69 Works

Data from: Non-invasive monitoring of temporal and spatial blood flow during bone graft healing using diffuse correlation spectroscopy

Songfeng Han, Michael D. Hoffman, Ashley R. Proctor, Emmanuel A. Mannoh, Nathaniel E. Barber, Hyun Jin Kim, Ki Won Jung, Danielle S. W. Benoit, Regine Choe & Joseph B. Vella
Vascular infiltration and associated alterations in microvascular blood flow are critical for complete bone graft healing. Therefore, real-time, longitudinal measurement of blood flow has the potential to successfully predict graft healing outcomes. Herein, we non-invasively measure longitudinal blood flow changes in bone autografts and allografts using diffuse correlation spectroscopy in a murine femoral segmental defect model. Blood flow was measured at several positions proximal and distal to the graft site before implantation and every week...

Data from: Crop domestication facilitated rapid geographical expansion of a specialist pollinator, the squash bee Peponapis pruinosa

Margarita M. López-Uribe, James H. Cane, Robert L. Minckley & Bryan N. Danforth
Squash was first domesticated in Mexico and is now found throughout North America (NA) along with Peponapis pruinosa, a pollen specialist bee species of the squash genus Cucurbita. The origin and spread of squash cultivation is well-studied archaeologically and phylogenetically; however, no study has documented how cultivation of this or any other crop has influenced species in mutualistic interactions. We used molecular markers to reconstruct the demographic range expansion and colonization routes of P. pruinosa...

Data from: Impact of point-of-care ultrasound on clinical decision-making at an urban emergency department in Tanzania

Teri Reynolds, Stas S. Amato, Irene Kulola, Jeffrey C. Chuan-Jay, Juma Mfinanga, Hendry Sawe, Teri Ann Reynolds & Hendry Robert Sawe
Background: Point of care ultrasound (PoCUS) is an efficient, inexpensive, safe, and portable imaging modality that can be particularly useful in resource-limited settings. However, its impact on clinical decision making in such settings has not been well studied. The objective of this study is to describe the utilization and impact of PoCUS on clinical decision making at an urban emergency department in Dar es Salaam, Tanzania. Methods: This was a prospective descriptive cross-sectional study of...

Data from: Allele-specific transcriptome and methylome analysis reveals stable inheritance and cis-regulation of DNA methylation in Nasonia

Xu Wang, John H. Werren & Andrew G. Clark
Gene expression divergence between closely related species could be attributed to both cis- and trans- DNA sequence changes during evolution, but it is unclear how the evolutionary dynamics of epigenetic marks are regulated. In eutherian mammals, biparental DNA methylation marks are erased and reset during gametogenesis, resulting in paternal or maternal imprints which lead to genomic imprinting. Whether DNA methylation reprogramming exists in insects is not known. Wasps of the genus Nasonia are non-social parasitoids...

Data from: Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles

John Sproul, Lindsey Barton & David Maddison
Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome’s component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have...

Directed Evolution of AAV for Efficient Gene Delivery to Canine and Primate Retina - Raw counts of variants from deep sequencing

Leah Byrne, Timothy Day, Meike Visel, Deniz Dalkara, Valerie Dufour, Felipe Pompeo Marinho, William Merigan, Gustavo Aguirre, William Beltran, David Schaffer & John Flannery
Efficient AAV-mediated gene delivery remains a significant obstacle to effective retinal gene therapies. Here, we apply the process of directed evolution – guided by deep sequencing and followed by direct in vivo secondary selection of high-performing vectors with a GFP-barcoded library – to create AAV viral capsids with new capabilities to deliver genes to the outer retina in large animals. The resulting vectors resulted in efficient targeting of photoreceptors, bipolar cells, and RPE cells in...

Data from: Islands of retroelements are major components of Drosophila centromeres

Ching-Ho Chang, Ankita Chanvan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-Ting Wu, Amanda M. Larracuente & Barbara G Mellone
Centromeres are essential chromosomal regions that mediate kinetochore assembly and spindle attachments during cell division. Despite their functional conservation, centromeres are amongst the most rapidly evolving genomic regions and can shape karyotype evolution and speciation across taxa. Although significant progress has been made in identifying centromere-associated proteins, the highly repetitive centromeres of metazoans have been refractory to DNA sequencing and assembly, leaving large gaps in our understanding of their functional organization and evolution. Here, we...

Data from: Mapping of craniofacial traits in outbred mice identifies major developmental genes involved in shape determination

Luisa F. Pallares, Peter Carbonetto, Shyam Gopalakrishnan, Clarissa C. Parker, Cheryl L. Ackert-Bicknell, Abraham A. Palmer & Diethard Tautz
The vertebrate cranium is a prime example of the high evolvability of complex traits. While evidence of genes and developmental pathways underlying craniofacial shape determination is accumulating, we are still far from understanding how such variation at the genetic level is translated into craniofacial shape variation. Here we used 3D geometric morphometrics to map genes involved in shape determination in a population of outbred mice (Carworth Farms White, or CFW). We defined shape traits via...

