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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.Ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project's interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team's modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB's expandability and flexible architecture allow it to serve as an example ecosystems database.

For the past decade, observations of carbonyl sulfide (OCS or COS) have been investigated as a proxy for carbon uptake by plants. OCS is destroyed by enzymes that interact with CO2 during photosynthesis, namely carbonic anhydrase (CA) and RuBisCO, where CA is the more important one. The majority of sources of OCS to the atmosphere are geographically separated from this large plant sink, whereas the sources and sinks of CO2 are co-located in ecosystems. The drawdown of OCS can therefore be related to the uptake of CO2 without the added complication of co-located emissions comparable in magnitude. Here we review the state of our understanding of the global OCS cycle and its applications to ecosystem carbon cycle science. OCS uptake is correlated well to plant carbon uptake, especially at the regional scale. OCS can be used in conjunction with other independent measures of ecosystem function, like solar-induced fluorescence and carbon and water isotope studies. More work needs to be done to generate global coverage for OCS observations and to link this powerful atmospheric tracer to systems where fundamental questions concerning the carbon and water cycle remain.

Systematic biases in eddy covariance measurements of net ecosystem-atmosphere carbon dioxide exchange (NEE) are ubiquitous in forests when turbulence is low at night. We propose an alternative to the conventional bias correction, the friction velocity (u*) filter, by hypothesizing that these biases have two separate, concurrent causes: (1) a subcanopy CO2 storage pool that eludes typical storage measurements, creating a turbulence-dependent bias, and (2) advective divergence loss of CO2, creating a turbulence-independent bias. We correct for (1) using a simple parametric model of missing storage (MS). Prior experiments have inferred (2) directly from atmospheric measurements (DRAINO). For sites at which DRAINO experiments have not been performed or are infeasible, we estimate (2) empirically using a PAR-extrapolated advective respiration loss (PEARL) approach. We compare u* filter estimates of advection and NEE to MS-PEARL estimates at one temperate forest and two tropical forest sites. We find that for tropical forests, u* filters can produce a range of extreme NEE estimates, from long-term forest carbon emission to sequestration, that diverge from independent assessments and are not physically sustainable. Our MS model eliminates the dependence of nighttime NEE on u*, consistent with findings from DRAINO studies that nighttime advective losses of CO2 are often not dependent on the strength of turbulence. Our PEARL estimates of mean advective loss agree with available DRAINO measurements. The MS-PEARL correction to long-term NEE produces better agreement with forest inventories at all three sites. Moreover, the correction retains all nighttime eddy covariance data and is therefore more widely applicable than the u* filter approach, which rejects substantial nighttime data—up to 93% at one of the tropical sites. The full MS-PEARL NEE correction is therefore an equally defensible and more practical alternative to the u* filter, but leads to different conclusions about the resulting carbon balance. Our results therefore highlight the need to investigate which approach's underlying hypotheses are more physically realistic.

The seasonal pattern of the carbon isotope content (δ13C) of atmospheric CO2 depends on local and nonlocal land-atmosphere exchange and atmospheric transport. Previous studies suggested that the δ13C of the net land-atmosphere CO2 flux (δsource) varies seasonally as stomatal conductance of plants responds to vapor pressure deficit of air (VPD). We studied the variation of δsource at seven sites across the United States representing forests, grasslands, and an urban center. Using a two-part mixing model, we calculated the seasonal δsource for each site after removing background influence and, when possible, removing δ13C variation of nonlocal sources. Compared to previous analyses, we found a reduced seasonal (March–September) variation in δsource at the forest sites (0.5‰ variation). We did not find a consistent seasonal relationship between VPD and δsource across forest (or other) sites, providing evidence that stomatal response to VPD was not the cause of the global, coherent seasonal pattern in δsource. In contrast to the forest sites, grassland and urban sites had a larger seasonal variation in δsource (5‰) dominated by seasonal transitions in C3/C4 grass productivity and in fossil fuel emissions, respectively. Our findings were sensitive to the location used to account for atmospheric background variation within the mixing model method that determined δsource. Special consideration should be given to background location depending on whether the intent is to understand site level dynamics or regional scale impacts of land-atmosphere exchange. The seasonal amplitude in δ13C of land-atmosphere CO2 exchange (δsource) varied across land cover types and was not driven by seasonal changes in vapor pressure deficit. The largest seasonal amplitudes of δsource were at grassland and urban sites, driven by changes in C3/C4 grass productivity and fossil fuel emissions, respectively. Mixing model approaches may incorrectly calculate δsource when background atmospheric observations are remote and/or prone to anthropogenic influence.

