Mechanistic Study into Free Radical-Activated Glycan Dissociations through Isotope-Labeled Cellobioses.

Inspired by the electron-activated dissociation technique, the most potent tool for glycan characterization, we recently developed free radical reagents for glycan structural elucidation. However, the underlying mechanisms of free radical-induced glycan dissociation remain unclear and, therefore, hinder the rational optimization of the free radical reagents and the interpretation of tandem mass spectra, especially the accurate assignment of the relatively low-abundant but information-rich ions. In this work, we selectively incorporate the 13C and/or 18O isotopes into cellobiose to study the mechanisms for free radical-induced dissociation of glycans. The eight isotope-labeled cellobioses include 1-13C, 3-13C, 1'-13C, 2'-13C, 3'-13C, 4'-13C, 5'-13C, and 1'-13C-4-18O-cellobioses. Upon one-step collisional activation, cross-ring (X ions), glycosidic bond (Y-, Z-, and B-related ions), and combinational (Y1 + 0,4X0 ion) cleavages are generated. These fragment ions can be unambiguously assigned and confirmed by the mass difference of isotope labeling. Importantly, the relatively low-abundant but information-rich ions, such as 1,5X0 + H, 1,4X0 + H, 2,4X0 + H-OH, Y1 + 0,4X0, 2,5X1-H, 3,5X0-H, 0,3X0-H, 1,4X0-H, and B2-3H, are confidently assigned. The mechanisms for the formations of these ions are investigated and supported by quantum chemical calculations. These ions are generally initiated by hydrogen abstraction followed by sequential ß-elimination and/or radical migration. Here, the mechanistic study for free radical-induced glycan dissociation allows us to interpret all of the free radical-induced fragment ions accurately and, therefore, enables the differentiation of stereochemical isomers. Moreover, it provides fundamental knowledge for the subsequent development of bioinformatics tools to interpret the complex free radical-induced glycan spectra.

Energies, structures, and harmonic frequencies of small water clusters from the direct random phase approximation.

The binding energies, structures, and vibrational frequencies of water clusters up to 20 molecules are computed at the direct random phase approximation (RPA) level of theory and compared to theoretical benchmarks. Binding energies of the WATER27 set, which includes neutral and positively and negatively charged clusters, are predicted to be too low in the complete basis set limit by an average of 7 kcal/mol (9%) and are worse than the results from the best density functional theory methods or from the Møller-Plesset theory. The RPA shows significant basis set size dependence for binding energies. The order of the relative energies of the water hexamer and dodecamer isomers is predicted correctly by the RPA. The mean absolute deviation for angles and distances for neutral clusters up to the water hexamer are 0.2° and 0.6 pm, respectively, using quintuple-ζ basis sets. The relative energetic order of the hexamer isomers is preserved upon optimization. Vibrational frequencies for these systems are underestimated by several tens of wavenumbers for large basis sets, and deviations increase with the basis set size. Overall, the direct RPA method yields accurate structural parameters but systematically underestimates binding energies and shows strong basis set size dependence.

Cytomegalovirus distribution and evolution in hominines.

Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.

Human impact erodes chimpanzee behavioral diversity.

Chimpanzees possess a large number of behavioral and cultural traits among nonhuman species. The "disturbance hypothesis" predicts that human impact depletes resources and disrupts social learning processes necessary for behavioral and cultural transmission. We used a dataset of 144 chimpanzee communities, with information on 31 behaviors, to show that chimpanzees inhabiting areas with high human impact have a mean probability of occurrence reduced by 88%, across all behaviors, compared to low-impact areas. This behavioral diversity loss was evident irrespective of the grouping or categorization of behaviors. Therefore, human impact may not only be associated with the loss of populations and genetic diversity, but also affects how animals behave. Our results support the view that "culturally significant units" should be integrated into wildlife conservation.

Stable isotope variation in savanna chimpanzees (Pan troglodytes verus) indicate avoidance of energetic challenges through dietary compensation at the limits of the range.

OBJECTIVES: Food scarcity is proposed to be a limitation to chimpanzees at the limits of their range; however, such a constraint has never been investigated in this context. We investigated patterns of δ13 C and δ15 N variation along a latitudinal gradient at the northwestern West African chimpanzee (Pan troglodytes verus) range limit with the expectation that isotope ratios of chimpanzees at the range limit will indicate different dietary strategies or higher physiological constraints than chimpanzees further from the edge. MATERIALS AND METHODS: We measured δ13 C and δ15 N values in hair (n = 81) and plant food (n = 342) samples from five chimpanzee communities located along a latitudinal gradient in Southeastern Senegal. RESULTS: We found clear grouping patterns in hair δ13 C and δ15 N in the four southern sites compared to the northernmost site. Environmental baseline samples collected from these sites revealed overall higher plant δ15 N values at the northernmost site, but similar δ13 C values across sites. By accounting for environmental baseline, Δ13 C and Δ15 N values were clustered for all five sites relative to total Pan variation, but indicated a 13 C-enriched diet at the range limit. DISCUSSION: Clustering in Δ13 C and Δ15 N values supports that strategic shifting between preferred and fallback foods is a likely ubiquitous but necessary strategy employed by these chimpanzees to cope with their environment, potentially allowing chimpanzees at their limits to avoid periods of starvation. These results also underline the necessity of accounting for local isotopic baseline differences during inter-site comparison.

