FISH mapping and molecular organization of the major repetitive sequences of tomato

This paper presents a bird's-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA](4), a microsatellite that also forms part of the pericentromeres, together with [GA](8), [GATA](4) and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer regio

Nondissipative Drag Conductance as a Topological Quantum Number

We show in this paper that the boundary condition averaged nondissipative drag conductance of two coupled mesoscopic rings with no tunneling, evaluated in a particular many-particle eigenstate, is a topological invariant characterized by a Chern integer. Physical implications of this observation are discussed.Comment: 4 pages, no figure. Title modified and significant revision made to the text. Final version appeared in PR

Syzygies in equivariant cohomology for non-abelian Lie groups

We extend the work of Allday-Franz-Puppe on syzygies in equivariant cohomology from tori to arbitrary compact connected Lie groups G. In particular, we show that for a compact orientable G-manifold X the analogue of the Chang-Skjelbred sequence is exact if and only if the equivariant cohomology of X is reflexive, if and only if the equivariant Poincare pairing for X is perfect. Along the way we establish that the equivariant cohomology modules arising from the orbit filtration of X are Cohen-Macaulay. We allow singular spaces and introduce a Cartan model for their equivariant cohomology. We also develop a criterion for the finiteness of the number of infinitesimal orbit types of a G-manifold.Comment: 28 pages; minor change

Wave attenuation at a salt marsh margin: A case study of an exposed coast on the Yangtze estuary

To quantify wave attenuation by (introduced) Spartina alterniflora vegetation at an exposed macrotidal coast in the Yangtze Estuary, China, wave parameters and water depth were measured during 13 consecutive tides at nine locations ranging from 10 m seaward to 50 m landward of the low marsh edge. During this period, the incident wave height ranged from <0.1 to 1.5 m, the maximum of which is much higher than observed in other marsh areas around the world. Our measurements and calculations showed that the wave attenuation rate per unit distance was 1 to 2 magnitudes higher over the marsh than over an adjacent mudflat. Although the elevation gradient of the marsh margin was significantly higher than that of the adjacent mudflat, more than 80% of wave attenuation was ascribed to the presence of vegetation, suggesting that shoaling effects were of minor importance. On average, waves reaching the marsh were eliminated over a distance of similar to 80 m, although a marsh distance of >= 100 m was needed before the maximum height waves were fully attenuated during high tides. These attenuation distances were longer than those previously found in American salt marshes, mainly due to the macrotidal and exposed conditions at the present site. The ratio of water depth to plant height showed an inverse correlation with wave attenuation rate, indicating that plant height is a crucial factor determining the efficiency of wave attenuation. Consequently, the tall shoots of the introduced S. alterniflora makes this species much more efficient at attenuating waves than the shorter, native pioneer species in the Yangtze Estuary, and should therefore be considered as a factor in coastal management during the present era of sea-level rise and global change. We also found that wave attenuation across the salt marsh can be predicted using published models when a suitable coefficient is incorporated to account for drag, which varies in place and time due to differences in plant characteristics and abiotic conditions (i.e., bed gradient, initial water depth, and wave action).

Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria

Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events

Does black-hole growth depend on the cosmic environment?

It is well known that environment affects galaxy evolution, which is broadly related to supermassive black hole (SMBH) growth. We investigate whether SMBH evolution also depends on host-galaxy local (sub-Mpc) and global (≈1–10 Mpc) environment. We construct the surface-density field (local environment) and cosmic web (global environment) in the Cosmic Evolution Survey (COSMOS) field at z = 0.3–3.0. The environments in COSMOS range from the field to clusters (Mhalo ≲ 1014 M⊙), covering the environments where ≈99 per cent of galaxies in the Universe reside. We measure sample-averaged SMBH accretion rate ( BHAR¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ ) from X-ray observations, and study its dependence on overdensity and cosmic-web environment at different redshifts while controlling for galaxy stellar mass (M⋆). Our results show that BHAR¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ does not significantly depend on overdensity or cosmic-web environment once M⋆ is controlled, indicating that environment-related physical mechanisms (e.g. tidal interaction and ram-pressure stripping) might not significantly affect SMBH growth. We find that BHAR¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ is strongly related to host-galaxy M⋆, regardless of environment

Entanglement and Quantum Phase Transitions via Adiabatic Quantum Computation

For a finite XY chain and a finite two-dimensional Ising lattice, it is shown that the paramagnetic ground state is adiabatically transformed to the GHZ state in the ferromagnetic phase by slowly turning on the magnetic field. The fidelity between the GHZ state and an adiabatically evolved state shows a feature of the quantum phase transition.Comment: Revise

