarized channel to a reservoir lead. As a result of quantum effects such as the Coulomb interaction in the cavity and global phase coherence, we show that the charge relaxation resistance $R_q$ is identical for weak and large transmissions and it changes from $h/2e^2$ to $h/e^2$ when the frequency (times $\hbar$) exceeds the level spacing of the cavity; $h$ is the Planck constant and $e$ the electron charge. For large cavities, we formulate a correspondence between the charge relaxation resistance $h/e^2$ and the Korringa-Shiba relation of the Kondo model. Furthermore, we introduce a general class of models, for which the charge relaxation resistance is universal. Our results emphasize that the charge relaxation resistance is a key observable to understand the dynamics of strongly correlated systems.Comment: 12 pages, 3 figure

Detecting the direction of a signal on high-dimensional spheres: Non-null and Le Cam optimality results

We consider one of the most important problems in directional statistics, namely the problem of testing the null hypothesis that the spike direction $\theta$ of a Fisher-von Mises-Langevin distribution on the $p$-dimensional unit hypersphere is equal to a given direction $\theta_0$. After a reduction through invariance arguments, we derive local asymptotic normality (LAN) results in a general high-dimensional framework where the dimension $p_n$ goes to infinity at an arbitrary rate with the sample size $n$, and where the concentration $\kappa_n$ behaves in a completely free way with $n$, which offers a spectrum of problems ranging from arbitrarily easy to arbitrarily challenging ones. We identify various asymptotic regimes, depending on the convergence/divergence properties of $(\kappa_n)$, that yield different contiguity rates and different limiting experiments. In each regime, we derive Le Cam optimal tests under specified $\kappa_n$ and we compute, from the Le Cam third lemma, asymptotic powers of the classical Watson test under contiguous alternatives. We further establish LAN results with respect to both spike direction and concentration, which allows us to discuss optimality also under unspecified $\kappa_n$. To investigate the non-null behavior of the Watson test outside the parametric framework above, we derive its local asymptotic powers through martingale CLTs in the broader, semiparametric, model of rotationally symmetric distributions. A Monte Carlo study shows that the finite-sample behaviors of the various tests remarkably agree with our asymptotic results.Comment: 47 pages, 4 figure

Non-Equilibrium Edge Channel Spectroscopy in the Integer Quantum Hall Regime

Heat transport has large potentialities to unveil new physics in mesoscopic systems. A striking illustration is the integer quantum Hall regime, where the robustness of Hall currents limits information accessible from charge transport. Consequently, the gapless edge excitations are incompletely understood. The effective edge states theory describes them as prototypal one-dimensional chiral fermions - a simple picture that explains a large body of observations and calls for quantum information experiments with quantum point contacts in the role of beam splitters. However, it is in ostensible disagreement with the prevailing theoretical framework that predicts, in most situations, additional gapless edge modes. Here, we present a setup which gives access to the energy distribution, and consequently to the energy current, in an edge channel brought out-of-equilibrium. This provides a stringent test of whether the additional states capture part of the injected energy. Our results show it is not the case and thereby demonstrate regarding energy transport, the quantum optics analogy of quantum point contacts and beam splitters. Beyond the quantum Hall regime, this novel spectroscopy technique opens a new window for heat transport and out-of-equilibrium experiments.Comment: 13 pages including supplementary information, Nature Physics in prin

Directed self-assembly of a helical nanofilament liquid crystal phase for use as structural color reflectors

The fabrication of molecular structures with a desired morphology, e.g., nanotubes, nanoribbons, nanosprings, and sponges, is essential for the advancement of nanotechnology. Unfortunately, realization of this objective is expensive and complicated. Here, we report that irradiating a film comprising azobenzene derivatives with UV light produces oriented arrays of helical nanofilaments via the photoisomerization-induced Weigert effect. As a result, structural colors are observed due to the extrinsic chiral reflection in the visible wavelength range, and the reflected color can be tuned by adjusting the molecular length of the azobenzene derivative. This simple fabrication method can be used for fabricating large, reversible, and patternable color reflectors, providing a new platform for interference-based structural coloration as it exists in nature, such as morpho butterflies, green-winged teal, and various beetles

The Arthrobacter Species FB24 Arth_1007 (DnaB) Intein Is a Pseudogene

An Arthrobacter species FB24 gene (locus tag Arth_1007) was previously annotated as a putative intein-containing DnaB helicase of phage origin (Arsp-FB24 DnaB intein). However, it is not a helicase gene because the sequence similarity is limited to inteins. In fact, the flanking exteins total only 66 amino acids. Therefore, the intein should be referred to as the Arsp-FB24 Arth_1007 intein. The Arsp-FB24 Arth_1007 intein failed to splice in its native precursor and in a model precursor. We previously noted that the Arsp-FB24 Arth_1007 intein is the only putative Class 3 intein that is missing the catalytically essential Cys at position 4 of intein Motif F, which is one of the three defining signature residues of this class. Additionally, a catalytically essential His in position 10 of intein Motif B is also absent; this His is the most conserved residue amongst all inteins. Splicing activity was not rescued when these two catalytically important positions were ‘reverted’ back to their consensus residues. This study restores the unity of the Class 3 intein signature sequence in active inteins by demonstrating that the Arsp-FB24 Arth_1007 intein is an inactive pseudogene