Nocturnal activity in wild chimpanzees (Pan troglodytes): Evidence for flexible sleeping patterns and insights into human evolution.

OBJECTIVES: We investigated occurrences and patterns of terrestrial nocturnal activity in wild chimpanzees (Pan troglodytes) and modelled the influence of various ecological predictors on nocturnal activity. METHODS: Data were extracted from terrestrial camera-trap footage and ecological surveys from 22 chimpanzee study sites participating in the Pan African Programme: The Cultured Chimpanzee. We described videos demonstrating nocturnal activity, and we tested the effects of the percentage of forest, abundance of predators (lions, leopards and hyenas), abundance of large mammals (buffalos and elephants), average daily temperature, rainfall, human activity, and percent illumination on the probability of nocturnal activity. RESULTS: We found terrestrial nocturnal activity to occur at 18 of the 22 study sites, at an overall average proportion of 1.80% of total chimpanzee activity, and to occur during all hours of the night, but more frequently during twilight hours. We found a higher probability of nocturnal activity with lower levels of human activity, higher average daily temperature, and at sites with a larger percentage of forest. We found no effect of the abundance of predators and large mammals, rainfall, or moon illumination. DISCUSSION: Chimpanzee terrestrial nocturnal activity appears widespread yet infrequent, which suggests a consolidated sleeping pattern. Nocturnal activity may be driven by the stress of high daily temperatures and may be enabled at low levels of human activity. Human activity may exert a relatively greater influence on chimpanzee nocturnal behavior than predator presence. We suggest that chimpanzee nocturnal activity is flexible, enabling them to respond to changing environmental factors.

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest.

Anthrax is a globally important animal disease and zoonosis. Despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. Here we show that the dynamics of an anthrax-causing agent, Bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. Using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of death for a broad range of mammalian hosts. We predict that this pathogen will accelerate the decline and possibly result in the extirpation of local chimpanzee (Pan troglodytes verus) populations. We present the epidemiology of a cryptic pathogen and show that its presence has important implications for conservation.

Comparative isotope ecology of African great apes.

The isotope ecology of great apes is a useful reference for palaeodietary reconstructions in fossil hominins. As extant apes live in C3-dominated habitats, variation in isotope signatures is assumed to be low compared to hominoids exploiting C4-plant resources. However, isotopic differences between sites and between and within individuals are poorly understood due to the lack of vegetation baseline data. In this comparative study, we included all species of free-ranging African great apes (Pan troglodytes, Pan paniscus, Gorilla sp.). First, we explore differences in isotope baselines across different habitats and whether isotopic signatures in apes can be related to feeding niches (faunivory and folivory). Secondly, we illustrate how stable isotopic variations within African ape populations compare to other extant and extinct primates and discuss possible implications for dietary flexibility. Using 701 carbon and nitrogen isotope data points resulting from 148 sectioned hair samples and an additional collection of 189 fruit samples, we compare six different great ape sites. We investigate the relationship between vegetation baselines and climatic variables, and subsequently correct great ape isotope data to a standardized plant baseline from the respective sites. We obtained temporal isotopic profiles of individual animals by sectioning hair along its growth trajectory. Isotopic signatures of great apes differed between sites, mainly as vegetation isotope baselines were correlated with site-specific climatic conditions. We show that controlling for plant isotopic characteristics at a given site is essential for faunal data interpretation. While accounting for plant baseline effects, we found distinct isotopic profiles for each great ape population. Based on evidence from habituated groups and sympatric great ape species, these differences could possibly be related to faunivory and folivory. Dietary flexibility in apes varied, but temporal variation was overall lower than in fossil hominins and extant baboons, shifting from C3 to C4-resources, providing new perspectives on comparisons between extinct and extant primates.

Thermochemistry and Geometries for Transition-Metal Chemistry from the Random Phase Approximation.

