Group additivity calculation of the standard molal thermodynamic properties of aqueous amino acids, polypeptides and unfolded proteins as a function of temperature, pressure and ionization state

International audienceThermodynamic calculation of the chemical speciation of proteins and the limits of protein metastability affords a quantitative understanding of the biogeochemical constraints on the distribution of proteins within and among different organisms and chemical environments. These calculations depend on accurate determination of the ionization states and standard molal Gibbs free energies of proteins as a function of temperature and pressure, which are not generally available. Hence, to aid predictions of the standard molal thermodynamic properties of ionized proteins as a function of temperature and pressure, calculated values are given below of the standard molal thermodynamic properties at 25°C and 1 bar and the revised Helgeson-Kirkham-Flowers equations of state parameters of the structural groups comprising amino acids, polypeptides and unfolded proteins. Group additivity and correlation algorithms were used to calculate contributions by ionized and neutral sidechain and backbone groups to the standard molal Gibbs free energy (? G°), enthalpy (? H°), entropy (S°), isobaric heat capacity (C°P), volume (V°) and isothermal compressibility (?°T) of multiple reference model compounds. Experimental values of C°P, V° and ?°T at high temperature were taken from the recent literature, which ensures an internally consistent revision of the thermodynamic properties and equations of state parameters of the sidechain and backbone groups of proteins, as well as organic groups. As a result, ? G°, ? H°, S° C°P, V° and ?°T of unfolded proteins in any ionization state can be calculated up to T~-300°C and P~-5000 bars. In addition, the ionization states of unfolded proteins as a function of not only pH, but also temperature and pressure can be calculated by taking account of the degree of ionization of the sidechain and backbone groups present in the sequence. Calculations of this kind represent a first step in the prediction of chemical affinities of many biogeochemical reactions, as well as of the relative stabilities of proteins as a function of temperature, pressure, composition and intra- and extracellular chemical potentials of O2 and H2, NH3, H2PO4 and CO2

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii

© The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 198 (2017): 131-150, doi:10.1016/j.gca.2016.10.029.The role of nitrogen cycling in submarine hydrothermal systems is far less studied than that of other biologically reactive elements such as sulfur and iron. In order to address this knowledge gap, we investigated nitrogen redox processes at Loihi Seamount, Hawaii, using a combination of biogeochemical and isotopic measurements, bioenergetic calculations and analysis of the prokaryotic community composition in venting fluids sampled during four cruises in 2006, 2008, 2009 and 2013. Concentrations of NH4+ were positively correlated to dissolved Si and negatively correlated to NO3-+NO2-, while NO2- was not correlated to NO3-+NO2-, dissolved Si or NH4+. This is indicative of hydrothermal input of NH4+ and biological mediation influencing NO2- concentrations. The stable isotope ratios of NO3- (d15N and d18O) was elevated with respect to background seawater, with d18O values exhibiting larger changes than corresponding d15N values, reflecting the occurrence of both production and reduction of NO3- by an active microbial community. d15N-NH4+ values ranged from 0‰ to +16.7‰, suggesting fractionation during consumption and potentially N-fixation as well. Bioenergetic calculations reveal that several catabolic strategies involving the reduction of NO3- and NO2- coupled to sulfide and iron oxidation could provide energy to microbes in Loihi fluids, while 16S rRNA gene sequencing of Archaea and Bacteria in the fluids reveals groups known to participate in denitrification and N-fixation. Taken together, our data support the hypothesis that microbes are mediating N-based redox processes in venting hydrothermal fluids at Loihi Seamount.This work was supported by the NSF Microbial Observatories program (MCB 0653265), the Gordon and Betty Moore Foundation (GBMF1609), NSF-OCE 0648287, the Center for Dark Energy Biosphere Investigations (C-DEBI) and the NASA Astrobiology Institute — Life Underground (NAI-LU). Sequence data was generated as part of the Alfred P. Sloan Foundation's ICoMM field project and the W. M. Keck Foundation

Microbial activity in the marine deep biosphere: progress and prospects

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth\u27s global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org)

