Entropy concepts and DNA investigations

Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a maximum of heterogeneity. It falls in the block length interval [5,7]. Maximum distinction between natural and artificial sequences is shifted on 1-3 position from the maximum of heterogeneity to the right as for metric as for topological entropy. This point on the specificity of real DNA sequences in the interval.Comment: 10 pages 7 figures submitted to PL

Laser induced surface acoustic wave combined with phase sensitive optical coherence tomography for superficial tissue characterization:a solution for practical application

Mechanical properties are important parameters that can be used to assess the physiologic conditions of biologic tissue. Measurements and mapping of tissue mechanical properties can aid in the diagnosis, characterisation and treatment of diseases. As a non-invasive, non-destructive and non-contact method, laser induced surface acoustic waves (SAWs) have potential to accurately characterise tissue elastic properties. However, challenge still exists when the laser is directly applied to the tissue because of potential heat generation due to laser energy deposition. This paper focuses on the thermal effect of the laser induced SAW on the tissue target and provides an alternate solution to facilitate its application in clinic environment. The solution proposed is to apply a thin agar membrane as surface shield to protect the tissue. Transient thermal analysis is developed and verified by experiments to study the effects of the high energy Nd:YAG laser pulse on the surface shield. The approach is then verified by measuring the mechanical property of skin in a Thiel mouse model. The results demonstrate a useful step toward the practical application of laser induced SAW method for measuring real elasticity of normal and diseased tissues in dermatology and other surface epithelia

Global search for autumn‐lead sea surface salinity predictors of winter precipitation in southwestern United States

Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 45 (2018): 8445-8454, doi:10.1029/2018GL079293.Sea surface salinity (SSS) is sensitive to changes in ocean evaporation and precipitation, that is, to changes in the oceanic water cycle. Through the close connection between the oceanic and terrestrial water cycle, SSS can be used as an indicator of rainfall on land. Here we search globally for teleconnections between autumn‐lead September‐October‐November SSS signals and winter December‐January‐February precipitation over southwestern United States. The SSS‐based model (R2 = 0.61) outperforms the sea surface temperature‐based model (R2 = 0.54). Further, a fresh tropical Pacific in autumn, indicated by low SSS, corresponds with wet winters. Recent studies suggest that anomalously high rainfall in the tropics may excite Rossby waves that can export water to the extratropics. Thus, incorporating SSS, a sensitive indicator of regional oceanic rainfall, can enhance the accuracy of existing precipitation prediction frameworks that rely on sea surface temperature‐based climate indices and, by extension, improve watershed management.NSF Grant Numbers: ICER‐1663704, ICER‐1663138, DGE1144152, DGE1745303; Woods Hole Oceanographic Institution2019-02-2

The role of the subtropical North Atlantic water cycle in recent US extreme precipitation events

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Climate Dynamics 50 (2018): 1291–1305, doi:10.1007/s00382-017-3685-y.The role of the oceanic water cycle in the record-breaking 2015 warm-season precipitation in the US is analyzed. The extreme precipitation started in the Southern US in the spring and propagated northward to the Midwest and the Great Lakes in the summer of 2015. This seasonal evolution of precipitation anomalies represents a typical mode of variability of US warm-season precipitation. Analysis of the atmospheric moisture flux suggests that such a rainfall mode is associated with moisture export from the subtropical North Atlantic. In the spring, excessive precipitation in the Southern US is attributable to increased moisture flux from the northwestern portion of the subtropical North Atlantic. The North Atlantic moisture flux interacts with local soil moisture which enables the US Midwest to draw more moisture from the Gulf of Mexico in the summer. Further analysis shows that the relationship between the rainfall mode and the North Atlantic water cycle has become more significant in recent decades, indicating an increased likelihood of extremes like the 2015 case. Indeed, two record-high warm-season precipitation events, the 1993 and 2008 cases, both occurred in the more recent decades of the 66 year analysis period. The export of water from the North Atlantic leaves a marked surface salinity signature. The salinity signature appeared in the spring preceding all three extreme precipitation events analyzed in this study, i.e. a saltier-than-normal subtropical North Atlantic in spring followed by extreme Midwest precipitation in summer. Compared to the various sea surface temperature anomaly patterns among the 1993, 2008, and 2015 cases, the spatial distribution of salinity anomalies was much more consistent during these extreme flood years. Thus, our study suggests that preseason salinity patterns can be used for improved seasonal prediction of extreme precipitation in the Midwest.LL is supported by the Postdoctoral Scholar Program at WHOI, with funding provided by the Oceans and Climate Change Institute. RWS is supported by NASA Grants NNX12AF59G and NNX14AH38G, and NSF Grant OCE-1129646. CCU is supported by NSF Grant AGS-1355339