Data from: What caused over a century of decline in general intelligence? Testing predictions from the genetic selection and neurotoxin hypotheses

Michael A. Woodley Of Menie, Matthew A. Sarraf, Mateo Peñaherrera-Aguirre, Heitor B.F. Fernandes & David Becker
Several converging lines of evidence indicate that general intelligence (g) has declined in Western populations. The causes of these declines are debated. Here, two hypotheses are tested: (1) selection acting against genetic variants that promote g causes the decline and (2) the presence of neurotoxic pollution in the environment causes the decline. A linear mixed model was devised to test (1) and (2), in which the secular decline in a “heritable g” (g.h) chronometric factor...

Data from: Macroevolutionary persistence of heritable endosymbionts: acquisition, retention, and expression of adaptive phenotypes in Spiroplasma

Tamara S. Haselkorn & John Jaenike
The phylogenetic incongruence between insects and their facultative maternally transmitted endosymbionts indicates that these infections are generally short-lived evolutionarily. Therefore, long-term persistence of many endosymbionts must depend on their ability to colonize and spread within new host species. At least 17 species of Drosophila are infected with endosymbiotic Spiroplasma that have various phenotypic effects. We transinfected five strains of Spiroplasma from three divergent clades into Drosophila neotestacea to test their capacity to spread in a...

Optimizing parameters for using the parallel auditory brainstem response (pABR) to quickly estimate hearing thresholds

Melissa Polonenko & Ross Maddox
Objectives: Timely assessments are critical to providing early intervention and better hearing and spoken language outcomes for children with hearing loss. To facilitate faster diagnostic hearing assessments in infants, the authors developed the parallel auditory brainstem response (pABR), which presents randomly timed trains of tone pips at five frequencies to each ear simultaneously. The pABR yields high-quality waveforms that are similar to the standard, single-frequency serial ABR but in a fraction of the recording time....

Constitutive model of erythrocyte membranes with distributions of spectrin orientations and lengths - pipette aspiration data and MatLab Code

Richard Waugh & Zhangli Peng
The speadsheet contains the original micropipette aspiration measurement of red blood cell membrane. There are five days of experiment each on its own tab, the first three of which are reported in the manuscript. The MatLab code used to generate theoretical predictions based on our new microstructurebased constitutive model are also included. This is the code used to generate least squared regression values for the material coefficients.

Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination

Xu Wang, Xiaozhu Wang, Xiao Xiong, Wenqi Cao, Chao Zhang & John Werren
Wolbachia are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced Wolbachia strains in the A, B, C, D, E and F supergroups. Phylogenomic analysis with these core genes indicate that all 33 Wolbachia strains maintain the supergroup relationship classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were...

Data from: Rapid evolution of asymmetric reproductive incompatibilities in stalk-eyed flies

Emily G. Rose, Cara L. Brand & Gerald S. Wilkinson
The steps by which isolated populations acquire reproductive incompatibilities remain poorly understood. One potentially important process is postcopulatory sexual selection because it can generate divergence between populations in traits that influence fertilization success after copulation. Here we present a comprehensive analysis of this form of reproductive isolation by conducting reciprocal crosses between variably diverged populations of stalk-eyed flies (Teleopsis dalmanni). First, we measure seven types of reproductive incompatibility between copulation and fertilization. We then compare...

Data from: Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella

Christopher A. Hamm, David J. Begun, Alexandre Vo, Chris C. R. Smith, Perot Saelao, Amanda O. Shaver, John Jaenike & Michael Turelli
Drosophila suzukii recently invaded North America and Europe. Populations in Hawaii, California, New York and Nova Scotia are polymorphic for Wolbachia, typically with <20% infection frequency. The Wolbachia in D. suzukii, denoted wSuz, is closely related to wRi, the variant prevalent in continental populations of D. simulans. wSuz is also nearly identical to Wolbachia found in D. subpulchrella, plausibly D. suzukii's sister species. This suggests vertical Wolbachia transmission through cladogenesis (“cladogenic transmission”). The widespread occurrence...

Data from: Cuticular hydrocarbon divergence in the jewel wasp Nasonia: evolutionary shifts in chemical communication channels?

Jan Buellesbach, Juergen Gadau, Leo W. Beukeboom, Felix Echinger, Rhitoban Raychoudhury, Jack H. Werren & Thomas Schmitt
The evolution and maintenance of intraspecific communication channels constitutes a key feature of chemical signaling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In the present study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyze their chemical divergence, and investigate their role as species-specific sexual signaling cues. Males and females of all four...

Data from: The genetic basis of behavioral isolation between Drosophila mauritiana and D. sechellia

Daniel R. McNabney
Understanding how species form is a fundamental question in evolutionary biology. Identifying the genetic bases of barriers that prevent gene flow between species provides insight into how speciation occurs. Here I analyze a poorly understood reproductive isolating barrier, prezygotic reproductive isolation. I perform a genetic analysis of prezygotic isolation between two closely related species of Drosophila, D. mauritiana and D. sechellia. I first confirm the existence of strong behavioral isolation between D. mauritiana females and...

