A Statistical Test of Network Analysis: Can it Detect Differences in Food Web Properties?

Ecological network analysis (ENA) is a modeling approach increasingly being used to examine food webs. However, most studies do not replicate networks, and a statistical evaluation of ENA is lacking. The major objectives of this study, therefore, were to evaluate statistically the effectiveness of ENA in detecting differences in food web properties and to compare ENA output with established community level indices. Quantitative trophic networks (n = 12) representing four high salt marsh ponds during three times (corresponding to low stress, high stress, and post-disturbance) were constructed from an extensive field sampling program augmented by literature values. Food webs of salt marsh ponds were used because these systems contain relatively simple food webs, have well defined boundaries, and allow for adequate replication. A null hypothesis was tested to determine how values of 12 indices from ENA output differed among the three stress/disturbance conditions (H _o: low stress = high stress = post-disturbance). Results of both ANOVA and Friedman’s tests indicated most ENA indices were significantly different among the three stress/disturbance conditions. The amount of covariance among the indices was relatively low (7 of 66 were significant). Results were compared to differences in community indices (richness, evenness, and diversity) among the three stress/disturbance conditions. ENA output identified differences beyond those recognized by the community indices. Overall, networks were unique enough under different environmental conditions to provide statistically significant differences in ENA results. Our findings are supportive of the use of carefully constructed networks in food web analysis and for decision making in ecosystem-based management. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Secretion and Uptake of α-Synuclein Via Extracellular Vesicles in Cultured Cells

In Parkinson’s disease and other Lewy body disorders, the propagation of pathology has been accredited to the spreading of extracellular α-synuclein (α-syn). Although the pathogenic mechanisms are not fully understood, cell-to-cell transfer of α-syn via exosomes and other extracellular vesicles (EVs) has been reported. Here, we investigated whether altered molecular properties of α-syn can influence the distribution and secretion of α-syn in human neuroblastoma cells. Different α-syn variants, including α-syn:hemi-Venus and disease-causing mutants, were overexpressed and EVs were isolated from the conditioned medium. Of the secreted α-syn, 0.1–2% was associated with vesicles. The major part of EV α-syn was attached to the outer membrane of vesicles, whereas a smaller fraction was found in their lumen. For α-syn expressed with N-terminal hemi-Venus, the relative levels associated with EVs were higher than for WT α-syn. Moreover, such EV-associated α-syn:hemi-Venus species were internalized in recipient cells to a higher degree than the corresponding free-floating forms. Among the disease-causing mutants, A53T α-syn displayed an increased association with EVs. Taken together, our data suggest that α-syn species with presumably lost physiological functions or altered aggregation properties may shift the cellular processing towards vesicular secretion. Our findings thus lend further support to the tenet that EVs can mediate spreading of harmful α-syn species and thereby contribute to the pathology in α-synucleinopathies.     

Fluxes and compartmentation of K+, Na+ and Cl−, and action of auxins in suspension-cultured Petroselinum cells

Transport of ⁸⁶Rb⁺/K⁺, ²²Na⁺, ³⁶Cl^?, and [³H]indole acetic acid (IAA) has been studied on suspension-cultured cells of the parsley, Petroselinum crispum (Mill) Nym. By compartmental analysis two intracellular compartments of K⁺, Na⁺, and Cl^? have been identified and ascribed to the cytoplasm and vacuole; half-times of exchange were around 200 s and 5 h, respectively. According to the Ussing-Teorell flux equation, active transport is required for the influx into the cytoplasm at the plasmalemma (K⁺, Cl^?) and the tonoplast (K⁺, Na⁺, Cl^?). The plasmalemma permeability pattern, P_K:P_Na:P_Cl=1.00:0.24:0.38, features an increased chloride permeability compared with cells from higher plant tissues. IAA uptake showed an exponential timecourse, was half-maximal after 10 min, and a linear function of the IAA concentration from 10^?9 to 10^?5 M. IAA and 2,4-dichlorophenoxy acetic acid reduce the apparent influx of K⁺, Na⁺, Cl^? during the initial 30 min after addition and subsequently accelerate both in- and efflux of these ions. We discuss that auxins could affect the ion fluxes in a complex way, e.g. by protonophorous activity and by control of the hypothetical proton pump.     

