A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

<p>Abstract</p> <p>Background</p> <p>As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models in other biological fields. Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution.</p> <p>Results</p> <p>We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket <it>Laupala kohalensis</it>. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web page</p> <p>Conclusion</p> <p>Orthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus <it>Laupala </it>have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic resources for three distinct but overlapping fields of inquiry: neurobiology, speciation, and molecular evolution.</p

Homeotic transformation induced by protein transduction

One of the most fundamental features of living organisms is that cells are separated from their external environment by a thin, but highly complex plasma membrane constituted of a lipid bilayer. Although, the lipid bilayer is only a few nanometers in width, it is impermeable to most molecules apart from small hydrophobic ones. The ability of small molecules to diffuse through a lipid bilayer is related to their lipid solubility. Hydrophilic macromolecular Antennapedia homeodomain peptide has been shown to be able to translocate from extracellular space into the cytoplasm of cells in a receptor-independent manner. Its third α-helix domain, designated as “Penetratin”, was proposed to be the functional transduction domain that is responsible for the translocation, and it is widely used for intracellular delivery of various exogenous proteins. Although Penetratin has been regarded to be the only element conferring the capacity of its parent polypeptide to penetrate through the plasma membrane, we found that the complete Antennapedia homeodomain exhibits an appreciably higher level of translocation efficiency as compared to Penetratin. Pharmacological analysis demonstrated that macropinocytic endocytosis plays a significant role underlying the process of the homeodomain internalization, and this is consistent with the observation that internalized polypeptide co-localizes with a fluid phase dye. Our studies identify macropinocytosis as a major mechanism by which Antennapedia homeodomain obtains the access to the interior of cells. In the process of macropinocytosis, signaling from the plasma membrane is required for actin remodeling to generate mechanical deformation forces; the interaction between positively charged Antennapedia homeodomain and negatively charged extracellular heparan sulfate could trigger the signaling cascade for fluid phase endocytosis. This would presumably explain why positively charged peptides, polymers, and liposomes are able to penetrate cells. As a fluid phase macropinocytosis provides cells with a way to non-selectively internalize large quantities of solute, it represents an effective means for drug delivery into cells. Both of “Penetratin” and Antennapedia homeodomain exploit macropinocytosis to a certain extent, the comparison between them may advance our understanding of the mechanisms triggering macropinocytotic endocytosis

Measuring enjoyment of physical activity in older adults: invariance of the physical activity enjoyment scale (paces) across groups and time

The purpose of this study was to validate the Physical Activity Enjoyment Scale (PACES) in a sample of older adults. Participants within two different exercise groups were assessed at two time points, 6 months apart. Group and longitudinal invariance was established for a novel, 8-item version of the PACES. The shortened, psychometrically sound measure provides researchers and practitioners an expedited and reliable instrument for assessing the enjoyment of physical activity

Methods for Evaluating the Content, Usability, and Efficacy of Commercial Mobile Health Apps

Commercial mobile apps for health behavior change are flourishing in the marketplace, but little evidence exists to support their use. This paper summarizes methods for evaluating the content, usability, and efficacy of commercially available health apps. Content analyses can be used to compare app features with clinical guidelines, evidence-based protocols, and behavior change techniques. Usability testing can establish how well an app functions and serves its intended purpose for a target population. Observational studies can explore the association between use and clinical and behavioral outcomes. Finally, efficacy testing can establish whether a commercial app impacts an outcome of interest via a variety of study designs, including randomized trials, multiphase optimization studies, and N-of-1 studies. Evidence in all these forms would increase adoption of commercial apps in clinical practice, inform the development of the next generation of apps, and ultimately increase the impact of commercial apps. Boudreaux, Rajani S Sadasivam, Sean P Mullen, Jennifer L Carey, Rashelle B Hayes, Eric Y Ding, Gary G Bennett, Sherry L Pagoto. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 18.12.2017

Ancient homology underlies adaptive mimetic diversity across butterflies

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time.We thank the governments of Ecuador, Costa Rica and the United States for permission to collect butterflies. In addition, we thank Larry Gilbert, Durrell Kapan, Ryan Hill, Kenny Kronforst and Nicholas Crawford for their assistance in collecting butterflies. The funding was provided by National Science Foundation awards to S. P. M., M. R. K. and R.D.R. (National Science Foundation

Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies.

