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

Direct evidence of soft mode behavior near the Burns' temperature in PbMg1/3_{1 / 3}Nb2/3_{2 / 3}O3_{3} (PMN) relaxor ferroectric

Inelastic neutron scattering measurements of the relaxor ferroelectric PbMg$_{1 / 3}$Nb$_{2 / 3}$O$_{3}$ (PMN) in the temperature range 490~K$<$T$<$880~K directly observe the soft mode (SM) associated with the Curie-Weiss behavior of the dielectric constant $\varepsilon$(T). The results are treated within the framework of the coupled SM and transverse optic (TO1) mode and the temperature dependence of the SM frequency at q=0.075 a* is determined. The parameters of the SM are consistent with the earlier estimates and the frequency exhibits a minimum near the Burns temperature ($\approx$ 650K)Comment: 6 figure

Perceived Partner Responsiveness Forecasts Behavioral Intimacy as Measured by Affectionate Touch

Affectionate touch is an important behavior in close relationships throughout the lifespan. Research has investigated the relational and individual psychological and physical benefits of affectionate touch, but the situational factors that give rise to it have been overlooked. Theorizing from the interpersonal process model of intimacy, the current studies tested whether perceived partner responsiveness forecasts affectionate touch in romantic couples. Following a preliminary integrative data analysis (N = 842), three prospective studies use ecologically valid behavioral (Studies 1 and 2) and daily (Studies 2 and 3) data, showing a positive association between perceived partner responsiveness and affectionate touch. Furthermore, in Study 3, we tested a theoretical extension of the interpersonal process of intimacy, finding that affectionate touch forecasts the partner’s perception of the touch-giver’s responsiveness the next day. Findings suggest affectionate touch may be an untested mechanism at the heart of the interpersonal process of intimacy

Defining the molecular pathology of pancreatic body and tail adenocarcinom

Background: Pancreatic ductal adenocarcinoma (PDAC) remains a dismal disease, with very little improvement in survival over the past 50 years. Recent large-scale genomic studies have improved understanding of the genomic and transcriptomic landscape of the disease, yet very little is known about molecular heterogeneity according to tumour location in the pancreas; body and tail PDACs especially tend to have a significantly worse prognosis. The aim was to investigate the molecular differences between PDAC of the head and those of the body and tail of the pancreas. Methods: Detailed correlative analysis of clinicopathological variables, including tumour location, genomic and transcriptomic data, was performed using the Australian Pancreatic Cancer Genome Initiative (APGI) cohort, part of the International Cancer Genome Consortium study. Results: Clinicopathological data were available for 518 patients recruited to the APGI, of whom 421 underwent genomic analyses; 179 of these patients underwent whole-genome and 96 RNA sequencing. Patients with tumours of the body and tail had significantly worse survival than those with pancreatic head tumours (12·1 versus 22·0 months; P = 0·001). Location in the body and tail was associated with the squamous subtype of PDAC. Body and tail PDACs enriched for gene programmes involved in tumour invasion and epithelial-to-mesenchymal transition, as well as features of poor antitumour immune response. Whether this is due to a molecular predisposition from the outset, or reflects a later time point on the tumour molecular clock, requires further investigation using well designed prospective studies in pancreatic cancer. Conclusion: PDACs of the body and tail demonstrate aggressive tumour biology that may explain worse clinical outcomes

The antiferromagnetic phi4 Model, II. The one-loop renormalization

It is shown that the four dimensional antiferromagnetic lattice phi4 model has the usual non-asymptotically free scaling law in the UV regime around the chiral symmetrical critical point. The theory describes a scalar and a pseudoscalar particle. A continuum effective theory is derived for low energies. A possibility of constructing a model with a single chiral boson is mentioned.Comment: To appear in Phys. Rev.