α-Synuclein Reduces Tension and Increases Undulations in Simulations of Small Unilamellar Vesicles

Using coarse-grained molecular dynamics simulations we have explored the effect of α-Synuclein (αSyn) on the structural and mechanical properties of small unilamellar vesicles in the fluid-phase. The study is motivated by observations that a high density of membrane-bound αSyn inhibits the fusion of synthetic small unilamellar vesicles. By combining three-dimensional pressure tensor calculations with our recently developed spherical harmonics fluctuation analysis approach, we show a reduction in membrane surface tension and increased membrane undulations when αSyn is bound to the vesicle’s outer leaflet at a 200:1 L/P. The protein effects these changes by decreasing the negative pressure in the headgroup region of the outer leaflet and increasing the positive pressure throughout the hydrocarbon core.     

Draining the Pool? Carbon Storage and Fluxes in Three Alpine Plant Communities

Shrub communities have expanded in arctic and alpine tundra during recent decades. Changes in shrub abundance may alter ecosystem carbon (C) sequestration and storage, with potential positive or negative feedback on global C cycling. To assess potential implications of shrub expansion in different alpine plant communities, we compared C fluxes and pools in one Empetrum-dominated heath, one herb- and cryptogam-dominated meadow, and one Salix-shrub community in Central Norway. Over two growing seasons, we measured Gross Ecosystem Photosynthesis, Ecosystem Respiration (ER), and C pools for above-ground vegetation, litter, roots, and soil separated into organic and mineral horizons. Both the meadow and shrub communities had higher rates of C fixation and ER, but the total ecosystem C pool in the meadow was twice that of the shrub community because of more C in the organic soil horizon. Even though the heath community had the lowest rates of C fixation, it stored one and a half times more C than the shrub community. The results indicate that the relatively high above-ground biomass sequestering C during the growing season is not associated with high C storage in shrub-dominated communities. Instead, shrub-dominated areas may be draining the carbon-rich alpine soils because of high rates of decomposition. These processes were not shown by mid-growing season C fluxes, but were reflected by the very different distribution of C pools in the three habitats.     

Proteomic Analysis of C2C12 Myoblast and Myotube Exosome-Like Vesicles: A New Paradigm for Myoblast-Myotube Cross Talk?

Exosomes are nanometer-sized microvesicles formed in multivesicular bodies (MVBs) during endosome maturation. Exosomes are released from cells into the microenvironment following fusion of MVBs with the plasma membrane. During the last decade, skeletal muscle-secreted proteins have been identified with important roles in intercellular communications. To investigate whether muscle-derived exosomes participate in this molecular dialog, we determined and compared the protein contents of the exosome-like vesicles (ELVs) released from C2C12 murine myoblasts during proliferation (ELV-MB), and after differentiation into myotubes (ELV-MT). Using a proteomic approach combined with electron microscopy, western-blot and bioinformatic analyses, we compared the protein repertoires within ELV-MB and ELV-MT. We found that these vesicles displayed the classical properties of exosomes isolated from other cell types containing components of the ESCRT machinery of the MVBs, as well as numerous tetraspanins. Specific muscle proteins were also identified confirming that ELV composition also reflects their muscle origin. Furthermore quantitative analysis revealed stage-preferred expression of 31 and 78 proteins in ELV-MB and ELV-MT respectively. We found that myotube-secreted ELVs, but not ELV-MB, reduced myoblast proliferation and induced differentiation, through, respectively, the down-regulation of Cyclin D1 and the up-regulation of myogenin. We also present evidence that proteins from ELV-MT can be incorporated into myoblasts by using the GFP protein as cargo within ELV-MT. Taken together, our data provide a useful database of proteins from C2C12-released ELVs throughout myogenesis and reveals the importance of exosome-like vesicles in skeletal muscle biology.     