Optical properties and radiative forcing of urban aerosols in Nanjing, China

AbstractContinuous measurements of atmospheric aerosols were made in Nanjing, a megacity in China, from 18 January to 18 April, 2011 (Phase 1) and from 22 April 2011 to 21 April 2012 (Phase 2). Aerosol characteristics, optical properties, and direct radiative forcing (DRF) were studied through interpretations of these measurements. We found that during Phase 1, mean PM2.5, black carbon (BC), and aerosol scattering coefficient (Bsp) in Nanjing were 76.1 ± 59.3 μg m−3, 4.1 ± 2.2 μg m−3, and 170.9 ± 105.8 M m−1, respectively. High pollution episodes occurred during Spring and Lantern Festivals when hourly PM2.5 concentrations reached 440 μg m−3, possibly due to significant discharge of fireworks. Temporal variations of PM2.5, BC, and Bsp were similar to each other. It is estimated that inorganic scattering aerosols account for about 49 ± 8.6% of total aerosols while BC only accounted for 6.6 ± 2.9%, and nitrate was larger than sulfate. In Phase 2, optical properties of aerosols show great seasonality. High relative humidity (RH) in summer (June, July, August) likely attributed to large optical depth (AOD) and small Angstrom exponent (AE) of aerosols. Due to dust storms, AE of total aerosols was the smallest in spring (March, April, May). Annual mean 550-nm AOD and 675/440-nm AE were 0.6 ± 0.3 and 1.25 ± 0.29 for total aerosols, 0.04 ± 0.02 and 1.44 ± 0.50 for absorbing aerosols, 0.48 ± 0.29 and 1.64 ± 0.29 for fine aerosols, respectively. Annual single scattering albedo of aerosols ranged from 0.90 to 0.92. Real time wavelength-dependent surface albedo from the Moderate Resolution Imaging Spectroradiometer (MODIS) was used to assess aerosol DRFs. Both total and absorbing aerosol DRFs had significant seasonal variations in Nanjing and they were the strongest in summer. Annual mean clear sky TOA DRF (including daytime and nighttime) of total and absorbing aerosols was about −6.9 and +4.5 W m−2, respectively. Aerosol DRFs were found to be sensitive to surface albedo. Over brighter surfaces, solar radiation was more absorbed by absorbing aerosols and less scattered by scattering aerosols

Propagators in Noncommutative Instantons

We explicitly construct Green functions for a field in an arbitrary representation of gauge group propagating in noncommutative instanton backgrounds based on the ADHM construction. The propagators for spinor and vector fields can be constructed in terms of those for the scalar field in noncommutative instanton background. We show that the propagators in the adjoint representation are deformed by noncommutativity while those in the fundamental representation have exactly the same form as the commutative case.Comment: 28 pages, Latex, v2: A few typos correcte

Structural and biophysical characterization of bacillus thuringiensis insecticidal proteins Cry34Ab1 and Cry35Ab1

Bacillus thuringiensis strains are well known for the production of insecticidal proteins upon sporulation and these proteins are deposited in parasporal crystalline inclusions. The majority of these insect-specific toxins exhibit three domains in the mature toxin sequence. However, other Cry toxins are structurally and evolutionarily unrelated to this three-domain family and little is known of their three dimensional structures, limiting our understanding of their mechanisms of action and our ability to engineer the proteins to enhance their function. Among the non-three domain Cry toxins, the Cry34Ab1 and Cry35Ab1 proteins from B. thuringiensis strain PS149B1 are required to act together to produce toxicity to the western corn rootworm (WCR) Diabrotica virgifera virgifera Le Conte via a pore forming mechanism of action. Cry34Ab1 is a protein of ∼14 kDa with features of the aegerolysin family (Pfam06355) of proteins that have known membrane disrupting activity, while Cry35Ab1 is a ∼44 kDa member of the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. The Cry34Ab1/Cry35Ab1 proteins represent an important seed trait technology having been developed as insect resistance traits in commercialized corn hybrids for control of WCR. The structures of Cry34Ab1 and Cry35Ab1 have been elucidated to 2.15 Å and 1.80 Å resolution, respectively. The solution structures of the toxins were further studied by small angle X-ray scattering and native electrospray ion mobility mass spectrometry. We present here the first published structure from the aegerolysin protein domain family and the structural comparisons of Cry34Ab1 and Cry35Ab1 with other pore forming toxins