Protein structure and conformational changes studied by Fourier transform infrared spectroscopy

Fourier transform infrared spectroscopy (FTIR) has been used to study a range of different proteins. These include:- i) Human serum transferrin, human lactoferrin and rabbit serum transferrin. A study has been made of the structural changes that accompany iron binding and release from these related proteins. Structural variations within this group of proteins have been shown. Thermal denaturation studies, using differential scanning calorimetric measurements, have been related to FTIR spectral changes and indicate that the crystal structure of iron-free human lactoferrin may not reflect the structure of this protein in solution. ii) Human placental transferrin receptor. This protein has been examined at extracellular and endosomal pH. Both the intact protein in detergent and its water soluble major extracellular fragment have been investigated. iii) The bacterial adhesive protein streptococcal antigen I/II. The solution structure and thermal stability of the native protein, the recombinant full-length protein and four recombinant fragments of this protein have been examined using both Fourier transform infrared spectroscopy and circular dichroism spectroscopy. iv) Albumin, IgG, Ribonuclease, Fibrinogen, A study of the thermal stability of these and other proteins has been undertaken to compare their denaturation properties in H2O and 2H2O solutions. v) Lysozyme, Ribonuclease These and several other proteins have been examined using Fourier transform infrared microscopy in order to compare the infrared spectra of these proteins, both in solution and also in the form of single crystals. Many of the proteins show similar spectra, whether recorded in solution or from a single crystal. In some cases, as with single crystals oi Endothia parasitica pepsin, Mucor pucillus pepsin and serum amyloid P component, the spectra differ from those recorded in solution. These differences may indicate that a rearrangement of turns structures occurs upon crystallisation. The major novel findings of this work are: i) There are small but significant structural differences between human serum transferrin, rabbit serum transferrin and human lactoferrin. The crystal structure of human lactoferrin may not represent the structure of this protein in solution. The apparent conflict between CD, FTIR and X-ray crystallographic estimates of secondary structural content of the transferrins can be explained by the fact that CD estimates are based on dihedral angles and not hydrogen bonding patterns. ii) Intact transferrin receptor precipitates out of solution at endosomal pH while the extracellular fragment remains soluble but undergoes a conformational change. This results in minor change in the secondary structural content of the protein and a reduction of thermal stability by approximately 15°C. iii) The recombinant polypeptides produced to study the structure of streptococcal antigen I/II have been shown to fold into defined secondary structures. Furthermore the structures of these fragments have been used to predict a possible structure for the native protein. iv) Quantitative analysis of thermally induced changes in the FTIR spectra of proteins in H2O solution may not offer any significant advantage to analyses performed in 2H2O due to problems associated with the different molar absorption coefficients of the separate secondary structures in H2O solution. v) Infrared spectroscopy/microscopy can be successfully be applied to the study of protein structure in both the solution and crystalline form

Addressing the accountability challenges of international policing in peace support operations

"There is increasing concern over the behaviour and accountability of international personnel, including CIVPOL contingents, deployed in peace-keeping and peace-building missions throughout the world. From the point of view of local populations the ‘internationals’ are typically perceived to be ‘above the law’. This is directly related to the fact that under status of forces or mission agreements (SOFAs or SOMAs) they are exempt from local host state jurisdiction. There are also significant practical problems in gathering and presenting evidence for disciplinary or criminal proceedings in their home states. This paper will analyse these problems in detail, based on a study of some recent European Union and international missions and suggest how a more co-operative home and host state approach to monitoring, investigation and adjudication of alleged misconduct might achieve more effective accountability and thus contribute to the overall success of CIVPOL missions." [auhtor's abstract

The gold standard: accurate stellar and planetary parameters for eight Kepler M dwarf systems enabled by parallaxes

