Hypothesis Tests on Mixture Model Components with Applications in Ecology and Agriculture

Multiple comparisons are widely used to compare gross features of distributions across populations. However, often a scientific hypothesis is more easily couched in terms of more focused null and alternative statistical hypotheses. For example, among distributions exhibiting clusters of continuous measurements across strata, are there clusters of measurements similar in terms of location, spread, or weight? We propose testing such hypotheses using a sequence of nested finite mixture models. Reasonable, data-driven priors are suggested based on estimates of the sample spreads and midpoints. Formal hypothesis testing is carried out through the computation of Bayes factors. The method is illustrated on Holling’s (Ecological Monographs 62:447–502, 1992) forest and prairie bird body mass data, and data on the time-to-abortion in dairy cows. Supplemental simulations are available online.     

Role of EphA4 and EphrinB3 in local neuronal circuits that control walking

Local circuits in the spinal cord that generate locomotion are termed central pattern generators (CPGs). These provide coordinated bilateral control over the normal limb alternation that underlies walking. The molecules that organize the mammalian CPG are unknown. Isolated spinal cords from mice lacking either the EphA4 receptor or its ligand ephrinB3 have lost left-right limb alternation and instead exhibit synchrony. We identified EphA4-positive neurons as an excitatory component of the locomotor CPG. Our study shows that dramatic locomotor changes can occur as a consequence of local genetic rewiring and identifies genes required for the development of normal locomotor behavior.     

Species from the Colletotrichum acutatum,Colletotrichum boninense and Colletotrichum gloeosporioides species complexes associated with tree tomato and mango crops in Colombia

Colletotrichum species cause typical anthracnose symptoms in tree tomato and mango. To characterize species of Colletotrichum in these two crops in Colombia, 91 isolates were collected from several localities. Phylogenetic analyses using nuclear gene sequencing of the ITS region and the glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) gene allowed the identification of three groups: acutatum, gloeosporioides and boninense. These three groups were further confirmed using two additional genomic regions (chitin synthase 1 and actin) for 30 isolates representative of the three previously identified complexes and one genomic region (ApMat) for the Colletotrichum gloeosporioides complex strains. The entire approach permitted a robust strain identification that allowed phylogenetic species recognition (PSR) based on the identification of well‐supported monophyletic clades and concordance between individual and multilocus phylogenies. Morphological and physiological assays were also conducted. Isolates that were morphologically identified as C. gloeosporioides showed high phenotypic diversity. Pathogenicity data revealed a considerable degree of host preference.     

Defense gene expression patterns of three SAR-induced tomato cultivars in the field

Plant activation is an appealing disease management tool, avoiding some of the challenges of traditional chemical control by not directly impacting the pathogen. This study examined effects of acibenzolar-S-methyl (ASM), a plant activator that induces systemic acquired resistance, on defense response activation in three field-grown tomato cultivars in New York. Salicylic acid, ethylene and jasmonic acid-mediated responses were monitored by following expression of a marker gene for each signaling pathway using quantitative real-time PCR over the course of two ASM applications. ASM induced salicylic acid and ethylene, but not jasmonic acid-regulated gene expression in all cultivars tested. All three cultivars demonstrated a significantly stronger gene expression response relative to the untreated control following the second ASM application. Implications of these findings on management practices are discussed.     

Are classification criteria for vasculitis useful in clinical practice? Observations and lessons from Colombia

Introduction

Idiopathic systemic vasculitis represents a group of clinical entities having non-specific etiology with the common characteristic of acute or chronic inflammatory compromise of the small and large vessels walls, associated with fibrinoid necrosis.

Objectives

To describe the most common inflammatory vascular diseases in a long historical cohort of patients from San Juan de Dios Hospital located in Bogota, Colombia using two different systems and a clinical histopathological correlation format, and to make a comparison between them.

Methods

We reviewed all previously ascertained cases of vasculitis confirmed by biopsy processed between 1953 and 1990, and systematically collected data on all new cases of vasculitis from 1991 to 1997 at the Hospital San Juan de Dios (Bogota – Colombia). The cases were classified in accordance with the Chapel Hill Consensus criteria, and the system proposed by J.T. Lie.

Results

Of 165,556 biopsy tissue specimens obtained during this period from our hospital, 0.18% had vasculitis, perivasculitis or vasculopathy. These included 304 histopathological biopsies from 292 patients. Cutaneous leukocytoclastic vasculitis (64 histological specimens) was the most frequently encountered type of "primary" vasculitis followed by thromboangiitis obliterans (38 specimens), and polyarteritis nodosa (24 specimens). Vasculitis associated with connective tissue diseases (33 specimens) and infection (20 specimens) were the main forms of secondary vasculitis, a category that was omitted from the Chapel Hill consensus report. We found that 65.8% of our histopathological diagnoses could not be classified according to the Chapel Hill classification, and 35.2% could not be classified according to the classification of Lie. Only 8.9% of cases remained unclassified by our system after clinical and histological correlation.

Conclusion

Current vasculitis classification schemes are designed for classification, rather that diagnosis of disease and do not adequately address some common forms of inflammatory vascular diseases, including those of infectious etiology and unusual etiology seen in clinical practice. Based on our clinical experience, we suggest a classification outline which practitioners can use which emphasizes correlation of the clinical picture to the histopathology findings for diagnosis and therapy, which may promote better clinical practice and standardization for clinical trials.

