Travel depth, a new shape descriptor for macromolecules: application to ligand binding

Depth is a term frequently applied to the shape and surface of macromolecules, describing for example the grooves in DNA, the shape of an enzyme active site, or the binding site for a small molecule in a protein. Yet depth is a difficult property to define rigorously in a macromolecule, and few computational tools exist to quantify this notion, to visualize it, or analyze the results. We present our notion of travel depth, simply put the physical distance a solvent molecule would have to travel from a surface point to a suitably defined reference surface. To define the reference surface, we use the limiting form of the molecular surface with increasing probe size: the convex hull. We then present a fast, robust approximation algorithm to compute travel depth to every surface point. The travel depth is useful because it works for pockets of any size and complexity. It also works for two interesting special cases. First, it works on the grooves in DNA, which are unbounded in one direction. Second, it works on the case of tunnels, that is pockets that have no "bottom", but go through the entire macromolecule. Our algorithm makes it straightforward to quantify discussions of depth when analyzing structures. High-throughput analysis of macromolecule depth is also enabled by our algorithm. This is demonstrated by analyzing a database of protein-small molecule binding pockets, and the distribution of bound magnesium ions in RNA structures. These analyses show significant, but subtle effects of depth on ligand binding localization and strength.     

Neutral currents in weak interactions and molecular asymmetry

Weak interactions are parity violating forces, i.e. they differentiate between mirror images. Therefore it is a very attractive hypothesis to invoke weak interactions in explaining the origin of molecular asymmetry. It is, however, not clear whether weak interactions may operate between electrons and/or between electrons and protons? For these types of interactions so called neutral currents are needed. Recent experiments with muon neutrinos at CERN gave some evidence for the existence of neutral currents. Thus we may suppose that parity violating forces are active in molecules. In the first part of this paper a very elementary theory of weak interactions is outlined with special reference to the discovery of neutral currents. In the second part we show how weak interactions may differentiate between mirror image molecules. The asymmetrically distributed static charges in chiral molecules represent a helical potential field. This potential field may exert an effect on the orbital electrons and therefore coupling of spins and momenta occurs. Thus the enantiomers are parity transformed images not only as geometrical bodies, but their orbital electrons are parity transformed too as "a helical electron gas". Weak interactions will differentiate between L and D forms because their orbital electrons have a nonzero spin polarization with respect to their velocity.     

Cooperativity: over the Hill

Cooperativity, the ability of ligand binding at one site on a macromolecule to influence ligand binding at a different site on the same macromolecule, is a fascinating biological property that is often poorly explained in textbooks. The Hill coefficient is commonly used in biophysical studies of cooperative systems although it is not a quantitative measure of cooperativity. The free energy of interaction between binding sites (ΔΔG) is a more stringent definition of cooperativity and provides a direct quantitative measure of how the binding of ligand at one site affects the ligand affinity of another site.     

Location-specific Responsiveness to Environmental Perturbations in Wedge-capped Capuchins (Cebus olivaceus)

We recorded the responses of the members of a captive group of wedge-capped capuchins to novel and familiar objects placed in different parts of their cage in a study of the spatial dependency of activity with objects. We focused on behavioral pattern variability across subjects and across object location. Results show that, according to the location of the object, a great deal of within-subject response variability exists. The dominant male was slow to interact physically with objects and presented social-like behaviors—essentially grooming—towards objects in only one site. Implicit to the ethological approach is the assumption that consistent spatial location is irrelevant or, at best, of little importance to the definition of stimuli. Nevertheless, stimuli would be best considered as perturbations insofar as the significance of an object or event depends on where and when it is encountered. In order to evaluate how monkey cognition operates, it seems essential to investigate the role of the primate's own spatial structure. As a working hypothesis, we introduce the processes of spatial facilitation and inhibition and suggest that they affect how an individual interacts with objects and events.     

