Evaluating the role of biotic interactions in structuring communities using a gradient analysis of multiple interacting guilds

The extent to which ecological communities are coherent entities as opposed to mere intersections of individual species distributions has long been one of the fundamental questions of ecology. Gradient analysis is one commonly used tool for addressing this question; however, all such studies have used organisms from a single taxon or guild. This risks missing important connections due to non‐competitive interactions, which should be more likely to occur between members of different guilds. Such organisms are unlikely to compete for resources and can have complementary niches that promote non‐competitive interactions. We examined the abundances of taxa in four interacting guilds along an elevation gradient in a forest in the southern Appalachian mountains. A causal discovery algorithm was used to investigate the relative frequencies of interguild and intraguild interactions. These were approximately equally common once taxonomic richness was taken into account. We used elements of metacommunity structure analysis to study the extent to which species distributions are non‐independent and tested the hypothesis that combinations of two or more interacting guilds exhibit more coherence than single guilds. In this analysis, all guilds other than collembola were classified as Clementsian or quasi‐Clementsian. (Collembola were classified as random.) When sets of multiple guilds were examined, Clementsian and quasi‐Clementsian structures predominated. We also compared boundary conjunction, measured as Morisita’s index (MI) for these sets of guilds to the weighted average of the guilds’ MI values. Only sets of directly interacting guilds had higher‐than‐baseline boundary conjunction values, and such boundary conjunction values are found in all but one set of directly interacting guilds. Our results highlight the importance of inter‐guild interactions in structuring patterns of cooccurrence. Trophic interactions and plant–fungus symbioses (mutualistic and/or pathogen–host) appear particularly important.     

Polymer Brushes under High Load

Polymer coatings are frequently used to provide repulsive forces between surfaces in solution. After 25 years of design and study, a quantitative model to explain and predict repulsion under strong compression is still lacking. Here, we combine experiments, simulations, and theory to study polymer coatings under high loads and demonstrate a validated model for the repulsive forces, proposing that this universal behavior can be predicted from the polymer solution properties.     

Postnatal Temporal,Spatial and Modality Tuning of Nociceptive Cutaneous Flexion Reflexes in Human Infants

Cutaneous flexion reflexes are amongst the first behavioural responses to develop and are essential for the protection and survival of the newborn organism. Despite this, there has been no detailed, quantitative study of their maturation in human neonates. Here we use surface electromyographic (EMG) recording of biceps femoris activity in preterm (<37 weeks gestation, GA) and term (≥37 weeks GA) human infants, less than 14 days old, in response to tactile, punctate and clinically required skin-breaking lance stimulation of the heel. We show that all infants display a robust and long duration flexion reflex (>4 seconds) to a single noxious skin lance which decreases significantly with gestational age. This reflex is not restricted to the stimulated limb: heel lance evokes equal ipsilateral and contralateral reflexes in preterm and term infants. We further show that infant flexion withdrawal reflexes are not always nociceptive specific: in 29% of preterm infants, tactile stimulation evokes EMG activity that is indistinguishable from noxious stimulation. In 40% of term infants, tactile responses are also present but significantly smaller than nociceptive reflexes. Infant flexion reflexes are also evoked by application of calibrated punctate von Frey hairs (vFh), 0.8–17.2 g, to the heel. Von Frey hair thresholds increase significantly with gestational age and the magnitude of vFh evoked reflexes are significantly greater in preterm than term infants. Furthermore flexion reflexes in both groups are sensitized by repeated vFh stimulation. Thus human infant flexion reflexes differ in temporal, modality and spatial characteristics from those in adults. Reflex magnitude and tactile sensitivity decreases and nociceptive specificity and spatial organisation increases with gestational age. Strong, relatively non-specific, reflex sensitivity in early life may be important for driving postnatal activity dependent maturation of targeted spinal cord sensory circuits.     

The Epidemiological Modelling of Major Depressive Disorder: Application for the Global Burden of Disease Study 2010

Background

Although the detrimental impact of major depressive disorder (MDD) at the individual level has been described, its global epidemiology remains unclear given limitations in the data. Here we present the modelled epidemiological profile of MDD dealing with heterogeneity in the data, enforcing internal consistency between epidemiological parameters and making estimates for world regions with no empirical data. These estimates were used to quantify the burden of MDD for the Global Burden of Disease Study 2010 (GBD 2010).

Method

Analyses drew on data from our existing literature review of the epidemiology of MDD. DisMod-MR, the latest version of the generic disease modelling system redesigned as a Bayesian meta-regression tool, derived prevalence by age, year and sex for 21 regions. Prior epidemiological knowledge, study- and country-level covariates adjusted sub-optimal raw data.

