Cardiac cell modelling: Observations from the heart of the cardiac physiome project

In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field

Optimization of insect odorant receptor trafficking and functional expression via transient transfection in HEK293 cells

Insect odorant receptors show a limited functional expression in various heterologous expression systems including insect and mammalian cells. This may be in part due to the absence of key components driving the release of these proteins from the endoplasmic reticulum and directing them to the plasma membrane. In order to mitigate this problem we took advantage of small export signals within the human HCN1 and Rhodopsin that have been shown to promote protein release from the endoplasmic reticulum and the trafficking of post-Golgi vesicles, respectively. Moreover, we designed a new vector based on a bidirectional expression cassette to drive the functional expression of the insect odorant receptor co-receptor (Orco) and an odor-binding odorant receptor, simultaneously. We show that this new method can be used to reliably express insect odorant receptors in HEK293 cells via transient transfection and that is highly suitable for downstream applications using automated and high-throughput imaging platforms

Marine latitude/altitude OH distributions: Comparison of Pacific Ocean observations with models

Reported here are tropical/subtropical Pacific basin OH observational data presented in a latitude/altitude geographical grid. They cover two seasons of the year (spring and fall) that reflect the timing of NASA's PEM-Tropics A (1996) and B (1999) field programs. Two different OH sensors were used to collect these data, and each instrument was mounted on a different aircraft platform (i.e., NASA's P-3B and DC-8). Collectively, these chemical snapshots of the central Pacific have revealed several interesting trends. Only modest decreases (factors of 2 to 3) were found in the levels of OH with increasing altitude (0-12 km). Similarly, only modest variations were found (factors of 1.5 to 3.5) when the data were examined as a function of latitude (30° N to 30° S). Using simultaneously recorded data for CO, O3, H2O, NO, and NMHCs, comparisons with current models were also carried out. For three out of four data subsets, the results revealed a high level of correspondence. On average, the box model results agreed with the observations within a factor of 1.5. The comparison with the three-dimensional model results was found to be only slightly worse. Overall, these results suggest that current model mechanisms capture the major photochemical processes controlling OH quite well and thus provide a reasonably good representation of OH levels for tropical marine environments. They also indicate that the two OH sensors employed during the PEM-Tropics B study generally saw similar OH levels when sampling a similar tropical marine environment. However, a modest altitude bias appears to exist between these instruments. More rigorous instrument intercomparison activity would therefore seem to be justified. Further comparisons of model predictions with observations are also recommended for nontropical marine environments as well as those involving highly elevated levels of reactive non-methane hydrocarbons. Copyright 2001 by the American Geophysical Union

Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function

The cardiac muscarinic receptor (M2R) regulates heart rate, in part, by modulating the ace-tylcholine (ACh) activated K⁺ current I$_{K,ACh}$ through dissociation of G-proteins, that in turn activate K$_{ ACh}$ channels. Recently, M2Rs were noted to exhibit intrinsic voltage sensitivity, i.e. their affinity for ligands varies in a voltage dependent manner. The voltage sensitivity of M2R implies that the affinity for Ach (and thus the Ach effect) varies throughout the time course of a cardiac electrical cycle. The aim of this study was to investigate the contribution of M2R voltage sensitivity to the rate and shape of the human sinus node action potentials in physiological and pathophysiological conditions. We developed a Markovian model of the I$_{K,ACh}$ modulation by voltage and integrated it into a computational model of human sinus node. We performed simulations with the integrated model varying Ach concentration and voltage sensitivity. Low Ach exerted a larger effect on I$_{K,ACh}$ at hyperpolarized versus depolarized membrane voltages. This led to a slowing of the pacemaker rate due to an attenuated slope of phase 4 depolarization with only marginal effect on action potential duration and amplitude. We also simulated the theoretical effects of genetic variants that alter the voltage sensitivity of M2R. Modest negative shifts in voltage sensitivity, predicted to increase the affinity of the receptor for ACh, slowed the rate of phase 4 depolarization and slowed heart rate, while modest positive shifts increased heart rate. These simulations support our hypothesis that altered M2R voltage sensitivity contributes to disease and provide a novel mechanistic foundation to study clinical disorders such as atrial fibrillation and inappropriate sinus tachycardia

