Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.

Back to basics: how measures of lexical diversity can help discriminate between CEFR levels

This study contributes to ongoing discussions on how measures of lexical diversity (LD) can help discriminate between essays from second language learners of English, whose work has been assessed as belonging to levels B1 to C2 of the Common European Framework of Reference (CEFR). The focus is in particular on how different operationalisations of what constitutes a “different word” (type) impact on the LD measures themselves and on their ability to discriminate between CEFR levels. The results show that basic measures of LD, such as the number of different words, the TTR (Templin 1957) and the Index of Guiraud (Guiraud 1954) explain more variance in the CEFR levels than sophisticated measures, such as D (Malvern et al. 2004), HD-D (McCarthy and Jarvis 2007) and MTLD (McCarthy 2005) provided text length is kept constant across texts. A simple count of different words (defined as lemma’s and not as word families) was the best predictor of CEFR levels and explained 22 percent of the variance in overall scores on the Pearson Test of English Academic in essays written by 176 test takers.

Schatten class Toeplitz operators on generalized Fock spaces

In this paper we characterize the Schatten p class membership of Toeplitz operators with positive measure symbols acting on generalized Fock spaces for the full range p>0.

Attention bias to emotional faces varies by IQ and anxiety in Williams syndrome

Individuals with Williams syndrome (WS) often experience significant anxiety. A promising approach to anxiety intervention has emerged from cognitive studies of attention bias to threat. To investigate the utility of this intervention in WS, this study examined attention bias to happy and angry faces in individuals with WS (N=46). Results showed a significant difference in attention bias patterns as a function of IQ and anxiety. Individuals with higher IQ or higher anxiety showed a significant bias toward angry, but not happy faces, whereas individuals with lower IQ or lower anxiety showed the opposite pattern. These results suggest that attention bias interventions to modify a threat bias may be most effectively targeted to anxious individuals with WS with relatively high IQ.

Knowledge of basic concepts in deaf/hard of hearing children

Basic concept knowledge of children who were deaf/hard of hearing was tested using the Bracken Basic Concept Scale: 3rd Edition. These children were given both the receptive and expressive portions of the test. Results indicate delays in overall basic concept knowledge in children who are deaf compared to their normal-hearing peers.

Non-steroidal anti-inflammatory drugs may modulate the protease activity of Candida albicans

The phenotypic pressure exerted by non-steroidal anti-inflammatory drugs (NSAIDs) on autochthonous and pathogenic microbiota remains sparsely known. In this study, we investigated if some NSAIDs increment or diminish the secretion of aspartyl-proteases (Sap) by Candida albicans grown under different phenotypes and oxygen availability using a set of SAP knock-out mutants and other set for genes (EFG1 and CPH1) that codify transcription factors involved in filamentation and protease secretion. Preconditioned cells were grown under planktonic and biofilm phenotypes, in normoxia and anoxia, in the presence of plasma concentrations of acetylsalicylic acid, diclofenac, indomethacin, nimesulide, piroxicam, ibuprofen, and acetaminophen. For diclofenac, indomethacin, nimesulide, and piroxicam the secretion rates of Sap by SAP1-6, EFG1. and CPH1 mutants were similar or, even, inferior to parental wildtype strain. This suggests that neither Sap 1-6 isoenzymes nor Efg1/Cph1 pathways may be entirely responsible for protease release when exposed to these NSAIDs. Ibuprofen and acetaminophen enhanced Sap secretion rates in three environmental conditions (normoxic biofilm, normoxic planktonic and anoxic planktonic). In other hand, aspirin seems to reduce the Sap-related pathogenic behavior of candidal biofilms. Modulation of Sap activity may occur according to candidal phenotypic state, oxygen availability, and type of NSAID to which the cells are exposed. (C) 2010 Elsevier Ltd. All rights reserved.

Detailed molecular characterization of cord blood-derived endothelial progenitors

Objective. Given their involvement in pathological and physiological angiogenesis, there has been growing interest in understanding and manipulating endothellial progenitor cells (EPC) for therapeutic purposes. However, detailed molecular analysis of EPC before and during endothelial differentiation is lacking and is the subject of the present study. Materials and Methods. We report a detailed microarray gene-expression profile of freshly isolated (day 0) human cord blood (CB)-derived EPC (CD133(+)KDR(+) or CD34(+)KDR(+)), and at different time points during in vitro differentiation (early: day 13; late: day 27). Results. Data obtained reflect an EPC transcriptome enriched in genes related to stem/progenitor cells properties (chromatin remodeling, self-renewal, signaling, cytoskeleton organization and biogenesis, recruitment, and adhesion). Using a complementary DNA microarray enriched in intronic transcribed sequences, we observed, as well, that naturally transcribed intronic noncoding RNAs were specifically expressed at the EPC stage. Conclusion. Taken together, we have defined the global gene-expression profile of CB-derived EPC during the process of endothelial differentiation, which can be used to identify genes involved in different vascular pathologies. (C) 2008 ISEH - Society for Hematology and Stem Cells. Published by Elsevier Inc.