We report parallaxes and proper motions from the Hawaii Infrared Parallax Program for eight nearby M dwarf stars with transiting exoplanets discovered by Kepler. We combine our directly measured distances with mass-luminosity and radius–luminosity relationships to significantly improve constraints on the host stars’ properties. Our astrometry enables the identification of wide stellar companions to the planet hosts. Within our limited sample, all the multi-transiting planet hosts (three of three) appear to be single stars, while nearly all (four of five) of the systems with a single detected planet have wide stellar companions. By applying strict priors on average stellar density from our updated radius and mass in our transit fitting analysis, we measure the eccentricity probability distributions for each transiting planet. Planets in single-star systems tend to have smaller eccentricities than those in binaries, although this difference is not significant in our small sample. In the case of Kepler-42bcd, where the eccentricities are known to be ≃0, we demonstrate that such systems can serve as powerful tests of M dwarf evolutionary models by working in L⋆ − ρ⋆ space. The transit-fit density for Kepler- 42bcd is inconsistent with model predictions at 2.1σ (22%), but matches more empirical estimates at 0.2σ (2%), consistent with earlier results showing model radii of M dwarfs are underinflated. Gaia will provide high-precision parallaxes for the entire Kepler M dwarf sample, and TESS will identify more planets transiting nearby, late-type stars, enabling significant improvements in our understanding of the eccentricity distribution of small planets and the parameters of late-type dwarfs.Support for Program number HST-HF2-51364.001-A was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555.Some of the data presented in this paper were obtained from the Mikulski Archive for Space Telescopes (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Support for MAST for non-HST data is provided by the NASA Office of Space Science via grant NNX09AF08G and by other grants and contracts. This paper includes data collected by the Kepler mission. Funding for the Kepler mission is provided by the NASA Science Mission directorate. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing HPC resources that have contributed to the research results reported within this paper. URL: http://www.tacc.utexas.edu. (HST-HF2-51364.001-A - NASA through Space Telescope Science Institute; NAS5-26555 - NASA; NNX09AF08G - NASA Office of Space Science; NASA Science Mission directorate

Propagation probability and spread rates of self-sustained smouldering fires under controlled moisture content and bulk density conditions

The consumption of large areas of peat during wildfires is due to self-sustained smouldering fronts that can remain active for weeks. We studied the effect of peat moisture content and bulk density on the horizontal propagation of smouldering fire in laboratory-scale experiments. We used milled peat with moisture contents between 25 and 250% (mass of water per mass of dry peat) and bulk densities between 50 and 150 kg m–3. An infrared camera monitored ignition, spread and extinction of each smouldering combustion front. Peats with a bulk density below 75 kg m–3 and a moisture content below 150% self-sustained smouldering propagation for more than 12 cm. Peat with a bulk density of 150 kg m–3 could self-sustain smouldering propagation up to a critical moisture content of 115%. A linear model estimated that increasing both moisture content and bulk density significantly reduced the median fire spread rate (which ranged between 1 and 5 cm h–1). Moisture content had a stronger effect size on the spread rate than bulk density. However, the effect of bulk density on spread rate depends upon the moisture content, with the largest effect of bulk density at low moisture contents.European Commission - European Regional Development FundEuropean Research CouncilHigher Education Authorit

The L 98-59 System: Three Transiting, Terrestrial-size Planets Orbiting a Nearby M Dwarf

We report the Transiting Exoplanet Survey Satellite (TESS) discovery of three terrestrial-size planets transiting L 98-59 (TOI-175, TIC 307210830)-a bright M dwarf at a distance of 10.6 pc. Using the Gaia-measured distance and broadband photometry, we find that the host star is an M3 dwarf. Combined with the TESS transits from three sectors, the corresponding stellar parameters yield planet radii ranging from 0.8 R ⊕ to 1.6 R ⊕. All three planets have short orbital periods, ranging from 2.25 to 7.45 days with the outer pair just wide of a 2:1 period resonance. Diagnostic tests produced by the TESS Data Validation Report and the vetting package DAVE rule out common false-positive sources. These analyses, along with dedicated follow-up and the multiplicity of the system, lend confidence that the observed signals are caused by planets transiting L 98-59 and are not associated with other sources in the field. The L 98-59 system is interesting for a number of reasons: the host star is bright (V = 11.7 mag, K = 7.1 mag) and the planets are prime targets for further follow-up observations including precision radial-velocity mass measurements and future transit spectroscopy with the James Webb Space Telescope; the near-resonant configuration makes the system a laboratory to study planetary system dynamical evolution; and three planets of relatively similar size in the same system present an opportunity to study terrestrial planets where other variables (age, metallicity, etc.) can be held constant. L 98-59 will be observed in four more TESS sectors, which will provide a wealth of information on the three currently known planets and have the potential to reveal additional planets in the system.Funding for the TESS mission is provided by NASA’s Science Mission directorate. Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) ERC grant agreement No. 336480, and from the ARC grant for Concerted Research Actions, financed by the Wallonia-Brussels Federatio

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper