pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis

Single molecule Förster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additional documentation including tutorials is hosted independently on ReadTheDocs. The code is available from the free hosting site Bitbucket. Through distribution of this software, we hope to lower the barrier for the adoption of smFRET experiments by other research groups and we encourage others to contribute modules for specific analysis needs

The discerning predator: decision rules underlying prey classification by a mosquito eating jumping spider

Evarcha culicivora is an East African jumping spider that feeds indirectly on vertebrate blood by choosing blood-fed female Anopheles mosquitoes as prey. Previous studies have shown that this predator can identify its preferred prey even when restricted to using only visual cues. Here, we used lures and virtual mosquitoes to investigate the optical cues underlying this predator's prey-choice behaviour. We made lures by dissecting and then reconstructing dead mosquitoes, combining the head plus thorax with different abdomens. Depending on the experiment, lures were either moving or motionless. Findings from the lure experiments suggested that, for E. culicivora, seeing a blood-fed female mosquito's abdomen on a lure was a necessary, but not sufficient, cue by which preferred prey was identified, as cues from the abdomen needed to be paired with cues from the head and thorax of a mosquito. Conversely, when abdomens were not visible or were identical, spiders based their decisions on the appearance of the head plus thorax of mosquitoes, choosing prey with female characteristics. Findings from a subsequent experiment using animated 3D virtual mosquitoes suggest that it is specifically the mosquito's antennae that influence E. culicivora's prey-choice decisions. Our results show that E. culicivora uses a complex process for prey classification. © 2012. Published by The Company of Biologists Ltd

Aggregation effects in mimicry

Many predators are averse to attacking ants and many palatable arthropods are Batesian mimics of ants. We considered whether aggregating Batesian mimics of ants can become more repelling to ant-averse predators by, as a group, resembling groups of ants (collective mimicry). Myrmarachne melanotarsa is a gregarious ant-like jumping spider (Salticidae) that resembles and associates with the ant Crematogaster sp. We used three large ant-averse salticids as predators in experiments. Besides M. melanotarsa and Crematogaster we used midges (Chaoborus sp.) and a small nonant-like, but gregarious, salticid (Menemerus sp.) as prey. The predators readily attacked both live midges and the nonant-like salticids that were presented singly or in groups but rarely attacked ants or ant mimics. Predators attacked ants and ant mimics presented in groups less often than they attacked solitary ants and ant mimics. In another experiment, motionless lures (groups of arthropods mounted in lifelike posture) were used. The findings showed that, independent of prey behaviour and movement, the predators were averse to being in close proximity to groups of ants and ant mimics, but had no evident aversion to the close proximity of groups of nonant-like salticids. Palatability tests demonstrated that the predators fed for long periods on M. melanotarsa, Menemerus and Chaoborus, but released Crematogaster almost immediately. Our results suggest that these predators have an innate aversion to ants and ant mimics and also that they are innately predisposed to perceive a group of ants (or ant mimics) as more repelling than solitary ants or ant mimics. © 2009 The Association for the Study of Animal Behaviour

Compound mimicry

Sexual dimorphism is pronounced in Myrmarachne, a large genus of ant-like jumping spiders (Salticidae) and one of the major animal groups in which Batesian mimicry of ants has evolved. Although adult females and juveniles of both sexes are distinctly ant-like in appearance, Myrmarachne males have elongated chelicerae that might appear to detract from their resemblance to ants. Experimental findings suggest that the Myrmarachne male's solution is to adopt compound mimicry (i.e. the male's model seems to be not simply an ant worker but a combination of an ant and something carried in the ant's mandibles: an 'encumbered ant'). By becoming a mimic of a particular subset of worker ants, Myrmarachne males may have retained their Batesian-mimicry defence against ant-averse predators, but at the price of receiving the unwanted attention of predators for which encumbered ants are preferred prey. Two salticid species were used as predators in the experiments. Portia fimbriata is known to choose other salticids as preferred prey and to avoid unencumbered ants and their mimics (Myrmarachne females). In experiments reported here, P. fimbriata avoided encumbered ants and Myrmarachne males. Ants are the preferred prey of Chalcotropis gulosus. In our experiments, C. gulosus chose safer encumbered ants in preference to more dangerous unencumbered ants, chose Myrmarachne males more often than Myrmarachne females and showed no evidence of distinguishing between Myrmarachne males and encumbered ants. The cost of reconciling sexual dimorphism with Batesian mimicry appears to be that Myrmarachne males attract the unwanted attention of specialist predators of their compound model. © 2005 The Royal Society

Spatial and Seasonal Distribution of American Whaling and Whales in the Age of Sail

American whalemen sailed out of ports on the east coast of the United States and in California from the 18th to early 20th centuries, searching for whales throughout the world’s oceans. From an initial focus on sperm whales (Physeter macrocephalus) and right whales (Eubalaena spp.), the array of targeted whales expanded to include bowhead whales (Balaena mysticetus), humpback whales (Megaptera novaeangliae), and gray whales (Eschrichtius robustus). Extensive records of American whaling in the form of daily entries in whaling voyage logbooks contain a great deal of information about where and when the whalemen found whales. We plotted daily locations where the several species of whales were observed, both those caught and those sighted but not caught, on world maps to illustrate the spatial and temporal distribution of both American whaling activity and the whales. The patterns shown on the maps provide the basis for various inferences concerning the historical distribution of the target whales prior to and during this episode of global whaling