Thin helium film on a glass substrate

We investigate by Monte Carlo simulations the structure, energetics and superfluid properties of thin helium-four films (up to four layers) on a glass substrate, at low temperature. The first adsorbed layer is found to be solid and "inert", i.e., atoms are localized and do not participate to quantum exchanges. Additional layers are liquid, with no clear layer separation above the second one. It is found that a single helium-three impurity resides on the outmost layer, not significantly further away from the substrate than helium-four atoms on the same layer.Comment: Six figures, submitted for publication to the Journal of Low Temperature Physic

Pancreatic cancer: from genome discovery to PRECISION-Panc

No abstract available

In-dept sequence analysis of the tomato chromosome 12 centromeric region: indentification of a large CAA block and characterization of pericentromere retrotranposons

We sequenced a continuous 326-kb DNA stretch of a microscopically defined centromeric region of tomato chromosome 12. A total of 84% of the sequence (270 kb) was composed of a nested complex of repeat sequences including 27 retrotransposons, two transposable elements, three MITEs, two terminal repeat retrotransposons in miniature (TRIMs), ten unclassified repeats and three chloroplast DNA insertions. The retrotransposons were grouped into three families of Ty3-Gypsy type long terminal repeat (LTR) retrotransposons (PCRT1¿PCRT3) and one LINE-like retrotransposon (PCRT4). High-resolution fluorescence in situ hybridization analyses on pachytene complements revealed that PCRT1a occurs on the pericentromere heterochromatin blocks. PCRT1 was the prevalent retrotransposon family occupying more than 60% of the 326-kb sequence with 19 members grouped into eight subfamilies (PCRT1a¿PCRT1h) based on LTR sequence. The PCRT1a subfamily is a rapidly amplified element occupying tens of megabases. The other PCRT1 subfamilies (PCRT1b¿PCRT1h) were highly degenerated and interrupted by insertions of other elements. The PCRT1 family shows identity with a previously identified tomato-specific repeat TGR2 and a CENP-B like sequence. A second previously described genomic repeat, TGR3, was identified as a part of the LTR sequence of an Athila-like PCRT2 element of which four copies were found in the 326-kb stretch. A large block of trinucleotide microsatellite (CAA)n occupies the centromere and large portions of the flanking pericentromere heterochromatin blocks of chromosome 12 and most of the other chromosomes. Five putative genes in the remaining 14% of the centromere region were identified, of which one is similar to a transcription regulator (ToCPL1) and a candidate jointless-2 gene. The sequence data from this study have been submitted to GenBank under accession no. AY85039

Seizure control by decanoic acid through direct AMPA receptor inhibition

The medium chain triglyceride ketogenic diet is an established treatment for drug-resistant epilepsy that increases plasma levels of decanoic acid and ketones. Recently, decanoic acid has been shown to provide seizure control in vivo, yet its mechanism of action remains unclear. Here we show that decanoic acid, but not the ketones β-hydroxybutryate or acetone, shows antiseizure activity in two acute ex vivo rat hippocampal slice models of epileptiform activity. To search for a mechanism of decanoic acid, we show it has a strong inhibitory effect on excitatory, but not inhibitory, neurotransmission in hippocampal slices. Using heterologous expression of excitatory ionotropic glutamate receptor AMPA subunits in Xenopus oocytes, we show that this effect is through direct AMPA receptor inhibition, a target shared by a recently introduced epilepsy treatment perampanel. Decanoic acid acts as a non-competitive antagonist at therapeutically relevant concentrations, in a voltage- and subunit-dependent manner, and this is sufficient to explain its antiseizure effects. This inhibitory effect is likely to be caused by binding to sites on the M3 helix of the AMPA-GluA2 transmembrane domain; independent from the binding site of perampanel. Together our results indicate that the direct inhibition of excitatory neurotransmission by decanoic acid in the brain contributes to the anti-convulsant effect of the medium chain triglyceride ketogenic diet

The Effective Lagrangian in the Randall-Sundrum Model and Electroweak Physics

We consider the two-brane Randall-Sundrum (RS) model with bulk gauge fields. We carefully match the bulk theory to a 4D low-energy effective Lagrangian. In addition to the four-fermion operators induced by KK exchange we find that large negative S and T parameters are induced in the effective theory. This is a tree-level effect and is a consequence of the shapes of the W and Z wave functions in the bulk. Such effects are generic in extra dimensional theories where the standard model (SM) gauge bosons have non-uniform wave functions along the extra dimension. The corrections to precision electroweak observables in the RS model are mostly dominated by S. We fit the parameters of the RS model to the experimental data and find somewhat stronger bounds than previously obtained; however, the standard model bound on the Higgs mass from precision measurements can only be slightly relaxed in this theory.Comment: 16 pages, LaTeX, 1 figure included, uses JHEP.cls, extended introduction, added reference