Tropical Vine Growth and the Effects on Forest Succession: A Review of the Ecology and Management of Tropical Climbing Plants

The climbing habit has evolved independently in many plant taxa, offering vines the ability to compete with non-climbing vegetation for resources such as light, nutrients, and water. This review examines the structural and functional characteristics that allow climbing plants to (1) achieve widespread dispersal, (2) transport large amounts of water throughout vessels, (3) maintain high photosynthesis levels through a large leaf area to biomass ratio, (4) achieve rapid vertical and horizontal expansion by fast growth rates and various climbing mechanisms and (5) survive and recover from disturbances. Due to the competitive effects of vines on trees, management of vine growth is used to preserve tropical timber plantations, combat invasive weeds, and promote rainforest recovery. In order to sustainably manage the vines into the future, it is necessary to understand the mechanisms by which they can alter tropical forest succession and the impacts of various management techniques.     

Palm Harvest Impacts in North-Western South America

Tropical forests harbor thousands of useful plants that are harvested and used in subsistence economies or traded in local, regional or international markets. The effect on the ecosystem is little known, and the forests resilience is badly understood. Palms are the most useful group of plants in tropical American forests. This paper introduces a cross-disciplinary study of the effects of harvesting palm products from the tropical forests in north-western South America. The size of the resource is estimated through palm community studies in the different forest formations that determines the number of species and individuals of all palm species. The genetic structure of useful palm species is studied to determine how much harvesting of the species contributes to genetic erosion of its populations, and whether extraction can be made without harm. Almost all palm species are used in rural communities for subsistence purposes Quantitative ethno-botanical research in different forest types have identified thousands of different ways of using palms for food, construction, tool-making, etc. Although most palms are used by the person harvesting them, many are sold on local markets as fruits, fiber, tools, construction materials etc., and a few have reached larger markets, including international markets. Palm populations are managed in various ways of which some are sustainable and others are destructive. National level mechanisms that governs extraction, trade and commercialization of palm products, are used to identify positive and negative policies in relation to resilience of ecosystems.     

<Emphasis Type=Italic>Aulonemia cochabambensis</Emphasis> (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae), an anomalous new species from Bolivia

Aulonemia cochabambensis (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae), a new species from the Department of Cochabamba, Bolivia, is described and illustrated. It has foliage leaves with delicate fimbriae, no sheath auricles, narrow blades, an abaxial dark marginal stripe, and intercostal sclerenchyma; few-flowered paniculate synflorescences; and robust, awned spikelets. The new species is compared with its putative relatives Aulonemia laxa and Arthrostylidium schomburgkii. A key to the species of Aulonemia in Bolivia is also included.     

Useful Species Richness,Proportion of Exotic Species,and Market Orientation on Amazonian Dark Earths and Oxisols<Superscript>1</Superscript>

Useful Species Richness, Proportion of Exotic Species, and Market Orientation on Amazonian Dark Earths and Oxisols Anthropogenic soils of Amazonia, known as Amazonian Dark Earths (ADE), are environments with elevated soil fertility that can produce crops that otherwise yield poorly on the leached and highly acidic Oxisols that dominate much of the basin. While ADE sites near urban centers often attract commercial horticultural production of nutrient–demanding exotics, these soils are also considered possibly unique reservoirs of endemic agrobiodiversity because of their relationship to pre–Columbian indigenous occupation. Through botanical surveys and interviews with smallholder farmers, this study compared useful species richness, proportion of exotic species, and market orientation of farms situated on ADE and non–anthropogenic Oxisols in the municipality of Borba in Central Brazilian Amazonia. Species richness was similar on Amazonian Dark Earth and Oxisol farms (19.6 spp vs. 18.3 spp); however, ADE farms showed significantly higher proportions of exotic species (39% vs. 26%; p = 0.025). Furthermore, ADE farms in Borba demonstrated significantly higher market orientation (61.0% vs. 47.3%; p = 0.028), likely a result of the advantage of Amazonian Dark Earths for production of crops that are nutrient–demanding or pH–sensitive crops that have higher values in the nearby regional market of Manaus.     

