De novo inference of protein function from coarse‐grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high‐throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse‐grained (CG) molecular dynamics trajectories were used to compute normalized root‐mean‐square‐fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three‐dimensional autocorrelation vectors. Our in‐house custom‐built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics‐signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof‐of‐principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom‐made CG FF, useful to all. Proteins 2014; 82:2443–2454. © 2014 Wiley Periodicals, Inc.     

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.     

Sex differences in leg dexterity are not present in elite athletes

We studied whether the time-varying forces that control unstable foot–ground interactions provide insight into the neural control of dynamic leg function. Twenty elite (10 F, 26.4 ± 3.5 yrs) and 20 recreational (10 F, 24.8 ± 2.4 yrs) athletes used an isolated leg to maximally compress a slender spring designed to buckle at low forces while seated. The foot forces during the compression at the edge of instability quantify the maximal sensorimotor ability to control dynamic foot–ground interactions. Using the nonlinear analysis technique of attractor reconstruction, we characterized the spatial (interquartile range IQR) and geometric (trajectory length TL, volume V, and sum of edge lengths SE) features of the dynamical behavior of those force time series. ANOVA confirmed the already published effect of sex, and a new effect of athletic ability, respectively, in TL (p = 0.014 and p < 0.001), IQR (p = 0.008 and p < 0.001), V (p = 0.034 and p = 0.002), and SE (p = 0.033 and p < 0.001). Further analysis revealed that, for recreational athletes, females exhibited weaker corrective actions and greater stochasticity than males as per their greater mean values of TL (p = 0.003), IQR (p = 0.018), V (p = 0.017), and SE (p = 0.025). Importantly, sex differences disappeared in elite athletes. These results provide an empirical link between sex, athletic ability, and nonlinear dynamical control. This is a first step in understanding the sensorimotor mechanisms for control of unstable foot–ground interactions. Given that females suffer a greater incidence of non-contact knee ligament injuries, these non-invasive and practical metrics of leg dexterity may be both indicators of athletic ability, and predictors of risk of injury.     

Nanoparticle transport and delivery in a heterogeneous pulmonary vasculature

Quantitative understanding of nanoparticles delivery in a complex vascular networks is very challenging because it involves interplay of transport, hydrodynamic force, and multivalent interactions across different scales. Heterogeneous pulmonary network includes up to 16 generations of vessels in its arterial tree. Modeling the complete pulmonary vascular system in 3D is computationally unrealistic. To save computational cost, a model reconstructed from MRI scanned images is cut into an arbitrary pathway consisting of the upper 4-generations. The remaining generations are represented by an artificially rebuilt pathway. Physiological data such as branch information and connectivity matrix are used for geometry reconstruction. A lumped model is used to model the flow resistance of the branches that are cut off from the truncated pathway. Moreover, since the nanoparticle binding process is stochastic in nature, a binding probability function is used to simplify the carrier attachment and detachment processes. The stitched realistic and artificial geometries coupled with the lumped model at the unresolved outlets are used to resolve the flow field within the truncated arterial tree. Then, the biodistribution of 200 nm, 700 nm and 2 µm particles at different vessel generations is studied. At the end, 0.2–0.5% nanocarrier deposition is predicted during one time passage of drug carriers through pulmonary vascular tree. Our truncated approach enabled us to efficiently model hemodynamics and accordingly particle distribution in a complex 3D vasculature providing a simple, yet efficient predictive tool to study drug delivery at organ level.     

Body size and area‐incidence relationships: is there a general pattern?

Aim This paper tests firstly for the existence of a general relationship between body size of terrestrial animals and their incidence across habitat patches of increasing size, and secondly for differences in this relationship between insects and vertebrates. Location The analysis was based on the occupancy pattern of 50 species from 15 different landscapes in a variety of ecosystems ranging from Central European grassland to Asian tropical forest. Methods The area‐occupancy relationship was described by incidence functions that were calculated using logistic regression. A correlation analysis between body size of the species and the patch area referring to the two given points of the incidence function was performed. In order to test for an effect of taxon (insects vs. vertebrates), an analysis of covariance was conducted. Results In all species, the incidence was found to increase with increasing patch area. The macroecological analysis showed a significant relationship between the incidence in habitat patches and the body size of terrestrial animals. The area requirement was found to increase linearly with increasing body size on a log‐log scale. This relationship did not differ significantly between insects and vertebrates. Conclusions The approach highlighted in this paper is to associate incidence functions with body size. The results suggest that body size is a general but rather rough predictor for the area requirements of animals. The relationship seems valid for a wide range of body sizes of terrestrial animals. However, further studies including isolation of habitats as well as additional species traits into the macroecological analysis of incidence functions are needed.     