Incorporating the geometry of dispersal and migration to understand spatial patterns of species distributions

Dispersal and migration can be important drivers of species distributions. Because the paths followed by individuals of many species are curvilinear, spatial statistical models based on rectilinear coordinates systems would fail to predict population connectivity or the ecological consequences of migration or species invasions. I propose that we view migration/dispersal as if organisms were moving along curvilinear geometrical objects called smooth manifolds. In that view, the curvilinear pathways become the ‘shortest realised paths’ arising from the necessity to minimise mortality risks and energy costs. One can then define curvilinear coordinate systems on such manifolds. I describe a procedure to incorporate manifolds and define appropriate coordinate systems, with focus on trajectories (1D manifolds), as parts of mechanistic ecological models. I show how a statistical method, known as ‘manifold learning’, enables one to define the manifold and the appropriate coordinate systems needed to calculate population connectivity or study the effects of migrations (e.g. in aquatic invertebrates, fish, insects and birds). This approach may help in the design of networks of protected areas, in studying the consequences of invasion, range expansions, or transfer of parasites/diseases. Overall, a geometrical view to animal movement gives a novel perspective to the understanding of the ecological role of dispersal and migration.     

Morphogenetic Processes: Application to Cambial Growth Dynamics

Both the physiological and the pathological morphogenetic processes that we can meet in embryogenesis, neogenesis and degenerative dysgenesis present common features: they are ruled by three different kinds of mechanisms, one related to cell migration, the second to cell differentiation and the third to cell proliferation. We deal here with an application to the cambial growth which essentially involves the third type of mechanism. Woody plants produce secondary tissue (secondary xylem and phloem) from a meristematic tissue called vascular cambium, responsible for the radial growth of a tree. This paper focuses on the formation of secondary xylem, considered in two dimensions in a cross-section framework. A new discrete modelling approach is used, based on the cellular scale, in order to attain a more accurate understanding of how the elementary microscopic behaviour of each cell takes part in the macroscopic morphogenesis. The mathematical model essentially uses an occurrence method simulating the main features of radial growth with simple geometric rules, such as Thom's division rule (Thom,1972)to account for the cell proliferation. The study applies to concrete instances in which the changes made in the geometrical cellular patterns of the vascular cambium clearly affect the shape of the tree, as in Pinus radiata (D. Don.).     

CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO

We have implemented in TOM/FRODO a protein crystallographic symmetry display and handling package, called CRYStallize. This package is designed as an aid in solving protein structures by molecular replacement methods. It allows the rotation/translation solutions provided by molecular replacement programs to be checked in a fast and easy way. Using CRYStallize, approximate solutions can also be improved by manual modifications. Symmetry-related objects, represented as surfaces, can be generated and handled in the same way as the reference molecules, thus permitting an efficient analysis of crystal packing and site accessibility. This program is available in the TOM/FRODO software release, which runs on the Silicon-Graphics workstations.     

The chain length of lignan macromolecule from flaxseed hulls is determined by the incorporation of coumaric acid glucosides and ferulic acid glucosides

Lignan macromolecule from flaxseed hulls is composed of secoisolariciresinol diglucoside (SDG) and herbacetin diglucoside (HDG) moieties ester-linked by 3-hydroxy-3-methylglutaric acid (HMGA), and of p-coumaric acid glucoside (CouAG) and ferulic acid glucoside (FeAG) moieties ester-linked directly to SDG. The linker molecule HMGA was found to account for 11% (w/w) of the lignan macromolecule. Based on the extinction coefficients and RP-HPLC data, it was determined that SDG contributes for 62.0% (w/w) to the lignan macromolecule, while CouAG, FeAG, and HDG contribute for 12.2, 9.0, and 5.7% (w/w), respectively.Analysis of fractions of lignan macromolecule showed that the higher the molecular mass, the higher the proportion of SDG was. An inverse relation between the molecular mass and the proportion (%) CouAG + FeAG was found. Together with the structural information of oligomers of lignan macromolecule obtained after partial saponification, it is hypothesized that the amount of CouAG + FeAG present during biosynthesis determines the chain length of lignan macromolecule.Furthermore, the chain length was estimated from a model describing lignan macromolecule based on structural and compositional data. The average chain length of the lignan macromolceule was calculated to be three SDG moieties with CouAG or FeAG at each of the terminal positions, with a variation between one and seven SDG moieties.     

