104 Works

Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

Rebecca Cheek, Brenna Forrester, Daryl Trumbo, Patricia Salerno, Nancy Chen, T. Scott Sillett, Scott Morrison, Cameron Ghalambor & W. Chris Funk
We present evidence for and investigate potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over...

Neural processing and perception of Schroeder‐phase harmonic tone complexes in the gerbil: Relating single‐unit neurophysiology to behavior

Friederike Steenken, Henning Oetjen, Rainer Beutelmann, Laurel H. Carney, Christine Koeppl & Georg M. Klump
Schroeder-phase harmonic tone complexes have been used in physiological and psychophysical studies in several species to gain insight into cochlear function. Each pitch period of the Schroeder stimulus contains a linear frequency sweep; the duty cycle, sweep velocity, and direction are controlled by parameters of the phase spectrum. Here, responses to a range of Schroeder-phase harmonic tone complexes were studied both behaviorally and in neural recordings from the auditory nerve and inferior colliculus of Mongolian...

Additional file 1 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 1: Fig. S1. Conditions for bulk RNA. Fig. S2. Improved performance of SHERRY2 on bulk RNA. Fig. S3. Conditions for single cells. Fig. S4. Accuracy of SHERRY2 for single cells. Fig. S5. Flow cytometry gating of single lymphocytes and single GC B cells. Fig. S6. DNase activity and performance in SHERRY2 library construction. Fig. S7. GC information gained from SHERRY2. Fig. S8. BCR sequences of single GC B cells identified by SHERRY2. Fig....

Additional file 3 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 3: Table S2.Comparison of SHERRY and SHERRY2 performances on bulk RNA. (recording data values of Additional file 1: Fig. S2).

Additional file 3 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 3: Table S2.Comparison of SHERRY and SHERRY2 performances on bulk RNA. (recording data values of Additional file 1: Fig. S2).

Data from: Anolis sex chromosomes are derived from a single ancestral pair

Tony Gamble, Anthony J. Geneva, Richard E. Glor & David Zarkower
To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis we compared the relative roles of sex chromosome conservation vs. turnover of sex determining mechanisms. We used model based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable...

Data from: Cis- and trans-acting genetic factors contribute to heterogeneity in the rate of crossing over between the Drosophila simulans clade species

M. Victoria Cattani, Sarah B. Kingan & Daven C. Presgraves
In the genus Drosophila, variation in recombination rates has been found within and between species. Genetic variation for both cis- and trans-acting factors has been shown to affect recombination rates within species, but little is known about the genetic factors that affect differences between species. Here we estimate rates of crossing over for seven segments that tile across the euchromatic length of the X chromosome in the genetic backgrounds of three closely related Drosophila species....

Data from: Maintenance of a male-killing Wolbachia in Drosophila innubila by male-killing dependent and male-killing independent mechanisms

Robert L. Unckless & John Jaenike
Many maternally inherited endosymbionts manipulate their host’s reproduction in various ways to enhance their own fitness. One such mechanism is male-killing, in which sons of infected mothers are killed by the endosymbiont during development. Several hypotheses have been proposed to explain the advantages of male-killing, including resource reallocation from sons to daughters of infected females, avoidance of inbreeding by infected females, and, if transmission is not purely maternal, the facilitation of horizontal transmission to uninfected...

Data from: Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group)

Anthony J. Geneva, Jared Hilton, Sabina Noll & Richard E. Glor
The distichus species group includes six species and 21 subspecies of trunk ecomorph anoles distributed across Hispaniola and its satellite islands as well as the northern Bahamas. Although this group has long served as a model system for studies of reproductive character displacement, adaptation, behavior and speciation, it has never been the subject of a comprehensive phylogenetic analysis. Our goal here is to generate a multilocus phylogenetic dataset (one mitochondrial and seven nuclear loci) and...

Data from: A new method to scan genomes for introgression in a secondary contact model

Anthony J. Geneva, Christina A. Muirhead, Sarah B. Kingan & Daniel Garrigan
Secondary contact between divergent populations or incipient species may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model. Gmin is defined as the ratio of the minimum between-population number of nucleotide differences in a genomic window to the average number of between-population differences. Although it is conceptually simple, one advantage of Gmin...

Data from: The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive

Amanda M. Larracuente
Background: Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster....

Data from: Electrophysiological correlates of semantic dissimilarity reflect the comprehension of natural, narrative speech

Michael P. Broderick, Andrew J. Anderson, Giovanni M. Di Liberto, Michael J. Crosse & Edmund C. Lalor
People routinely hear and understand speech at rates of 120–200 words per minute [1, 2]. Thus, speech comprehension must involve rapid, online neural mechanisms that process words’ meanings in an approximately time-locked fashion. However, in the context of continuous speech, electrophysiological evidence for such time-locked processing has been lacking. Whilst valuable insights into the semantic processing of speech have been provided by the “N400 component” of the event-related potential [3-6], this literature has been dominated...

Data from: Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

Colin D. Meiklejohn, Emily L. Landeen, Kathleen E. Gordon, Thomas Rzatkiewicz, Sarah B. Kingan, Anthony J. Geneva, Jeffrey P. Vedanayagam, Christina A. Muirhead, Daniel Garrigan, David L. Stern & Daven C. Presgraves
During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow...