Climate models require an understanding of ecosystem-scale respiration and photosynthesis, yet there is no way of measuring these two fluxes directly; here, new instrumentation is used to determine these fluxes in a temperate forest, showing, for instance, that respiration is less during the day than at night. Seasonal variation in forest productivity Much of the carbon dioxide emitted into the atmosphere is taken up by forest ecosystems. Forest carbon sink estimates are based on the idea that ecosystem respiration is greater during the day than at night and that the efficiency of photosynthetic light use declines after spring. Rick Wehr et al. determine ecosystem photosynthesis and daytime respiration in a temperate deciduous forest over a three-year period on the basis of the isotopic composition of net ecosystem exchange. The work reveals that ecosystem respiration is in fact lower during the day than at night -- evidence of the inhibition of leaf respiration by light (the Kok effect) at the ecosystem scale. The authors argue that current approaches for estimating photosynthesis and daytime respiration do not take this effect into account and therefore overestimate ecosystem photosynthesis and daytime respiration at their forest site, and portray ecosystem photosynthetic light-use efficiency as declining when it is in fact stable. The findings may have implications for estimates of biospheric productivity and carbon cycle-climate interactions. Terrestrial ecosystems currently offset one-quarter of anthropogenic carbon dioxide (CO.sub.2) emissions because of a slight imbalance between global terrestrial photosynthesis and respiration.sup.1. Understanding what controls these two biological fluxes is therefore crucial to predicting climate change.sup.2. Yet there is no way of directly measuring the photosynthesis or daytime respiration of a whole ecosystem of interacting organisms; instead, these fluxes are generally inferred from measurements of net ecosystem-atmosphere CO.sub.2 exchange (NEE), in a way that is based on assumed ecosystem-scale responses to the environment. The consequent view of temperate deciduous forests (an important CO.sub.2 sink) is that, first, ecosystem respiration is greater during the day than at night; and second, ecosystem photosynthetic light-use efficiency peaks after leaf expansion in spring and then declines.sup.3, presumably because of leaf ageing or water stress. This view has underlain the development of terrestrial biosphere models used in climate prediction.sup.4,5 and of remote sensing indices of global biosphere productivity.sup.5,6. Here, we use new isotopic instrumentation.sup.7 to determine ecosystem photosynthesis and daytime respiration.sup.8 in a temperate deciduous forest over a three-year period. We find that ecosystem respiration is lower during the day than at night--the first robust evidence of the inhibition of leaf respiration by light.sup.9,10,11 at the ecosystem scale. Because they do not capture this effect, standard approaches.sup.12,13 overestimate ecosystem photosynthesis and daytime respiration in the first half of the growing season at our site, and inaccurately portray ecosystem photosynthetic light-use efficiency. These findings revise our understanding of forest-atmosphere carbon exchange, and provide a basis for investigating how leaf-level physiological dynamics manifest at the canopy scale in other ecosystems., Author(s): R. Wehr [sup.1] , J. W. Munger [sup.2] , J. B. McManus [sup.3] , D. D. Nelson [sup.3] , M. S. Zahniser [sup.3] , E. A. Davidson [sup.4] , [...]

