A reference map of the human binary protein interactome

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships^1,2. Here, we present a human “all-by-all” reference interactome map of human binary protein interactions, or “HuRI”. With ~53,000 high-quality protein-protein interactions (PPIs), HuRI has approximately four times more such interactions than high-quality curated interactions from small-scale studies. Integrating HuRI with genome³, transcriptome⁴, and proteome⁵ data enables the study of cellular function within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying specific subcellular roles of PPIs. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms underlying tissue-specific phenotypes of Mendelian diseases. HuRI represents a systematic proteome-wide reference linking genomic variation to phenotypic outcomes.

Tracking forest phenology and seasonal physiology using digital repeat photography: a critical assessment

Digital repeat photography is becoming widely used for near-surface remote sensing of vegetation. Canopy greenness, which has been used extensively for phenological applications, can be readily quantified from camera images. Important questions remain, however, as to whether the observed changes in canopy greenness are directly related to changes in leaf-level traits, changes in canopy structure, or some combination thereof. We investigated relationships between canopy greenness and various metrics of canopy structure and function, using five years (2008–2012) of automated digital imagery, ground observations of phenological transitions, leaf area index (LAI) measurements, and eddy covariance estimates of gross ecosystem photosynthesis from the Harvard Forest, a temperate deciduous forest in the northeastern United States. Additionally, we sampled canopy sunlit leaves on a weekly basis throughout the growing season of 2011. We measured physiological and morphological traits including leaf size, mass (wet/dry), nitrogen content, chlorophyll fluorescence, and spectral reflectance and characterized individual leaf color with flatbed scanner imagery. Our results show that observed spring and autumn phenological transition dates are well captured by information extracted from digital repeat photography. However, spring development of both LAI and the measured physiological and morphological traits are shown to lag behind spring increases in canopy greenness, which rises very quickly to its maximum value before leaves are even half their final size. Based on the hypothesis that changes in canopy greenness represent the aggregate effect of changes in both leaf-level properties (specifically, leaf color) and changes in canopy structure (specifically, LAI), we developed a two end-member mixing model. With just a single free parameter, the model was able to reproduce the observed seasonal trajectory of canopy greenness. This analysis shows that canopy greenness is relatively insensitive to changes in LAI at high LAI levels, which we further demonstrate by assessing the impact of an ice storm on both LAI and canopy greenness. Our study provides new insights into the mechanisms driving seasonal changes in canopy greenness retrieved from digital camera imagery. The nonlinear relationship between canopy greenness and canopy LAI has important implications both for phenological research applications and for assessing responses of vegetation to disturbances.

A synthetic five amino acid propeptide increases dopamine neuron differentiation and neurochemical function

A major consequence of Parkinson's disease (PD) involves the loss of dopaminergic neurons in the substantia nigra (SN) and a subsequent loss of dopamine (DA) in the striatum. We have shown that glial cell line-derived neurotrophic factor (GDNF) shows robust restorative and protective effects for DA neurons in rats, non-human primates and possibly in humans. Despite GDNF's therapeutic potential, its clinical value has been questioned due to its limited diffusion to target areas from its large size and chemical structure. Several comparatively smaller peptides are thought to be generated from the prosequence. A five amino-acid peptide, dopamine neuron stimulating peptide-5 (DNSP-5), has been proposed to demonstrate biological activity relevant to neurodegenerative disease. We tested the in vitro effects of DNSP-5 in primary dopaminergic neurons dissected from the ventral mesencephalon of E14 Sprague Dawley rat fetuses. Cells were treated with several doses (0.03, 0.1, 1.0, 10.0 ng/mL) of GDNF, DNSP-5, or an equivalent volume of citrate buffer (vehicle). Morphological features of tyrosine hydroxylase positive neurons were quantified for each dose. DNSP-5 significantly increased (p < 0.001) all differentiation parameters compared to citrate vehicle (at one or more dose). For in vivo studies, a unilateral DNSP-5 treatment (30 μg) was administered directly to the SN. Microdialysis in the ipsilateral striatum was performed 28 days after treatment to determine extracellular levels of DA and its primary metabolites (3,4-dihydroxyphenylacetic acid and homovanillic acid). A single treatment significantly increased (~66%) extracellular DA levels compared to vehicle, while DA metabolites were unchanged. Finally, the protective effects of DNSP-5 against staurosporine-induced cytotoxicity were investigated in a neuronal cell line showing substantial protection by DNSP-5. Altogether, these studies strongly indicate biological activity of DNSP-5 and suggest that DNSP-5 has neurotrophic-like properties that may be relevant to the treatment of neurodegenerative diseases like PD.