Cytokine Profile in Human Eyes: Contribution of a New Cytokine Combination for Differential Diagnosis between Intraocular Lymphoma or Uveitis

Primary intraocular lymphoma (PIOL), also called primary vitreoretinal lymphomas, often masquerades as uveitis. This misdiagnosis can result in subsequent brain involvement and oculocerebral lymphoma (OCL). In this study, we sought to characterize the helper T-cell type 1 (Th1)/Th2 cytokine profile in vitreous samples from patients with PIOL, OCL, uveitis and controls with non-inflammatory disease. Vitreous and aqueous humor samples from 87 patients with PIOL (n = 30), OCL (n = 12), uveitis (n = 34), and retinal detachment (RD) without hemorrhage (n = 11) were analyzed and their concentrations of interleukin (IL)-2, IL-4, IL-6, IL-10, interferon (IFN)-γ, and tumor necrosis factor (TNF)-α were determined by flow cytometric bead arrays (CBA). The IL-10 levels determined by CBA were compared with those by ELISA. IL-10 concentrations measured by CBA and ELISA were highly correlated. IL-2, IL-4, and TNFα were not detected in any sample. The only cytokine detected at a significant level in samples from RD vitreous was IL-6. The IL-10/IL-6 ratio, as previously reported, was slightly higher in PIOL than in uveitis samples, but not for all patients. Cytokine profiles from PIOL and OCL samples did not differ. The combination of the IL-10/IL-6 and IL-10/IFNγ ratios was highly informative for discriminating PIOL/OCL from uveitis samples and for therapeutic follow up of PIOL. This strategy might be very helpful as an initial screening to rule out PIOL in patients thought to have uveitis.     

Changes in Bacterial Community Structure of Agricultural Land Due to Long-Term Organic and Chemical Amendments

Community level physiological profiling and pyrosequencing-based analysis of the V1-V2 16S rRNA gene region were used to characterize and compare microbial community structure, diversity, and bacterial phylogeny from soils of chemically cultivated land (CCL), organically cultivated land (OCL), and fallow grass land (FGL) for 16 years and were under three different land use types. The entire dataset comprised of 16,608 good-quality sequences (CCL, 6,379; OCL, 4,835; FGL, 5,394); among them 12,606 sequences could be classified in 15 known phylum. The most abundant phylum were Proteobacteria (29.8%), Acidobacteria (22.6%), Actinobacteria (11.1%), and Bacteroidetes (4.7%), while 24.3% of the sequences were from bacterial domain but could not be further classified to any known phylum. Proteobacteria, Bacteroidetes, and Gemmatimonadetes were found to be significantly abundant in OCL soil. On the contrary, Actinobacteria and Acidobacteria were significantly abundant in CCL and FGL, respectively. Our findings supported the view that organic compost amendment (OCL) activates diverse group of microorganisms as compared with conventionally used synthetic chemical fertilizers. Functional diversity and evenness based on carbon source utilization pattern was significantly higher in OCL as compared to CCL and FGL, suggesting an improvement in soil quality. This abundance of microbes possibly leads to the enhanced level of soil organic carbon, soil organic nitrogen, and microbial biomass in OCL and FGL soils as collated with CCL. This work increases our current understanding on the effect of long-term organic and chemical amendment applications on abundance, diversity, and composition of bacterial community inhabiting the soil for the prospects of agricultural yield and quantity of soil.     