An overview of the binary collision impact theory of spectral line shapes has been given to provide a unified statistical mechanical approach to line-shape theory, laser theory, nonlinear optics, and transport phenomena in dilute gases. The computation of spectral line profiles corresponding to those obtained from ultra-high-resolution spectral line-shape measurements requires numerical ab initio calculation of scattering amplitudes directly from the underlying dynamics of collisions between radiatively active molecules and their perturbers. The Wigner distribution function-density matrix is utilized to describe the kinetic theory of spectral line shapes and to discuss the various collisional processes that contribute to the kernel of kinetic equations. The influence of features of the potential energy surface on spectral parameters is also discussed, and the importance of comparing experimental line profiles directly with numerically computed line shapes obtained from reliable interaction potentials is emphasized. This contrasts sharply with the universal practice of comparing experimental line widths and shifts using some average or approximate theoretical scattering cross- sections and it contrasts sharply with fitting experimental profiles to some convenient analytical line-shape model; hence the phrase 'a paradigm shift' in the title of this work. PACS Nos.: 32.70.Jz, 33.20.-t, 33.70.Gj, 34.50.-s. Nous avons presente une revue de la theorie du profile de raies spectrales suite a des collisions binaires, de facon a developper une approche unifiee de mecanique statistique pour la theorie du profile de raie, l'optique non lineaire, la theorie des lasers et les phenomenes de transport dans les gaz dilues. Le calcul du profil des raies spectrales qui correspondent a ces mecanismes exige un calcul ab initio des amplitudes de diffusion directement a partir de la dynamique des collisions entre des molecules a impact radiatif et les mecanismes perturbateurs. Nous couplons la fonction de distribution de Wigner et la matrice de densite pour decrire la theorie cinetique du profile de raie spectrale et discuter les differents mecanismes de collision qui contribuent au noyau des equations cinetiques. Nous analysons egalement l'influence des particularites de la surface d'energie sur les parametres spectraux et nous insistons sur l'importance de comparer les profiles experimentaux de raie directement avec les profiles de raie calcules a partir de potentiels fiables. Ceci contraste nettement avec la pratique universelle ou on compare les valeurs experimentales des largeurs et deplacements de raie en utilisant des sections efficaces approximatives quelconques, theoriques ou moyennes et contraste nettement avec l'ajustement des profiles de raie experimentaux a une forme analytique commode; d'ou l'expression << un changement de paradigm >> dans le titre. [Traduit par la Redaction], 1. Introduction The impact theory of spectral line shapes has been around for about a century, beginning with the classical theory of Lorentz [1], and was essentially completed with the [...]

An infrared laser spectrometer based on difference-frequency generation in LiI[O.sub.3] is described. The spectrometer has a frequency uncertainty of less than 1 MHz and a signal-to-noise ratio between 3000:1 and 10,000:1. These properties allow the spectrometer to be used for studies of the non-Lorentzian and non-Voigt character of absorption line shapes in atmospheric trace gases. OCIS codes: 300.1030, 300.6190, 300.6320, 300.6340, 300.6360, 300.6390.

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The 0310 ← 0110 parallel Q branch of N2O has been studied at 297 K and over the pressure range 1–130 torr. Absorption spectra were recorded using a high resolution (1.5 MHz or 5 × 10-5 cm-1) and high signal-to-noise (>3500:1) mid-infrared spectrometer based on difference-frequency infrared generation in AgGaS2. In the low-pressure range (1–11 torr) we obtained accurate values for the line strengths, the broadening coefficients, the weak mixing coefficients, and the overall shifting of the branch. The medium pressure results, ranging from 23 to 130 torr, were analyzed by treating the band as a whole, using a relaxation matrix formalism, based on an energy gap scaling law. We find, effectively, that only 36% of the rotationally inelastic collisions are associated with Q branch mixing, the rest presumably being associated with Q–P and Q–R mixing in the same vibrational band. The pressure shifting coefficient of the 0310 ← 0110 Q branch as a whole was also determined and found to be 5.8 × 10-3 cm-1/atm towards lower frequencies. [Copyright &y& Elsevier]