Parasite-mediated intraguild predation as one of the drivers of co-existence and exclusion among invasive and native amphipods (Crustacea)

Parasitism is emerging as one of the forces determining the outcome of biological invasions. Using field survey and laboratory experiments, we investigate parasitism as one of the factors mediating the interactions among invasive and native amphipods. An extensive survey (100 sites) of a small British island, revealed the native Gammarus duebeni celticus to be parasitised by the muscle wasting microsporidian Pleistophora mulleri and the acanthocephalan duck parasite Polymorphus minutus, the introduced European Gammarus pulex only by P. minutus and the North American Crangonyx pseudogracilis by neither. While Gammarus spp. were widespread in rivers (one or both species present in 64% of sites), C. pseudogracilis had a restricted distribution (7% of sites) and always co-occurred with Gammarus spp. In contrast, Gammarus spp. were absent from all pond/reservoir sites, with C. pseudogracilis present in over 90%. While the negative association of C. pseudogracilis with Gammarus spp. undoubtedly results from factors such as physico-chemical tolerance and predation as C. pseudogracilis can be heavily predated by Gammarus spp., it was notable that C. pseudogracilis co-occurred with Gammarus spp. more frequently when the latter were parasitised. Laboratory experiments clearly showed that predation on C. pseudogracilis was greatly diminished when G. d. celticus was parasitised by P. mulleri and G. pulex by P. minutus. Our study provides evidence that parasitism, by mediating a key interspecific interaction, is one of an array of interacting factors that may have a role in driving patterns of exclusion and co-existence in natives and invaders.     

Biased competition through variations in amplitude of <Emphasis Type="Italic">γ</Emphasis>-oscillations

Experiments in visual cortex have shown that the firing rate of a neuron in response to the simultaneous presentation of a preferred and non-preferred stimulus within the receptive field is intermediate between that for the two stimuli alone (stimulus competition). Attention directed to one of the stimuli drives the response towards the response induced by the attended stimulus alone (selective attention). This study shows that a simple feedforward model with fixed synaptic conductance values can reproduce these two phenomena using synchronization in the gamma-frequency range to increase the effective synaptic gain for the responses to the attended stimulus. The performance of the model is robust to changes in the parameter values. The model predicts that the phase locking between presynaptic input and output spikes increases with attention.     

NS-kNN: a modified <Emphasis Type="Italic">k</Emphasis>-nearest neighbors approach for imputing metabolomics data

Introduction

A common problem in metabolomics data analysis is the existence of a substantial number of missing values, which can complicate, bias, or even prevent certain downstream analyses. One of the most widely-used solutions to this problem is imputation of missing values using a k-nearest neighbors (kNN) algorithm to estimate missing metabolite abundances. kNN implicitly assumes that missing values are uniformly distributed at random in the dataset, but this is typically not true in metabolomics, where many values are missing because they are below the limit of detection of the analytical instrumentation.

Objectives

Here, we explore the impact of nonuniformly distributed missing values (missing not at random, or MNAR) on imputation performance. We present a new model for generating synthetic missing data and a new algorithm, No-Skip kNN (NS-kNN), that accounts for MNAR values to provide more accurate imputations.

Methods

We compare the imputation errors of the original kNN algorithm using two distance metrics, NS-kNN, and a recently developed algorithm KNN-TN, when applied to multiple experimental datasets with different types and levels of missing data.

Results

Our results show that NS-kNN typically outperforms kNN when at least 20–30% of missing values in a dataset are MNAR. NS-kNN also has lower imputation errors than KNN-TN on realistic datasets when at least 50% of missing values are MNAR.

Conclusion

Accounting for the nonuniform distribution of missing values in metabolomics data can significantly improve the results of imputation algorithms. The NS-kNN method imputes missing metabolomics data more accurately than existing kNN-based approaches when used on realistic datasets.