Cell-cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris

RpfG is a paradigm for a class of widespread bacterial two-component regulators with a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. In the plant pathogen Xanthomonas campestris pv. campestris (Xcc), a two-component system comprising RpfG and the complex sensor kinase RpfC is implicated in sensing and responding to the diffusible signaling factor (DSF), which is essential for cell-cell signaling. RpfF is involved in synthesizing DSF, and mutations of rpfF, rpfG, or rpfC lead to a coordinate reduction in the synthesis of virulence factors such as extracellular enzymes, biofilm structure, and motility. Using yeast two-hybrid analysis and fluorescence resonance energy transfer experiments in Xcc, we show that the physical interaction of RpfG with two proteins with diguanylate cyclase (GGDEF) domains controls a subset of RpfG-regulated virulence functions. RpfG interactions were abolished by alanine substitutions of the three residues of the conserved GYP motif in the HD-GYP domain. Changing the GYP motif or deletion of the two GGDEF-domain proteins reduced Xcc motility but not the synthesis of extracellular enzymes or biofilm formation. RpfG-GGDEF interactions are dynamic and depend on DSF signaling, being reduced in the rpfF mutant but restored by DSF addition. The results are consistent with a model in which DSF signal transduction controlling motility depends on a highly regulated, dynamic interaction of proteins that influence the localized expression of cyclic di-GMP.

Terror Management Theory and Belief in an Afterlife

Research has shown that belief in an afterlife, a form of symbolic immortality, can alleviate the negative emotions associated with one’s mortality (Deschesne et. al, 2003). We found this aspect of TMT particularly interesting, but lacking any substantial research. Therefore, we set out to determine if belief in an afterlife could diminish the effects of mortality salience. As far as we know, our study is the first to use a pre-screening process to determine participants’ prior beliefs. One prediction might be that those who believe in an afterlife will be less affected by the effects of mortality salience.

Differential Habituation of Male Betta Splendens to Qualitatively Different Stimuli

Habituation is a learning mechanism that functions to decrease the amount of energy and attention focused on a certain stimuli. Male Siamese Fighting Fish, Betta splendens, are territorial animals that defend their territories using a number of aggressive displays. Male Bettas have previously shown the ability to habituate to the presence of a conspecific male when visually exposed to each other. Due to the costly nature of many of the male Betta’s displays, I hypothesized that male Bettas should differentially habituate to qualitatively different stimuli. I presented each of three groups of male Betta splendens with a different stimulus, each presenting a different level of interactivity. I predicted that the Bettas would be more likely to habituate to a less interactive stimulus than a more interactive one. No significant habituation was observed in any of the groups and no significant differences in latency to display or length of display between all three groups were observed. However, overall data trends suggest that habituation was indeed occurring and that the three different stimuli elicited different levels of display. The limited amount of visual exposure to the stimuli in this experiment might account for why results were insignificant.

The role of TaABF1 in abscisic acid-mediated suppression of -amylase gene expression in cereal grains

The phytohormones gibberellin (GA) and abscisic acid (ABA) regulate important developments events in germinating seeds. Specifically, GA induces the expression of hyrolase genes, like the α-amylase gene Amy32b, which mobilizes starch reserves to be used by the embryo, and ABA suppresses this induction. Recent advancements identified ABA and GA receptors and key components in the signaling pathways, however, the mechanism of crosstalk between the hormones remains largely unknown. To further elucidate the mechanism of ABA suppression of GA-induced genes, we focused on the transcription factor TaABF1, a member of the ABA response element binding factor family. TaABF1 has been shown to physically interact with the SnRK2 kinase PKABA1 and overexpression of TaABF1 or PKABA1 can suppress Amy32b. We carried out particle bombardment experiments to investigate how TaABF1 suppresses Amy32b and how TaABF1 is activated by ABA. The role of TaABF1 in ABA-mediated suppression of Amy32b is more complicated than hypothesized. Unlike PKABA1, overexpression of TaABF1 did not cause a decrease of GAMyb expression and in fact resulted in an increase of GAMyb expression. When TaABF1 and GAMyb were simultaneously overexpressed in aleurone, the GAMyb induction of Amy32b was unaffected, indicating that the target of TaABF1 action must be upstream of GAMyb. Furthermore, TaABF1 and ABA demonstrated an additive effect on the suppression of Amy32b. Based on our findings, we propose a model in which PKABA1 activates two separate targets, one being TaABF1 which then modifies an unknown target upstream of GAMyb and the other being an unknown transcription factor that suppresses GAMyb transcription.