Causes and consequences of tipping points in river delta social-ecological systems

The sustainability of social-ecological systems within river deltas globally is in question as rapid development and environmental change trigger "negative” or “positive” tipping points depending on actors’ perspectives, e.g., regime shift from abundant sediment deposition to sediment shortage, agricultural sustainability to agricultural collapse or shift from rural to urban land. Using a systematic review of the literature, we show how cascading effects across anthropogenic, ecological, and geophysical processes have triggered numerous tipping points in the governance, hydrological and land use management of the world’s river deltas. Crossing tipping points had both positive and negative effects that generally enhanced economic development to the detriment of the environment. Assessment of deltas that featured prominently in the review revealed how outcomes of tipping points can inform the long-term trajectory of deltas towards sustainability or collapse. Management of key drivers at the delta scale can trigger positive tipping points to place social-ecological systems on a pathway towards sustainable development

Parasitism of Lepidopterous Stem Borers in Cultivated and Natural Habitats

Plant infestation, stem borer density, parasitism, and parasitoid abundance were assessed during two years in two host plants, Zea mays (L.) (Cyperales: Poaceae) and Sorghum bicolor (L.) (Cyperales: Poaceae), in cultivated habitats. The four major host plants (Cyperus spp., Panicum spp., Pennisetum spp., and Sorghum spp.) found in natural habitats were also assessed, and both the cultivated and natural habitat species occurred in four agroecological zones in Kenya. Across habitats, plant infestation (23.2%), stem borer density (2.2 per plant), and larval parasitism (15.0%) were highest in maize in cultivated habitats. Pupal parasitism was not higher than 4.7% in both habitats, and did not vary with locality during each season or with host plant between each season. Cotesia sesamiae (Cameron) and C. flavipes Cameron (Hymenoptera: Braconidae) were the key parasitoids in cultivated habitats (both species accounted for 76.4% of parasitized stem borers in cereal crops), but not in natural habitats (the two Cotesia species accounted for 14.5% of parasitized stem borers in wild host plants). No single parasitoid species exerted high parasitism rates on stem borer populations in wild host plants. Low stem borer densities across seasons in natural habitats indicate that cereal stem borer pests do not necessarily survive the non-cropping season feeding actively in wild host plants. Although natural habitats provided refuges for some parasitoid species, stem borer parasitism was generally low in wild host plants. Overall, because parasitoids contribute little in reducing cereal stem borer pest populations in cultivated habitats, there is need to further enhance their effectiveness in the field to regulate these pests

Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences

<p>Abstract</p> <p>Background</p> <p>Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune suppression if animals are infected with an ncp biotype during early gestation, followed by a subsequent infection of the cp biotype. The molecular mechanisms that underscore the complex disease etiology leading to immune suppression in cattle caused by BVDV are not well understood.</p> <p>Results</p> <p>Using proteomics, we evaluated the effect of cp and ncp BVDV infection of bovine monocytes to determine their role in viral immune suppression and uncontrolled inflammation. Proteins were isolated by differential detergent fractionation and identified by 2D-LC ESI MS/MS. We identified 137 and 228 significantly altered bovine proteins due to ncp and cp BVDV infection, respectively. Functional analysis of these proteins using the Gene Ontology (GO) showed multiple under- and over- represented GO functions in molecular function, biological process and cellular component between the two BVDV biotypes. Analysis of the top immunological pathways affected by BVDV infection revealed that pathways representing macropinocytosis signalling, virus entry via endocytic pathway, integrin signalling and primary immunodeficiency signalling were identified only in ncp BVDV-infected monocytes. In contrast, pathways like actin cytoskeleton signalling, RhoA signalling, clathrin-mediated endocytosis signalling and interferon signalling were identified only in cp BDVD-infected cells. Of the six common pathways involved in cp and ncp BVDV infection, acute phase response signalling was the most significant for both BVDV biotypes. Although, most shared altered host proteins between both BVDV biotypes showed the same type of change, integrin alpha 2b (ITGA2B) and integrin beta 3 (ITGB3) were down- regulated by ncp BVDV and up- regulated by cp BVDV infection.</p> <p>Conclusions</p> <p>This study shows that, as we expected, there are significant functional differences in the host proteins that respond to cp or ncp BVDV infection. The combined use of GO and systems biology network modelling facilitated a better understanding of host-pathogen interactions.</p