Extracting Structural Information of a Heteropolymer from Force-Extension Curves

We present a theory for the reverse analysis on the sequence information of a single H/P two-letter random hetero-polymer (RHP) from its force-extension(f-z) curves during quasi static stretching. Upon stretching of a self-assembled RHP, it undergoes several structural transitions. The typical elastic response of a hetero-polymeric globule is a set of overlapping saw-tooth patterns. With consideration of the height and the position of the overlapping saw-tooth shape, we analyze the possibility of extracting the binding energies of the internal domains and the corresponding block sizes of the contributing conformations.Comment: 5 figures 7 page

Growth performances, chemical composition, and microbiological loads of mealworm reared with brewery spent grains and bread leftovers

Tenebrio molitor (mealworm) larvae are one of the most intriguing edible insects, and they may be raised on a variety of substrates, including by-products, side-stream products, and former foodstuff. The substrates could affect drastically the productive performances as well as the chemical-nutritional value of the larvae. In this study we tested two main substrate ingredients, brewery spent grains (SG) and bread leftovers (B), without adding any other dry ingredients. In order to correlate the chemical composition of the substrates to the larvae characteristics, five different diets were tested as 100% of a single ingredient (SG100 and B100), 75–25% mixes (SG75B25 and SG25B75) and 50–50% mixes (SG50B50). The effects of the substrate were tested on the development rates, chemical composition, and microbial loads of mealworm larvae. The effects of fasting, washing, and cooking were also tested on the microbiological determinations. Results indicate that all the parameters were affected by the chemical compositions of the substrates. The larvae fed the higher contents of SG showed the best growth performances along with higher nutritional values. The diet with only bread (B100) showed the worst parameters, both on the growth performances and on the nutritive values. Microbial loads were also affected by the diets, with minor effects in relation to the washing and fasting procedures, while cooking drastically reduced all the microbial loads. Taking into account that the two employed ingredients were former foodstuff or by-products it is important to highlight the capacity of mealworms to positively convert side-stream materials into rich nutritional animal products.Highlights Mealworm could be proficiently reared on brewery spent grains and bread leftovers converting them into nutritional animal products. Mealworm productive performances and nutritional value could be affected by the employed substrate. Evidence of high mealworms plasticity and potential tailor made of the final outcomes

Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry

P pili are multisubunit fibers essential for the attachment of uropathogenic Escherichia coli to the kidney. These fibers are formed by the noncovalent assembly of six different homologous subunit types in an array that is strictly defined in terms of both the number and order of each subunit type. Assembly occurs through a mechanism termed “donor-strand exchange (DSE)” in which an N-terminal extension (Nte) of one subunit donates a β-strand to an adjacent subunit, completing its Ig fold. Despite structural determination of the different subunits, the mechanism determining specificity of subunit ordering in pilus assembly remained unclear. Here, we have used noncovalent mass spectrometry to monitor DSE between all 30 possible pairs of P pilus subunits and their Ntes. We demonstrate a striking correlation between the natural order of subunits in pili and their ability to undergo DSE in vitro. The results reveal insights into the molecular mechanism by which subunit ordering during the assembly of this complex is achieved

First Order Bipolaronic Transition at Finite Temperature in the Holstein Model

We investigate the Holstein model by using the dynamical mean-field theory combined with the exact diagonalization method. Below a critical temperature Tcr, a coexistence of the polaronic and the bipolaronic solutions is found for the same value of the electron-phonon coupling $ in the range gc1(T)<g<gc2(T). In the coexistence region, the system shows a first order phase transition from the bipolaronic to the polaronic states as T decreases at T=Tp(<Tcr), where the double occupancy and the lattice fluctuation together with the anharmonicity of the effective ion potential change discontinuously without any symmetry breaking. The obtained bipolaronic transition seems to be consistent with the rattling transition in the beta-pyrochlore oxide KOs2O6.Comment: 5 pages, 5 figures, J. Phys. Soc. Jpn. 79 (2010) 09370

Surface diffusion coefficients by thermodynamic integration: Cu on Cu(100)