An overview of the binary collision impact theory of spectral line shapes has been given to provide a unified statistical mechanical approach to line-shape theory, laser theory, nonlinear optics, and transport phenomena in dilute gases. The computation of spectral line profiles corresponding to those obtained from ultra-high-resolution spectral line-shape measurements requires numerical ab initio calculation of scattering amplitudes directly from the underlying dynamics of collisions between radiatively active molecules and their perturbers. The Wigner distribution function-density matrix is utilized to describe the kinetic theory of spectral line shapes and to discuss the various collisional processes that contribute to the kernel of kinetic equations. The influence of features of the potential energy surface on spectral parameters is also discussed, and the importance of comparing experimental line profiles directly with numerically computed line shapes obtained from reliable interaction potentials is emphasized. This contrasts sharply with the universal practice of comparing experimental line widths and shifts using some average or approximate theoretical scattering cross-sections and it contrasts sharply with fitting experimental profiles to some convenient analytical line-shape model; hence the phrase 'a paradigm shift' in the title of this work. [ABSTRACT FROM AUTHOR]

Aqueous self-assembly of amphiphilic block copolymers is studied extensively for biomedical applications like drug delivery and nanoreactors. The commonly used hydrophilic block poly(ethylene oxide) (PEO), however, suffers from several drawbacks. As a potent alternative, poly(glycidol) (PG) has gained increasing interest, benefiting from its easy synthesis, high biocompatibility and flexibility as well as enhanced functionality compared to PEO. In this study, we present a quick and well-controlled synthesis of poly(butylene oxide)- block -poly(glycidol) (PBO- b -PG) amphiphilic diblock copolymers together with a straight-forward self-assembly protocol. Depending on the hydrophilic mass fraction of the copolymer, nanoscopic micelles, worms and polymersomes were formed as well as microscopic giant unilamellar vesicles. The particles were analysed regarding their size and shape, using dynamic and static light scattering, TEM and Cryo-TEM imaging as well as confocal laser scanning microscopy. We have discovered a strong dependence of the formed morphology on the self-assembly method and show that only solvent exchange leads to the formation of homogenous phases. Thus, a variety of different structures can be obtained from a highly flexible copolymer, justifying a potential use in biomedical applications., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Controllable attachment of proteins to material surfaces is very attractive for many applications including biosensors, bioengineered scaffolds or drug screening. Especially, redox proteins have received considerable attention as a model system not only to understand the mechanism of electron transfer in biological systems, but also the development of novel biosensors. However, current research attempts suffer from denaturation of the protein after its attachment to solid substrates. Here, we present how lipid, polymer and hybrid membranes based on mixtures of lipids and copolymers on a solid support provide a more favorable environment to drive selective and functional attachment of a model redox protein, cytochrome  c (cyt c ). Polymer membranes provided chemical versatility to support covalent attachment of cyt c , whereas lipid membranes provided flexibility and biocompatibility to support insertion of cyt c through its hydrophobic part. Hybrid membranes combine the most promising characteristics of both lipids and polymers and allowed attachment of cyt  c with both covalent attachment and insertion driven by hydrophobic interactions. We then investigated the effect of different attachment strategies on the accessibility and peroxidase-like activity of cyt c , in the presence of different membranes. The real-time combination of cyt c with the planar membranes was investigated by quartz crystal microbalance with dissipation. It was possible to selectively drive the insertion of cyt c into a specific lipid domain of hybrid membranes. In addition, protein accessibility and its functionality were dependent on the specificity of the combination strategy: covalent conjugation of cyt c to polymer and hybrid membranes promoted higher accessibility and supported higher peroxidase-like activity. Taking together, the combination of biomolecules with planar membranes can be modulated in such a way to improve the accessibility of the biomolecules and their resulting functionality for the development of efficient "active surfaces".