Performance of the random phase approximation (RPA) is tested for thermochemistry and geometries of transition-metal chemistry using various benchmarks obtained either computationally or experimentally. Comparison is made to popular (semi)local meta- and hybrid density functionals as well as to the second-order Møller-Plesset perturbation theory (MP2) and its spin-component-scaled derivatives. The benchmark sets include reaction energies, barrier heights, and dissociation energies of prototype bond-activation reactions, dissociation energies for a set of large transition-metal complexes, bond lengths and dissociation energies of metal hydride ions, and bond lengths and angles of a set of closed-shell first-row transition-metal complexes. The emphasis is on first-row transition-metal chemistry, though for energies, elements beyond the first-row are included. Attention is paid to the basis set convergence of RPA. For thermochemistry, RPA performs on par or better than the density functional theory (DFT) functionals presented and is significantly more accurate than MP2. The largest errors are observed in dissociation energies where the electronic environment is altered substantially. For structural parameters, very good results were obtained, and RPA meets the high quality of structures from DFT. In most cases, well-converged structures are obtained with basis sets of triple-zeta quality. MP2 optimized values can often not be obtained and are on average of inferior quality. Though chemical accuracy is not reached, the RPA method is a step forward toward a systematic, parameter-free, all-round method to describe transition-metal chemistry.

Chimpanzee accumulative stone throwing.

The study of the archaeological remains of fossil hominins must rely on reconstructions to elucidate the behaviour that may have resulted in particular stone tools and their accumulation. Comparatively, stone tool use among living primates has illuminated behaviours that are also amenable to archaeological examination, permitting direct observations of the behaviour leading to artefacts and their assemblages to be incorporated. Here, we describe newly discovered stone tool-use behaviour and stone accumulation sites in wild chimpanzees reminiscent of human cairns. In addition to data from 17 mid- to long-term chimpanzee research sites, we sampled a further 34 Pan troglodytes communities. We found four populations in West Africa where chimpanzees habitually bang and throw rocks against trees, or toss them into tree cavities, resulting in conspicuous stone accumulations at these sites. This represents the first record of repeated observations of individual chimpanzees exhibiting stone tool use for a purpose other than extractive foraging at what appear to be targeted trees. The ritualized behavioural display and collection of artefacts at particular locations observed in chimpanzee accumulative stone throwing may have implications for the inferences that can be drawn from archaeological stone assemblages and the origins of ritual sites.

FDE-vdW: A van der Waals inclusive subsystem density-functional theory.

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation-dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.

Analytical First-Order Molecular Properties and Forces within the Adiabatic Connection Random Phase Approximation.

The random phase approximation (RPA) is an increasingly popular method for computing molecular ground-state correlation energies within the adiabatic connection fluctuation-dissipation theorem framework of density functional theory. We present an efficient analytical implementation of first-order RPA molecular properties and nuclear forces using the resolution-of-the-identity (RI) approximation and imaginary frequency integration. The centerpiece of our approach is a variational RPA energy Lagrangian invariant under unitary transformations of occupied and virtual reference orbitals, respectively. Its construction requires the solution of a single coupled-perturbed Kohn-Sham equation independent of the number of perturbations. Energy gradients with respect to nuclear displacements and other first-order properties such as one-particle densities or dipole moments are obtained from partial derivatives of the Lagrangian. Our RPA energy gradient implementation exhibits the same [Formula: see text] scaling with system size N as a single-point RPA energy calculation. In typical applications, the cost for computing the entire gradient vector with respect to nuclear displacements is ∼5 times that of a single-point RPA energy calculation. Derivatives of the quadrature nodes and weights used for frequency integration are essential for RPA gradients with an accuracy consistent with RPA energies and can be included in our approach. The quality of RPA equilibrium structures is assessed by comparison to accurate theoretical and experimental data for covalent main group compounds, weakly bonded dimers, and transition metal complexes. RPA outperforms semilocal functionals as well as second-order Møller-Plesset (MP2) theory, which fails badly for the transition metal compounds. Dipole moments of polarizable molecules and weakly bound dimers show a similar trend. RPA harmonic vibrational frequencies are nearly of coupled cluster singles, doubles, and perturbative triples quality for a set of main group compounds. Compared to the ring-coupled cluster based implementation of Rekkedal et al. [J. Chem. Phys. 2013, 139, 081101.], our method scales better by two powers of N and supports a semilocal Kohn-Sham reference. The latter is essential for the good performance of RPA in small-gap systems.

Controls on coarse wood decay in temperate tree species: birth of the LOGLIFE experiment.

Dead wood provides a huge terrestrial carbon stock and a habitat to wide-ranging organisms during its decay. Our brief review highlights that, in order to understand environmental change impacts on these functions, we need to quantify the contributions of different interacting biotic and abiotic drivers to wood decomposition. LOGLIFE is a new long-term 'common-garden' experiment to disentangle the effects of species' wood traits and site-related environmental drivers on wood decomposition dynamics and its associated diversity of microbial and invertebrate communities. This experiment is firmly rooted in pioneering experiments under the directorship of Terry Callaghan at Abisko Research Station, Sweden. LOGLIFE features two contrasting forest sites in the Netherlands, each hosting a similar set of coarse logs and branches of 10 tree species. LOGLIFE welcomes other researchers to test further questions concerning coarse wood decay that will also help to optimise forest management in view of carbon sequestration and biodiversity conservation.