Uncertainty in eddy covariance measurements and its application to physiological models

Flux data are noisy, and this uncertainty is largely due to random measurement error. Knowledge of uncertainty is essential for the statistical evaluation of modeled and measured fluxes, for comparison of parameters derived by fitting models to measured fluxes and in formal data-assimilation efforts. We used the difference between simultaneous measurements from two towers located less than 1 km apart to quantify the distributional characteristics of the measurement error in fluxes of carbon dioxide (CO2) and sensible and latent heat (H and LE, respectively). Flux measurement error more closely follows a double exponential than a normal distribution. The CO2 flux uncertainty is negatively correlated with mean wind speed, whereas uncertainty in H and LE is positively correlated with net radiation flux. Measurements from a single tower made 24 h apart under similar environmental conditions can also be used to characterize flux uncertainty. Uncertainty calculated by this method is somewhat higher than that derived from the two-tower approach. We demonstrate the use of flux uncertainty in maximum likelihood parameter estimates for simple physiological models of daytime net carbon exchange. We show that inferred model parameters are highly correlated, and that hypothesis testing is therefore possible only when the joint distribution of the model parameters is taken into account.

Spectral reflectance of Picea rubens (Pinaceae) and Abies balsamea (Pinaceae) needles along an elevational gradient, Mt. Moosilauke, New Hampshire, USA

Relationships among elevation, foliar morphology, spectral reflectance, and chlorophyll fluorescence of two co-occurring montane conifers, red spruce (Picea rubens Sarg.) and balsam fir (Abies balsamea [L.] Mill.), were investigated along two transects from 460 to 1460 m on Mt. Moosilauke in the White Mountains of New Hampshire, USA. Spectral reflectance (300-1100 nm wavelengths) and the chlorophyll fluorescence F(v)/F(m) ratio were measured on dark-adapted needles. Foliar morphology (needle size, shape, and mass) and nitrogen concentrations were measured in the laboratory. Reflectance spectra varied between species and with elevation. Two chlorophyll measures, red edge position and a chlorophyll-based difference index (Chl NDI = R750 - R705/R750 + R705), indicated more chlorophyll in fir than in spruce and decreasing chlorophyll with increasing elevation in both species. The structure-independent pigment index (SIPI = R800 - R445/R800 - R680) increased with elevation, indicating an increasing carotenoid : chlorophyll ratio. The photochemical reflectance index (PRI = R531 - R570/R531 + R570), a measure of photosynthetic radiation use efficiency, decreased with increasing elevation up to 1370 m. In the highest elevation site, within the stunted alpine krummholz at 1460 m, PRI was higher than at 1370 m, but still lower than at 1070 m. This same pattern was evident in the chlorophyll fluorescence F(v)/F(m) measurements. These independent indices indicate higher stress in spruce than fir, which may be related to the "spruce decline" reported in the northeastern USA. Results also indicate progressively increasing stress with increasing elevation up to 1370 m. Stress appears to be lower at 1460 m than at 1370 m, despite the harsher conditions at the very summit of Mt. Moosilauke. This may be a consequence of stress-tolerant physiology and/or prostrate architecture.