Schistocephalus solidus and Ligula intestinalis: Pinocytosis by the tegument

Using ruthenium red as a macromolecule, endocytosis was demonstrated in the plerocercoid of Ligula intestinalis and adult Schistocephalus solidus. Uptake, transport across the tegument, and exocytosis across the basal plasma membrane occurred within 6 min. The types of vesicles in the tegument of L. intestinalis are redescribed and their former classification is modified. The vertical and longitudinal distribution of pinosomes in the tegument of adult S. solidus and L. intestinalis plerocercoids were determined. The possible role of macromolecular uptake in the economy of pseudophyllidean tapeworms is discussed with particular reference to growth and defence of an unencysted larval stage in the tissues of the intermediate host.     

The reactivity of lactyl-oxythiamin implies the role of the amino-pyrimidine in thiamin catalyzed decarboxylation

It has previously been established that the deprotonated amino substituent of the pyrimidine of thiamin diphosphate (ThDP) acts as an internal base to accept the C2H of the thiazolium in ThDP-dependent enzymes. The amino group has also been implicated in assisting the departure of the aldehydic product formed after loss of CO₂ from ketoacid substrates. However, the potential role for the pyrimidine amino group in the key decarboxylation step has not been assessed. Oxythiamin contains a hydroxyl group in place of the pyrimidine amino group in thiamin, providing a basis for comparison of reactivity. Lactyl-oxythiamin (LOTh), the conjugate of pyruvic acid and oxythiamin was prepared by condensation of ethyl pyruvate and hydroxyl-protected oxythiamin followed by deprotection and acidic hydrolysis of the ethyl ester. The rate constants observed for the decarboxylation of LOTh in neutral and acidic solutions are about four times smaller than those for the corresponding compound that contains the amino group, lactylthiamin. The difference in reactivity is consistent with the amino group’s participation in facilitating the decarboxylation step by allowing a competitive addition pathway that produces bicarbonate and has implications for the corresponding enzymic reaction.     

A measure of spatial stratified heterogeneity

Spatial stratified heterogeneity, referring to the within-strata variance less than the between strata-variance, is ubiquitous in ecological phenomena, such as ecological zones and many ecological variables. Spatial stratified heterogeneity reflects the essence of nature, implies potential distinct mechanisms by strata, suggests possible determinants of the observed process, allows the representativeness of observations of the earth, and enforces the applicability of statistical inferences. In this paper, we propose a q-statistic method to measure the degree of spatial stratified heterogeneity and to test its significance. The q value is within [0,1] (0 if a spatial stratification of heterogeneity is not significant, and 1 if there is a perfect spatial stratification of heterogeneity). The exact probability density function is derived. The q-statistic is illustrated by two examples, wherein we assess the spatial stratified heterogeneities of a hand map and the distribution of the annual NDVI in China.     

Identification of soil quality indicators for assessing the effect of different tillage practices through a soil quality index in a semi-arid environment

Tillage is known to potentially affect soil quality in various ways. In this study, a soil quality index (SQI) was developed by quantifying several soil attributes either sensitive or insensitive to physical disturbance, using factor analysis as a dimension reduction technique, in order to discriminate different tillage systems. Soil properties including physical (MWD), chemical (pH, organic C, total N, available P and POM contents) and microbial (MBC, MBN, PCM, PNM and three enzymes) parameters were measured to establish a minimum data set (MDS) for the assessment of overall SQI. The soil attributes were determined on samples (0–20 cm depth) collected under moldboard (MP) and disk (DP) plows as conventional tillage (CT), and rotary (RP) and chisel (CP) plows as reduced tillage (RT) systems with a similar plant C input rate and cover crop over a period of six years (2005–2011) in a semi-arid calcareous soil (Calcixerepts) from Central Iran. Results indicated a clear difference in soil quality among the tillage systems with a significant increase of SQI under RT over time, particularly under CP practices. Although RT improved most soil microbial attributes, not all attributes contributed to SQI because of their close interrelationship. The final SQI consisted only of geometric mean of microbial activity (GMA, the square root of the product of PCM and PNM) and geometric mean of enzyme activity (GME, the cube root of the product of enzyme activities). Soil GME and GMA were found to be as key indicators contributing 55% and 36% to SQI, respectively. Therefore, the GME and GMA were the most important indicators effectively discriminating tillage systems, and could be used to monitor the enhancement of soil quality under RT in this semiarid environment. The influence of tillage year on SQI was greater than that of tillage practices. In conclusion, RT systems were characterized by a higher value of SQI, suggesting a good recovery of soil capacity and functions after abandoning CT in the studied area. Smallholder farmers should therefore be aware of the potential for high soil quality in future as a result of continuing RT systems, especially with surface tillage using CP practices.