Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits

For human complex traits, non-additive genetic variation has been invoked to explain “missing heritability,” but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP2 and δSNP2) in unrelated individuals based on an orthogonal model where the estimate of hSNP2 is independent of that of δSNP2. With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of δSNP2 averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP2 = 0.15). There were a few traits that showed substantial estimates of δSNP2, none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem.     

Viscoelastic Transient of Confined Red Blood Cells

The unique ability of a red blood cell to flow through extremely small microcapillaries depends on the viscoelastic properties of its membrane. Here, we study in vitro the response time upon flow startup exhibited by red blood cells confined into microchannels. We show that the characteristic transient time depends on the imposed flow strength, and that such a dependence gives access to both the effective viscosity and the elastic modulus controlling the temporal response of red cells. A simple theoretical analysis of our experimental data, validated by numerical simulations, further allows us to compute an estimate for the two-dimensional membrane viscosity of red blood cells, ηmem2D ∼ 10⁻⁷ N⋅s⋅m⁻¹. By comparing our results with those from previous studies, we discuss and clarify the origin of the discrepancies found in the literature regarding the determination of ηmem2D, and reconcile seemingly conflicting conclusions from previous works.     

Controlling Electron Transfer between the Two Cofactor Chains of Photosystem I by the Redox State of One of Their Components

Two functional electron transfer (ET) chains, related by a pseudo-C₂ symmetry, are present in the reaction center of photosystem I (PSI). Due to slight differences in the environment around the cofactors of the two branches, there are differences in both the kinetics of ET and the proportion of ET that occurs on the two branches. The strongest evidence that this is indeed the case relied on the observation that the oxidation rates of the reduced phylloquinone (PhQ) cofactor differ by an order of magnitude. Site-directed mutagenesis of residues involved in the respective PhQ-binding sites resulted in a specific alteration of the rates of semiquinone oxidation. Here, we show that the PsaA-F689N mutation results in an ∼100-fold decrease in the observed rate of PhQA− oxidation. This is the largest change of PhQA− oxidation kinetics observed so far for a single-point mutation, resulting in a lifetime that exceeds that of the terminal electron donor, P700+. This situation allows a second photochemical charge separation event to be initiated before PhQA− has decayed, thereby mimicking in PSI a situation that occurs in type II reaction centers. The results indicate that the presence of PhQA− does not impact the overall quantum yield and leads to an almost complete redistribution of the fractional utilization of the two functional ET chains, in favor of the one that does not bear the charged species. The evolutionary implications of these results are also briefly discussed.     