Atmospheric sampling of Supertyphoon Mireille with NASA DC-8 aircraft on September 27,1991, during PEM-West A

The DC-8 mission of September 27, 1991, was designed to sample air flowing into Typhoon Mireille in the boundary layer, air in the upper tropospheric eye region, and air emerging from the typhoon and ahead of the system, also in the upper troposphere. The objective was to find how a typhoon redistributes trace constituents in the West Pacific region and whether any such redistribution is important on the global scale. The boundary layer air (300 m), in a region to the SE of the eye, contained low mixing ratios of the tracer species O3, CO, C2H6, C2H2, C3H8, C6H6and CS2 but high values of dimethylsulfide (DMS). The eye region relative to the boundary layer, showed somewhat elevated levels of CO, substantially increased levels of O3, CS2 and all nonmethane hydrocarbons (NMHCs), and somewhat reduced levels of DMS. Ahead of the eye, CO and the NMHCs remained unchanged, O3 and CS2 showed a modest decrease, and DMS showed a substantial decrease. There was no evidence from lidar cross sections of ozone for the downward entrainment of stratospheric air into the eye region; these sections show that low ozone values were measured in the troposphere. The DMS data suggest substantial entrainment of boundary layer air into the system, particularly into the eye wall region. Estimates of the DMS sulphur flux between the boundary layer and the free troposphere, based on computations of velocity potential and divergent winds, gave values of about 69 μg S m−2 d−1 averaged over a 17.5° grid square encompassing the typhoon. A few hours after sampling with the DC-8, Mireille passed over Oki Island, just to the north of Japan, producing surface values of ozone of 5.5 ppbv. These O3 levels are consistent with the low tropospheric values found by lidar and are more typical of equatorial regions. We suggest that the central eye region may act like a Taylor column which has moved poleward from low latitudes. The high-altitude photochemical environment within Typhoon Mireille was found to be quite active as evidenced by significant levels of measured gas phase H2O2 and CH3OOH and model-computed levels of OH

Chemical Characteristics of Continental Outflow from Asia to the Troposphere Over the Western Pacific Ocean during February - March 1994: Results from PEM-West B

We present here the chemical composition of outflow from the Asian continent to the atmosphere over the western Pacific basin during the Pacific Exploratory Mission-West (PEM-West B) in February-March 1994. Comprehensive measurements of important tropospheric trace gases and aerosol particulate matter were performed from the NASA DC-8 airborne laboratory. Backward 5 day isentropic trajectories were used to partition the outflow from two major source regions- continental north (greater than 20 deg N) and continental south (less than 20 deg N). Air parcels that had not passed over continental areas for the previous 5 days were classified as originating from an aged marine source. The trajectories and the chemistry together indicated that there was extensive rapid outflow of air parcels at altitudes below 5 km, while aged marine air was rarely encountered and only at less than 20 deg N latitude. The outflow at low altitudes had enhancements in common industrial solvent vapors such as C2Cl4, CH3CCl3, and C6H6, intermixed with the combustion emission products C2H2, C2H6, CO, and NO. The mixing ratios of all species were up to tenfold greater in outflow from the continental north compared to the continental south source region, with Pb-210 concentrations reaching 38 fCi (10(exp -15) curies) per standard cubic meter. In the upper troposphere we again observed significant enhancements in combustion-derived species in the 8-10 km altitude range, but water-soluble trace gases and aerosol species were depleted. These observations suggest that ground level emissions were lofted to the upper troposphere by wet convective systems which stripped water-soluble components from these air parcels. There were good correlations between C2H2 and CO and C2H6 (r(sup 2) = 0.70 - 0.97) in these air parcels and much weaker ones between C2H2 and H2O2 or CH3OOH (r(sup 2) = 0.50). These correlations were the strongest in the continental north outflow where combustion inputs appeared to be recent (1 - 2 days old). Ozone and PAN showed general correlation in these same air parcels but not with the combustion products. It thus appears that several source inputs were intermixed in these upper tropospheric air masses, with possible contributions from European or Middle Eastern source regions. In aged marine air mixing ratios of 03 (approximately equals 20 parts per billion by volume) and PAN (less than or equal to 10 parts per trillion by volume) were nearly identical at less than 2 km and 10 - 12 km altitudes due to extensive convective uplifting of marine boundary layer air over the equatorial Pacific even in wintertime. Comparison of the Pacific Exploratory Mission-West A and PEM-West B data sets shows significantly larger mixing ratios of SO2 and H2O2 during PEM-West A. Emissions from eruption of Mount Pinatubo are a likely cause for the former, while suppressed photochemical activity in winter was probably responsible for the latter. This comparison also highlighted the twofold enhancement in C2H2, C2H6, and C3H8 in the continental north outflow during /PEM-West B. Although this could be due to reduced OH oxidation rates of these species in wintertime, we argue that increased source emissions are primarily responsible

