Neoseiulus paspalivorus,a predator from coconut,as a candidate for controlling dry bulb mites infesting stored tulip bulbs

The dry bulb mite, Aceria tulipae, is the most important pest of stored tulip bulbs in The Netherlands. This tiny, eriophyoid mite hides in the narrow space between scales in the interior of the bulb. To achieve biological control of this hidden pest, candidate predators small enough to move in between the bulb scales are required. Earlier experiments have shown this potential for the phytoseiid mite, Neoseiulus cucumeris, but only after the bulbs were exposed to ethylene, a plant hormone that causes a slight increase in the distance between tulip bulb scales, just sufficient to allow this predator to reach the interior part of the bulb. Applying ethylene, however, is not an option in practice because it causes malformation of tulip flowers. In fact, to prevent this cosmetic damage, bulb growers ventilate rooms where tulip bulbs are stored, thereby removing ethylene produced by the bulbs (e.g. in response to mite or fungus infestation). Recently, studies on the role of predatory mites in controlling another eriophyoid mite on coconuts led to the discovery of an exceptionally small phytoseiid mite, Neoseiulus paspalivorus. This predator is able to move under the perianth of coconuts where coconut mites feed on meristematic tissue of the fruit. This discovery prompted us to test N. paspalivorus for its ability to control A. tulipae on tulip bulbs under storage conditions (ventilated rooms with bulbs in open boxes; 23 °C; storage period June–October). Using destructive sampling we monitored predator and prey populations in two series of replicated experiments, one at a high initial level of dry bulb mite infestation, late in the storage period, and another at a low initial dry bulb mite infestation, halfway the storage period. The first and the second series involved treatment with N. paspalivorus and a control experiment, but the second series had an additional treatment in which the predator N. cucumeris was released. Taking the two series of experiments together we found that N. paspalivorus controlled the populations of dry bulb mites both on the outer scale of the bulbs as well as in the interior part of the bulbs, whereas N. cucumeris significantly reduced the population of dry bulb mites on the outer scale, but not in the interior part of the bulb. Moreover, N. paspalivorus was found predominantly inside the bulb, whereas N. cucumeris was only found on the outer scale, thereby confirming our hypothesis that the small size of N. paspalivorus facilitates access to the interior of the bulbs. We argue that N. paspalivorus is a promising candidate for the biological control of dry bulb mites on tulip bulbs under storage conditions in the Netherlands.     

Morphological plasticity in mangrove trees: salinity-related changes in the allometry of Avicennia germinans

Key Message

Morphological plasticity helps plants to cope to environmental conditions. Allometric responses of the mangrove Avicennia germinans to increasing salinity are easily detectable when focusing on the top height trees.

Abstract

Several studies show that mangrove trees possess high species- and site-related trait allometry, suggesting large morphological plasticity that might be related to environmental conditions, but the causes of such variation are not clearly understood and systematic quantification is still missing. Both aspects are essential for a mechanistic understanding of the development and functioning of forests. We analyzed the role of salinity in the allometric relations of the mangrove Avicennia germinans, using: (1) the top height trees (trees with the largest diameters at breast height, which reflect forest properties at the maximum use of resources); (2) the slenderness coefficient (which indicates competition and environmental conditions); and (3) the crown to DBH ratio. These standard tools for forest scientists dealing with terrestrial forests are suitable to analyze the plastic responses of mangroves to salinity. First, the top height trees help to recognize structural forest properties that are not detectable when studying the whole stand. Second, we found that at salinities above 55 ‰, trees are less slender and develop wider crowns in relation to DBH than when growing at lower salinities. Our results suggest a significant change in allometric traits in relation to salinity, and reflect the plastic responses of tree traits in response to environmental variation. Understanding the plastic responses of plants to their environment can help to better model, predict, and manage forests in changing environments.     

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

As the more recent next-generation sequencing (NGS) technologies provide longer read sequences, the use of sequencing datasets for complete haplotype phasing is fast becoming a reality, allowing haplotype reconstruction of a single sequenced genome. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. In this paper, we describe a novel maximum-likelihood estimation framework, HapTree, for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing technologies. For triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.     

Absence of Intestinal PPARγ Aggravates Acute Infectious Colitis in Mice through a Lipocalin-2–Dependent Pathway

To be able to colonize its host, invading Salmonella enterica serovar Typhimurium must disrupt and severely affect host-microbiome homeostasis. Here we report that S. Typhimurium induces acute infectious colitis by inhibiting peroxisome proliferator-activated receptor gamma (PPARγ) expression in intestinal epithelial cells. Interestingly, this PPARγ down-regulation by S. Typhimurium is independent of TLR-4 signaling but triggers a marked elevation of host innate immune response genes, including that encoding the antimicrobial peptide lipocalin-2 (Lcn2). Accumulation of Lcn2 stabilizes the metalloproteinase MMP-9 via extracellular binding, which further aggravates the colitis. Remarkably, when exposed to S. Typhimurium, Lcn2-null mice exhibited a drastic reduction of the colitis and remained protected even at later stages of infection. Our data suggest a mechanism in which S. Typhimurium hijacks the control of host immune response genes such as those encoding PPARγ and Lcn2 to acquire residence in a host, which by evolution has established a symbiotic relation with its microbiome community to prevent pathogen invasion.     

Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity

Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.     

Expression of the Arabidopsis vacuolar H+‐pyrophosphatase gene (AVP1) improves the shoot biomass of transgenic barley and increases grain yield in a saline field

Cereal varieties with improved salinity tolerance are needed to achieve profitable grain yields in saline soils. The expression of AVP1, an Arabidopsis gene encoding a vacuolar proton pumping pyrophosphatase (H⁺‐PPase), has been shown to improve the salinity tolerance of transgenic plants in greenhouse conditions. However, the potential for this gene to improve the grain yield of cereal crops in a saline field has yet to be evaluated. Recent advances in high‐throughput nondestructive phenotyping technologies also offer an opportunity to quantitatively evaluate the growth of transgenic plants under abiotic stress through time. In this study, the growth of transgenic barley expressing AVP1 was evaluated under saline conditions in a pot experiment using nondestructive plant imaging and in a saline field trial. Greenhouse‐grown transgenic barley expressing AVP1 produced a larger shoot biomass compared to null segregants, as determined by an increase in projected shoot area, when grown in soil with 150 mm NaCl. This increase in shoot biomass of transgenic AVP1 barley occurred from an early growth stage and also in nonsaline conditions. In a saline field, the transgenic barley expressing AVP1 also showed an increase in shoot biomass and, importantly, produced a greater grain yield per plant compared to wild‐type plants. Interestingly, the expression of AVP1 did not alter barley leaf sodium concentrations in either greenhouse‐ or field‐grown plants. This study validates our greenhouse‐based experiments and indicates that transgenic barley expressing AVP1 is a promising option for increasing cereal crop productivity in saline fields.     

Low Birth Weight in Perinatally HIV-Exposed Uninfected Infants: Observations in Urban Settings in Cameroon

Background

The consequences of maternal HIV infection for fetal growth are controversial. Here, we estimated the frequency of small for gestational age and gender (SGAG) among neonates born to HIV-infected or uninfected mothers and assessed the contribution, if any, of maternal HIV to the risk of SGAG.

Methods

The data used were obtained from the ANRS-Pediacam cohort in Cameroon. Pairs of newborns, one to a HIV-infected mother and the other to an uninfected mother, were identified during the first week of life, and matched on gender and recruitment site from 2007–2010. SGAG was defined in line with international recommendations as a birth weight Z-score adjusted for gestational age at delivery and gender more than two standard deviations below the mean (−2SD). Considering the matched design, logistic regression modeling was adjusted on site and gender to explore the effect of perinatal HIV exposure on SGAG.

Results

Among the 4104 mother-infant pairs originally enrolled, no data on birth weight and/or gestational age were available for 108; also, 259 were twins and were excluded. Of the remaining 3737 mother-infant pairs, the frequency of SGAG was 5.3% (95%CI: 4.6–6.0), and was significantly higher among HIV-infected infants (22.4% vs. 6.3%; p<.001) and lower among HIV-unexposed uninfected infants (3.5% vs. 6.3%; p<.001) than among HIV-exposed uninfected infants. Similarly, SGAG was significantly more frequent among HIV-infected infants (aOR: 4.1; 2.0–8.1) and less frequent among HIV-unexposed uninfected infants (aOR: 0.5; 0.4–0.8) than among HIV-exposed uninfected infants. Primiparity (aOR: 1.9; 1.3–2.7) and the presence of any disease during pregnancy (aOR: 1.4; 1.0–2.0) were identified as other contributors to SGAG.

Conclusion

Maternal HIV infection was independently associated with SGAG for HIV-exposed uninfected infants. This provides further evidence of the need for adapted monitoring of pregnancy in HIV-infected women, especially if they are symptomatic, to minimize additional risk factors for SGAG.     

Myeloid Mineralocorticoid Receptor Deficiency Inhibits Aortic Constriction-Induced Cardiac Hypertrophy in Mice

Mineralocorticoid receptor (MR) blockade has been shown to suppress cardiac hypertrophy and remodeling in animal models of pressure overload (POL). This study aims to determine whether MR deficiency in myeloid cells modulates aortic constriction-induced cardiovascular injuries. Myeloid MR knockout (MMRKO) mice and littermate control mice were subjected to abdominal aortic constriction (AAC) or sham operation. We found that AAC-induced cardiac hypertrophy and fibrosis were significantly attenuated in MMRKO mice. Expression of genes important in generating reactive oxygen species was decreased in MMRKO mice, while that of manganese superoxide dismutase increased. Furthermore, expression of genes important in cardiac metabolism was increased in MMRKO hearts. Macrophage infiltration in the heart was inhibited and expression of inflammatory genes was decreased in MMRKO mice. In addition, aortic fibrosis and inflammation were attenuated in MMRKO mice. Taken together, our data indicated that MR deficiency in myeloid cells effectively attenuated aortic constriction-induced cardiac hypertrophy and fibrosis, as well as aortic fibrosis and inflammation.