Moduli of ADHM Sheaves and Local Donaldson-Thomas Theory

The ADHM construction establishes a one-to-one correspondence between framed torsion free sheaves on the projective plane and stable framed representations of a quiver with relations in the category of complex vector spaces. This paper studies the geometry of moduli spaces of representations of the same quiver with relations in the abelian category of coherent sheaves on a smooth complex projective curve $X$. In particular it is proven that this moduli space is virtually smooth and related byrelative Beilinson spectral sequence to the curve counting construction via stable pairs of Pandharipande and Thomas. This yields a new conjectural construction for the local Donaldson-Thomas theory of curves as well as a natural higher rank generalization.Comment: 61 pages AMS Latex; v2: minor corrections, reference added; v3: some proofs corrected using the GIT construction of the moduli space due to A. Schmitt; main results unchanged; final version to appear in J. Geom. Phy

Boosting endoplasmic reticulum folding capacity reduces unfolded protein response activation and intracellular accumulation of human kidney anion exchanger 1 in Saccharomyces cerevisiae

Human kidney anion exchanger 1 (kAE1) facilitates simultaneous efflux of bicarbonate and absorption of chloride at the basolateral membrane of α-intercalated cells. In these cells, kAE1 contributes to systemic acid–base balance along with the proton pump v-H+-ATPase and the cytosolic carbonic anhydrase II. Recent electron microscopy analyses in yeast demonstrate that heterologous expression of several kAE1 variants causes a massive accumulation of the anion transporter in intracellular membrane structures. Here, we examined the origin of these kAE1 aggregations in more detail. Using various biochemical techniques and advanced light and electron microscopy, we showed that accumulation of kAE1 mainly occurs in endoplasmic reticulum (ER) membranes which eventually leads to strong unfolded protein response (UPR) activation and severe growth defect in kAE1 expressing yeast cells. Furthermore, our data indicate that UPR activation is dose dependent and uncoupled from the bicarbonate transport activity. By using truncated kAE1 variants, we identified the C-terminal region of kAE1 as crucial factor for the increased ER stress level. Finally, a redistribution of ER-localized kAE1 to the cell periphery was achieved by boosting the ER folding capacity. Our findings not only demonstrate a promising strategy for preventing intracellular kAE1 accumulation and improving kAE1 plasma membrane targeting but also highlight the versatility of yeast as model to investigate kAE1-related research questions including the analysis of structural features, protein degradation and trafficking. Furthermore, our approach might be a promising strategy for future analyses to further optimize the cell surface targeting of other disease-related PM proteins, not only in yeast but also in mammalian cells. Take Away We analysed the intracellular transport of human kAE1 to the yeast plasma membrane. We studied the effect of human kAE1 expression on yeast growth and UPR activation. We investigated the impact of different kAE1 truncation variants on UPR induction We implemented intervention strategies to improve PM targeting of kAE1

Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana

Relating molecular variation to phenotypic diversity is a central goal in evolutionary biology. In Arabidopsis thaliana, FLOWERING LOCUS C (FLC) is a major determinant of variation in vernalization—the acceleration of flowering by prolonged cold. Here, through analysis of 1307 A. thaliana accessions, we identify five predominant FLC haplotypes defined by noncoding sequence variation. Genetic and transgenic experiments show that they are functionally distinct, varying in FLC expression level and rate of epigenetic silencing. Allelic heterogeneity at this single locus accounts for a large proportion of natural variation in vernalization that contributes to adaptation of A. thaliana

Artificial quantum confinement in LAO3/STO heterostructure

Heterostructures of transition metal oxides (TMO) perovskites represent an ideal platform to explore exotic phenomena involving the complex interplay between the spin, charge, orbital and lattice degrees of freedom available in these compounds. At the interface between such materials, this interplay can lead to phenomena that are present in none of the original constituents such as the formation of the interfacial 2D electron system (2DES) discovered at the LAO3/STO3 (LAO/STO) interface. In samples prepared by growing a LAO layer onto a STO substrate, the 2DES is confined in a band bending potential well, whose width is set by the interface charge density and the STO dielectric properties, and determines the electronic band structure. Growing LAO (2 nm) /STO (x nm)/LAO (2 nm) heterostructures on STO substrates allows us to control the extension of the confining potential of the top 2DES via the thickness of the STO layer. In such samples, we explore the dependence of the electronic structure on the width of the confining potential using soft X-ray ARPES combined with ab-initio calculations. The results indicate that varying the thickness of the STO film modifies the quantization of the 3d t2g bands and, interestingly, redistributes the charge between the dxy and dxz/dyz bands

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression.

While genetic variation at chromatin loops is relevant for human disease, the relationships between contact propensity (the probability that loci at loops physically interact), genetics, and gene regulation are unclear. We quantitatively interrogate these relationships by comparing Hi-C and molecular phenotype data across cell types and haplotypes. While chromatin loops consistently form across different cell types, they have subtle quantitative differences in contact frequency that are associated with larger changes in gene expression and H3K27ac. For the vast majority of loci with quantitative differences in contact frequency across haplotypes, the changes in magnitude are smaller than those across cell types; however, the proportional relationships between contact propensity, gene expression, and H3K27ac are consistent. These findings suggest that subtle changes in contact propensity have a biologically meaningful role in gene regulation and could be a mechanism by which regulatory genetic variants in loop anchors mediate effects on expression