Protein and DNA sequence determinants of thermophilic adaptation

Prokaryotes living at extreme environmental temperatures exhibit pronounced signatures in the amino acid composition of their proteins and nucleotide compositions of their genomes reflective of adaptation to their thermal environments. However, despite significant efforts, the definitive answer of what are the genomic and proteomic compositional determinants of Optimal Growth Temperature of prokaryotic organisms remained elusive. Here the authors performed a comprehensive analysis of amino acid and nucleotide compositional signatures of thermophylic adaptation by exhaustively evaluating all combinations of amino acids and nucleotides as possible determinants of Optimal Growth Temperature for all prokaryotic organisms with fully sequences genomes.. The authors discovered that total concentration of seven amino acids in proteomes, IVYWREL, serves as a universal proteomic predictor of Optimal Growth Temperature in prokaryotes. Resolving the old-standing controversy the authors determined that the variation in nucleotide composition (increase of purine load, or A+G content with temperature) is largely a consequence of thermal adaptation of proteins. However, the frequency with which A and G nucleotides appear as nearest neighbors in genome sequences is strongly and independently correlated with Optimal Growth Temperature. as a result of codon bias in corresponding genomes. Together these results provide a complete picture of proteomic and genomic determinants of thermophilic adaptation.Comment: in press PLoS Computational Biology; revised versio

Practical guidance for applying the ADNEX model from the IOTA group to discriminate between different subtypes of adnexal tumors.

All gynecologists are faced with ovarian tumors on a regular basis, and the accurate preoperative diagnosis of these masses is important because appropriate management depends on the type of tumor. Recently, the International Ovarian Tumor Analysis (IOTA) consortium published the Assessment of Different NEoplasias in the adneXa (ADNEX) model, the first risk model that differentiates between benign and four types of malignant ovarian tumors: borderline, stage I cancer, stage II-IV cancer, and secondary metastatic cancer. This approach is novel compared to existing tools that only differentiate between benign and malignant tumors, and therefore questions may arise on how ADNEX can be used in clinical practice. In the present paper, we first provide an in-depth discussion about the predictors used in ADNEX and the ability for risk prediction with different tumor histologies. Furthermore, we formulate suggestions about the selection and interpretation of risk cut-offs for patient stratification and choice of appropriate clinical management. This is illustrated with a few example patients. We cannot propose a generally applicable algorithm with fixed cut-offs, because (as with any risk model) this depends on the specific clinical setting in which the model will be used. Nevertheless, this paper provides a guidance on how the ADNEX model may be adopted into clinical practice

H-ATLAS: a candidate high redshift cluster/protocluster of star-forming galaxies

We investigate the region around the Planck-detected z=3.26 gravitationally lensed galaxy HATLAS J114637.9-001132 (hereinafter HATLAS12-00) using both archival Herschel data from the H-ATLAS survey and using submm data obtained with both LABOCA and SCUBA2. The lensed source is found to be surrounded by a strong overdensity of both Herschel-SPIRE sources and submm sources. We detect 17 bright (S870 >~7 mJy) sources at >4sigma closer than 5 arcmin to the lensed object at 850/870 microns. Ten of these sources have good cross-identifications with objects detected by Herschel-SPIRE which have redder colours than other sources in the field, with 350 micron flux > 250 micron flux, suggesting that they lie at high redshift. Submillimeter Array (SMA) observations localise one of these companions to ~1 arcsecond, allowing unambiguous cross identification with a 3.6 and 4.5 micron Spitzer source. The optical/near-IR spectral energy distribution (SED) of this source is measured by further observations and found to be consistent with z>2, but incompatible with lower redshifts. We conclude that this system may be a galaxy cluster/protocluster or larger scale structure that contains a number of galaxies undergoing starbursts at the same time

Isotope effect in impure high T_c superconductors

The influence of various kinds of impurities on the isotope shift exponent \alpha of high temperature superconductors has been studied. In these materials the dopant impurities, like Sr in La_{2-x}Sr_xCuO_4, play different role and usually occupy different sites than impurities like Zn, Fe, Ni {\it etc} intentionally introduced into the system to study its superconducting properties. In the paper the in-plane and out-of-plane impurities present in layered superconductors have been considered. They differently affect the superconducting transition temperature T_c. The relative change of isotope shift coefficient, however, is an universal function of T_c/T_{c0} (T_{c0} reffers to impurity free system) {\it i.e.} for angle independent scattering rate and density of states function it does not depend whether the change of T_c is due to in- or out-of-plane impurities. The role of the anisotropic impurity scattering in changing oxygen isotope coefficient of superconductors with various symmetries of the order parameter is elucidated. The comparison of the calculated and experimental dependence of \alpha/\alpha_0, where \alpha_0 is the clean system isotope shift coefficient, on T_c/T_{c0} is presented for a number of cases studied. The changes of \alpha calculated within stripe model of superconductivity in copper oxides resonably well describe the data on La_{1.8}Sr_{0.2}Cu_{1-x}(Fe,Ni)_xO_4, without any fitting parameters.Comment: 8 pages, 6 figures, Phys. Rev. B67 (2003) accepte

