32 Works

Data from: Fine mapping quanitative trait loci affecting murine external ear tissue regeneration in the LG/J by SM/J advanced intercross line

Ellen Heber-Katz, James M. Cheverud, Heather A. Lawson, Kristine Bouckaert, Elizabeth P. Blankenhorn, Laura Cort, Andrew V. Kossenkov, Louise C. Showe, Khamilia Bedelbaeva, Dmitri Gourevitch & Yong Zhang
External ear hole closure in LG/J mice represents a model of regenerative response. It is accompanied by the formation of a blastema-like structure and the re-growth of multiple tissues including cartilage. The ability to regenerate tissue is heritable. An F34 advanced intercross line of mice (Wustl:LG,SM-G34) was generated to identify genomic loci involved in ear hole closure over a 30 day healing period. We mapped nineteen quantitative trait loci (QTL) for ear hole closure. Individual...

Data from: On the relationship between ontogenetic and static allometry

Christophe Pelabon, Geir Hysing Bolstad, Camilla Kalvatn Egset, James M. Cheverud, Mihaela Pavlicev & Gunilla Rosenqvist
Ontogenetic and static allometries describe how a character changes in size when the size of the organism changes during ontogeny and among individuals measured at the same developmental stage, respectively. Understanding the relationship between these two types of allometry is crucial to understanding the evolution of allometry and, more generally, the evolution of shape. However, the effects of ontogenetic allometry on static allometry remain largely unexplored. Here, we first show analytically how individual variation in...

Data from: Repetitive concussive traumatic brain injury interacts with post-injury foot shock stress to worsen social and depression-like behavior in mice

Kristen C. Klemenhagen, Scott P. O'Brien, David L. Brody & Scott P. O’Brien
The debilitating effects of repetitive concussive traumatic brain injury (rcTBI) have been increasingly recognized in both military and civilian populations. rcTBI may result in significant neurological, cognitive, and affective sequelae, and is often followed by physical and/or psychological post-injury stressors that may exacerbate the effects of the injury and prolong the recovery period for injured patients. However, the consequences of post-injury stressors and their subsequent effects on social and emotional behavior in the context of...

Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Minseung Choi, Diane P. Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger & Charles D. Laird
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity...

Supplemental Data for Cerebral Oxygen Metabolic Stress, Microstructural Injury, and Infarction in Adults With Sickle Cell Disease

Yan Wang, Slim Fellah, Melanie Fields, Kristin Guilliams, Michael Binkley, Cihat Eldeniz, Joshua Shimony, Martin Reis, Katie Vo, Yasheng Chen, Jin-Moo Lee, Hongyu An & Andria Ford
Supplemental data to manuscript

Data from: Cambrian origin of the CYP27C1-mediated vitamin A1-to-A2 switch, a key mechanism of vertebrate sensory plasticity

Ala Morshedian, Matthew B. Toomey, Gabriel E. Pollock, Rikard Frederiksen, Jennifer M. Enright, Stephen D. McCormick, M. Carter Cornwall, Gordon L. Fain & Joseph C. Corbo
The spectral composition of ambient light varies across both space and time. Many species of jawed vertebrates adapt to this variation by tuning the sensitivity of their photoreceptors via the expression of CYP27C1, an enzyme that converts vitamin A1 into vitamin A2, thereby shifting the ratio of vitamin A1-based rhodopsin to red-shifted vitamin A2-based porphyropsin in the eye. Here, we show that the sea lamprey (Petromyzon marinus), a jawless vertebrate that diverged from jawed vertebrates...

Data from: Echidna venom gland transcriptome provides insights into the evolution of monotreme venom

Emily S. W. Wong, Stewart Nichol, Wesley C. Warren, Katherine Belov & Stewart Nicol
Monotremes (echidna and platypus) are egg-laying mammals. One of their most unique characteristic is that males have venom/crural glands that are seasonally active. Male platypuses produce venom during the breeding season, delivered via spurs, to aid in competition against other males. Echidnas are not able to erect their spurs, but a milky secretion is produced by the gland during the breeding season. The function and molecular composition of echidna venom is as yet unknown. Hence,...