The global increase in species richness toward the tropics across continents and taxonomic groups, referred to as the latitudinal diversity gradient, stimulated the formulation of many hypotheses to explain the underlying mechanisms of this pattern. We evaluate several of these hypotheses to explain spatial diversity patterns in a butterfly family, the Nymphalidae, by assessing the contributions of speciation, extinction, and dispersal, and also the extent to which these processes differ among regions at the same latitude. We generate a time-calibrated phylogeny containing 2,866 nymphalid species (~45% of extant diversity). Neither speciation nor extinction rate variations consistently explain the latitudinal diversity gradient among regions because temporal diversification dynamics differ greatly across longitude. The Neotropical diversity results from low extinction rates, not high speciation rates, and biotic interchanges with other regions are rare. Southeast Asia is also characterized by a low speciation rate but, unlike the Neotropics, is the main source of dispersal events through time. Our results suggest that global climate change throughout the Cenozoic, combined with tropical niche conservatism, played a major role in generating the modern latitudinal diversity gradient of nymphalid butterflies

Pasteurellaceae ComE1 Proteins Combine the Properties of Fibronectin Adhesins and DNA Binding Competence Proteins

A novel fibronectin-binding protein from Pasteurella multocida (PM1665) that binds to the fibronectin type III9-10 modules via two helix-hairpin-helix motifs has recently been described [1]. This protein shares homology with competence-related DNA-binding and uptake proteins (ComEA and ComE) from Gram-positive and Gram-negative bacteria. Here, we show that recombinant PM1665 (now designated ComE1) also binds to DNA through the same helix-hairpin-helix motifs required for fibronectin-binding. This binding to DNA is non sequence-specific and is confined to double-stranded DNA. We have cloned and expressed ComE1 proteins from five members of the Pasteurellaceae in order to further investigate the function(s) of these proteins. When expressed as recombinant GST-fusion proteins, all of the homologues bound both to fibronectin and to double-stranded DNA. Inactivation of the gene encoding the ComE1 homologue in Actinobacillus pleuropneumoniae indicates major roles for these proteins in at least two processes: natural transformation, and binding of bacteria to fibronectin

Importance of Achromatic Contrast in Short-Range Fruit Foraging of Primates

Trichromatic primates have a ‘red-green’ chromatic channel in addition to luminance and ‘blue-yellow’ channels. It has been argued that the red-green channel evolved in primates as an adaptation for detecting reddish or yellowish objects, such as ripe fruits, against a background of foliage. However, foraging advantages to trichromatic primates remain unverified by behavioral observation of primates in their natural habitats. New World monkeys (platyrrhines) are an excellent model for this evaluation because of the highly polymorphic nature of their color vision due to allelic variation of the L-M opsin gene on the X chromosome. In this study we carried out field observations of a group of wild, frugivorous black-handed spider monkeys (Ateles geoffroyi frontatus, Gray 1842, Platyrrhini), consisting of both dichromats (n = 12) and trichromats (n = 9) in Santa Rosa National Park, Costa Rica. We determined the color vision types of individuals in this group by genotyping their L-M opsin and measured foraging efficiency of each individual for fruits located at a grasping distance. Contrary to the predicted advantage for trichromats, there was no significant difference between dichromats and trichromats in foraging efficiency and we found that the luminance contrast was the main determinant of the variation of foraging efficiency among red-green, blue-yellow and luminance contrasts. Our results suggest that luminance contrast can serve as an important cue in short-range foraging attempts despite other sensory cues that could be available. Additionally, the advantage of red-green color vision in primates may not be as salient as previously thought and needs to be evaluated in further field observations

Imaging body-mind crosstalk in young adults

Objective There is evidence that complex relationships exist between motor functions, brain structure, and cognitive functions, particularly in the aging population. However, whether such relationships observed in older adults could extend to other age groups (e.g., younger adults) remains to be elucidated. Thus, the current study addressed this gap in the literature by investigating potential associations between motor functions, brain structure, and cognitive functions in a large cohort of young adults Methods In the current study, data from 910 participants (22–35 yr) were retrieved from the Human Connectome Project. Interactions between motor functions (i.e., cardiorespiratory fitness, gait speed, hand dexterity, and handgrip strength), brain structure (i.e., cortical thickness, surface area, and subcortical volumes), and cognitive functions were examined using linear mixed-effects models and mediation analyses. The performance of different machine-learning classifiers to discriminate young adults at three different levels (related to each motor function) was compared Results Cardiorespiratory fitness and hand dexterity were positively associated with fluid and crystallized intelligence in young adults, whereas gait speed and handgrip strength were correlated with specific measures of fluid intelligence (e.g., inhibitory control, flexibility, sustained attention, and spatial orientation; false discovery rate [FDR] corrected, p < 0.05). The relationships between cardiorespiratory fitness and domains of cognitive function were mediated by surface area and cortical volume in regions involved in the default mode, sensorimotor, and limbic networks (FDR corrected, p < 0.05). Associations between handgrip strength and fluid intelligence were mediated by surface area and volume in regions involved in the salience and limbic networks (FDR corrected, p < 0.05). Four machine-learning classifiers with feature importance ranking were built to discriminate young adults with different levels of cardiorespiratory fitness (random forest), gait speed, hand dexterity (support vector machine with the radial kernel), and handgrip strength (artificial neural network) Conclusions In summary, similar to observations in older adults, the current study provides empirical evidence (i) that motor functions in young adults are positively related to specific measures of cognitive functions, and (ii) that such relationships are at least partially mediated by distinct brain structures. Furthermore, our analyses suggest that machine-learning classifier has a promising potential to be used as a classification tool and decision support for identifying populations with below-average motor and cognitive functions