Current role of beta-adrenergic blockers in the treatment of chronic congestive heart failure

Recent findings on the use of beta-adrenergic blockers in patients with congestive heart failure (CHF) are reviewed. CHF is a progressive, debilitating disease that afflicts 4.6 million patients in the United States. Treatment has traditionally consisted of a diuretic, an angiotensin-converting-enzyme (ACE) inhibitor, and digoxin. Despite advances in ACE-inhibitor therapy, the five-year mortality rate remains nearly 50%. Overstimulation of the sympathetic nervous system is believed to contribute to mortality. Beta-blockers have recently been added to the standard of care for patients with New York Heart Association functional class II or III heart failure. Four randomized, double-blind, placebo-controlled clinical trials were recently completed that addressed the benefits of beta-blockers in CHF. The overall mortality rate was reduced 65% by carvedilol, 34% by metoprolol, and 33% by bisoprolol; all these reductions were significant compared with placebo, and the trials were ended early. Bucindolol, however, did not have a significant effect on mortality. These drugs are hepatically metabolized and may require dosage adjustment in hepatically impaired patients. Decompensation of heart failure is another consideration; a beta-blocker should be added only for patients with stable CHF. Dosages must be slowly adjusted to targeted levels. Adverse effects do not differ significantly among beta-blockers. In addition to their effect on mortality, beta-blockers reduce CHF-related morbidity, such as all-cause hospitalization. Carvedilol, metoprolol, and bisoprolol decrease the mortality and morbidity associated with CHF and can be used with limited adverse effects. The choice among these agents does not affect clinical outcomes; bucindolol, however, has proven ineffective.

Gas-phase molecular structures of third row transition-metal hexafluorides WF6, ReF6, OsF6, IrF6, and PtF6. An electron-diffraction and ab initio study

The molecular structures of WF6, ReF6, OsF6, IrF6, and PtF6 have been measured by electron diffraction from the gases, the last from both PtF6 itself and from a vapor assumed to consist of a mixture of O2 and PtF6 obtained by heating the salt O2PtF6. For models of Oh symmetry the bond lengths in the first three members of the series are essentially identical, but the Ir-F and Pt-F bonds are respectively about 0.01 and 0.02 A longer. Models of D4h symmetry were also tested for ReF6, OsF6, and IrF6 in which operation of the Jahn-Teller effect is thought possible. For these models the same trend was seen in the average bond-length values. The effect of three-atom multiple scattering was also investigated, and experimental estimates of the effects of vibrational averaging ("shrinkage") on the distances were obtained. Normal-coordinate analyses based on the observed wavenumbers yielded stretching force constants consistent with the usual inverse bond-length/force-constant relationship. Ab initio molecular orbital optimizations of the molecules constrained to Oh symmetry were carried out at several levels of theory and basis-set size. Less extensive optimizations of ReF6, OsF6, and IrF6 with D4h symmetry were also carried out. The best overall agreement with both the experimental values and the distance trend for Oh symmetry was obtained with the Hay-Wadt (n+1)VDZ basis on the metals and the aug-cc-pVTZ on the fluorines at the MP2 level, but these bases with B3P86 and B3PW91 density functional theory were nearly as good and with B3LYP only slightly worse. The D4h structures for ReF6, OsF6, and IrF6 with the cited bases at the B3P86 level were slightly more stable (respectively 0.8, 2.6, and 1.4 kcal/mol) with the axial bonds shorter by about 0.04 A in ReF6 and 0.07 A in OsF6, but about 0.05 A longer in IrF6. The significance of these values is uncertain. The experimental bond lengths (rg/A) with estimated 2sigma uncertainties for the models of Oh symmetry are W-F = 1.829(2), Re-F = 1.829(2), Os-F = 1.828(2), Ir-F = 1.839(2), and Pt-F = 1.852(2); the Pt-F value from the O2PtF6 sample was 1.851(2) A. Although the experimental data neither confirm nor refute the existence of the Jahn-Teller effect in ReF6, OsF6, and IrF6, they ensure that if present the distortion from Oh symmetry must be small.