Indolicidin Binding Induces Thinning of a Lipid Bilayer

We use all-atom molecular dynamics simulations on a massive scale to compute the standard binding free energy of the 13-residue antimicrobial peptide indolicidin to a lipid bilayer. The analysis of statistical convergence reveals systematic sampling errors that correlate with reorganization of the bilayer on the microsecond timescale and persist throughout a total of 1.4 ms of sampling. Consistent with experimental observations, indolicidin induces membrane thinning, although the simulations significantly overestimate the lipophilicity of the peptide.Antimicrobial peptides are a component of the innate immune system of eukaryotes (1). As such, they must interact with pathogenic membranes, either during translocation or by disrupting their structural integrity (2). Here we examine the binding of the 13-residue cationic antimicrobial peptide indolicidin (3) (ILPWKWPWWPWRR-NH₂) to a lipid membrane as a first step towards elucidating its mechanism of action.Molecular solutes interact with lipid membranes in many cellular processes (4). Computational approaches such as molecular dynamics simulations have been widely used to characterize these interactions (5). However, molecular dynamics simulations can require unfeasibly long times to reach equilibrium (6). Therefore, it is common to compute equilibrium properties of solute insertion into lipid bilayers using umbrella sampling (7) simulations in which the solute is restrained along the bilayer normal using harmonic restraining potentials, or umbrellas, centered at zi0 values distributed between bulk water and the bilayer center.It is often assumed that equilibrium properties rapidly attain convergence in umbrella sampling simulations; accordingly, convergence measures are rarely published (8). However, we have recently shown that umbrella sampling simulations require up to 100 ns per umbrella (3 μs in total) to eliminate systematic sampling errors in the standard free energy of binding, ΔGbind0, of an arginine side-chain analog from bulk water to a lipid bilayer (8). The fact that umbrella sampling has been used to investigate the bilayer insertion of substantially larger solutes (9) motivates a systematic evaluation of statistical sampling convergence of ΔGbind0 for indolicidin in a lipid bilayer.To estimate ΔGbind0 of indolicidin to a lipid bilayer, we conducted 60 sets of umbrella-sampling simulations while systematically varying the initial conformation. In each umbrella sampling simulation, each umbrella was simulated for 1.5 μs, yielding a total simulation time of 1.4 ms and 60 independent free energy or potential of mean force (PMF) profiles from bulk water to the center of a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer.The PMF profiles indicate that indolicidin strongly binds to the bilayer, partitioning inside the lipid headgroups (Fig. 1, A and E). Importantly, the mean estimate of ΔGbind0 decays exponentially with equilibration time t_eq, indicating that systematic sampling errors in individual simulations continued to decrease throughout the 1.5-μs interval as rare events led to more favorable states (Fig. 1 B). The low frequency of transitions to more favorable states exacerbates the requirement for massive sampling using multiple independent simulations.Open in a separate windowFigure 1PMF for indolicidin partitioning into a POPC bilayer. (A) Average PMF from 60 independent umbrella-sampling simulations based on 1 < t ≤ 1.5 μs/umbrella. (B) Average ΔGbind0 from 50-ns time intervals per umbrella (t_eq < t ≤ t_eq+50 ns) as a function of equilibration time, t_eq. (Solid line) Single exponential fit to the mean over 0.5 < t_eq ≤ 1.5 μs. (C) Mean values of ΔGbind0 from the 10-μs/umbrella simulations (crosses) together with the mean values of ΔGbind0 (triangles) and exponential fit from panel B. PMF and ΔGbind0 profiles obtained from each of the 60 independent simulations are shown in Fig. S1 in the Supporting Material. (D–F) Representative conformations after 1.5 μs of simulation at zi0 = (D) 3 nm, (E) 1.2 nm, and (F) 0.0 nm. To see this figure in color, go online.Computational limitations precluded extending all 60 sets of umbrella-sampling simulations to even longer times. Instead, we identified the two simulations at each umbrella that appeared to be most representative of equilibrium and extended each to 10 μs per umbrella (see Methods in the Supporting Material). The resulting estimates of ΔGbind0 continued to decrease until t_eq = 4 μs (68 μs in total), after which they stabilized at the asymptotic limit of the exponential fit of the shorter simulation data (ΔGbind0 = −26 ± 5 kcal/mol; Fig. 1 C).As indolicidin approaches the bilayer, it is drawn closer (Fig. 2 A) as salt bridges form between the peptide and the phospholipid headgroups (Fig. 2 