Data from: Rhythmic motor behavior influences perception of visual time

Alice Tomassini, Tiziana Vercillo, Francesco Torricelli & Maria Concetta Morrone
Temporal processing is fundamental for an accurate synchronization between motor behavior and sensory processing. Here we investigate how motor timing during rhythmic tapping influences perception of visual time. Participants listen to a sequence of four auditory tones played at 1 Hz and continue the sequence (without auditory stimulation) by tapping four times with their finger. During finger tapping, they are presented with an empty visual interval and are asked to judge its length compared to...

Data from: All-optical recording and stimulation of retinal neurons in vivo in retinal degeneration mice

Soon Keen Cheong, Jennifer M. Strazzeri, David R. Williams & William H. Merigan
Here we demonstrate the application of a method that could accelerate the development of novel therapies by allowing direct and repeatable visualization of cellular function in the living eye, to study loss of vision in animal models of retinal disease, as well as evaluate the time course of retinal function following therapeutic intervention. We use high-resolution adaptive optics scanning light ophthalmoscopy to image fluorescence from the calcium sensor GCaMP6s. In mice with photoreceptor degeneration (rd10),...

Data from: Single molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

Daniel Emerson Khost, Danna G. Eickbush & Amanda M. Larracuente
Highly-repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses a challenge for genome assembly and makes progress on the detailed study of satDNA structure difficult. Here we use single-molecule sequencing long reads from Pacific Biosciences (PacBio) to determine the detailed structure of all major autosomal complex satDNA loci in Drosophila melanogaster, with a particular focus on...

Data from: Life-history strategy and behavioral type: risk-tolerance reflects growth rate and energy allocation in ant colonies

Sarah E. Bengston, Min Shin & Anna Dornhaus
Despite the recent interest in animal personality and behavioral syndromes, there is a paucity of explanations for why distinct behavioral traits should evolve to correlate. We investigate whether such correlations across apparently distinct behavioral traits may be explained by variation in life history strategy among individual ant colonies. Life history theory predicts that the way in which individuals allocate energy towards somatic maintenance or reproduction drives several distinct traits in physiology, morphology, and energy use;...

Data from: Hosts do not simply outsource pathogen resistance to protective symbionts

Jan Hrcek, Benjamin J. Parker, Ailsa H.C. McLean, Jean-Christophe Simon, Ciara M. Mann & H. Charles J. Godfray
Microbial symbionts commonly protect their hosts from natural enemies, but it is unclear how protective symbionts influence the evolution of host immunity to pathogens. One possibility is that ‘extrinsic’ protection provided by symbionts allows hosts to reduce investment in ‘intrinsic’ immunological resistance mechanisms. We tested this idea using pea aphids (Acyrthosiphon pisum) and their facultative bacterial symbionts that increase host resistance to the fungal pathogen Pandora neoaphidis. The pea aphid taxon is composed of multiple...

Data from: Correlates of decisional dynamics in the dorsal anterior cingulate cortex

Habiba Azab & Benjamin Y. Hayden
We hypothesized that during binary economic choice, decision makers use the first option they attend as a default to which they compare the second. To test this idea, we recorded activity of neurons in the dorsal anterior cingulate cortex (dACC) of macaques choosing between gambles presented asynchronously. We find that ensemble encoding of the value of the first offer includes both choice-dependent and choice-independent aspects, as if reflecting a partial decision. That is, its responses...

Exposing distinct subcortical components of the auditory brainstem response evoked by continuous naturalistic speech

Melissa J Polonenko & Ross K Maddox
Speech processing is built upon encoding by the auditory nerve and brainstem, yet we know very little about how these processes unfold in specific subcortical structures. These structures are deep and respond quickly, making them difficult to study during ongoing speech. Recent techniques begin to address this problem, but yield temporally broad responses with consequently ambiguous neural origins. Here we describe a method that pairs re-synthesized 'peaky' speech with deconvolution analysis of EEG recordings. We...

Data from: Adult MTM1-related myopathy carriers: classification based on deep phenotyping

Benjamin T. Cocanougher, Lauren Flynn, Pomi Yun, Minal Jain, Ruhi Vasavada, Jason Wittenbach, Sabine De Chastonay, Sameer Chhibber, A. Micheil Innes, Linda MacLaren, Tahseen Mozaffar, Andrew E. Arai, Sandra Donkervoort, Carsten G. Bönnemann & A. Reghan Foley
Objective To better characterize adult MTM1-related myopathy carriers and recommend a phenotypic classification. Methods This cohort study was performed at the National Institutes of Health Clinical Center. Participants were required to carry a confirmed MTM1 mutation and were recruited via the Congenital Muscle Disease International Registry (n=8), a traveling local clinic of the Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, NIH and Cure CMD (n=1) and direct physician referral (n=1). Neuromuscular examinations, muscle MRI,...

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