Data from: Bio-inspired imager improves sensitivity in near-infrared fluorescence image-guided surgery

Missael Garcia, Christopher Edmiston, Timothy York, Radoslav Marinov, Suman Mondal, Nan Zhu, Gail P. Sudlow, Walter J. Akers, Julie Margenthaler, Samuel Achilefu, Rongguang Liang, Mohamed A. Zayed, Marta Y. Pepino & Viktor Gruev
Image-guided surgery can enhance cancer treatment by decreasing, and ideally eliminating, positive tumor margins and iatrogenic damage to healthy tissue. Current state-of-the-art near-infrared fluorescence imaging systems are bulky and costly, lack sensitivity under surgical illumination, and lack co-registration accuracy between multimodal images. As a result, an overwhelming majority of physicians still rely on their unaided eyes and palpation as the primary sensing modalities for distinguishing cancerous from healthy tissue. Here we introduce an innovative design,...

Data from: Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis

Shiloh R. Lueschow, Jessica Stumphy, Huiyu Gong, Stacy L. Kern, Timothy G. Elgin, Mark A. Underwood, Karen M. Kalanetra, David A. Mills, Melissa H. Wong, David K. Meyerholz, Misty Good & Steven J. McElroy
Necrotizing enterocolitis (NEC) remains the leading cause of gastrointestinal morbidity and mortality in premature infants. Human and animal studies suggest a role for Paneth cells in NEC pathogenesis. Paneth cells play critical roles in host-microbial interactions and epithelial homeostasis. The ramifications of eliminating Paneth cell function on the immature host-microbial axis remains incomplete. Paneth cell function was depleted in the immature murine intestine using chemical and genetic models, which resulted in intestinal injury consistent with...

Data from: Rapid quantitative pharmacodynamic imaging by a novel method: theory, simulation testing and proof of principle

Kevin J. Black, Jonathan M. Koller, Bradley D. Miller & Brad D. Miller
Pharmacological challenge imaging has mapped, but rarely quantified, the sensitivity of a biological system to a given drug. We describe a novel method called rapid quantitative pharmacodynamic imaging. This method combines pharmacokinetic-pharmacodynamic modeling, repeated small doses of a challenge drug over a short time scale, and functional imaging to rapidly provide quantitative estimates of drug sensitivity including EC50 (the concentration of drug that produces half the maximum possible effect). We first test the method with...

Data from: Differential Expression Analysis for Pathways

Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins & Eugene Kolker
Life science technologies generate a deluge of data that hold the keys to unlocking the secrets of important biological functions and disease mechanisms. We present DEAP, Differential Expression Analysis for Pathways, which capitalizes on information about biological pathways to identify important regulatory patterns from differential expression data. DEAP makes significant improvements over existing approaches by including information about pathway structure and discovering the most differentially expressed portion of the pathway. On simulated data, DEAP significantly...

Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

Nathan P. McNulty, Wu Meng, Alison R. Erickson, Chongle Pan, Brian K. Erickson, Eric C. Martens, Nicholas A. Pudlo, Brian D. Muegge, Bernard Henrissat, Robert L. Hettich, Jeffrey I. Gordon & Meng Wu
The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed...

Data from: Expression of and choice for condition-dependent carotenoid-based color in an urbanizing context

Mathieu Giraudeau, Matthew B. Toomey, Pierce Hutton & Kevin J. McGraw
Urban environments create a unique suite of conditions, leading to changes in animal behavior, morphology, phenology or physiology. Condition-dependent traits such as the carotenoid-based coloration offer a unique opportunity to assess the impacts of urbanization on organisms because they reflect the nutrition, health or other resource-based attributes of their bearers and they play an essential role in intra- and inter-sex interactions. To determine if and how the carotenoid-based coloration of male house finches (Haemorhous mexicanus)...