B), inducing their protrusion (Figs. 1 D and ​and22 C). At large separation distances, this state is attained only when the peptide becomes highly extended (Fig. 2, D and E). As indolicidin is inserted more deeply, the surface of the lipid bilayer invaginates (Figs. 1 E and ​and22 C), maintaining peptide-lipid salt bridges (Fig. 2 B) and leading to the formation of a pore when the solute is near the bilayer center (Figs. 1 F and ​and22 C, and see Fig. S2, Fig. S3, Fig. S4, and Fig. S5 in the Supporting Material). These Boltzmann-weighted ensemble averages may not be mechanistically representative of nonequilibrium binding events (8,10).Open in a separate windowFigure 2Slow equilibration of bilayer and peptide. (A–D) Color quantifies conformational reorganization for t_eq < t ≤ t_eq + 100 ns as a function of t_eq and |zi0|. (A) Deviation of insertion depth, z, from zi0, Δz ≡ z − zi0; (B) number of peptide-lipid salt bridges, N_SB; (C) volume change of the bilayer’s proximal leaflet in the radial vicinity of the solute, V_ε; and (D) peptide end-to-end distance (EED). There is no sampling for t > 0.5 μs at |zi0| ≥ 4.5 nm. (E) Representative time-series of a trajectory at zi0 = 3.9 nm. (F) Representative conformation at 10 μs for |zi0| = 1.2 nm. To see this figure in color, go online.The reorganization of the peptide, the bilayer, and the ionic interactions between them became more pronounced with increasing simulation time at peptide insertion depths shallower than the global free energy minimum (|zi0| >1.4 nm; Fig. 1 A and Fig. 2, B–D). These conformational transitions are likely the source of the systematic drift of ΔGbind0. Reorganization of the bilayer also controls the rate of equilibration during membrane insertion of an arginine side chain (8,9) and a cyclic arginine nonamer (11), suggesting that slow reorganization of lipids around cationic solutes presents a general impediment to simulation convergence.Consistent with the perturbation of membrane thickness observed by in situ atomic force microscopy (12), our results suggest that indolicidin insertion induces local thinning of the bilayer (Fig. 1, E and F, and Fig. 2, C and F). The different conformational ensembles sampled by the peptide in water and in the lipid bilayer (Fig. 2 D) are consistent with the observations that indolicidin is disordered in solution (13) and adopts stable conformations in the presence of detergent (14). Although the peptide’s conformation continued to change when it was deeply inserted (Fig. 2 D), the amount of water in the bilayer’s hydrophobic core converged relatively rapidly (see Fig. S2). Indolicidin can induce the formation of hydrated, porelike defects (see Fig. S2, Fig. S3, Fig. S4, and Fig. S5) but does not act as a chloride carrier (see Fig. S6 and Fig. S7). Future studies of the mechanism of indolicidin action will examine the effect of multiple peptide binding.The PMF profile presented in this Letter is strikingly different from that computed by Yeh et al. (15) using different force field parameters for indolicidin partitioning into a DMPC (1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine) bilayer, from which the binding free energy was estimated to be 0 kcal/mol (15). However, that study comprised only 25 ns per umbrella and likely suffers from systematic sampling errors induced by initial conditions (see Fig. S8).Our estimate of the binding affinity is much larger than the values obtained for indolicidin and large unilamellar POPC vesicles using isothermal titration calorimetry, −7.4 kcal/mol (16), and equilibrium dialysis, −8.8 kcal/mol (13). Such a discrepancy suggests that the relative accuracy of binding free energies for amino-acid side-chain analogs (8,9,17) does not necessarily extend to polypeptides. Although more work is needed to elucidate the source of this discrepancy, this study underlines the importance of attaining convergence before evaluating force-field accuracy.Importantly, this work also highlights the extensive sampling required to remove systematic errors induced by initial conditions in atomistic simulations of peptides in membranes. Slow equilibration of the system is due to rare transitions across hidden free energy barriers involving reorganization of the membrane. Two simple recommendations are 1), evaluating the time-dependence of ensemble averages, and 2), conducting multiple simulations with different initial conditions. We have recently shown that by using enhanced sampling techniques it is possible to identify the locations of hidden free energy barriers without a priori knowledge (9). Future research will examine strategies for speeding up the crossing of these barriers, such as optimized order parameters including bilayer reorganization and enhanced sampling techniques including a random walk along the order parameter (9).     