Data from: Age and sex differences in burnout, career satisfaction, and well-being in US neurologists

Kathrin LaFaver, Janis M. Miyasaki, Christopher M. Keran, Carol Rheaume, Lisa Gulya, Kerry H. Levin, Elaine C. Jones, Heidi B. Schwarz, Jennifer R. Molano, Amy Hessler, Divya Singhal, Tait D. Shanafelt, Jeff A. Sloan, Paul J. Novotny, Terrence L. Cascino & Neil A. Busis
Objective: To examine age and sex differences in burnout, career satisfaction, and well-being in US neurologists. Methods: Quantitative and qualitative analyses of men’s (n = 1,091) and women’s (n = 580) responses to a 2016 survey of US neurologists. Results: Emotional exhaustion in neurologists initially increased with age, then started to decrease as neurologists got older. Depersonalization decreased as neurologists got older. Fatigue and overall quality of life in neurologists initially worsened with age, then...

Endothelial glycocalyx layer properties and its ability to limit leukocyte adhesion

Luis Delgadillo
The endothelial glycocalyx layer (EGL), consisting of long proteoglycans protruding from the endothelium, acts as a regulator of inflammation by preventing leukocyte engagement with adhesion molecules on the endothelial surface. The amount of resistance to adhesive events the EGL provides is the result of two properties: EGL thickness and stiffness. To determine these, we used an atomic force microscope to indent the surfaces of cultured endothelial cells with a glass bead and evaluated two different...

The lexical and grammatical sources of neg-raising inferences

Hannah Y. An & Aaron S. White

PRISM-HD: Patient-Reported Impact of Symptoms in Huntington Disease

Alistair M Glidden, Elizabeth A Luebbe, Molly J Elson, Steven B Goldenthal, Christopher W Snyder, Christine E Zizzi, E Ray Dorsey & Chad R Heatwole
OBJECTIVE: To determine the frequency and relative importance of symptoms experienced by adults with Huntington disease (HD) and to identify factors associated with a higher disease burden. METHODS: We performed 40 qualitative interviews (n = 20 with HD, n = 20 caregivers) and analyzed 2,082 quotes regarding the symptomatic burden of HD. We subsequently performed a cross-sectional study with 389 participants (n = 156 with HD [60 of whom were prodromal], n = 233 caregivers)...

Perceptual restoration fails to recover unconscious processing for smooth eye movements after occipital stroke

Sunwoo Kwon, Jude Mitchell & Krystel Huxlin
Visual pathways that guide actions do not necessarily mediate conscious perception. Patients with primary visual cortex (V1) damage lose conscious perception but often retain unconscious abilities (e.g. blindsight). Here, we asked if saccade accuracy and post-saccadic following responses (PFRs) that automatically track target motion upon saccade landing are retained when conscious perception is lost. We contrasted these behaviors in the blind and intact fields of 8 chronic V1-stroke patients, and in 8 visually-intact controls. Saccade...

Clumped-isotope constraint on upper-tropospheric cooling during the Last Glacial Maximum

Asmita Banerjee, Laurence Yeung, Lee Murray, Xin Tie, Jessica Tierney & Allegra LeGrande
Ice cores and other paleotemperature proxies, together with general circulation models, have provided information on past surface temperatures and the atmosphere’s composition in different climates. Little is known, however, about past temperatures at high altitudes, which play a crucial role in Earth’s radiative energy budget. Paleoclimate records at high-altitude sites are sparse, and the few that are available show poor agreement with climate model predictions. These disagreements could be due to insufficient spatial coverage, spatiotemporal...

Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

Ching-Ho Chang, Lauren Gregory, Kathleen Gordon, Colin Meiklejohn & Amanda Larracuente
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological...

Additional file 1 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 1: Fig. S1. Conditions for bulk RNA. Fig. S2. Improved performance of SHERRY2 on bulk RNA. Fig. S3. Conditions for single cells. Fig. S4. Accuracy of SHERRY2 for single cells. Fig. S5. Flow cytometry gating of single lymphocytes and single GC B cells. Fig. S6. DNase activity and performance in SHERRY2 library construction. Fig. S7. GC information gained from SHERRY2. Fig. S8. BCR sequences of single GC B cells identified by SHERRY2. Fig....

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

Data from: The Caenorhabditis elegans Myc-Mondo/Mad complexes integrate diverse longevity signals

David W. Johnson, Jesse R. Llop, Sara F. Farrell, Jie Yuan, Lindsay R. Stolzenburg & Andrew Vaughn Samuelson
The Myc family of transcription factors regulates a variety of biological processes, including the cell cycle, growth, proliferation, metabolism, and apoptosis. In Caenorhabditis elegans, the “Myc interaction network” consists of two opposing heterodimeric complexes with antagonistic functions in transcriptional control: the Myc-Mondo:Mlx transcriptional activation complex and the Mad:Max transcriptional repression complex. In C. elegans, Mondo, Mlx, Mad, and Max are encoded by mml-1, mxl-2, mdl-1, and mxl-1, respectively. Here we show a similar antagonistic role...

Data from: Using genomic data to revisit a classic example of reproductive character displacement in Haitian Anolis lizards

Shea M. Lambert, Anthony J. Geneva, D. Luke Mahler & Richard E. Glor
The pattern of reproductive character displacement (RCD)—in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation—is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies of RCD to include molecular genetic data was described 40 years ago in a complex of Haitian trunk...

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