Comparability of Mixed IC50 Data – A Statistical Analysis

The biochemical half maximal inhibitory concentration (IC₅₀) is the most commonly used metric for on-target activity in lead optimization. It is used to guide lead optimization, build large-scale chemogenomics analysis, off-target activity and toxicity models based on public data. However, the use of public biochemical IC₅₀ data is problematic, because they are assay specific and comparable only under certain conditions. For large scale analysis it is not feasible to check each data entry manually and it is very tempting to mix all available IC₅₀ values from public database even if assay information is not reported. As previously reported for K_i database analysis, we first analyzed the types of errors, the redundancy and the variability that can be found in ChEMBL IC₅₀ database. For assessing the variability of IC₅₀ data independently measured in two different labs at least ten IC₅₀ data for identical protein-ligand systems against the same target were searched in ChEMBL. As a not sufficient number of cases of this type are available, the variability of IC₅₀ data was assessed by comparing all pairs of independent IC₅₀ measurements on identical protein-ligand systems. The standard deviation of IC₅₀ data is only 25% larger than the standard deviation of K_i data, suggesting that mixing IC₅₀ data from different assays, even not knowing assay conditions details, only adds a moderate amount of noise to the overall data. The standard deviation of public ChEMBL IC₅₀ data, as expected, resulted greater than the standard deviation of in-house intra-laboratory/inter-day IC₅₀ data. Augmenting mixed public IC₅₀ data by public K_i data does not deteriorate the quality of the mixed IC₅₀ data, if the K_i is corrected by an offset. For a broad dataset such as ChEMBL database a K_i- IC₅₀ conversion factor of 2 was found to be the most reasonable.     

Why Does the Giant Panda Eat Bamboo? A Comparative Analysis of Appetite-Reward-Related Genes among Mammals

Background

The giant panda has an interesting bamboo diet unlike the other species in the order of Carnivora. The umami taste receptor gene T1R1 has been identified as a pseudogene during its genome sequencing project and confirmed using a different giant panda sample. The estimated mutation time for this gene is about 4.2 Myr. Such mutation coincided with the giant panda''s dietary change and also reinforced its herbivorous life style. However, as this gene is preserved in herbivores such as cow and horse, we need to look for other reasons behind the giant panda''s diet switch.

Methodology/Principal Findings

Since taste is part of the reward properties of food related to its energy and nutrition contents, we did a systematic analysis on those genes involved in the appetite-reward system for the giant panda. We extracted the giant panda sequence information for those genes and compared with the human sequence first and then with seven other species including chimpanzee, mouse, rat, dog, cat, horse, and cow. Orthologs in panda were further analyzed based on the coding region, Kozak consensus sequence, and potential microRNA binding of those genes.

Conclusions/Significance

Our results revealed an interesting dopamine metabolic involvement in the panda''s food choice. This finding suggests a new direction for molecular evolution studies behind the panda''s dietary switch.     

Potential Transfer of Polyglutamine and CAG-Repeat RNA in Extracellular Vesicles in Huntington’s Disease: Background and Evaluation in Cell Culture

In Huntington’s disease (HD) the imperfect expanded CAG repeat in the first exon of the HTT gene leads to the generation of a polyglutamine (polyQ) protein, which has some neuronal toxicity, potentially mollified by formation of aggregates. Accumulated research, reviewed here, implicates both the polyQ protein and the expanded repeat RNA in causing toxicity leading to neurodegeneration in HD. Different theories have emerged as to how the neurodegeneration spreads throughout the brain, with one possibility being the transport of toxic protein and RNA in extracellular vesicles (EVs). Most cell types in the brain release EVs and these have been shown to contain neurodegenerative proteins in the case of prion protein and amyloid-beta peptide. In this study, we used a model culture system with an overexpression of HTT-exon 1 polyQ-GFP constructs in human 293T cells and found that the EVs did incorporate both the polyQ-GFP protein and expanded repeat RNA. Striatal mouse neural cells were able to take up these EVs with a consequent increase in the green fluorescent protein (GFP) and polyQ-GFP RNAs, but with no evidence of uptake of polyQ-GFP protein or any apparent toxicity, at least over a relatively short period of exposure. A differentiated striatal cell line expressing endogenous levels of Hdh mRNA containing the expanded repeat incorporated more of this mRNA into EVs as compared to similar cells expressing this mRNA with a normal repeat length. These findings support the potential of EVs to deliver toxic expanded trinucleotide repeat RNAs from one cell to another, but further work will be needed to evaluate potential EV and cell-type specificity of transfer and effects of long-term exposure. It seems likely that expanded HD-associated repeat RNA may appear in biofluids and may have use as biomarkers of disease state and response to therapy.     

