Acquiring nutrients from tree leaves: effects of leaf maturity and development type on a generalist caterpillar

The rapid growth and prolific reproduction of many insect herbivores depend on the efficiencies and rates with which they acquire nutrients from their host plants. However, little is known about how nutrient assimilation efficiencies are affected by leaf maturation or how they vary between plant species. Recent work showed that leaf maturation can greatly decrease the protein assimilation efficiency (PAE) of Lymantria dispar caterpillars on some tree species, but not on species in the willow family (Salicaceae). One trait of many species in the Salicaceae that potentially affects PAE is the continuous (or “indeterminate”) development of leaves throughout the growing season. To improve our understanding of the temporal and developmental patterns of nutrient availability for tree-feeding insects, this study tested two hypotheses: nutrients (protein and carbohydrate) are more efficiently assimilated from immature than mature leaves, and, following leaf maturation, nutrients are more efficiently assimilated from indeterminate than determinate tree species. The nutritional physiology and growth of a generalist caterpillar (L. dispar) were measured on five determinate and five indeterminate tree species while their leaves were immature and again after they were mature. In support of the first hypothesis, caterpillars that fed on immature leaves had significantly higher PAE and carbohydrate assimilation efficiency (CAE), as well as higher protein assimilation rates and growth rates, than larvae that fed on mature leaves. Contrary to the second hypothesis, caterpillars that fed on mature indeterminate tree leaves did not have higher PAE than those that fed on mature determinate leaves, while CAE differed by only 3% between tree development types. Instead, “high-PAE” and “low-PAE” tree species were found across taxonomic and development categories. The results of this study emphasize the importance of physiological mechanisms, such as nutrient assimilation efficiency, to explain the large variation in host plant quality for insect herbivores.     

Telephone genetic counseling for high-risk women undergoing BRCA1 and BRCA2 testing: rationale and development of a randomized controlled trial

Genetic counseling and testing, particularly for adult onset conditions, has become increasingly available over the last decade, and it is expected that this trend will continue as additional genes are identified and as such testing diffuses into mainstream clinical care. To meet the increased demand for services, it will become necessary to explore alternative avenues to traditional face-to-face genetic counseling. One such modality is the use of telephone genetic counseling (TGC), which is easy to implement and still allows for comprehensive service delivery. Although TGC has been used with increased frequency, there is a paucity of data about its effectiveness and impact on important patient outcomes. This paper provides an overview of the evolution of telephone counseling in nongenetics and genetics settings. The rationale and aims of the largest randomized clinical trial to be performed with this mode of counseling in the context of cancer susceptibility testing for mutations in the BRCA1 and BRCA2 genes are also explained. In addition, procedural aspects of the genetic counseling intervention and the novel tools developed to facilitate this process and to ensure adequate counselor training and quality assurance are described.     

Model-based Analysis of ChIP-Seq (MACS)

We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.     

Sensorimotor gating: startle submits to presynaptic inhibition

Prepulse inhibition is a type of sensorimotor gating that is disrupted in some neuropsychiatric disorders. Its cellular basis has eluded investigators but now, using a molluscan model system, a cellular mechanism has been established.     

Neuropeptidomic analysis of the brain and thoracic ganglion from the Jonah crab,Cancer borealis

Mass spectrometric methods were applied to determine the peptidome of the brain and thoracic ganglion of the Jonah crab (Cancer borealis). Fractions obtained by high performance liquid chromatography were characterized using MALDI-TOF MS and ESI-Q-TOF MS/MS. In total, 28 peptides were identified within the molecular mass range 750-3000Da. Comparison of the molecular masses obtained with MALDI-TOF MS with the calculated molecular masses of known crustacean peptides revealed the presence of at least nine allatostatins, three orcokinin precursor derived peptides, namely FDAFTTGFGHS, [Ala(13)]-orcokinin, and [Val(13)]-orcokinin, and two kinins, a tachykinin-related peptide and four FMRFamide-related peptides. Eight other peptides were de novo sequenced by collision induced dissociation on the Q-TOF system and yielded AYNRSFLRFamide, PELDHVFLRFamide or EPLDHVFLRFamide, APQRNFLRFamide, LNPFLRFamide, DVRTPALRLRFamide, and LRNLRFamide, which belong to the FMRFamide related peptide family, as well as NFDEIDRSGFA and NFDEIDRSSFGFV, which display high sequence similarity to peptide sequences within the orcokinin precursor of Orconectes limosus. Our paper is the first (neuro)peptidomic analysis of the crustacean nervous system.     

The Relationship between Mental and Somatic Practices and Wisdom

In this study we sought to explore how experience with specific mental and somatic practices is associated with wisdom, using self-report measures of experience and wisdom. We administered standard surveys to measure wisdom and experience among four groups of practitioners of mental and somatic practices, namely, meditators, practitioners of the Alexander Technique, practitioners of the Feldenkrais Method, and classical ballet dancers. We additionally administered surveys of trait anxiety and empathy to all participants to explore possible mediating relationships of experience and wisdom by characteristics thought to be components of wisdom. Wisdom was higher on average among meditation practitioners, and lowest among ballet dancers, and this difference held when controlling for differences in age between practices, supporting the view that meditation is linked to wisdom and that ballet is not. However, we found that increased experience with meditation and ballet were both positively associated with wisdom, and that lowered trait anxiety mediated this positive association among meditation practitioners, and, non-significantly, among ballet dancers. These results suggest that not all practices that are purported to affect mental processing are related to wisdom to the same degree and different kinds of experience appear to relate to wisdom in different ways, suggesting different mechanisms that might underlie the development of wisdom with experience.     

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes

Background

Bacterial viruses (phages) play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage.

Methodology/Principal Findings

To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles), and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL) or of a whole genome shotgun library (WGSL), or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling.

Conclusions/Significance

These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.     

The Absorption Hypothesis: Learning to Hear God in Evangelical Christianity

ABSTRACT  In this article, we use a combination of ethnographic data and empirical methods to identify a process called "absorption," which may be involved in contemporary Christian evangelical prayer practice (and in the practices of other religions). The ethnographer worked with an interdisciplinary team to identify people with a proclivity for "absorption." Those who seemed to have this proclivity were more likely to report sharper mental images, greater focus, and more unusual spiritual experience. The more they prayed, the more likely they were to have these experiences and to embrace fully the local representation of God. Our results emphasize learning, a social process to which individuals respond in variable ways, and they suggest that interpretation, proclivity, and practice are all important in understanding religious experience. This approach builds on but differs from the approach to religion within the culture-and-cognition school.