Classifying medical devices according to their maintenance sensitivity: a practical, risk-based approach to PM program management

Many medical equipment items need periodic attention to ensure that they continue to operate properly and safely; and most inspecting agencies require healthcare facilities to have a competent equipment maintenance program that is focused on the most critical of those devices. There is however a long-standing lack of consensus on how best to determine which devices should be included in this critical device category, and which can reasonably be excluded. A new methodology is proposed for establishing a logical, fact-based framework for determining which devices should be included. It is based in part on a new FDA-sanctioned definition of what an appropriate regimen of planned maintenance activities for a medical device should include. This new definition addresses the medical device users' concerns about periodic performance verification and safety testing as well as detecting and correcting the wear or progressive deterioration of any non-durable parts, which is the primary focus of the conventional preventive maintenance programs found in less critical industries. The analytical approach proposed utilizes technical information that is either already available or which can be easily developed. It characterizes each different device by means of a 3-letter maintenance sensitivity profile that can be used to analyze the effectiveness of the maintenance procedures as well as quantify the device's sensitivity to planned maintenance. A collaborative effort to assemble and organize this data would provide the industry with a sound, logical platform for narrowing the scope of most PM programs and allow us to redirect a significant amount of scarce technical manpower into more productive activities such as device user training.     

PGE2 MEDIATES OENOCYTOID CELL LYSIS VIA A SODIUM‐POTASSIUM‐CHLORIDE COTRANSPORTER

Prostaglandin E₂ (PGE₂) mediates immune responses of the beet armyworm, Spodoptera exigua, including oenocytoid cell lysis (a class of lepidopteran hemocytes: OCL) via its specific membrane receptor to release inactive prophenoloxidase (PPO) into hemolymph. PPO is activated into phenoloxidase in the plasma to play crucial roles in the immune responses of S. exigua. The mechanism of OCL has not been elucidated, however we posed the hypothesis that a rapid accumulation of sodium ions within the oenocytoids allows a massive influx of water by the ion gradient, which leads to the cell lysis. It remains unclear which sodium channel is responsible for the OCL in response to PGE₂. This study identified a specific sodium channel called sodium‐potassium‐chloride cotransporter 1 (Se‐NKCC1) expressed in hemocytes of S. exigua and analyzed its function in the OCL in response to PGE₂. Se‐NKCC1 encodes a basic membrane protein (pI value = 8.445) of 1,066 amino acid residues, which contains 12 putative transmembrane domains. Se‐NKCC1 was expressed in all developmental stages and tissues. qPCR showed that bacterial challenge significantly induced its expression. A specific inhibitor of NKCC, bumetanide, prevented the OCL in a dose‐dependent manner. When RNA interference (RNAi) using double‐stranded RNA specific to Se‐NKCC1 suppressed its expression, the OCL and PPO activation were significantly inhibited in response to PGE₂. The RNAi treatment also reduced nodule formation to bacterial challenge. These results suggest that Se‐NKCC1 is associated with OCL by facilitating inward transport of ions in response to PGE₂.     

A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes

Avoiding collisions is one of the most basic needs of any mobile agent, both biological and technical, when searching around or aiming toward a goal. We propose a model of collision avoidance inspired by behavioral experiments on insects and by properties of optic flow on a spherical eye experienced during translation, and test the interaction of this model with goal-driven behavior. Insects, such as flies and bees, actively separate the rotational and translational optic flow components via behavior, i.e. by employing a saccadic strategy of flight and gaze control. Optic flow experienced during translation, i.e. during intersaccadic phases, contains information on the depth-structure of the environment, but this information is entangled with that on self-motion. Here, we propose a simple model to extract the depth structure from translational optic flow by using local properties of a spherical eye. On this basis, a motion direction of the agent is computed that ensures collision avoidance. Flying insects are thought to measure optic flow by correlation-type elementary motion detectors. Their responses depend, in addition to velocity, on the texture and contrast of objects and, thus, do not measure the velocity of objects veridically. Therefore, we initially used geometrically determined optic flow as input to a collision avoidance algorithm to show that depth information inferred from optic flow is sufficient to account for collision avoidance under closed-loop conditions. Then, the collision avoidance algorithm was tested with bio-inspired correlation-type elementary motion detectors in its input. Even then, the algorithm led successfully to collision avoidance and, in addition, replicated the characteristics of collision avoidance behavior of insects. Finally, the collision avoidance algorithm was combined with a goal direction and tested in cluttered environments. The simulated agent then showed goal-directed behavior reminiscent of components of the navigation behavior of insects.     