The rate of diffusion of a Cu adatom on the Cu(100) surface is calculated using thermodynamic integration within the transition state theory. The results are found to be in excellent agreement with the essentially exact values from molecular-dynamics simulations. The activation energy and related entropy are shown to be effectively independent of temperature, thus establishing the validity of the Arrhenius law over a wide range of temperatures. Our study demonstrates the equivalence of diffusion rates calculated using thermodynamic integration within the transition state theory and direct molecular-dynamics simulations.Comment: 4 pages (revtex), two figures (postscript

Periscope Proteins are variable-length regulators of bacterial cell surface interactions

Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal “Periscope Proteins” as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly available long-read genome sequencing data, we propose that this class could contain over 50 distinct proteins, including those implicated in host colonization and biofilm formation by human pathogens. In large multidomain proteins, sequence divergence between adjacent domains appears to reduce interdomain misfolding. Periscope Proteins break this “rule,” suggesting that their length variability plays an important role in regulating bacterial interactions with host surfaces, other bacteria, and the immune system

Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed 'clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length

Interpreting Overdiagnosis Estimates in Population-based Mammography Screening

Estimates of overdiagnosis in mammography screening range from 1% to 54%. This review explains such variations using gradual implementation of mammography screening in the Netherlands as an example. Breast cancer incidence without screening was predicted with a micro-simulation model. Observed breast cancer incidence (including ductal carcinoma in situ and invasive breast cancer) was modeled and compared with predicted incidence without screening during various phases of screening program implementation. Overdiagnosis was calculated as the difference between the modeled number of breast cancers with and the predicted number of breast cancers without screening. Estimating overdiagnosis annually between 1990 and 2006 illustrated the importance of the time at which overdiagnosis is measured. Overdiagnosis was also calculated using several estimators identified from the literature. The estimated overdiagnosis rate peaked during the implementation phase of screening, at 11.4% of all predicted cancers in women aged 0–100 years in the absence of screening. At steady-state screening, in 2006, this estimate had decreased to 2.8%. When different estimators were used, the overdiagnosis rate in 2006 ranged from 3.6% (screening age or older) to 9.7% (screening age only). The authors concluded that the estimated overdiagnosis rate in 2006 could vary by a factor of 3.5 when different denominators were used. Calculations based on earlier screening program phases may overestimate overdiagnosis by a factor 4. Sufficient follow-up and agreement regarding the chosen estimator are needed to obtain reliable estimates

Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein.

Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed 'clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.This research was supported by Biotechnology and Biological Research Council Grants BB/J006459/1 (D.T.G. and J.C.), BB/J005029/1 (F.W. and J.R.P), BB/G019452/1 (O.E.F and D.J.B) and BB/G020671/1 (C.G.B. and J.R.P.). H.K.H.F. is supported by a studentship from a Wellcome Trust 4-year PhD programme (WT095024MA). C.M.J. is supported by the German Federal Ministry of Education and Research (BMBF), grant BIOSCAT (contract N° 05K12YE1). J.C. is a Wellcome Trust Senior Research Fellow (WT/095195). J.R.P holds a British Heart Foundation Senior Basic Science Fellowship (FS/12/36/29588). The authors acknowledge the use of EMBL SAXS beamline P12 at Petra-3 (DESY, Hamburg, Germany) and Maxim Petoukhov (EMBL) for providing a modified version of SASR EF. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under BioStruct-X (grant agreement N°283570). The authors would like to thank Diamond Light Source for beamtime (proposal mx-7864) and Johan Turkenburg and Sam Hart for assistance with crystal testing and data collection.This is the final version of the article. It first appeared from NPG via http://dx.doi.org/10.1038/ncomms827

How Graphene Is Cut upon Oxidation?

Our first principles calculations reveal that oxidative cut of graphene is realized by forming epoxy and then carbonyl pairs. Direct forming carbonyl pair to tear graphene up from an edge position is not favorable in energy. This atomic picture is valuable for developing effective graphene manipulation means. The proposed epoxy pairs may be related to some long puzzling experimental observations on graphene oxide