LOFAR/H-ATLAS: The low-frequency radio luminosity - star-formation rate relation

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society. © 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society.Radio emission is a key indicator of star-formation activity in galaxies, but the radio luminosity-star formation relation has to date been studied almost exclusively at frequencies of 1.4 GHz or above. At lower radio frequencies the effects of thermal radio emission are greatly reduced, and so we would expect the radio emission observed to be completely dominated by synchrotron radiation from supernova-generated cosmic rays. As part of the LOFAR Surveys Key Science project, the Herschel-ATLAS NGP field has been surveyed with LOFAR at an effective frequency of 150 MHz. We select a sample from the MPA-JHU catalogue of SDSS galaxies in this area: the combination of Herschel, optical and mid-infrared data enable us to derive star-formation rates (SFRs) for our sources using spectral energy distribution fitting, allowing a detailed study of the low-frequency radio luminosity--star-formation relation in the nearby Universe. For those objects selected as star-forming galaxies (SFGs) using optical emission line diagnostics, we find a tight relationship between the 150 MHz radio luminosity ($L_{150}$) and SFR. Interestingly, we find that a single power-law relationship between $L_{150}$ and SFR is not a good description of all SFGs: a broken power law model provides a better fit. This may indicate an additional mechanism for the generation of radio-emitting cosmic rays. Also, at given SFR, the radio luminosity depends on the stellar mass of the galaxy. Objects which were not classified as SFGs have higher 150-MHz radio luminosity than would be expected given their SFR, implying an important role for low-level active galactic nucleus activity.Peer reviewedFinal Published versio

Cortical Factor Feedback Model for Cellular Locomotion and Cytofission

Eukaryotic cells can move spontaneously without being guided by external cues. For such spontaneous movements, a variety of different modes have been observed, including the amoeboid-like locomotion with protrusion of multiple pseudopods, the keratocyte-like locomotion with a widely spread lamellipodium, cell division with two daughter cells crawling in opposite directions, and fragmentations of a cell to multiple pieces. Mutagenesis studies have revealed that cells exhibit these modes depending on which genes are deficient, suggesting that seemingly different modes are the manifestation of a common mechanism to regulate cell motion. In this paper, we propose a hypothesis that the positive feedback mechanism working through the inhomogeneous distribution of regulatory proteins underlies this variety of cell locomotion and cytofission. In this hypothesis, a set of regulatory proteins, which we call cortical factors, suppress actin polymerization. These suppressing factors are diluted at the extending front and accumulated at the retracting rear of cell, which establishes a cellular polarity and enhances the cell motility, leading to the further accumulation of cortical factors at the rear. Stochastic simulation of cell movement shows that the positive feedback mechanism of cortical factors stabilizes or destabilizes modes of movement and determines the cell migration pattern. The model predicts that the pattern is selected by changing the rate of formation of the actin-filament network or the threshold to initiate the network formation

Primary leptomeningeal oligodendrogliomatosis

Primary leptomeningeal oligodendrogliomas (PLOs) are rare intracranial malignancies where tumors grow in the subarachnoid space without an obvious connection to the brain or spinal cord parenchyma. Adding to the three previously reported cases of PLO with no parenchymal involvement we report a fourth case of the same in this paper in a 50-year-old woman presenting with unrelenting headaches. CT scan of her head revealed hydrocephalus and MRI revealed diffuse enhancement of her leptomeninges throughout her brain and spine, prominent over the basilar region. Biopsy obtained using a frameless stereotactic biopsy showed sharply defined cell borders, clear cytoplasm, and rounded nuclei consistent with an oligodendroglioma. Our case suggests that PLO can mimic diffuse forms of granulomatous meningitis and should be suspected in patients that clinically and radiographically present like granulomatous meningitis but without blood or CSF markers for the same

Transgressing the moral economy: Wheelerism and management of the nationalised coal industry in Scotland

This article illuminates the links between managerial style and political economy in post-1945 Britain, and explores the origins of the 1984–1985 miners' strike, by examining in longer historical context the abrasive attitudes and policies of Albert Wheeler, Scottish Area Director of the National Coal Board (NCB). Wheeler built on an earlier emphasis on production and economic criteria, and his micro-management reflected pre-existing centralising tendencies in the industries. But he was innovative in one crucial aspect, transgressing the moral economy of the Scottish coalfield, which emphasised the value of economic security and changes by joint industrial agreement

Modelling direct and indirect water requirements of construction

Water consumed directly by the construction industry is known to be of little importance. However, water consumed in the manufacture of goods and services required by construction may be significant in the context of a building\u27s life cycle water requirements and the national water budget. This paper evaluates the significance of water embodied in the construction of individual buildings. To do this, an input-output-based hybrid embodied water analysis was undertaken on 17 Australian non-residential case studies. It was found that there is a considerable amount of water embodied in construction. The highest value was 20.1 kilolitres (kL)/m2 gross floor area (GFA), representing many times the enclosed volume of the building, and many years worth of operational water. The water required by the main construction process is minimal. However, the water embodied in building materials is considerable. These findings suggest that the selection of elements and materials has a great impact on a building\u27s embodied water. This research allows the construction industry to evaluate design and construction in broad environmental terms to select options that might be cost neutral or possibly cost positive while retaining their environmental integrity. The research suggests policies focused on operational water consumption alone are inadequate. <br /