Stable kilohertz rate molecular beam laser ablation sources

A stable kilohertz (kHz) rate laser ablation/desorption supersonic molecular beam source for use in kHz rate laser experiments was discussed. The source was based based upon strong nonresonant interaction of a dithering laser focus with a rotating and translating solid rod. The kHz laser ablation of a high temperature refractory metal (niobium) for use in studied of metal clusters was also demonstrated. The kHz laser desorption and jet cooling of an involatile biomolecule (the DNA based guanine) for use in spectroscopic and dynamical studies was described.open151

Determining the Contribution of Epidermal Cell Shape to Petal Wettability Using Isogenic Antirrhinum Lines

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

A 3D Cu‐Naphthalene‐Phosphonate Metal–Organic Framework with Ultra‐High Electrical Conductivity

A conductive phosphonate metal–organic framework (MOF), [{Cu(H2O)}(2,6‐NDPA)0.5] (NDPA = naphthalenediphosphonic acid), which contains a 2D inorganic building unit (IBU) comprised of a continuous edge‐sharing sheet of copper phosphonate polyhedra is reported. The 2D IBUs are connected to each other via polyaromatic 2,6‐NDPA's, forming a 3D pillared‐layered MOF structure. This MOF, known as TUB40, has a narrow band gap of 1.42 eV, a record high average electrical conductance of 2 × 102 S m−1 at room temperature based on single‐crystal conductivity measurements, and an electrical conductance of 142 S m−1 based on a pellet measurement. Density functional theory (DFT) calculations reveal that the conductivity is due to an excitation from the highest occupied molecular orbital on the naphthalene‐building unit to the lowest unoccupied molecular orbital on the copper atoms. Temperature‐dependent magnetization measurements show that the copper atoms are antiferromagnetically coupled at very low temperatures, which is also confirmed by the DFT calculations. Due to its high conductance and thermal/chemical stability, TUB40 may prove useful as an electrode material in supercapacitors

Hole-Hole Contact Interaction in the t-J Model

Using an analytical variational approach we calculate the hole-hole contact interaction on the N\'{e}el background. Solution of the Bethe-Salpeter equation with this interaction gives bound states in $d$- and p-waves with binding energies close to those obtained by numerical methods. At $t/J \ge 2-3$ the bound state disappears. In conclusion we discuss the relation between short range and long range interactions and analogy with the problem of pion condensation in nuclear matter.Comment: 11 pp. (LATEX), 7 figures (PostScript) appended, report N

AP-1 imprints a reversible transcriptional program of senescent cells

Senescent cells affect many physiological and pathophysiological processes. While select genetic and epigenetic elements for senescence induction have been identified, the dynamics, epigenetic mechanisms and regulatory networks defining senescence competence, induction and maintenance remain poorly understood, precluding the deliberate therapeutic targeting of senescence for health benefits. Here, we examined the possibility that the epigenetic state of enhancers determines senescent cell fate. We explored this by generating time-resolved transcriptomes and epigenome profiles during oncogenic RAS-induced senescence and validating central findings in different cell biology and disease models of senescence. Through integrative analysis and functional validation, we reveal links between enhancer chromatin, transcription factor recruitment and senescence competence. We demonstrate that activator protein 1 (AP-1) ‘pioneers’ the senescence enhancer landscape and defines the organizational principles of the transcription factor network that drives the transcriptional programme of senescent cells. Together, our findings enabled us to manipulate the senescence phenotype with potential therapeutic implications

Genomic Position Mapping Discrepancies of Commercial SNP Chips

The field of genetics has come to rely heavily on commercial genotyping arrays and accompanying annotations for insights into genotype-phenotype associations. However, in order to avoid errors and false leads, it is imperative that the annotation of SNP chromosomal positions is accurate and unambiguous. We report on genomic positional discrepancies of various SNP chips for human, cattle and mouse species, and discuss their causes and consequences

Lower cardiorespiratory fitness contributes to increased insulin resistance and fasting glycaemia in middle-aged South Asian compared with European men living in the UK

AIMS/HYPOTHESIS: This study aimed to determine the extent to which increased insulin resistance and fasting glycaemia in South Asian men, compared with white European men, living in the UK, was due to lower cardiorespiratory fitness (maximal oxygen uptake [[Formula: see text]]) and physical activity. METHODS: One hundred South Asian and 100 age- and BMI-matched European men without diagnosed diabetes, aged 40–70 years, had fasted blood taken for measurement of glucose concentration, HOMA-estimated insulin resistance (HOMA(IR)), plus other risk factors, and underwent assessment of physical activity (using accelerometry), [Formula: see text], body size and composition, and demographic and other lifestyle factors. For 13 South Asian and one European man, HbA(1c) levels were >6.5% (>48 mmol/mol), indicating potential undiagnosed diabetes; these men were excluded from the analyses. Linear regression models were used to determine the extent to which body size and composition, fitness and physical activity variables explained differences in HOMA(IR) and fasting glucose between South Asian and European men. RESULTS: HOMA(IR) and fasting glucose were 67% (p < 0.001) and 3% (p < 0.018) higher, respectively, in South Asians than Europeans. Lower [Formula: see text], lower physical activity and greater total adiposity in South Asians individually explained 68% (95% CI 45%, 91%), 29% (11%, 46%) and 52% (30%, 80%), respectively, and together explained 83% (50%, 119%) (all p < 0.001) of the ethnic difference in HOMA(IR). Lower [Formula: see text] and greater total adiposity, respectively, explained 61% (9%, 111%) and 39% (9%, 76%) (combined effect 63% [8%, 115%]; all p < 0.05) of the ethnic difference in fasting glucose. CONCLUSIONS/INTERPRETATION: Lower cardiorespiratory fitness is a key factor associated with the excess insulin resistance and fasting glycaemia in middle-aged South Asian, compared with European, men living in the UK. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00125-013-2969-y) contains peer-reviewed but unedited supplementary material, which is available to authorised users