A proposed mechanism for IS607-family serine transposases

Background The transposases encoded by the IS607 family of mobile elements are unusual serine recombinases with an inverted domain order and minimal specificity for target DNA.<p></p> Results Structural genomics groups have determined three crystal structures of the catalytic domains of IS607 family transposases. The dimers formed by these catalytic domains are very different from those seen for other serine recombinases and include interactions that usually only occur upon formation of a synaptic tetramer.<p></p> Conclusions Based on these structures, we propose a model for how IS607-family transposases could form a synaptic tetramer. The model suggests that, unlike other serine recombinases, these enzymes carry out sequence-specific DNA binding and catalysis in trans: the DNA binding and catalytic domains of each subunit are proposed to interact with different DNA duplexes. The model also suggests an explanation for the minimal target DNA specificity.<p></p&gt

Scaled Correlations of Critical Points of Random Sections on Riemann Surfaces

In this paper we prove that as N goes to infinity, the scaling limit of the correlation between critical points z1 and z2 of random holomorphic sections of the N-th power of a positive line bundle over a compact Riemann surface tends to 2/(3pi^2) for small sqrt(N)|z1-z2|. The scaling limit is directly calculated using a general form of the Kac-Rice formula and formulas and theorems of Pavel Bleher, Bernard Shiffman, and Steve Zelditch.Comment: 55 pages. LaTeX. output.txt is the output of running heisenberg_simpler.mpl through maple. heisenberg_simpler.mpl can be run by maple at the command line by saying 'maple -q heisenberg_simpler.mpl' to see the maple calculations that generated the matrices U(t) and D(t) described in the paper's appendix. It may also be run by opening it with GUI mapl

Spatial variation in directional swimming enables juvenile sea turtles to reach and remain in productive waters

Ocean currents play an important role in the movement and distribution of organisms and for small animals it is often assumed that their movements in the ocean are determined by passive drift. Here we challenge this assumption by conducting an experiment at the scale of an entire ocean basin to test whether small (∼35 cm) juvenile loggerhead sea turtles Caretta caretta move independently of ocean currents. By comparing the trajectories of 46 satellite tracked turtles (11502 positions, 12850 tracking days) with Lagrangian drifters (3716303 positions, 927529 tracking days) and virtual particles tracked within the Hybrid Coordinate Ocean Model (HYCOM), we found that in certain areas turtles moved in a similar manner to ocean currents, but in other areas turtle movement was markedly different from ocean currents, with turtles moving to areas thousands of kilometres from where they would have drifted passively. We further found that turtles were distributed in more-productive areas than would be expected if their movement depended on passive transport only. These findings demonstrate that regional variation in directional swimming contributes to young sea turtles reaching more favourable developmental habitats and supports laboratory work suggesting that young turtles have a map sense to determine their location in a seemingly featureless ocean

Triton photodisintegration in three-dimensional approach

Two- and three- particles photodisintegration of the triton is investigated in a three-dimensional (3D) Faddeev approach. For this purpose the Jacobi momentum vectors for three particles system and spin-isospin quantum numbers of the individual nucleons are considered. Based on this picture the three-nucleon Faddeev integral equations with the two-nucleon interaction are formulated without employing the partial wave decomposition. The single nucleon current as well as $\pi-$ and $\rho-$ like exchange currents are used in an appropriate form to be employed in 3D approach. The exchange currents are derived from AV18 NN force. The two-body t-matrix, Deuteron and Triton wave functions are calculated in the 3D approach by using AV18 potential. Benchmarks are presented to compare the total cross section for the two- and three- particles photodisintegration in the range of $E_{\gamma}<30 MeV$. The 3D Faddeev approach shows promising results

Omega-6 to omega-3 polyunsaturated fatty acid ratio and subsequent mood disorders in young people with at-risk mental states: a 7-year longitudinal study

While cross-sectional studies suggest that patients with mood disorders have a higher ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) and lower levels of omega-3 PUFAs, it is unknown if a high n-6/3 ratio indicates vulnerability for depression. We tested this hypothesis in a 7-year follow-up study of young individuals with an ultra-high risk (UHR) phenotype. We conducted a secondary analysis of the Vienna omega-3 study, a longitudinal study of omega-3 PUFAs in individuals at UHR for psychosis (n = 69). Levels of n-6 and n-3 PUFAs were measured in the phosphatidylethanolamine fraction of erythrocyte membranes at intake into the study. Mood disorder diagnosis was ascertained with the Structured Clinical Interview for DSM-IV-TR and confirmed by review of medical records and interviews of caregivers. A higher n-6/3 PUFA ratio at baseline predicted mood disorders in UHR individuals over a 7-year (median) follow-up (odds ratio = 1.89, 95% CI = 1.075-3.338, P = 0.03). This association remained significant after adjustment for age, gender, smoking, severity of depressive symptoms at baseline and n-3 supplementation. Consistent results were obtained for individual PUFAs, including lower levels of eicosapentaenoic acid and docosahexaenoic acid. The predictive capacity of these findings was specific to mood disorders as no associations were found for any other psychiatric disorder. To our knowledge, our data provide the first prospective evidence that the n-6/3 PUFA ratio is associated with an increased risk for mood disorders in young people exhibiting an UHR phenotype. These findings may have important implications for treatment and risk stratification beyond clinical characteristics