Results

There were over 298 million cases of MDD globally at any point in time in 2010, with the highest proportion of cases occurring between 25 and 34 years. Global point prevalence was very similar across time (4.4% (95% uncertainty: 4.2–4.7%) in 1990, 4.4% (4.1–4.7%) in 2005 and 2010), but higher in females (5.5% (5.0–6.0%) compared to males (3.2% (3.0–3.6%) in 2010. Regions in conflict had higher prevalence than those with no conflict. The annual incidence of an episode of MDD followed a similar age and regional pattern to prevalence but was about one and a half times higher, consistent with an average duration of 37.7 weeks.

Conclusion

We were able to integrate available data, including those from high quality surveys and sub-optimal studies, into a model adjusting for known methodological sources of heterogeneity. We were also able to estimate the epidemiology of MDD in regions with no available data. This informed GBD 2010 and the public health field, with a clearer understanding of the global distribution of MDD.     

Systems biological approach to investigate the lack of familial link between Down's Syndrome & Neural Tube Disorders

Systems Biology involves the study of the interactions of biological systems and ultimately their functions. Down''s syndrome (DS) is one of the most common genetic disorders which are caused by complete, or occasionally partial, triplication of chromosome 21, characterized by cognitive and language dysfunction coupled with sensory and neuromotor deficits. Neural Tube Disorders (NTDs) are a group of congenital malformations of the central nervous system and neighboring structures related to defective neural tube closure during the first trimester of pregnancy usually occurring between days 18-29 of gestation. Several studies in the past have provided considerable evidence that abnormal folate and methyl metabolism are associated with onset of DS & NTDs. There is a possible common etiological pathway for both NTDs and Down''s syndrome. But, various research studies over the years have indicated very little evidence for familial link between the two disorders. Our research aimed at the gene expression profiling of microarray datasets pertaining to the two disorders to identify genes whose expression levels are significantly altered in these conditions. The genes which were 1.5 fold unregulated and having a p-value <0.05 were filtered out and gene interaction network were constructed for both NTDs and DS. The top ranked dense clique for both the disorders were recognized and over representation analysis was carried out for each of the constituent genes. The comprehensive manual analysis of these genes yields a hypothetical understanding of the lack of familial link between DS and NTDs. There were no genes involved with folic acid present in the dense cliques. Only – CBL, EGFR genes were commonly present, which makes the allelic variants of these genes – good candidates for future studies regarding the familial link between DS and NTDs.

Abbreviations

NTD - Neural Tube Disorders, DS - Down''s Syndrome, MTHFR - Methylenetetrahydrofolate reductase, MTRR– 5 - methyltetrahydrofolate-homocysteine methyltransferase reductase.     

A plant growth-promoting pseudomonad is closely related to the Pseudomonas syringae complex of plant pathogens

Pseudomonas putida GR12-2 is well known as a plant growth-promoting rhizobacterium; however, phylogenetic analysis using the 16S rRNA gene and four housekeeping genes indicated that this strain forms a monophyletic group with the Pseudomonas syringae complex, which is composed of several species of plant pathogens. On the basis of these sequence analyses, we suggest that P. putida GR12-2 be redesignated as P. syringae GR12-2. To compare the ecological roles of P. syringae GR12-2 with its close relatives P. syringae pathovar (pv.) tomato DC3000 and P. syringae pv. syringae B728a, we investigated their ability to cause disease and promote plant growth. When introduced on tobacco or tomato leaves, P. syringae GR12-2 was unable to elicit a hypersensitive response or cause disease, which are characteristic responses of P. syringae DC3000 and B728a, nor were type III secretion system genes required for virulence detected in P. syringae GR12-2 by PCR or DNA hybridization. In contrast to P. syringae GR12-2, neither of the phytopathogens was able to promote root growth when inoculated onto canola seeds. Although commensals and nonpathogens have been reported among the strains of the P. syringae complex, P. syringae GR12-2 is a mutualist and a phytostimulator.     

Uptake of picophytoplankton,bacterioplankton and virioplankton by a fringing coral reef community (Ningaloo Reef,Australia)

We examined the importance of picoplankton and virioplankton to reef trophodynamics at Ningaloo Reef, (north-western Australia), in May and November 2008. Picophytoplankton (Prochlorococcus, Synechococcus and picoeukaryotes), bacterioplankton (inclusive of bacteria and Archaea), virioplankton and chlorophyll a (Chl a) were measured at five stations following the consistent wave-driven unidirectional mean flow path of seawater across the reef and into the lagoon. Prochlorococcus, Synechococcus, picoeukaryotes and bacterioplankton were depleted to similar levels (~40% on average) over the fore reef, reef crest and reef flat (=‘active reef’), with negligible uptake occurring over the sandy bottom lagoon. Depletion of virioplankton also occurred but to more variable levels. Highest uptake rates, m, of picoplankton occurred over the reef crest, while uptake coefficients, S (independent of cell concentration), were similarly scaled over the reef zones, indicating no preferential uptake of any one group. Collectively, picophytoplankton, bacterioplankton and virioplankton accounted for the uptake of 29 mmol C m⁻² day⁻¹, with Synechococcus contributing the highest proportion of the removed C. Picoplankton and virioplankton accounted for 1–5 mmol N m⁻² day⁻¹ of the removed N, with bacterioplankton estimated to be a highly rich source of N. Results indicate the importance of ocean–reef interactions and the dependence of certain reef organisms on picoplanktonic supply for reef-level biogeochemistry processes.     