Preparation and Characterization of Stable pH-Sensitive Vesicles Composed of α-Tocopherol Hemisuccinate

The current study aims to develop a stable pH-sensitive drug delivery system. First, cleavable polyethylene glycol-α-tocopherol hemisuccinate (PEG-THS) was synthesized. Conventional pH-sensitive vesicles composed of the Tris salt of α-tocopherol hemisuccinate (THST) were then prepared using the detergent removal technique. The vesicles had a mean particle size of (163.8 ± 5.5) nm and a zeta potential of −74.5 ± 6.4 mV. The THST vesicles were then modified using PEG-THS or uncleavable PEG-cholesterol (PEG-CHOL) (THST/PEG-lipids, 100:6 molar ratio). The mean vesicle particle size and absolute zeta potential decreased with increasing PEG-THS proportion. When the pH was decreased, the vesicle particle size and calcein release rate increased. The THST vesicles were initially Ca²⁺-unstable but exhibited significantly improved stability after modification with PEG-THS, especially at PEG-lipid ratios above 6%. Incubation in an acid serum increased the calcein release rate of conventional THST vesicles to 45 ± 1.98% at 10 min. However, the release rate of the PEG-CHOL vesicles remained low. The calcein release rate of PEG-THS vesicles was between those of conventional and PEG-CHOL-V. Therefore, PEG-THS can protect vesicles in serum and reconstitute their pH sensitivity in acidic conditions. Cleavable PEG-THS can be used in stable pH-sensitive preparations without loss of pH sensitivity. Free calcein and conventional vesicles eliminated from the plasma soon after injection, as well as the half-life (t_1/2) and area under the curve of PEG-THS-V encapsulating calcein, were dramatically increased. This phenomenon indicates that the use of PEG-lipid derivatives has gained a favorably long circulation effect in mice.Key words: cleavage, long circulation, PEG-α-tocopherol hemisuccinate, pH-sensitive, vesicles     

Analysis of proteins involved in the production of MAA?s in two Cyanobacteria Synechocystis PCC 6803 and Anabaena cylindrica

Mycosporine- like amino acids (MAAs) are small (<400Da), colourless, water soluble compounds composed of cyclohexenone or cyclohexinimine chromophere conjugated with the nitrogen substituent of amino acid or its amino alcohol. These compounds are known for their UV- absorbing role in various organisms and seem to have evolutionary significance. The biosynthesis of MAAs is presumed to occur via the first part of shikimate pathway. In the present work two cyanobacteria Synechocystis PCC 6803 and Anabaena cylindrica were tested for their ability to synthesize MAAs and protein involved in the production of MAAs. It was found that protein sequence 3-phosphoshikimate 1-carboxyvinyltransferase is involved in producing mycosporine glycine in Synechocystis PCC 6803 and 3-dehydroquinate synthase is involved for producing shinorine in Anabaena cylindrica. Phylogenetic and bioinformatic analysis of Mycosporine like amino acid producing protein sequence of both cyanobacterial species Synechocystis PCC 6803 and Anabaena cylindrica provide a useful framework to understand the relationship of the different forms and how they have evolved from a common ancestor. These products seem to be conserved but the residues are prone to variation which might be due the fact that different cyanobacteria show different physiological process in response of Ultraviolet stress.     