Changing fates on the road to neuronal diversity

One of the longstanding goals of neurobiologists is to describe, in molecular terms, how a neural progenitor cell (NPC) can generate an ordered series of uniquely fated neurons and glia. Recent studies reveal that many, or all, neural-subtype identities can be linked to sequentially changing regulatory programs within NPCs. Two new studies, in this issue of Developmental Cell, provide novel insights into the molecular details of how Drosophila NPCs transition from one offspring identity program to the next.     

Variation in the OC Locus of Acinetobacter baumannii Genomes Predicts Extensive Structural Diversity in the Lipooligosaccharide

Lipooligosaccharide (LOS) is a complex surface structure that is linked to many pathogenic properties of Acinetobacter baumannii. In A. baumannii, the genes responsible for the synthesis of the outer core (OC) component of the LOS are located between ilvE and aspS. The content of the OC locus is usually variable within a species, and examination of 6 complete and 227 draft A. baumannii genome sequences available in GenBank non-redundant and Whole Genome Shotgun databases revealed nine distinct new types, OCL4-OCL12, in addition to the three known ones. The twelve gene clusters fell into two distinct groups, designated Group A and Group B, based on similarities in the genes present. OCL6 (Group B) was unique in that it included genes for the synthesis of L-Rhamnosep. Genetic exchange of the different configurations between strains has occurred as some OC forms were found in several different sequence types (STs). OCL1 (Group A) was the most widely distributed being present in 18 STs, and OCL6 was found in 16 STs. Variation within clones was also observed, with more than one OC locus type found in the two globally disseminated clones, GC1 and GC2, that include the majority of multiply antibiotic resistant isolates. OCL1 was the most abundant gene cluster in both GC1 and GC2 genomes but GC1 isolates also carried OCL2, OCL3 or OCL5, and OCL3 was also present in GC2. As replacement of the OC locus in the major global clones indicates the presence of sub-lineages, a PCR typing scheme was developed to rapidly distinguish Group A and Group B types, and to distinguish the specific forms found in GC1 and GC2 isolates.     

SWEET-DB: an attempt to create annotated data collections for carbohydrates

Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use modern web techniques to annotate and/or cross-reference carbohydrate-related data collections which allow glycoscientists to find important data for compounds of interest in a compact and well-structured representation. Currently, reference data taken from three data sources can be retrieved for a given carbohydrate (sub)structure. The sources are CarbBank structures and literature references (linked to NCBI PubMed service), NMR data taken from SugaBase and 3D co-ordinates generated with SWEET-II. The main purpose of SWEET-DB is to enable an easy access to all data stored for one carbohydrate structure entering a complete sequence or parts thereof. Access to SWEET-DB contents is provided with the help of separate input spreadsheets for (sub)structures, bibliographic data, general structural data like molecular weight, NMR spectra and biological data. A detailed online tutorial is available at http://www.dkfz.de/spec2/sweetdb/nar/.     

Do You Really Want to Know? Elementary Music Programs and Potential in Utah

This is the first of two articles reporting the results of a study by the author regarding the status of elementary music education in the state of Utah. This article focuses on how elementary music programs are structured (regular instruction with a music specialist, truncated programs, delegated programs, no formal music instruction, no music instruction). Factors that shape those structures are also addressed. While over 90 percent of elementary schools in the United States provide regular music instruction taught by certified music specialists to over 90 percent of their student populations, less than 10 percent of Utah's elementary population receives such instruction. Nearly half of the elementary students in the state receive no designated music instruction other than that provided by their regular elementary classroom teachers. The influence of budget constraints, school funding policies, No Child Left Behind, other accountability measures, high-stakes testing, urban/rural populations, and demographics are highlighted. Policy considerations are discussed.     