Fosalvudine tidoxil is a prodrug derived from the nucleoside reverse transcriptase inhibitor 3-deoxy-3-fluorothymidine (FLT; alovudine). FLT effectively inhibits resistant human immunodeficiency virus type 1, but its clinical development was stopped due to bone marrow and liver toxicity. In this study, we examined the long-term in vivo effects of fosalvudine tidoxil on the mitochondrial DNA (mtDNA) contents in rats. Sprague-Dawley rats received fosalvudine tidoxil (15, 40, or 100 mg/kg of body weight/day) by oral gavage during a period of 8 weeks. Didanosine (100 mg/kg/day) was used as a positive control for mitochondrial toxicity. mtDNA levels in liver, gastrocnemius muscle, sciatic nerve, and inguinal fat pad tissues were quantified by real-time PCR. In hepatic mitochondria, fosalvudine tidoxil induced significant mtDNA depletion. At doses of 15, 40, and 100 mg/kg, the mean hepatic mtDNA values were 62, 64, and 47% of control values, respectively. Rats exposed to 100 mg/kg of fosalvudine tidoxil, unlike all other groups, had slightly elevated levels of glutamate pyruvate transaminase in sera. Didanosine induced a loss of mtDNA (to 48% of the control level) similar to that induced by fosalvudine tidoxil. mtDNA levels in skeletal, neural, and adipose tissues in the negative control and treatment groups were similar. Our results suggest that fosalvudine tidoxil induces mitochondrial hepatotoxicity and that this effect warrants scrutiny in clinical trials.

The ATP-binding cassette transporter G1 (ABCG1) catalyzes export of cellular cholesterol from macrophages and hepatocytes. Here we identify an additional function of ABCG1 in the regulation of adiposity in screens of the Drosophila melanogaster and the New Zealand obese (NZO) mouse genomes. Insertion of modified transposable elements of the P-family upstream of CG17646, the Drosophila ortholog of Abcg1, generated lines of flies with increased triglyceride stores. In NZO mice, an Abcg1 variant was identified in a suggestive adiposity quantitative trait locus and was associated with higher expression of the gene in white adipose tissue. Targeted disruption of Abcg1 in mice resulted in reduced body weight gain (8.42+/-0.6 g in Abcg1-/- vs. 13.07+/-1.1 g in Abcg1+/+ mice) and adipose tissue mass gain (3.78+/-1.3 g in Abcg1-/- vs. 9.39+/-1.6 g in Abcg1+/+ mice) detected over a period of 12 wk. The reduction of adipose tissue mass in Abcg1-/- mice was associated with markedly decreased size of the adipocytes. In contrast to their wild-type littermates, male Abcg1-/- mice exhibited no high-fat diet-induced impairment of glucose tolerance and fatty liver. Furthermore, Abcg1-/- mice possess decreased food intake and elevated total energy expenditure (Abcg1-/- mice, 748.1+/-5.4 kJ/kg metabolic body mass; Abcg1+/+ mice, 684.3+/-5.0 kJ/kg metabolic body mass; P=0.011), body temperature (Abcg1-/- mice, 37.82+/-0.29 C; Abcg1+/+ mice, 36.83+/-0.24 C; P<0.05), and locomotor activity (Abcg1-/- mice, 3655+/-189 counts/12 h during dark phase; Abcg1+/+ mice, 2445+/-235 counts/12 h during dark phase; P<0.01). Our data indicate a previously unrecognized role of ABCG1 in the regulation of energy balance and triglyceride storage.

Skeletal muscle uncoupling by ectopic expression of mitochondrial uncoupling protein 1 (UCP1) has been shown to result in a lean phenotype in mice characterized by increased energy expenditure (EE), resistance to diet-induced obesity, and improved glucose tolerance. Here, we investigated in detail the effect of ectopic UCP1 expression in skeletal muscle on thermoregulation and energy homeostasis in HSA-mUCP1 transgenic mice. Thermoneutrality was determined to be approximately 30 degrees C for both wild-type (WT) and transgenic mice. EE, body temperature (Tb), activity, and respiratory quotient (RQ) were then measured over 24 h at ambient temperatures (Ta) of 30, 22, and 5 degrees C. HSA-mUCP1 transgenic mice showed increased activity-related EE and heat loss but similar basal metabolic rate compared with WT. Tb at resting periods was progressively decreased with declining Ta in HSA-mUCP1 transgenic mice but not in WT. Compared with WT littermates, the transgenic HSA-mUCP1 mice displayed increased RQ levels during night time, indicative of increased overall glucose oxidation, and failed to decrease their RQ levels with declining Ta. Thus increased EE caused by skeletal muscle uncoupling is clearly due to a decreased muscle energy efficiency during activity combined with increased glucose oxidation and a compromised thermoregulation associated with increased overall heat loss. At Tas below thermoneutrality, this puts increasing energy demands on the animals, whereas at thermoneutrality most differences in energy metabolism are not apparent any more.

We have built a high-resolution and high-signal-to-noise ratio spectrometer for line shape studies of greenhouse gases in the mid infrared. The infrared radiation is generated in a AgGaS2 nonlinear crystal by the well-known difference-frequency method. The choice of crystal is explained, and a brief literature review is presented. With two tunable dye lasers and a type I, 90 degrees phase-matching geometry, the infrared is continuously tunable from 7 to 9 microm when Rhodamine 6G and Sulforhodamine 640 dyes are used. The total infrared power exceeds 30 nW and is limited by both the damage threshold and thermal loading of the crystal. Phase-sensitive detection allows us to reach signal-to-noise ratios in excess of 3500:1 while maintaining an instrumental linewidth of 1.5 MHz. However, we show that the spectrometer may be used to measure the positions of spectral lines within +/-400 kHz.

The temperature and pressure cycles inside a pressure modulator cell (PMC) of the type used for gas-correlation radiometry aboard the Measurements of Pollution in the Troposphere (MOPITT) satellite instrument have been determined from dynamic measurements of the spectral line shapes of the R(0) and R(18) transitions in the fundamental vibrational-rotational band of carbon monoxide. The line strengths and linewidths were used to calculate the temperature and pressure, respectively, with a temporal resolution of approximately 200 micros, or 1/100 of a PMC cycle. The results are compared with a thermodynamic box model.

The past few years have seen an increase in interest about the molecular and genetic events regulating pancreas development. Transcription factors such as Pdx1, p48 and Nkx2.2 have been shown to be essential for the proper differentiation of exocrine and endocrine tissue; however, pancreas development also involves intricate interactions between the pancreatic epithelium and its surrounding mesenchyme. Signalling factors emanating from the notochord have been shown to repress Sonic hedgehog expression in the endoderm whereas signals originating from the pancreatic mesenchyme determine the proportion of exocrine to endocrine tissue. Understanding the molecular and genetic events underlying pancreas development also opens the door for devising new therapeutic strategies against pancreatic diseases such as diabetes and cancer.

The developing hindbrain is segmented in a series of repetitive bulges called neuromeres or rhombomeres. In the mouse, first molecular evidence for segmentation of the hindbrain came from rhombomeres 3- and 5-specific expression of the Krox-20 gene. The hindbrain segments are linked with the expression of different Hox genes which have a role in patterning the hindbrain and branchial region of the vertebrate head. Here we identified by subtractive hybridization a gene, mouse neuronatin, that is downregulated in P19 embryo carcinoma cells that have undergone a partial differentiation process. Neuronatin encodes putative transmembrane proteins of 54, 55, and 81 amino acids that might serve as protein ligands, cofactors, or small cell adhesion molecules. The neuronatin gene is transiently expressed in rhombomeres 3 and 5 during early hindbrain development and in the floor of the foregut pocket. In addition, expression is observed in the early Rathke's pouch, in the derived adenohypophysis, and in the developing inner ear. During later embryogenesis the neuronatin gene is strongly expressed in the major part of the central and peripheral nervous system. These results suggest that neuronatin participates in the maintenance of segment identity in the hindbrain and pituitary development and maturation or maintenance of the overall structure of the nervous system.