How Can Dolphins Recognize Fish According to Their Echoes? A Statistical Analysis of Fish Echoes

Echo-based object classification is a fundamental task of animals that use a biosonar system. Dolphins and porpoises should be able to rely on echoes to discriminate a predator from a prey or to select a desired prey from an undesired object. Many studies have shown that dolphins and porpoises can discriminate between objects according to their echoes. All of these studies however, used unnatural objects that can be easily characterized in human terminologies (e.g., metallic spheres, disks, cylinders). In this work, we collected real fish echoes from many angles of acquisition using a sonar system that mimics the emission properties of dolphins and porpoises. We then tested two alternative statistical approaches in classifying these echoes. Our results suggest that fish species can be classified according to echoes returning from porpoise- and dolphin-like signals. These results suggest how dolphins and porpoises can classify fish based on their echoes and provide some insight as to which features might enable the classification.     

Azathioprine, a clastogen in human somatic cells? Analysis of chromosome damage and SCE in lymphocytes after exposure in vivo and in vitro

Chromosomal analyses in lymphocytes of 28 patients with multiple sclerosis were carried out before, during and after Azathioprine (Aza) therapy. Only a higher incidence of gaps was found in treated patients than in a group of healthy persons but not in comparison with untreated patients. Similarly, no significant clastogenic effect was observed in vitro after short-term and long-term treatment of unstimulated and stimulated lymphocytes with concentrations of 1--100 microgram Aza per ml. Treatment of cultures with 0.0001--4.0 microgram/ml did not yield increased SCE frequencies. The absence of any significant clastogenic effect of therapeutic doses of Aza on human somatic cells is deduced from an evaluation of previously published data and from the present results.     

What's in a crowd? Analysis of face-to-face behavioral networks

The availability of new data sources on human mobility is opening new avenues for investigating the interplay of social networks, human mobility and dynamical processes such as epidemic spreading. Here we analyze data on the time-resolved face-to-face proximity of individuals in large-scale real-world scenarios. We compare two settings with very different properties, a scientific conference and a long-running museum exhibition. We track the behavioral networks of face-to-face proximity, and characterize them from both a static and a dynamic point of view, exposing differences and similarities. We use our data to investigate the dynamics of a susceptible-infected model for epidemic spreading that unfolds on the dynamical networks of human proximity. The spreading patterns are markedly different for the conference and the museum case, and they are strongly impacted by the causal structure of the network data. A deeper study of the spreading paths shows that the mere knowledge of static aggregated networks would lead to erroneous conclusions about the transmission paths on the dynamical networks.     

Is cribra orbitalia synonymous with anemia? Analysis and interpretation of cranial pathology in Sudan

Cribra orbitalia is a porotic or sieve-like lesion in the bony orbital roof. Its cause has been the object of research and discussion since the end of the 19th century. Since about 1960, most scientists have started to agree on the hypothesis that the lesion is a result of hypertrophy of the red bone marrow, and therefore is proof of anemia. However, recent investigations showed that in some cases, the histologic bone structure does not support the diagnosis of anemia. The status of cribra orbitalia as an indicator then becomes uncertain. We carried out a histologic examination of thin-ground sections in polarized light to clarify the possible sources of orbital roof lesions in a Nubian population from Missiminia, northern Sudan (n = 333). In at least 56.5% of cribra orbitalia cases, there were no histologic features indicating changes due to anemia. Signs of other pathological conditions, such as inflammation or osteoporosis, as well as pseudopathological cases, were found.     

Direct Observation of α-Synuclein Amyloid Aggregates in Endocytic Vesicles of Neuroblastoma Cells