Magnetotransport near a quantum critical point in a simple metal

We use geometric considerations to study transport properties, such as the conductivity and Hall coefficient, near the onset of a nesting-driven spin density wave in a simple metal. In particular, motivated by recent experiments on vanadium-doped chromium, we study the variation of transport coefficients with the onset of magnetism within a mean-field treatment of a model that contains nearly nested electron and hole Fermi surfaces. We show that most transport coefficients display a leading dependence that is linear in the energy gap. The coefficient of the linear term, though, can be small. In particular, we find that the Hall conductivity $\sigma_{xy}$ is essentially unchanged, due to electron-hole compensation, as the system goes through the quantum critical point. This conclusion extends a similar observation we made earlier for the case of completely flat Fermi surfaces to the immediate vicinity of the quantum critical point where nesting is present but not perfect.Comment: 11 pages revtex, 4 figure

Development of large fish farm numerical modeling techniques with in situ mooring tension comparisons

Author Posting. © Elsevier B.V., 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Aquacultural Engineering 36 (2007): 137-148, doi:10.1016/j.aquaeng.2006.10.001.A study is conducted to validate a numerical model for calculating mooring system tensions of a large fish farm containing 20 net pens in the absence of waves. The model is forced using measured current velocity values obtained outside of the farm. Mooring line tensions calculated with the numerical model are compared with load cell field data sets. The approach considers current velocity reduction and load characteristics that occur through the net pen system for both clean and fouled net conditions. Without accounting for the reduction, the numerical model produces excessively conservative results. With reduction, a substantial improvement occurs. Understanding these differences will help to establish appropriate safety factors when designing large marine fish farms using the model. Additional validation studies should be conducted with wave and current forcing to investigate the modeling large fish farms for exposed or open ocean sites.The authors would also like to express sincere thanks the National Oceanic and Atmospheric Administration for funding this project through the Saltonstall-Kennedy program under Grant NAO3NMF4270183

Formation of two-dimensional weak localization in conducting Langmuir-Blodgett films

We report the magnetotransport properties up to 7 T in the organic highly conducting Langmuir-Blodgett(LB) films formed by a molecular association of the electroactive donor molecule bis(ethylendioxy)tetrathiafulvalene (BEDO-TTF) and stearic acid CH$_3$(CH$_2$)$_{16}$COOH. We show the logarithmic decrease of dc conductivity and the negative transverse magnetoresistance at low temperature. They are interpreted in the weak localization of two-dimensional (2D) electronic system based on the homogeneous conducting layer with the molecular size thickness of BEDO-TTF. The electronic length with phase memory is given at the mesoscopic scale, which provides for the first time evidence of the 2D coherent charge transport in the conducting LB films.Comment: 5 pages, 1 Table and 5 figure

Targeting Toll-like receptor-4 to tackle preterm birth and fetal inflammatory injury

Every year, 15 million pregnancies end prematurely, resulting in more than 1 million infant deaths and long-term health consequences for many children. The physiological processes of labour and birth involve essential roles for immune cells and pro-inflammatory cytokines in gestational tissues. There is compelling evidence that the mechanisms underlying spontaneous preterm birth are initiated when a premature and excessive inflammatory response is triggered by infection or other causes. Exposure to pro-inflammatory mediators is emerging as a major factor in the 'fetal inflammatory response syndrome' that often accompanies preterm birth, where unscheduled effects in fetal tissues interfere with normal development and predispose to neonatal morbidity. Toll-like receptors (TLRs) are critical upstream gatekeepers of inflammatory activation. TLR4 is prominently involved through its ability to sense and integrate signals from a range of microbial and endogenous triggers to provoke and perpetuate inflammation. Preclinical studies have identified TLR4 as an attractive pharmacological target to promote uterine quiescence and protect the fetus from inflammatory injury. Novel small-molecule inhibitors of TLR4 signalling, specifically the non-opioid receptor antagonists (+)-naloxone and (+)-naltrexone, are proving highly effective in animal models for preventing preterm birth induced by bacterial mimetic LPS, heat-killed Escherichia coli, or the TLR4-dependent pro-inflammatory lipid, platelet-activating factor (PAF). Here, we summarise the rationale for targeting TLR4 as a master regulator of inflammation in fetal and gestational tissues, and the potential utility of TLR4 antagonists as candidates for preventative and therapeutic application in preterm delivery and fetal inflammatory injury.Sarah A Robertson, Mark R Hutchinson, Kenner C Rice, Peck-Yin Chin, Lachlan M Moldenhauer, Michael J Stark, David M Olson, Jeffrey A Keela

Effect of stress-triaxiality on void growth in dynamic fracture of metals: a molecular dynamics study

The effect of stress-triaxiality on growth of a void in a three dimensional single-crystal face-centered-cubic (FCC) lattice has been studied. Molecular dynamics (MD) simulations using an embedded-atom (EAM) potential for copper have been performed at room temperature and using strain controlling with high strain rates ranging from 10^7/sec to 10^10/sec. Strain-rates of these magnitudes can be studied experimentally, e.g. using shock waves induced by laser ablation. Void growth has been simulated in three different conditions, namely uniaxial, biaxial, and triaxial expansion. The response of the system in the three cases have been compared in terms of the void growth rate, the detailed void shape evolution, and the stress-strain behavior including the development of plastic strain. Also macroscopic observables as plastic work and porosity have been computed from the atomistic level. The stress thresholds for void growth are found to be comparable with spall strength values determined by dynamic fracture experiments. The conventional macroscopic assumption that the mean plastic strain results from the growth of the void is validated. The evolution of the system in the uniaxial case is found to exhibit four different regimes: elastic expansion; plastic yielding, when the mean stress is nearly constant, but the stress-triaxiality increases rapidly together with exponential growth of the void; saturation of the stress-triaxiality; and finally the failure.Comment: 35 figures, which are small (and blurry) due to the space limitations; submitted (with original figures) to Physical Review B. Final versio