Effects of lycopene supplementation on antioxidant status,oxidative stress,performance and carcass characteristics in heat-stressed Japanese quail

Lycopene, a carotenoid present predominantly in tomatoes, is one of the most efficient antioxidants. This experiment was conducted to evaluate the effects of dietary lycopene supplementation on performance, carcass characteristics, biomarkers of oxidative stress (malondialdehyde (MDA) and homocysteine), and concentrations of vitamins C, E, A, cholesterol, triglyceride, and glucose in Japanese quails (Coturnix coturnix Japonica) exposed to high-ambient temperature of 34 °C. Two hundred and forty Japanese quails (10 day-old) were randomly assigned to eight treatment groups consisting of 10 replicates of three birds. The birds were kept at a temperature-controlled room at 22 °C (Thermoneutral, TN groups) or 34 °C (for 12 h/day; 09.00 am–05.00 pm; Heat stress, HS groups). Birds were fed either a basal (control) diet (TN and HS) or the basal diet supplemented with 50, 100 or 200 mg of lycopene/kg of diet. Lycopene supplementation linearly increased feed intake (P=0.05$P=0.05$), live weight gain (P=0.01$P=0.01$), feed efficiency (P=0.01$P=0.01$) and cold carcass weight (P=0.01$P=0.01$) and yield (P=0.05$P=0.05$) under heat stress conditions but did not show the same effect at thermoneutral conditions (P>0.05$P>0.05$). The interaction Serum vitamin C, E, and A (P=0.01$P=0.01$) concentrations increased linearly in birds reared at high temperature while non-significant changes occurred at TN groups. Homocysteine level in serum and malondialdehyde (MDA) levels in serum, liver, and heart (P=0.001$P=0.001$) linearly decreased in all birds of both TN and HS groups as dietary lycopene supplementation increased. Heat stress-induced increase in serum cholesterol (P=0.01$P=0.01$), triglycerides (P=0.05$P=0.05$) and glucose (P=0.01$P=0.01$) concentrations were linearly reversed by lycopene supplementation. Supplementation of lycopene increased the HDL concentration whereas, the VLDL and LDL concentrations reduced with lycopene supplementation (P=0.01$P=0.01$, linear), particularly at a dietary concentration of 200 mg/kg. Lycopene could not be detected in control birds while a linear increase was observed in the sera of lycopene supplemented birds The results of the study indicate that lycopene supplementation attenuated the increase in oxidative stress and depletion in antioxidants caused by heat stress in Japanese quails.     

Hierarchical Model of Fibrillar Collagen Organization for Interpreting the Second-Order Susceptibility Tensors in Biological Tissue

The second-order nonlinear polarization properties of fibrillar collagen in various rat tissues (vertebrae, tibia, tail tendon, dermis, and cornea) are investigated with polarization-dependent second-harmonic generation (P-SHG) microscopy. Three parameters are extracted: the second-order susceptibility ratio, R = χZZZ(2)′/χZXX(2)′; a measure of the fibril distribution asymmetry, |A|; and the weighted-average fibril orientation, 〈δ〉. A hierarchical organizational model of fibrillar collagen is developed to interpret the second-harmonic generation polarization properties. Highlights of the model include: collagen type (e.g., type-I, type-II), fibril internal structure (e.g., straight, constant-tilt), and fibril architecture (e.g., parallel fibers, intertwined, lamellae). Quantifiable differences in internal structure and architecture of the fibrils are observed. Occurrence histograms of R and |A| distinguished parallel from nonparallel fibril distributions. Parallel distributions possessed low parameter values and variability, whereas nonparallel distributions displayed an increase in values and variability. From the P-SHG parameters of vertebrae tissue, a three-dimensional reconstruction of lamellae of intervertebral disk is presented.     

Reproductive biology of the horned viper,Cerastes cerastes gasperettii in the central region of Saudi Arabia

The reproductive biology of the horned viper, Cerastes cerastes gasperettii, in Riyadh region of Saudi Arabia was investigated over a period of one year. Study of reproductive cycle of male and female C. c. gasperettii revealed that the breeding season is relatively short (April and May). Thereafter females laid eggs by mid of July and hatching probably had taken place by the end of September. No activity was observed during winter, this may indicate just a single clutch per year. Relative testis weight to body weight was drastically increased (X¯ = 0.88%) during the peak of reproductive activity (May) where maximal expansion of seminiferous tubules was also attained during April and May (X¯ = 209 μm and 191 μm, respectively). Likewise, the ovarian activity was the highest during May where ovarian parameters were greater in terms of relative ovarian weight to body weight and ova diameter being 0.46% and 2.29 mm, respectively. Fat body weight was increased drastically just before the peak of reproductive activity then started to decline during June. It could be concluded that the harsh desert conditions and similar environments certainly affect reproductive activity of Saudi Arabian reptiles including snakes.     