     

In Vitro Studies on the Putative Function of N-acetylaspartate as an Osmoregulator

Efflux and tissue content of N-acetylaspartate (NAA) and amino acids were evaluated from cultured and acutely prepared hippocampal slices in response to changes in osmolarity. The osmoregulator taurine, but not NAA, was lost from both types of slices after moderate reductions in extracellular osmolarity (−60 mOsm) for 10–48 h. Hypoosmotic shock (−166 mOsm) for 5 min resulted in unselective efflux of several amino acids from acutely prepared slices. Notably, the efflux of taurine, but not NAA, was prominent also after the shock. Efflux of NAA was markedly enhanced by NMDA and high K⁺, in particular after the stimulation period. The high K⁺-mediated efflux was decreased by high extracellular osmolarity and a NMDA-receptor antagonist. The results indicate that NAA efflux can be induced by a sudden non-physiological decrease in extracellular osmolarity but not by prolonged more moderate changes in osmolarity. The mechanisms behind the efflux of NAA by high K⁺ are complex and may involve both swelling and activation of NMDA-receptors.     

Inflammation-associated S100 proteins: new mechanisms that regulate function

This review focuses on new aspects of extracellular roles of the calgranulins. S100A8, S100A9 and S100A12 are constitutively expressed in neutrophils and induced in several cell types. The S100A8 and S100A9 genes are regulated by pro- and anti-inflammatory mediators and their functions may depend on cell type, mediators within a particular inflammatory milieu, receptors involved in their recognition and their post-translational modification. The S100A8 gene induction in macrophages is dependent on IL-10 and potentiated by immunosuppressive agents. S100A8 and S100A9 are oxidized by peroxide, hypochlorite and nitric oxide (NO). HOCl generates intra-chain sulfinamide bonds; stronger oxidation promotes cross-linked forms that are seen in human atheroma. S100A8 is >200-fold more sensitive to oxidative cross-linking than low-density lipoprotein and may reduce oxidative damage. S100A8 and S100A9 can be S-nitrosylated. S100A8–SNO suppresses mast cell activation and inflammation in the microcirculation and may act as an NO transporter to regulate vessel tone in inflammatory lesions. S100A12 activates mast cells and is a monocyte and mast cell chemoattractant; a G-protein-coupled mechanism may be involved. Structure–function studies are discussed in relation to conservation and divergence of functions in S100A8. S100A12 induces cytokines in mast cells, but not monocytes/macrophages. It forms complexes with Zn²⁺ and, by chelating Zn²⁺, S100A12 significantly inhibits MMPs. Zn²⁺ in S100A12 complexes co-localize with MMP-9 in foam cells in atheroma. In summary, S100A12 has pro-inflammatory properties that are likely to be stable in an oxidative environment, because it lacks Cys and Met residues. Conversely, S100A8 and S100A9 oxidation and S-nitrosylation may have important protective mechanisms in inflammation.     

Human Alzheimer’s disease synaptic <Emphasis Type=Italic>O</Emphasis>-GlcNAc site mapping and iTRAQ expression proteomics with ion trap mass spectrometry

Neuronal synaptic functional deficits are linked to impaired learning and memory in Alzheimer’s disease (AD). We recently demonstrated that O-GlcNAc, a novel cytosolic and nuclear carbohydrate post-translational modification, is enriched at neuronal synapses and positively regulates synaptic plasticity linked to learning and memory in mice. Reduced levels of O-GlcNAc have been observed in AD, suggesting a possible link to deficits in synaptic plasticity. Using lectin enrichment and mass spectrometry, we mapped several human cortical synaptic O-GlcNAc modification sites. Overlap in patterns of O-GlcNAcation between mouse and human appears to be high, as previously mapped mouse synaptic O-GlcNAc sites in Bassoon, Piccolo, and tubulin polymerization promoting protein p25 were identified in human. Novel O-GlcNAc modification sites were identified on Mek2 and RPN13/ADRM1. Mek2 is a signaling component of the Erk 1/2 pathway involved in synaptic plasticity. RPN13 is a component of the proteasomal degradation pathway. The potential interplay of phosphorylation with mapped O-GlcNAc sites, and possible implication of those sites in synaptic plasticity in normal versus AD states is discussed. iTRAQ is a powerful differential isotopic quantitative approach in proteomics. Pulsed Q dissociation (PQD) is a recently introduced fragmentation strategy that enables detection of low mass iTRAQ reporter ions in ion trap mass spectrometry. We optimized LTQ ion trap settings for PQD-based iTRAQ quantitation and demonstrated its utility in O-GlcNAc site mapping. Using iTRAQ, abnormal synaptic expression levels of several proteins previously implicated in AD pathology were observed in addition to novel changes in synaptic specific protein expression including Synapsin II.