Predator Mimicry: Metalmark Moths Mimic Their Jumping Spider Predators

Cases of mimicry provide many of the nature's most convincing examples of natural selection. Here we report evidence for a case of predator mimicry in which metalmark moths in the genus Brenthia mimic jumping spiders, one of their predators. In controlled trials, Brenthia had higher survival rates than other similarly sized moths in the presence of jumping spiders and jumping spiders responded to Brenthia with territorial displays, indicating that Brenthia were sometimes mistaken for jumping spiders, and not recognized as prey. Our experimental results and a review of wing patterns of other insects indicate that jumping spider mimicry is more widespread than heretofore appreciated, and that jumping spiders are probably an important selective pressure shaping the evolution of diurnal insects that perch on vegetation

Primate modularity and evolution: first anatomical network analysis of primate head and neck musculoskeletal system

Network theory is increasingly being used to study morphological modularity and integration. Anatomical network analysis (AnNA) is a framework for quantitatively characterizing the topological organization of anatomical structures and providing an operational way to compare structural integration and modularity. Here we apply AnNA for the first time to study the macroevolution of the musculoskeletal system of the head and neck in primates and their closest living relatives, paying special attention to the evolution of structures associated with facial and vocal communication. We show that well-defined left and right facial modules are plesiomorphic for primates, while anthropoids consistently have asymmetrical facial modules that include structures of both sides, a change likely related to the ability to display more complex, asymmetrical facial expressions. However, no clear trends in network organization were found regarding the evolution of structures related to speech. Remarkably, the increase in the number of head and neck muscles – and thus of musculoskeletal structures – in human evolution led to a decrease in network density and complexity in humans

An Anti-Human ICAM-1 Antibody Inhibits Rhinovirus-Induced Exacerbations of Lung Inflammation

Human rhinoviruses (HRV) cause the majority of common colds and acute exacerbations of asthma and chronic obstructive pulmonary disease (COPD). Effective therapies are urgently needed, but no licensed treatments or vaccines currently exist. Of the 100 identified serotypes, ∼90% bind domain 1 of human intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, making this an attractive target for development of therapies; however, ICAM-1 domain 1 is also required for host defence and regulation of cell trafficking, principally via its major ligand LFA-1. Using a mouse anti-human ICAM-1 antibody (14C11) that specifically binds domain 1 of human ICAM-1, we show that 14C11 administered topically or systemically prevented entry of two major groups of rhinoviruses, HRV16 and HRV14, and reduced cellular inflammation, pro-inflammatory cytokine induction and virus load in vivo. 14C11 also reduced cellular inflammation and Th2 cytokine/chemokine production in a model of major group HRV-induced asthma exacerbation. Interestingly, 14C11 did not prevent cell adhesion via human ICAM-1/LFA-1 interactions in vitro, suggesting the epitope targeted by 14C11 was specific for viral entry. Thus a human ICAM-1 domain-1-specific antibody can prevent major group HRV entry and induction of airway inflammation in vivo

Ownership-dependent mating tactics of minor males of the beetle Librodor japonicus (Nitidulidae) with intra-sexual dimorphism of mandibles

Intra-sexual dimorphism is found in the weapons of many male beetles. Different behavioral tactics to access females between major and minor males, which adopt fighting and alternative tactics, respectively, are thought to maintain the male dimorphism. In these species major males have enlarged weapons that they use in fights with rival males. Minor males also have small weapons in some of these species, and it is unclear why these males possess weapons. We examined the hypothesis that minor males might adopt a fighting tactic when their status was relatively high in comparison with that of other males (e.g., ownership of a territory). We observed the behavioral tactics of major and minor males of the beetle Librodor japonicus, whose males have a dimorphism of their mandibles. Major males fought for resources, whereas minor males adopted two status-dependent tactics, fighting and sneaking, to access females, depending on their ownership of a sap site. We suggest that ownership status-dependent mating tactics in minor males may maintain the intra-sexual dimorphism in this beetle.</p

Pediatric Cushing disease: disparities in disease severity and outcomes in the Hispanic and African-American populations.

BackgroundLittle is known about the contribution of racial and socioeconomic disparities to severity and outcomes in children with Cushing disease (CD).MethodsA total of 129 children with CD, 45 Hispanic/Latino or African-American (HI/AA) and 84 non-Hispanic White (non-HW), were included in this study. A 10-point index for rating severity (CD severity) incorporated the degree of hypercortisolemia, glucose tolerance, hypertension, anthropomorphic measurements, disease duration, and tumor characteristics. Race, ethnicity, age, gender, local obesity prevalence, estimated median income, and access to care were assessed in regression analyses of CD severity.ResultsThe mean CD severity in the HI/AA group was worse than that in the non-HW group (4.9±2.0 vs. 4.1±1.9, P=0.023); driving factors included higher cortisol levels and larger tumor size. Multiple regression models confirmed that race (P=0.027) and older age (P=0.014) were the most important predictors of worse CD severity. When followed up a median of 2.3 years after surgery, the relative risk for persistent CD combined with recurrence was 2.8 times higher in the HI/AA group compared with that in the non-HW group (95% confidence interval: 1.2-6.5).ConclusionOur data show that the driving forces for the discrepancy in severity of CD are older age and race/ethnicity. Importantly, the risk for persistent and recurrent CD was higher in minority children