In vitro validation of acetyltransferase activity of GlmU as an antibacterial target in Haemophilus influenzae

GlmU is a bifunctional enzyme that is essential for bacterial growth, converting D-glucosamine 1-phosphate into UDP-GlcNAc via acetylation and subsequent uridyl transfer. A biochemical screen of AstraZeneca's compound library using GlmU of Escherichia coli identified novel sulfonamide inhibitors of the acetyltransferase reaction. Steady-state kinetics, ligand-observe NMR, isothermal titration calorimetry, and x-ray crystallography showed that the inhibitors were competitive with acetyl-CoA substrate. Iterative chemistry efforts improved biochemical potency against gram-negative isozymes 300-fold and afforded antimicrobial activity against a strain of Haemophilus influenzae lacking its major efflux pump. Inhibition of precursor incorporation into bacterial macromolecules was consistent with the antimicrobial activity being caused by disruption of peptidoglycan and fatty acid biosyntheses. Isolation and characterization of two different resistant mutant strains identified the GlmU acetyltransferase domain as the molecular target. These data, along with x-ray co-crystal structures, confirmed the binding mode of the inhibitors and explained their relative lack of potency against gram-positive GlmU isozymes. This is the first example of antimicrobial compounds mediating their growth inhibitory effects specifically via GlmU.     

Structural and signaling requirements of the human melanocortin 4 receptor for MAP kinase activation

In addition to its well known stimulation of cAMP production, the human melanocortin type 4 (hMC4) receptor recently has been shown to mediate p44/42 MAPK activation. This finding opens new questions about the structural and signaling mechanisms that connect the receptor to this alternate cell signaling pathway. Point mutants in the hMC4 receptor that have been associated with obesity were constructed and transfected into HEK 293 cells. Functional analyses then were done to determine if these mutations would similarly impact cAMP formation and p44/42 MAPK signaling. Whereas a D90N mutation in the second transmembrane domain and a D298A mutation in the seventh transmembrane domain impaired both cAMP formation and p44/42 MAPK activation, a more conservative D298N mutation retained cAMP formation but abolished p44/42 MAPK activation. The D298N mutation identified, for the first time, differential structural requirements of the hMC4 receptor for activation of the cAMP and p44/42 MAPK pathways. Furthermore, functional characterizations of a series of chimeric receptors combining the hMC4 receptor and the hMC3 subtype, a receptor that does not couple to p44/42 MAPK activation despite stimulating adenylyl cyclase, indicate that the hMC4 cytoplasmic tail is a necessary structural element for p44/42 MAPK signaling. Subsequent investigation of the signaling requirements for p44/42 MAPK activation demonstrated that the adenylyl cyclase inhibitor 2', 5'-dideoxyadenosine blocked agonist-induced p44/42 MAPK activation, but the PKA inhibitor Rp cAMPS did not. Taken together, these data indicate that cAMP is required, but not sufficient for p44/42 MAPK activation and suggest structural elements required for hMC4 receptor signaling.     

Reaction tissue formation and stem tensile modulus properties in wild-type and p-coumarate-3-hydroxylase downregulated lines of alfalfa, Medicago sativa (Fabaceae)

To our knowledge, xylary reaction tissue has never been reported in a forage crop species. Here we report the discovery of reaction tissue in a transgenic line of Medicago sativa (pC3H, for the gene for p-coumarate-3-hydroxylase) with reduced lignin content and in the wild-type (WT) line. Based on microscopy and biomechanical testing of internodal alfalfa branch sections, the transgenic (pC3H-I) line, relative to the WT (1) apparently formed more reaction tissue containing gelatinous fibers with adjacent thick-walled fibers (presumed to be "intermediate" tissue) more rapidly, (2) had more xylem tissue, and (3) had comparable tensile dynamic modulus properties. These findings thus establish the (limited) ability of this perennial angiosperm to form (inducible) reaction tissue in a manner somewhat analogous to that of woody arborescent angiosperms. The potential of effectuating reductions in lignin amounts in (woody) angiosperms with increased formation of reaction (tension wood) tissue is discussed because reaction tissues are often viewed as a deleterious trait in processing for many agronomic/industrial applications, especially with the current interest in biofuels.