A new cost‐distance model for human accessibility and an evaluation of accessibility bias in permanent vegetation plots in Great Smoky Mountains National Park,USA

Question: Can a new cost‐distance model help us to evaluate the potential for accessibility bias in ecological observations? How much accessibility bias is present in the vegetation monitoring plots accumulated over the last three decades in Great Smoky Mountains National Park? Location: Great Smoky Mountains National Park, North Carolina and Tennessee, USA. Methods: Distance, slope, stream crossings, and vegetation density were incorporated into a least‐cost model of energetic expenditure for human access to locations. Results: Estimated round‐trip energy costs for the park ranged from 0 to 1.62 × 10⁵ J kg^?1. The estimated round‐trip energetic expenditure for the surveys ranged from 53 to 1.51 × 10⁵ J kg^?1. Their distribution was more accessible than the random expectation. Ten (17%) of the vegetation types in the park are significantly under‐sampled relative to their area, and 16 (29%) are over‐sampled. Plots in 18 of the 40 vegetation types exhibited a significant positive correlation with accessibility. Conclusions: The least‐cost model is an improvement over previous attempts to quantify accessibility. The bias in plot locations suggests using a least‐cost model to test for bias in cases in which human accessibility is confounded with other sources of ecosystem variation.     

The Human Intestinal Microbiome: A New Frontier of Human Biology

To analyze the vast number and variety of microorganisms inhabitingthe human intestine, emerging metagenomic technologies are extremelypowerful. The intestinal microbes are taxonomically complexand constitute an ecologically dynamic community (microbiota)that has long been believed to possess a strong impact on humanphysiology. Furthermore, they are heavily involved in the maturationand proliferation of human intestinal cells, helping to maintaintheir homeostasis and can be causative of various diseases,such as inflammatory bowel disease and obesity. A simplifiedanimal model system has provided the mechanistic basis for themolecular interactions that occur at the interface between suchmicrobes and host intestinal epithelia. Through metagenomicanalysis, it is now possible to comprehensively explore thegenetic nature of the intestinal microbiome, the mutually interactingsystem comprising the host cells and the residing microbialcommunity. The human microbiome project was recently launchedas an international collaborative research effort to furtherpromote this newly developing field and to pave the way to anew frontier of human biology, which will provide new strategiesfor the maintenance of human health.     

Rapid dispersal and establishment of a benthic Ponto-Caspian goby in Lake Erie: diel vertical migration of early juvenile round goby

The round goby, Apollonia melanostoma, a molluscivore specialist, was introduced to the Great Lakes in the early 1990s and rapidly expanded its distribution, especially in Lake Erie. Adult round goby morphology suggests low dispersal and migration potential due to the lack of a swim bladder and benthic life style. Given that the larval stage occurs inside the benthic egg, and juveniles have adult morphologies, it has been suspected that dispersal and invasion potential is low for early life stages also. However, we identified early juvenile round gobies in the nocturnal pelagic in Lake Erie and thus we conducted a sampling study to determine the extent to which this life stage uses the nocturnal pelagic. Replicate ichthyoplankton samples were collected at 3-h intervals (1900–0700 h) at three depths (2 m, 5 m, 8 m) in western Lake Erie (water depth = 10 m) in July and August 2002 and June 2006. Early juvenile round gobies (6–23 mm TL) were present almost exclusively in the nocturnal samples (2200 h, 0100 h, 0400 h) with peak densities approaching 60 individuals per 100 m³ of water sampled. Nocturnal density was also significantly greater at 8-m depth versus 2-m and only the smallest fish (6–8 mm TL) migrated to the surface (2-m). Analyses of diet clearly demonstrated that these fish are foraging on plankton at night and thus may not be light limited for foraging in ship ballast tanks. In ships that take on thousands of tonnes of water for ballast, nocturnal ballasting could easily result in transport of thousands of young round gobies at a time. Additionally, within-lake dispersal at this lifestage is likely common and may facilitate downstream passage across barriers designed to limit range expansion.     

Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 Å Crystal Structure of the Active Form of ScpA

The crystal structure of an active form of ScpA has been solved to 1.9 Å resolution. ScpA is a multidomain cell-envelope subtilase from Streptococcus pyogenes that cleaves complement component C5a. The catalytic triad of ScpA is geometrically consistent with other subtilases, clearly demonstrating that the additional activation mechanism proposed for the Streptococcus agalactiae homologue (ScpB) is not required for ScpA. The ScpA structure revealed that access to the catalytic site is restricted by variable regions in the catalytic domain (vr7, vr9, and vr11) and by the presence of the inserted protease-associated (PA) domain and the second fibronectin type III domains (Fn2). Modeling of the ScpA-C5a complex indicates that the substrate binds with carboxyl-terminal residues (65-74) extended through the active site and core residues (1-64) forming exosite-type interactions with the Fn2 domain. This is reminiscent of the two-site mechanism proposed for C5a binding to its receptor. In the nonprime region of the active site, interactions with the substrate backbone are predicted to be more similar to those observed in kexins, involving a single β-strand in the peptidase. However, in contrast to kexins, there would be diminished emphasis on side-chain interactions, with little charged character in the S3-S1 and S6-S4 subsites occupied by the side chains of residues in vr7 and vr9. Substrate binding is anticipated to be dominated by ionic interactions in two distinct regions of ScpA. On the prime side of the active site, salt bridges are predicted between P1′, P2′, and P7′ residues, and residues in the catalytic and PA domains. Remote to the active site, a larger number of ionic interactions between residues in the C5a core and the Fn2 domain are observed in the model. Thus, both PA and Fn2 domains are expected to play significant roles in substrate recognition.     

Differential Processing of Amyloid-�� Precursor Protein Directs Human Embryonic Stem Cell Proliferation and Differentiation into Neuronal Precursor Cells

The amyloid-β precursor protein (AβPP) is a ubiquitously expressed transmembrane protein whose cleavage product, the amyloid-β (Aβ) protein, is deposited in amyloid plaques in neurodegenerative conditions such as Alzheimer disease, Down syndrome, and head injury. We recently reported that this protein, normally associated with neurodegenerative conditions, is expressed by human embryonic stem cells (hESCs). We now report that the differential processing of AβPP via secretase enzymes regulates the proliferation and differentiation of hESCs. hESCs endogenously produce amyloid-β, which when added exogenously in soluble and fibrillar forms but not oligomeric forms markedly increased hESC proliferation. The inhibition of AβPP cleavage by β-secretase inhibitors significantly suppressed hESC proliferation and promoted nestin expression, an early marker of neural precursor cell (NPC) formation. The induction of NPC differentiation via the non-amyloidogenic pathway was confirmed by the addition of secreted AβPPα, which suppressed hESC proliferation and promoted the formation of NPCs. Together these data suggest that differential processing of AβPP is normally required for embryonic neurogenesis.The amyloid-β precursor protein (AβPP)⁵ is a ubiquitously expressed transmembrane protein whose cleavage product, the amyloid-β (Aβ) protein, is deposited in amyloid plaques in the aged brain, following head injury, and in the neurodegenerative conditions of Alzheimer disease (AD) and Down syndrome (DS). AβPP has structural similarity to growth factors (1) and modulates several important neurotrophic functions, including neuritogenesis, synaptogenesis, and synaptic plasticity (2). The function of AβPP during early embryogenesis and neurogenesis has not been well described.AβPP is processed by at least two pathways, the non-amyloidogenic and amyloidogenic pathways. Non-amyloidogenic processing of AβPP yields secreted AβPPα (sAβPPα), the secreted extracellular domain of AβPP that acts as a growth factor for many cell types and promotes neuritogenesis (3). Amyloidogenic processing of AβPP releases sAβPPβ, the AβPP intracellular domain, and Aβ proteins. The Aβ protein has both neurotoxic and neurotrophic properties (4) dependent on the differentiation state of the neuron; Aβ is neurotoxic to differentiating neurons via a mechanism involving differentiation-associated increases in the phosphorylation of the microtubule-associated protein tau (5) but neurotrophic to undifferentiated embryonic neurons. Evidence supporting a neurotrophic function for Aβ during development include its neurogenic activity toward rat neural stem cells (4–6). Consistent with these data, two studies have demonstrated increased hippocampal neurogenesis in young transgenic mice overexpressing human APP_Sw,Ind (7, 8).Recently we reported that human embryonic stem cells (hESCs) express AβPP and that both the stemness of the cells and the pregnancy-associated hormone human chorionic gonadotropin alter AβPP expression (9). These results suggest a functional role for AβPP during early human embryogenesis. To further investigate the function of AβPP and its cleavage products during early embryonic neurogenesis, we examined the expression and processing of this protein and its role in proliferation and differentiation of hESCs into neural precursor cells (NPCs). We found that amyloidogenic processing of AβPP promotes hESC proliferation whereas non-amyloidogenic processing induces hESC differentiation into NPCs. These data reveal an important function for AβPP during early human embryonic neurogenesis. Our data imply that any dysregulation in AβPP processing that leads to altered sAβPPα/Aβ production could result in aberrant neurogenesis as reported in the AD and DS brains.     