Beta-Adrenergic Stimulation Maintains Cardiac Function in Serca2 Knockout Mice

Previous studies on Serca2 knockout (KO) mice showed that cardiac function is sustained in vivo for several weeks after knockout, whereas SERCA protein levels decrease and calcium dynamics are significantly impaired. In this study, we reconcile observed cellular and organ level contractile function using a cardiac multiscale model. We identified and quantified the changes in cellular function that are both consistent with observations and able to compensate for the decrease in SERCA. Calcium transients were used as input for multiscale computational simulations to predict whole-organ response. Although this response matched experimental pressure-volume (PV) measurements in healthy mice, the reduced magnitude calcium transients observed in KO cells were insufficient to trigger ventricular ejection. To replicate the effects of elevated catecholamine levels observed in vivo, cells were treated with isoproterenol. Incorporation of the resulting measured β-adrenergically stimulated calcium transients into the model resulted in a close match with experimental PV loops. Changes in myofilament properties, when considered in isolation, were not able to increase tension development to levels consistent with measurements, further confirming the necessity of a high β-adrenergic state. Modeling additionally indicated that increased venous return observed in the KO mice helps maintain a high ejection fraction via the Frank-Starling effect. Our study shows that increased β-adrenergic stimulation is a potentially highly significant compensatory mechanism by which cardiac function is maintained in Serca2 KO mice, producing the increases in both systolic and diastolic calcium, consistent with the observed contractile function observed in experimental PV measurements.     

Projected US distributions of transgenic and wildtype zebra danios, Danio rerio, based on temperature tolerance data

A genetically modified version of the south Asian, zebra danio, Danio rerio, a common aquarium fish, has become the first transgenic pet sold in the USA. Mean chronic lethal maxima of wildtype (39.8 °C, n=16$n=16$) and transgenic (39.3 °C, n=10$n=10$) zebra danios initially acclimated to 30 °C were statistically (but not dramatically) different as were mean chronic lethal minima of wildtype (5.3 °C, n=16$n=16$) and transgenic (5.6 °C, n=20$n=20$) zebra danios initially acclimated to 20 °C. These temperature tolerance values were used to estimate potential geographic distributions of the two varieties in the USA. Distributions of these D. rerio varieties in the USA should not be limited by their upper temperature tolerances, and low-temperature tolerance data suggest that both varieties are capable of overwintering in some southern and western US waters.     

Ultrashort echo imaging of cyclically loaded rabbit patellar tendon

Tendinopathy affects individuals who perform repetitive joint motion. Magnetic resonance imaging (MRI) is frequently used to qualitatively assess tendon health, but quantitative evaluation of inherent MRI properties of loaded tendon has been limited. This study evaluated the effect of cyclic loading on _T2^?${T_2}^{?}$ values of fresh and frozen rabbit patellar tendons using ultra short echo (UTE) MRI. Eight fresh and 8 frozen rabbit lower extremities had MR scans acquired for tendon _T2^?${T_2}^{?}$ evaluation. The tendons were then manually cyclically loaded for 100 cycles to 45 N at approximately 1 Hz. The MR scanning was repeated to reassess the _T2^?${T_2}^{?}$ values. Analyses were performed to detect differences of tendon _T2^?${T_2}^{?}$ values between fresh and frozen samples prior to and after loading, and to detect changes of tendon _T2^?${T_2}^{?}$ values between the unloaded and loaded configurations. No difference of _T2^?${T_2}^{?}$ was found between the fresh and frozen samples prior to or after loading, p=0.8 and p  =0.1, respectively. The tendons had significantly shorter _T2^?${T_2}^{?}$ values, p  =0.023, and reduced _T2^?${T_2}^{?}$ variability, p  =0.04, after cyclic loading. Histologic evaluation confirmed no induced tendon damage from loading. Shorter _T2^?${T_2}^{?}$, from stronger spin–spin interactions, may be attributed to greater tissue organization from uncrimping of collagen fibrils and lateral contraction of the tendon during loading. Cyclic tensile loading of tissue reduces patellar tendon _T2^?${T_2}^{?}$ values and may provide a quantitative metric to assess tissue organization.     