Data from: Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth

Noah J. Mathis, Emily N. Adaniya, Lauren M. Smith, Alexander G. Robling, Karl J. Jepsen & Stephen H. Schlecht
Administration of sclerostin-neutralizing antibody (Scl-Ab) treatment has been shown to elicit an anabolic bone response in growing and adult mice. Prior work characterized the response of individual mouse strains but did not establish whether the impact of Scl-Ab on whole bone strength would vary across different inbred mouse strains. Herein, we tested the hypothesis that two inbred mouse strains (A/J and C57BL/6J (B6)) will show different whole bone strength outcomes following sclerostin-neutralizing antibody (Scl-Ab) treatment...

YAP and TAZ maintain PROX1 expression in the developing lymphatic and lymphovenous valves in response to VEGF-C signaling

Boksik Cha, Yen-Chun Ho, Xin Geng, , Lijuan Chen, Yeunhee Kim, Dongwon Choi, Tae Hoon Kim, Gwendalyn Randolph, Xinwei Cao, Hong Chen & R. Sathish Srinivasan
Lymphatic vasculature is an integral part of digestive, immune and circulatory systems. The homeobox transcription factor PROX1 is necessary for the development of lymphatic vessels, lymphatic valves (LVs) and lymphovenous valves (LVVs). We and others previously reported a feedback loop between PROX1 and Vascular Endothelial Growth Factor-C (VEGF-C) signaling. PROX1 promotes the expression of the VEGF-C receptor VEGFR3 in lymphatic endothelial cells (LECs). In turn, VEGF-C signaling maintains PROX1 expression in LECs. However, the mechanisms...

Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

Estienne C. Swart, John R. Bracht, Vincent Magrini, Patrick Minx, Xiao Chen, Yi Zhou, Jaspreet S. Khurana, Aaron D. Goldman, Mariusz Nowacki, Klaas Schotanus, Seolkyoung Jung, Robert S. Fulton, Amy Ly, Sean McGrath, Kevin Haub, Jessica L. Wiggins, Donna Storton, John C. Matese, Lance Parsons, Wei-Jen Chang, Michael S. Bowen, Nicholas A. Stover, Thomas A. Jones, Sean R. Eddy, Thomas G. Doak … & Laura F. Landweber
The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions,...

A genetic mechanism for sexual dichromatism in birds

Miguel Carneiro, Malgorzata Gazda, Pedro Araújo, Ricardo Lopes, Matthew Toomey, Pedro Andrade, Sandra Afonso, Cristiana Marques, Luís Nunes, Paulo Pereira, Sandra Trigo, Geofrey Hill & Joseph Corbo
Sexual dichromatism — a difference in coloration between males and females — is central to the study of ornamentation, mate choice, and sexual selection. Here, we show that carotenoid-based dichromatism in mosaic canaries, a hybrid product between the sexually dichromatic red siskin and monochromatic canaries, is controlled by the carotenoid-cleaving enzyme Beta-Carotene Oxygenase 2 (BCO2). Dichromatism in mosaic canaries is explained by differential carotenoid degradation in the integument of each sex, rather than sex-specific variation...

Data from: A liquid-like organelle at the root of motile ciliopathy

Ryan L. Huizar, Chanjae Lee, Alexander A. Boulgakov, Amjad Horani, Fan Tu, Edward M. Marcotte, Steven L. Brody & John B. Wallingford
Motile ciliopathies are characterized by specific defects in cilia beating that result in chronic airway disease, subfertility, ectopic pregnancy, and hydrocephalus. While many patients harbor mutations in the dynein motors that drive cilia beating, the disease also results from mutations in so-called Dynein Axonemal Assembly Factors (DNAAFs) that act in the cytoplasm. The mechanisms of DNAAF action remain poorly defined. Here, we show that DNAAFs concentrate together with axonemal dyneins and chaperones into organelles that...

Data from: Validation of diffusion tensor imaging measures of nigrostriatal neurons in macaques

Joshua S. Shimony, Jerrel Rutlin, Morvarid Karimi, Linlin Tian, Abraham Z. Snyder, Susan K. Loftin, Scott A. Norris & Joel S. Perlmutter
Objective: Interpretation of diffusion MRI in the living brain requires validation against gold standard histological measures. We compared diffusion values of the nigrostriatal tract to PET and histological results in non-human primates (NHPs) with varying degrees of unilateral nigrostriatal injury induced by MPTP, a toxin selective for dopaminergic neurons. Methods: Sixteen NHPs had MRI and PET scans of three different presynaptic radioligands and blinded video-based motor ratings before and after unilateral carotid artery infusion of...