Basis set convergence of molecular correlation energy differences within the random phase approximation.

The basis set convergence of energy differences obtained from the random phase approximation (RPA) to the correlation energy is investigated for a wide range of molecular interactions. For dispersion bound systems the basis set incompleteness error is most pronounced, as shown for the S22 benchmark [P. Jurecka et al., Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The use of very large basis sets (> quintuple-zeta) or extrapolation to the complete basis set (CBS) limit is necessary to obtain a reliable estimate of the binding energy for these systems. Counterpoise corrected results converge to the same CBS limit, but counterpoise correction without extrapolation is insufficient. Core-valence correlations do not play a significant role. For medium- and short-range correlation, quadruple-zeta results are essentially converged, as demonstrated for relative alkane conformer energies, reaction energies dominated by intramolecular dispersion, isomerization energies, and reaction energies of small organic molecules. Except for weakly bound systems, diffuse augmentation almost universally slows down basis set convergence. For most RPA applications, quadruple-zeta valence basis sets offer a good balance between accuracy and efficiency.

Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration.

The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller-Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [A. Tajti et al., J. Chem. Phys. 121, 11599 (2004)] and MOLEKEL [F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998)] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N(4) log N) operations and O(N(3)) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30-40 grid points yield muH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn-Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [J. Jung et al., Phys. Rev. B 70, 205107 (2004)]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.

The influence of initial conditions on charge transfer dynamics.

In this work we address the influence of the initial state on electron transfer dynamics by comparing two different ways of setting up the initial state, namely by taking an electron from the HOMO of a DFT ground state, or by using constrained DFT to self-consistently create the initial state. We solve the TDKS equations for the benzyl-pentafluorobenzene cation. The neutral molecule has a localised HOMO, which gives a natural partitioning in donor and acceptor group. We compare the electronic dynamics for varying angle between donor and acceptor and for varying basis set. We show that the methods lead to essentially equivalent results, but that the use of cDFT gives higher currents and a more consistent initial state with respect to variation of basis set and geometry.

Dynamics of molecules in strong oscillating electric fields using time-dependent Hartree-Fock theory.

Restricted and unrestricted forms of time-dependent Hartree-Fock theory have been implemented and used to study the electronic dynamics of ethene, benzene, and the formaldehyde cation subjected to both weak and strong oscillating electric fields. Absorption spectra and frequency-dependent polarizabilities are calculated via the instantaneous dipole moment and its derivative. In the weak field limit the computed excitation energies agree very well with those obtained using linearized time-dependent Hartree-Fock theory, which is valid only in the low-field perturbation limit. For strong fields the spectra show higher-order excitations, and a shift in the position of the excitations, which is due to the nonadiabatic response of the molecules to the field. For open-shell systems in the presence of strong oscillating electric fields, unrestricted time-dependent Hartree-Fock theory predicts the value of S(2) to vary strongly with time.

The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3.

BACKGROUND: SH3 domains are small protein modules of 60-85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the alpha-spectrin SH3 domain (Spc-SH3). RESULTS: Here we present the high-resolution structure of the complex between the R21A mutant of Spc-SH3 and p41 derived from NMR data. Thermodynamic parameters of binding of p41 to both WT and R21A Spc-SH3 were measured by a combination of isothermal titration and differential scanning calorimetry. Mutation of arginine 21 to alanine in Spc-SH3 increases 3- to 4-fold the binding affinity for p41 due to elimination at the binding-site interface of the steric clash produced by the longer arginine side chain. Amide hydrogen-deuterium experiments on the free and p41-bound R21A Spc-SH3 domain indicate that binding elicits a strong reduction in the conformational flexibility of the domain. Despite the great differences in the thermodynamic magnitudes of binding, the structure of the R21A Spc-SH3:P41 complex is remarkably similar to that of the Abl-SH3:P41 complex, with only few differences in protein-ligand contacts at the specificity pocket. Using empirical methods for the prediction of binding energetics based on solvent-accessible surface area calculations, the differences in experimental energetics of binding between the two complexes could not be properly explained only on the basis of the structural differences observed between the complexes. We suggest that the experimental differences in binding energetics can be at least partially ascribed to the absence in the R21A Spc-SH3:P41 complex of several buried water molecules, which have been proposed previously to contribute largely to the highly negative enthalpy and entropy of binding in the Abl-SH3:P41 complex. CONCLUSION: Based on a deep structural and thermodynamic analysis of a low and high affinity complex of two different SH3 domains with the same ligand p41, we underline the importance of taking into account in any effective strategy of rational design of ligands, factors different from the direct protein-ligand interactions, such as the mediation of interactions by water molecules or the existence of cooperative conformational effects induced by binding.