Sustaining Plants and People: Traditional Q’eqchi’ Maya Botanical Knowledge and Interactive Spatial Modeling in Prioritizing Conservation of Medicinal Plants for Culturally Relative Holistic Health Promotion

Ethnobotanical surveys were conducted to locate culturally important, regionally scarce, and disappearing medicinal plants via a novel participatory methodology which involves healer-expert knowledge in interactive spatial modeling to prioritize conservation efforts and thus facilitate health promotion via medicinal plant resource sustained availability. These surveys, conducted in the Maya Mountains, Belize, generate ethnobotanical, ecological, and geospatial data on species which are used by Q’eqchi’ Maya healers in practice. Several of these mountainous species are regionally scarce and the healers are expressing difficulties in finding them for use in promotion of community health and wellness. Based on healers’ input, zones of highest probability for locating regionally scarce, disappearing, and culturally important plants in their ecosystem niches can be facilitated by interactive modeling. In the present study, this is begun by choosing three representative species to train an interactive predictive model. Model accuracy was then assessed statistically by testing for independence between predicted occurrence and actual occurrence of medicinal plants. A high level of accuracy was achieved using a small set of exemplar data. This work demonstrates the potential of combining ethnobotany and botanical spatial information with indigenous ecosystems concepts and Q’eqchi’ Maya healing knowledge via predictive modeling. Through this approach, we may identify regions where species are located and accordingly promote for prioritization and application of in situ and ex situ conservation strategies to protect them. This represents a significant step toward facilitating sustained culturally relative health promotion as well as overall enhanced ecological integrity to the region and the earth.     

Cole–Cole, linear and multivariate modeling of capacitance data for on-line monitoring of biomass

This work evaluates three techniques of calibrating capacitance (dielectric) spectrometers used for on-line monitoring of biomass: modeling of cell properties using the theoretical Cole–Cole equation, linear regression of dual-frequency capacitance measurements on biomass concentration, and multivariate (PLS) modeling of scanning dielectric spectra. The performance and robustness of each technique is assessed during a sequence of validation batches in two experimental settings of differing signal noise. In more noisy conditions, the Cole–Cole model had significantly higher biomass concentration prediction errors than the linear and multivariate models. The PLS model was the most robust in handling signal noise. In less noisy conditions, the three models performed similarly. Estimates of the mean cell size were done additionally using the Cole–Cole and PLS models, the latter technique giving more satisfactory results.     

QSRA – a quality-value guided de novo short read assembler

Background  

New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data.     

Panmixia postponed: ancestry-related assortative mating in contemporary human populations

A study of two different populations reveals that in both the choice of a spouse is non-random not only in respect of broad ethnic group but also in regard to specific ancestries within that group. The cause of this surprising bias remains unclear.