Shared circulation in parabiosis leads to the transfer of bone phenotype from gld to the wild-type mice

We have previously shown that mice with generalised lymphoproliferative disorder (gld) have increased bone mass in addition to autoimmune disease characterised by the accumulation of double negative (dn) T lymphocytes (CD3(+)CD4(-)CD8(-)CD45R(+)). To further explore the association of the immune disorder with the bone phenotype of gld mice, we established parabiotic circulation between gld and wild-type animals (C57BL/6, B6). One week after the surgery, the proportion of dn T lymphocytes increased in peripheral blood, bone marrow, spleen, and lymph nodes of wild-type members of the B6-gld parabiotic pair and decreased in tissues of gld pair members. The mixing of cells continued during four weeks of parabiosis. Number of osteoclast-like (OCL) cells in bone marrow cultures from a wild-type member of B6-gld parabiotic pair at the end of the first week decreased from 266+/-52 to 120+/-5OCL/cm(2), P<0.05, comparable with gld mice (99+/-21OCL/cm(2)), while the number of osteoblast colonies did not change. After four weeks, number of OCL cells formed from the bone marrow of B6 parabiotic mice was still similar to the number of OCL cells in their gld counterparts (150+/-18 and 131+/-24OCL/cm(2), respectively). In addition, the number of osteoblast colonies in B6 members of B6-gld parabiotic pairs increased (from 6+/-2 to 18+/-1colonies/cm(2), P<0.05) thus resembling the cell cultures of gld mice (18+/-1colonies/cm(2)). Taken together, these data show that the circulation of cells, including dn T lymphocytes established by parabiosis confers the osteoclast and osteoblast phenotype of gld to wild-type animals.     

Chain-length specificities of maize starch synthase I enzyme: studies of glucan affinity and catalytic properties

It is widely known that some of the starch synthases and starch-branching enzymes are trapped inside the starch granule matrix during the course of starch deposition in amyloplasts. The objective of this study was to use maize SSI to further our understanding of the protein domains involved in starch granule entrapment and identify the chain-length specificities of the enzyme. Using affinity gel electrophoresis, we measured the dissociation constants of maize SSI and its truncated forms using various glucans. The enzyme has a high degree of specificity in terms of its substrate-enzyme dissociation constant, but has a greatly elevated affinity for increasing chain lengths of alpha-1, 4 glucans. Deletion of the N-terminal arm of SSI did not affect the Kd value. Further small deletions of either N- or C-terminal domains resulted in a complete loss of any measurable affinity for its substrate, suggesting that the starch-affinity domain of SSI is not discrete from the catalytic domain. Greater affinity was displayed for the amylopectin fraction of starch as compared to amylose, whereas glycogen revealed the lowest affinity. However, when the outer chain lengths (OCL) of glycogen were extended using the phosphorylase enzyme, we found an increase in affinity for SSI between an average OCL of 7 and 14, and then an apparently exponential increase to an average OCL of 21. On the other hand, the catalytic ability of SSI was reduced several-fold using these glucans with extended chain lengths as substrates, and most of the label from [14C]ADPG was incorporated into shorter chains of dp < 10. We conclude that the rate of catalysis of SSI enzyme decreases with the OCL of its glucan substrate, and it has a very high affinity for the longer glucan chains of dp approximately 20, rendering the enzyme catalytically incapable at longer chain lengths. Based on the observations in this study, we propose that during amylopectin synthesis shorter A and B1 chains are extended by SSI up to a critical chain length that soon becomes unsuitable for catalysis by SSI and hence cannot be elongated further by this enzyme. Instead, SSI is likely to become entrapped as a relatively inactive protein within the starch granule. Further glucan extension for continuation of amylopectin synthesis must require a handover to other SS enzymes which can extend the glucan chains further or for branching by branching enzymes. If this is correct, this proposal provides a biochemical basis to explain how the specificities of various SS enzymes determine and set the limitations on the length of A, B, C chains in the starch granule.