Data from: A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch

Matthew B. Toomey, Cristiana I. Marques, Pedro Andrade, Pedro Miguel Araújo, Stephen Sabatino, Malgorzata A. Gazda, Sandra Afonso, Ricardo J. Lopes, Joseph C. Corbo & Miguel Carneiro
Discrete color morphs coexisting within a single population are common in nature. In a broad range of organisms, sympatric color morphs often display major differences in other traits, including morphology, physiology, or behavior. Despite the repeated occurrence of this phenomenon, our understanding of the genetics that underlie multi-trait differences and the factors that promote the long-term maintenance of phenotypic variability within a freely interbreeding population are incomplete. Here, we investigated the genetic basis of red...

Data from: High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds

Matthew B. Toomey, Ricardo J. Lopes, Pedro M. Araújo, James D. Johnson, Malgorzata A. Gazda, Sandra Afonso, Paulo G. Mota, Rebecca E. Koch, Geoffrey E. Hill, Joseph C. Corbo & Miguel Carneiro
Yellow, orange, and red coloration is a fundamental aspect of avian diversity and serves as an important signal in mate choice and aggressive interactions. This coloration is often produced through the deposition of diet-derived carotenoid pigments, yet the mechanisms of carotenoid uptake and transport are not well-understood. The white recessive breed of the common canary (Serinus canaria), which carries an autosomal recessive mutation that renders its plumage pure white, provides a unique opportunity to investigate...

Data from: Bacterial quorum sensing and metabolic incentives to cooperate

Ajai A. Dandekar, Sudha Chugani & E. Peter Greenberg
The opportunistic pathogen Pseudomonas aeruginosa uses a cell-cell communication system termed “quorum sensing” to control production of public goods, extracellular products that can be used by any community member. Not all individuals respond to quorum-sensing signals and synthesize public goods. Such social cheaters enjoy the benefits of the products secreted by cooperators. There are some P. aeruginosa cellular enzymes controlled by quorum sensing, and we show that quorum sensing–controlled expression of such private goods can...

Neurology paper \"Sequence of Alzheimer disease biomarker changes in cognitively normal adults: A cross-sectional study\" Table e-1

Jingqin Luo & Chengjie Xiong
Our Neurology 2020 paper titled "Sequence of Alzheimer disease biomarker changes in cognitively normal adults: A cross-sectional study" explores the cascades of changes of several well-known Alzheimer disease (AD) markers including cerebrow spinal fluid (CSF), imaging (PET-PIB and MRI) and cognitive markers in cognitively normal participants. The baseline marker data of participants is modeled as a piecewise linear function of baseline age allowing one change point, without and with adjustment for covariates. The change point...

Data from: Healing quantitative trait loci in a combined cross analysis using related mouse strain crosses

James M. Cheverud, Heather A. Lawson, Ryan Funk, Jia Zhou, Elizabeth P. Blankenhorn & Ellen Heber-Katz
Inbred mouse strains MRL and LG share the ability to fully heal ear hole punches with the full range of appropriate tissues without scarring. They also share a common ancestry, MRL being formed from a multi-strain cross with two final backcrosses to LG before being inbred by brother-sister mating. Many gene mapping studies for healing ability have been performed using these two strains, resulting in the location of about 20 quantitative trait loci (QTLs). Here,...

Data from: Genotype-dependent responses to levels of sibling competition over maternal resources in mice

Reinmar Hager, James M. Cheverud & Jason B. Wolf
Research on phenotypic plasticity has often focused on how a given genotype responds to changing physical environments. However, for many species the social environment plays an equally important role due to competition for resources. During early development, the level of competition for limited resources will often depend critically on the number of siblings. Therefore, competition among siblings should drive the evolution of genes that allow flexible responses to realized levels of competition and maternal resource...

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