Agelasine F from a Philippine Agelas sp. sponge exhibits in vitro antituberculosis activity

Marine sponge samples were collected in Baler, Aurora, Philippines, and extracts were tested for in vitro antituberculosis activity. An orange Agelas sp. sponge yielded the known compound, agelasine F, which inhibited some drug resistant strains of Mycobacterium tuberculosis in vitro at concentrations as low as 3.13 micrograms/ml. Activity against M. tuberculosis residing within macrophages required concentrations of 13-22 micrograms/ml which was below the IC50 for Vero cells (34 micrograms/ml).

Foliar plasticity of hybrid spruce in relation to crown position and stand age

This study examined the foliar response of putative hybrid Engelmann × white × Sitka spruce (Picea engelmannii Parry × Picea glauca (Moench) Voss × Picea sitchensis (Bong.) Carr) needles in relation to crown position and across three stages of development (15, 55, and 145 years). We focused on the morphological and anatomical response, and used physiological measures (photosynthesis and stomatal conductance) to emphasize the important relationship between structure and function. We found that needles from the upper outer crown position were adaptated to reduce stress from evapotranspiration. Trees from the 15- and 55-year-old stands generally responded the most, and trees from the 145-year-old stand responded the least. As they mature, these spruce trees may have reduced ability to adapt to their environment. Some of our results contradict what the literature considers "typical" for sun-shade dimorphism in temperate forests. For example, in all stands, sun needles were broader than shade needles and, in the two younger stands, sun needles were larger in area, not smaller, than shade needles. Also, in the youngest stand, stomatal pores were longer on sun needles than on shade needles. There were no definite patterns in stomatal spacing with regard to crown position. Our results are indicative of the strategies adopted to increase competitiveness in a resource-limited environment. We suggest that, in the 15-year-old stand, neither water nor light is limiting; in the 55-year-old stand, both water and light are highly limiting; and in the 145-year-old stand, water is most limiting.Key words: drought, foliar plasticity, needle anatomy, photosynthesis, Picea, stand development, sun-shade.

Effect of race on hypertension and antihypertensive therapy

The presence of hypertension in individual patients confers significant risk in terms of coronary artery disease, myocardial infarction, stroke and congestive heart failure. However, it is also a modifiable risk factor, as risk may be decreased through either lifestyle changes or pharmacotherapy to reduce the elevated blood pressure. Over the past 3 decades, there has been strenuous debate among clinical scientists regarding the role played by racial background in both the pathogenesis and response to pharmacotherapy. A number of studies, such as the third National Health and Nutrition Examination Survey (NHANES III) have demonstrated a higher prevalence of hypertension in black populations. The Hispanic Health and Nutrition Examination Survey (HHANES) suggested that the prevalence of hypertension in Hispanics of Caribbean descent was similar to that of African Americans, while Mexican Americans had lower rates of the disease. It appears that the pathophysiological consequences of elevated blood pressure may also be more severe in black patients. Thus, these patients will have a worse prognosis than their white counterparts at any given blood pressure level. The incidence of end-stage renal disease has been reported to be as much as 17 times more common in African American patients. A number of individual factors have been postulated for these differences including increased sodium intake, differences in sodium handling, decreased potassium intake, decreased calcium intake, elevated fasting insulin levels, lower levels of plasma renin activity and urinary kallikrein excretion. These differences in prevalence and pathophysiology have resulted in recommendations for differential therapeutic approaches in the treatment of hypertension. A major trial conducted in the Veteran Affairs Medical Centers in the USA noted that African Americans are generally more responsive to diuretics and calcium channel blockers than to ACE inhibitors or beta-blockers. However, it has been reported that this resistance may be overcome by increasing the dose of these agents. It has been postulated that these differences may be related to lower plasma renin activity noted in the black population, since diuretics and calcium channel blockers appear to be better suited to this population. These differential therapeutic recommendations will be reviewed in light of our current knowledge of the disease.