On estimation of genetic variance within families using genome-wide identity-by-descent sharing

Background

Traditionally, heritability and other genetic parameters are estimated from between-family variation. With the advent of dense genotyping, it is now possible to compute the proportion of the genome that is shared by pairs of sibs and thus undertake the estimation within families, thereby avoiding environmental covariances of family members. Formulae for the sampling variance of estimates have been derived previously for families with two sibs, which are relevant for humans, but sampling errors are large. In livestock and plants much larger families can be obtained, and simulation has shown sampling variances are then much smaller.

Methods

Based on the assumptions that realised relationship of sibs can be obtained from genomic data and that data are analyzed by restricted maximum likelihood, formulae were derived for the sampling variance of the estimates of genetic variance for arbitrary family sizes. The analysis used statistical differentiation, assuming the variance of relationships is small.

Results

The variance of the estimate of the additive genetic variance was approximately proportional to 1/ (fn²σR2), for f families of size n and variance of relationships σR2.

Conclusions

Because the standard error of the estimate of heritability decreased in proportion to family size, the use of within-family information becomes increasingly efficient as the family size increases. There are however, limitations, such as near complete confounding of additive and dominance variances in full sib families.     

Genetic variation for growth and selection in adult plants of Eucalyptus badjensis

The aim of this study was to evaluate Eucalyptus badjensis concerning the genetic variation for growth traits and the potential of the species in supporting a breeding programme. The field trial was a provenance/progeny test established in Campina da Alegria, Santa Catarina, Brazil (latitude 26°52′05.1″ S, longitude 51°48′47.5″ W, altitude 1,015 m) in a soil classified as Latossolic Alumino-Ferric Brown Nitosol. The experiment comprised 60 open-pollinated progenies from the provenances Glenbog and Badja State Forest, New South Wales, Australia. Ten replicates and plots with six plants in row were used. At the age of 17 years, 279 trees were assessed for diameter of the bole at breast height (DBH), total tree height (H) and volume of wood with bark (Vol). After submitting the data to statistical genetic analysis, the overall means for DBH, H and Vol were 45.17 cm, 33.30 m and 2.84 m³, and the estimates of additive coefficient of variation [CV^a(%)] were 12.59%, 5.91% and 26.51%, respectively. Heritability coefficients of additive effects (h^a2) were also estimated and the following values were found: 0.443, 0.312 and 0.358. Thirty-nine trees from 25 different progenies were selected. The expected means of the provenances after improvement were 50.02 cm, 34.35 m and 3.47 m³ for DBH, H and Vol, respectively.     

Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs

Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl₂ or 1 M KCl. The ΔG37∘ loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47–2.06 kcal/mol more favorable for the RNA bulge loops. The ΔG37∘ loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride.     

The catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2)

Methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) is a new drug target that is expressed in cancer cells but not in normal adult cells, which provides an Achilles heel to selectively kill cancer cells. Despite the availability of crystal structures of MTHFD2 in the inhibitor- and cofactor-bound forms, key information is missing due to technical limitations, including (a) the location of absolutely required Mg²⁺ ion, and (b) the substrate-bound form of MTHFD2. Using computational modeling and simulations, we propose that two magnesium ions are present at the active site whereby (i) Arg233, Asp225, and two water molecules coordinate MgA2+, while MgA2+ together with Arg233 stabilize the inorganic phosphate (P_i); (ii) Asp168 and three water molecules coordinate MgB2+, and MgB2+ further stabilizes P_i by forming a hydrogen bond with two oxygens of P_i; (iii) Arg201 directly coordinates the P_i; and (iv) through three water-mediated interactions, Asp168 contributes to the positioning and stabilization of MgA2+, MgB2+ and P_i. Our computational study at the empirical valence bond level allowed us also to elucidate the detailed reaction mechanisms. We found that the dehydrogenase activity features a proton-coupled electron transfer with charge redistribution connected to the reorganization of the surrounding water molecules which further facilitates the subsequent cyclohydrolase activity. The cyclohydrolase activity then drives the hydration of the imidazoline ring and the ring opening in a concerted way. Furthermore, we have uncovered that two key residues, Ser197/Arg233, are important factors in determining the cofactor (NADP⁺/NAD⁺) preference of the dehydrogenase activity. Our work sheds new light on the structural and kinetic framework of MTHFD2, which will be helpful to design small molecule inhibitors that can be used for cancer treatment.     