Smoking among morbidly obese patients

<p>Abstract</p> <p>Background</p> <p>Smokers usually have a lower Body Mass Index (BMI) when compared to non-smokers. Such a relationship, however, has not been fully studied in obese and morbidly obese patients. The objective of this study was to evaluate the relationship between smoking and BMI among obese and morbidly obese subjects.</p> <p>Methods</p> <p>In a case-control study design, 1022 individuals of both genders, 18-65 years of age, were recruited and grouped according to their smoking status (smokers, ex-smokers, and non-smokers) and nutritional state according to BMI (normal weight, overweight, obese, and morbidly obese).</p> <p>Results</p> <p>No significant differences were detected in the four BMI groups with respect to smoking status. However, there was a trend towards a higher frequency of smokers among the overweight, obese, and morbidly obese subjects compared to normal weight individuals (p = 0.078). In a logistic regression, after adjusting for potential confounders, morbidly obese subjects had an adjusted OR of 2.25 (95% CI, 1.52-3.34; p < 0.001) to be a smoker when compared to normal weight individuals.</p> <p>Discussion</p> <p>In this sample, while the frequency of smokers diminished in normal weight subjects as the BMI increased, such a trend was reversed in overweight, obese, and morbidly obese patients. In the latter group, the prevalence of smokers was significantly higher compared to the other groups. A patient with morbid obesity had a 2-fold increased risk of becoming a smoker. We speculate that these finding could be a consequence of various overlapping risk behaviors because these patients also are generally less physically active and prefer a less healthy diet, in addition to having a greater alcohol intake in relation to their counterparts. The external validity of these findings must be confirmed.</p

Calculation of the relative metastabilities of proteins using the CHNOSZ software package

<p>Abstract</p> <p>Background</p> <p>Proteins of various compositions are required by organisms inhabiting different environments. The energetic demands for protein formation are a function of the compositions of proteins as well as geochemical variables including temperature, pressure, oxygen fugacity and pH. The purpose of this study was to explore the dependence of metastable equilibrium states of protein systems on changes in the geochemical variables.</p> <p>Results</p> <p>A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules.</p> <p>Conclusion</p> <p>Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations.</p

Microbial activity in the marine deep biosphere: progress and prospects

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology.Keywords: Subsurface microbiology, Biogeochemistry, C-DEBI, Deep biosphere, IODP, Sediment, Oceanic crustKeywords: Subsurface microbiology, Biogeochemistry, C-DEBI, Deep biosphere, IODP, Sediment, Oceanic crus

Anthropogenic perturbation of the carbon fluxes from land to ocean

A substantial amount of the atmospheric carbon taken up on land through photosynthesis and chemical weathering is transported laterally along the aquatic continuum from upland terrestrial ecosystems to the ocean. So far, global carbon budget estimates have implicitly assumed that the transformation and lateral transport of carbon along this aquatic continuum has remained unchanged since pre-industrial times. A synthesis of published work reveals the magnitude of present-day lateral carbon fluxes from land to ocean, and the extent to which human activities have altered these fluxes. We show that anthropogenic perturbation may have increased the flux of carbon to inland waters by as much as 1.0 Pg C yr-1 since pre-industrial times, mainly owing to enhanced carbon export from soils. Most of this additional carbon input to upstream rivers is either emitted back to the atmosphere as carbon dioxide (~0.4 Pg C yr-1) or sequestered in sediments (~0.5 Pg C yr-1) along the continuum of freshwater bodies, estuaries and coastal waters, leaving only a perturbation carbon input of ~0.1 Pg C yr-1 to the open ocean. According to our analysis, terrestrial ecosystems store ~0.9 Pg C yr-1 at present, which is in agreement with results from forest inventories but significantly differs from the figure of 1.5 Pg C yr-1 previously estimated when ignoring changes in lateral carbon fluxes. We suggest that carbon fluxes along the land–ocean aquatic continuum need to be included in global carbon dioxide budgets.Peer reviewe

Adolescents’ beverage choice at school and the impact on sugar intake

Background/Objectives: To examine students’ beverage choice in school, with reference to its contribution to students’ intake of non-milk extrinsic (NME) sugars. Subjects/Methods: Beverage and food selection data for students aged 11–18 years (n=2461) were collected from two large secondary schools in England, for a continuous period of 145 (school A) and 125 (school B) school days. Descriptive analysis followed by cluster analysis of the beverage data were performed separately for each school. Results: More than a third of all items selected by students were beverages, and juice-based beverages were students’ most popular choice (school A, 38.6%; school B, 35.2%). Mean NME sugars derived from beverages alone was high (school A, 16.7 g/student-day; school B, 12.9 g/student-day). Based on beverage purchases, six clusters of students were identified at each school (school A: ‘juice-based’, ‘assorted’, ‘water’, ‘cartoned flavoured milk’, ‘bottled flavoured milk’, ‘high volume juice-based’; school B: ‘assorted’, ‘water with juice-based’, ‘sparkling juice/juice-based’, ‘water’, ‘high volume water’, ‘high volume juice-based’). Both schools included ‘high volume juice-based’ clusters with the highest NME sugar means from beverages (school A, 28.6 g/student-day; school B, 24.4 g/student-day), and ‘water’ clusters with the lowest. A hierarchy in NME sugars was found according to cluster; students in the ‘high volume juice-based’ cluster returned significantly higher levels of NME sugars than students in other clusters. Conclusions: This study reveals the contribution that school beverages combined with students’ beverage choice behaviour is making to students’ NME sugar intake. These findings inform school food initiatives, and more generally public health policy around adolescents’ dietary intake