Aggregation of α-synuclein has been linked to both familial and sporadic Parkinson’s disease. Recent studies suggest that α-synuclein aggregates may spread from cell to cell and raise questions about the propagation of neurodegeneration. While continuous progress has been made characterizing α-synuclein aggregates in vitro, there is a lack of information regarding the structure of these species inside the cells. Here, we use confocal fluorescence microscopy in combination with direct stochastic optical reconstruction microscopy, dSTORM, to investigate α-synuclein uptake when added exogenously to SH-SY5Y neuroblastoma cells, and to probe in situ morphological features of α-synuclein aggregates with near nanometer resolution. We demonstrate that using dSTORM, it is possible to follow noninvasively the uptake of extracellularly added α-synuclein aggregates by the cells. Once the aggregates are internalized, they move through the endosomal pathway and accumulate in lysosomes to be degraded. Our dSTORM data show that α-synuclein aggregates remain assembled after internalization and they are shortened as they move through the endosomal pathway. No further aggregation was observed inside the lysosomes as speculated in the literature, nor in the cytoplasm of the cells. Our study thus highlights the super-resolution capability of dSTORM to follow directly the endocytotic uptake of extracellularly added amyloid aggregates and to probe the morphology of in situ protein aggregates even when they accumulate in small vesicular compartments.     

α-Synuclein in Extracellular Vesicles: Functional Implications and Diagnostic Opportunities

Fibrillar inclusions of intraneuronal α-synuclein can be detected in certain brain areas from patients with Parkinson’s disease (PD) and other disorders with Lewy body pathology. These insoluble protein aggregates do not themselves appear to have a prominent neurotoxic effect, whereas various α-synuclein oligomers appear harmful. Although it is incompletely known how the prefibrillar species may be pathogenic, they have been detected both within and on the outside of exosomes and other extracellular vesicles (EVs), suggesting that such structures may mediate toxic α-synuclein propagation between neurons. Vesicular transfer of α-synuclein may thereby contribute to the hierarchical spreading of pathology seen in the PD brain. Although the regulation of α-synuclein release via EVs is not understood, data suggest that it may involve other PD-related molecules, such as LRRK2 and ATP13A2. Moreover, new evidence indicates that CNS-derived EVs in plasma have the potential to serve as biomarkers for diagnostic purposes. In a recent study, levels of α-synuclein were found to be increased in L1CAM-positive vesicles isolated from plasma of PD patients compared to healthy controls, and follow-up studies will reveal whether α-synuclein in EVs could be developed as a future disease biomarker. Preferentially, toxic prefibrillar α-synuclein oligomers should then be targeted as a biomarker—as evidence suggests that they reflect the disease process more closely than total α-synuclein content. In such studies, it will be essential to adopt stringent EV isolation protocols in order to avoid contamination from the abundant pool of free plasma α-synuclein in different aggregational states.     

Statistical mechanical treatment of α-helices and extended structures in proteins with inclusion of short- and medium-range interactions

A statistical mechanical model of protein conformation with medium-range interactions between theith and (i+k)^th residues (k<-4) is presented. Two two-state models, an α-helix-coil and an extended-structure-coil model, are formulated using the same form of the partition function, but the two models are applied independently to predict the locations of α-helical, extended, and coil segments; in the relatively few cases (<2%) where the predictions from the two models are in conflict, the prediction is scored as an incorrect one. Two independent sets of statistical weights (one set for each model) are derived to describe the interactions between the 20 amino acid residues for each range of interactionk; they are evaluated by minimizing an objective function so that the probability profiles for the α-helix or extended structure, respectively, in proteins computed from these statistical weights correlate optimally with the experimentally observed native conformations of these proteins. Examination of the resulting statistical weights shows that those for the interactions between hydrophobic residues and between a hydrophobic and a hydrophilic residue have reasonable magnitudes compared to what would be expected from the spatial arrangements of the side chains in the α-helix and the extended structure, and that those for the α-helix-coil model correlate well with experimentally determined values of the Zimm-Bragg parameterss and σ of the helix-coil transition theory. From the point of view of a method to predict the conformational states (i.e., α-helix, extended structure, and coil) of each residue, the statistical weights (as inall empirical prediction schemes) depend very much on the proteins used for the data base, since the presently available set of proteins of known structure is still too small for very high predictability; as a result, the correctness of the prediction is not very good for proteins not included in the data base. However, the correctness of the prediction, at least for the 37 proteins utilized as the data base in this study, is 91% and 87% for the α-helix-coil and the extended-structure-coil models, respectively; further, 79% of all the residues are predicted correctly when both the α-helix-coil and extended-structure-coil models are applied independently.