A Scaling Law of Vascular Volume

Vascular volume is of fundamental significance to the function of the cardiovascular system. An accurate prediction of blood volume in patients is physiologically and clinically significant. This study proposes what we believe is a novel volume scaling relation of the form: Vc=KvDs2/3Lc, where V_c and L_c are cumulative vessel volume and length, respectively, in the tree, and D_s is the diameter of the vessel segment. The scaling relation is validated in vascular trees of various organs including the heart, lung, mesentery, muscle, and eye of different species. Based on the minimum energy hypothesis and volume scaling relation, four structure-function scaling relations are predicted, including the diameter-length, volume-length, flow-diameter, and volume-diameter relations, with exponent values of 3/7, 127, 2⅓, and 3, respectively. These four relations are validated in the various vascular trees, which further confirm the volume scaling relation. This scaling relation may serve as a control reference to estimate the blood volume in various organs and species. The deviation from the scaling relation may indicate hypovolemia or hypervolemia and aid diagnosis.     

Topography Mediates the Influence of Cover Crops on Soil Nitrate Levels in Row Crop Agricultural Systems

Supplying adequate amounts of soil N for plant growth during the growing season and across large agricultural fields is a challenge for conservational agricultural systems with cover crops. Knowledge about cover crop effects on N comes mostly from small, flat research plots and performance of cover crops across topographically diverse agricultural land is poorly understood. Our objective was to assess effects of both leguminous (red clover) and non-leguminous (winter rye) cover crops on potentially mineralizable N (PMN) and NO3--N levels across a topographically diverse landscape. We studied conventional, low-input, and organic managements in corn-soybean-wheat rotation. The rotations of low-input and organic managements included rye and red clover cover crops. The managements were implemented in twenty large undulating fields in Southwest Michigan starting from 2006. The data collection and analysis were conducted during three growing seasons of 2011, 2012 and 2013. Observational micro-plots with and without cover crops were laid within each field on three contrasting topographical positions of depression, slope and summit. Soil samples were collected 4–5 times during each growing season and analyzed for NO3--N and PMN. The results showed that all three managements were similar in their temporal and spatial distributions of NO₃ ^—N. Red clover cover crop increased NO3--N by 35% on depression, 20% on slope and 32% on summit positions. Rye cover crop had a significant 15% negative effect on NO3--N in topographical depressions but not in slope and summit positions. The magnitude of the cover crop effects on soil mineral nitrogen across topographically diverse fields was associated with the amount of cover crop growth and residue production. The results emphasize the potential environmental and economic benefits that can be generated by implementing site-specific topography-driven cover crop management in row-crop agricultural systems.     

Epidemic dynamics on semi-directed complex networks

In this paper an SIS model for epidemic spreading on semi-directed networks is established, which can be used to examine and compare the impact of undirected and directed contacts on disease spread. The model is analyzed for the case of uncorrelated semi-directed networks, and the basic reproduction number _R0$R_0$ is obtained analytically. We verify that the _R0$R_0$ contains the outbreak threshold on undirected networks and directed networks as special cases. It is proved that if _R0<1$R_0<1$ then the disease-free equilibrium is globally asymptotically stable, otherwise the disease-free equilibrium is unstable and the unique endemic equilibrium exists, which is globally asymptotically stable. Finally the numerical simulations holds for these analytical results are given.