     

Effects of biological,economic and management factors on tuna and billfish stock status

Commercial tunas and billfishes (swordfish, marlins and sailfish) provide considerable catches and income in both developed and developing countries. These stocks vary in status from lightly exploited to rebuilding to severely depleted. Previous studies suggested that this variability could result from differences in life‐history characteristics and economic incentives, but differences in exploitation histories and management measures also have a strong effect on current stock status. Although the status (biomass and fishing mortality rate) of major tuna and billfish stocks is well documented, the effect of these diverse factors on current stock status and the effect of management measures in rebuilding stocks have not been analysed at the global level. Here, we show that, particularly for tunas, stocks were more depleted if they had high commercial value, were long‐lived species, had small pre‐fishing biomass and were subject to intense fishing pressure for a long time. In addition, implementing and enforcing total allowable catches (TACs) had the strongest positive influence on rebuilding overfished tuna and billfish stocks. Other control rules such as minimum size regulations or seasonal closures were also important in reducing fishing pressure, but stocks under TAC implementations showed the fastest increase of biomass. Lessons learned from this study can be applied in managing large industrial fisheries around the world. In particular, tuna regional fisheries management organizations should consider the relative effectiveness of management measures observed in this study for rebuilding depleted large pelagic stocks.     

Comment on "Dynamics of dpp signaling and proliferation control"

Wartlick et al. (Research Articles, 4 March 2011, p. 1154) reported that growth rates in the Drosophila wing disc correlate with increasing Dpp signaling levels, suggesting that the rate of Dpp increase determines the cell-cycle length. Contradicting their model, we found that cells in which the increase of Dpp signaling levels was genetically abrogated grew at rates comparable to those of wild-type cells.     

Membrane stability and mitochondrial activity of bovine sperm frozen with low-density lipoproteins and trehalose

Cryopreservation results in the destabilization of the sperm plasma membrane, leading to negative side effects such as premature cryocapacitation, apoptosis and the low mitochondrial activity of bovine spermatozoa. Low-density lipoproteins (LDL) and trehalose have been used in seminal freezing to protect the integrity and stability of sperm membranes. Likewise, trehalose can increase the mitochondrial activity of sperm. The objective of this study was to evaluate the membrane stability and mitochondrial activity of bovine sperm after being frozen and treated with LDL sources and trehalose. Ten ejaculates from five bulls were cryopreserved under the treatments, CEY: chicken egg yolk (20% v/v); CCEY: centrifuged CEY (20% v/v); LDL: LDL (8% v/v); T: trehalose (100 mM); and TLDL: T (100 mM) plus LDL (8% v/v). After thawing, membrane stability and mitochondrial membrane potential (ΔΨM) were assessed by flow cytometry through the M-540/Yopro-1 and DiOC6/PI probes. The structural membrane integrity (SMI) was evaluated by fluorescence microscopy using SYBR14/PI dyes. A generalized linear model was adjusted, and the means were compared using the Tukey test. Centrifuged chicken egg yolk and LDL had a higher proportion of non-cryocapacitated non-apoptotic sperm (M−Y−), while CEY and T had the largest populations of cryocapacitated non-apoptotic sperm (M+Y−) and cryocapacitated apoptotic sperm (M+Y+). Centrifuged chicken egg yolk also showed a higher proportion of sperm with high-ΔΨM. Treatments that included egg yolk or purified LDL had a positive effect on SMI. Centrifuged chicken egg yolk has a superior cryoprotective effect on membrane stability and mitochondrial activity of bovine semen over the conventional use of CEY or the individual or simultaneous use of LDL and trehalose.     

Genotypic and phenotypic characterization of Streptomyces species associated with potato crops in the central part of Colombia

In Colombia, Streptomyces scabiei (syn. S. scabies) is commonly believed to be the causal organism of scab disease in local potato crops. However, very little is known about this organism and about the diversity and pathogenicity of the Streptomyces species associated with potato crops in Colombia. This study, therefore, aimed to elucidate aspects regarding the diversity of these bacteria associated with potato crops in a particular region of Colombia and evaluate their pathogenicity. We obtained 33 isolates of Streptomyces from netted, superficial and deep-pitted potato scab lesions from two main potato-producing regions in Colombia. Of these, 17 were pathogenic based on in vitro and in planta assays. None of these isolates carried the txtA, txtB, or nec1 genes, commonly associated with pathogenicity in Streptomyces, and characteristic of the pathogenicity island (PAI). We also characterized all isolates based on phenotypic characteristics and analysed their phylogenetic relationships using the 16S rRNA, atpD, recA, rpoB, and trpB genes. The isolates were highly diverse, placed in nine clades with 15 different phenotypes. The 17 pathogenic isolates were placed into three clades, namely S. pratensis, S. xiamenensis, and unknown species. This study is a preliminary investigation towards understanding scab disease in Colombia through the study of both pathogenic and nonpathogenic species present in scab disease lesions in potatoes. Also, this is the first report of Streptomyces species associated with potato tubers in Colombia.