Leaf wax <i>n</i>-alkane distributions record ecological changes during the Younger Dryas at Trzechowskie paleolake (northern Poland) without temporal delay

While of higher plant origin, a specific source assignment of sedimentary leaf wax n-alkanes remains difficult. In addition, it is unknown how fast a changing catchment vegetation would be reflected in sedimentary leaf wax archives. In particular, for a quantitative interpretation of n-alkane C and H isotope ratios in terms of paleohydrological and paleoecological changes, a better understanding of transfer times and dominant sedimentary sources of leaf wax n-alkanes is required.In this study we tested to what extent compositional changes in leaf wax n-alkanes can be linked to known vegetation changes by comparison with high-resolution palynological data from the same archive. We analyzed leaf wax n-alkane concentrations and distributions in decadal resolution from a sedimentary record from Trzechowskie paleolake (TRZ, northern Poland), covering the Late Glacial to early Holocene (13&thinsp;360–9940&thinsp;yr&thinsp;BP). As an additional source indicator of targeted n-alkanes, compound-specific carbon isotopic data have been generated in lower time resolution. The results indicated rapid responses of n-alkane distribution patterns coinciding with major climatic and paleoecological transitions. We found a shift towards higher average chain length (ACL) values at the Allerød–Younger Dryas (YD) transition between 12&thinsp;680 and 12&thinsp;600&thinsp;yr&thinsp;BP, coevaled with a decreasing contribution of arboreal pollen (mainly Pinus and Betula) and a subsequently higher abundance of pollen derived from herbaceous plants (Poaceae, Cyperaceae, Artemisia), shrubs, and dwarf shrubs (Juniperus and Salix). The termination of the YD was characterized by a successive increase in n-alkane concentrations coinciding with a sharp decrease in ACL values between 11&thinsp;580 and 11&thinsp;490&thinsp;yr&thinsp;BP, reflecting the expansion of woodland vegetation at the YD–Holocene transition. A gradual reversal to longer chain lengths after 11&thinsp;200&thinsp;yr&thinsp;BP, together with decreasing n-alkane concentrations, most likely reflects the early Holocene vegetation succession with a decline of Betula.These results show that n-alkane distributions reflect vegetation changes and that a fast (i.e., subdecadal) signal transfer occurred. However, our data also indicate that a standard interpretation of directional changes in biomarker ratios remains difficult. Instead, responses such as changes in ACL need to be discussed in the context of other proxy data. In addition, we find that organic geochemical data integrate different ecological information compared to pollen, since some gymnosperm genera, such as Pinus, produce only a very low amount of n-alkanes and for this reason their contribution may be largely absent from biomarker records. Our results demonstrate that a combination of palynological and n-alkane data can be used to infer the major sedimentary leaf wax sources and constrain leaf wax transport times from the plant source to the sedimentary sink and thus pave the way towards quantitative interpretation of compound-specific hydrogen isotope ratios for paleohydrological reconstructions.</p