27 Works

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Clément Goubert, Jainy Thomas, Lindsay Payer, Jeffrey Kidd, Julie Feusier, W. Scott Watkins, Kathleen Burns, Lynn Jorde & Cédric Feschotte
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses...

Cell-autonomous light sensitivity via Opsin3 regulates fuel utilization in brown adipocytes

Mari Sato, Tadataka Tsuji, Kunyan Yang, Jonathan Dreyfuss, Tian Lian Huang, Chih-Hao Wang, Farnaz Shamsi, Luiz Leiria, Matthew Lynes, Yu-Hua Tseng, Xiaozhi Ren & King-Wai Yau
Opsin3 (Opn3) is a transmembrane heptahelical G-protein-coupled receptor (GPCR) with the potential to produce a non-visual photoreceptive effect. Interestingly, anatomical profiling of GPCRs reveals that Opn3 mRNA is highly expressed in adipose tissue. The photosensitive functions of Opn3 in mammals are poorly understood, and whether Opn3 has a role in fat is entirely unknown. In this study, we found that Opn3-knockout (Opn3-KO) mice were prone to diet-induced obesity and insulin-resistance. At the cellular level, Opn3-KO...

Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild

Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, Olga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, Shaikha Salem Al Dhaheri, David Wildt, Shireen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden & Klaus‐Peter Koepfli
Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (Oryx dammah) is a North African antelope that has...

What does it mean to be wild? Assessing human influence on the environments of nonhuman primate specimens in museum collections

Andrea Eller, Stephanie Canington, Sana Saiyed, Rita Austin, Courtney Hofman & Sabrina Sholts
Natural history collections are often thought to represent environments in a pristine natural state, free from human intervention – the so-called “wild”. In this study, we aim to assess the level of human influence represented by natural history collections of wild-collected primates over 120 years at the Smithsonian Institution’s National Museum of Natural History (NMNH). Our sample consisted of 875 catarrhine primate specimens in NMNH collections, representing 13 genera collected in 39 countries from 1882...

Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals

Siobhán B. Cooke, Liliana M. Dávalos, Alexis M. Mychajliw, Samuel T. Turvey & Nathan S. Upham
The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals...

Data from: Stroke patients with psychiatric comorbidities have lower carotid revascularization rates

Diana M. Bongiorno, Gail L. Daumit, Rebecca F. Gottesman & Roland Faigle
Objective: We investigated whether mental illness is associated with lower rates of CEA/CAS after stroke due to carotid stenosis. Methods: In this retrospective cross-sectional study, ischemic stroke cases due to carotid stenosis were identified in the 2007-2014 Nationwide (National) Inpatient Sample. Psychiatric conditions were identified by secondary ICD9-CM diagnosis codes for schizophrenia/psychoses, bipolar disorder, depression, anxiety, or substance use disorders. Using logistic regression, we tested the association between psychiatric conditions and CEA/CAS, controlling for demographic,...

Plant species fed on by wild ring-tailed lemurs (Lemur catta) at nine sites

Stephanie Canington
A key aspect of a primate’s ecology is its food source – the very nature of which is spatially and seasonally dependent, and may be affected by anthropic pressures. One of the most endangered, yet best-studied, strepsirrhine primates is the ring-tailed lemur (Lemur catta) – a species that has experienced significant human-induced habitat loss over many decades. To help understand feeding variability across time and space, I present a literature review of plant species (and...

Neurofilament light chain (NfL) as a biomarker of hereditary transthyretin-mediated amyloidosis

Paul Nioi, Simina Ticau, Gautham V. Sridharan, Shira Tsour, William L. Cantley, Amy Chan, Jason A. Gilbert, David Erbe, Emre Aldinc, Mary M. Reilly, David Adams, Michael Polydefkis, Kevin Fitzgerald & Akshay Vaishnaw
To identify changes in the proteome associated with onset and progression of ATTRv amyloidosis, we performed an observational, case-controlled study which compared proteomes of patients with ATTRv amyloidosis and healthy controls. Plasma levels of >1,000 proteins were measured in patients with ATTRv amyloidosis with polyneuropathy who received either placebo or patisiran in the APOLLO study and in healthy controls. The impact of patisiran on the time profile of each protein was determined by linear mixed...

Data from: Myelin basic protein induces neuron-specific toxicity by directly damaging the neuronal plasma membrane

Jie Zhang, Xin Sun, Sixin Zheng, Xiao Liu, Jinghua Jin, Yi Ren & Jianhong Luo
The central nervous system (CNS) insults may cause massive demyelination and lead to the release of myelin-associated proteins including its major component myelin basic protein (MBP). MBP is reported to induce glial activation but its effect on neurons is still little known. Here we found that MBP specifically bound to the extracellular surface of the neuronal plasma membrane and induced neurotoxicity in vitro. This effect of MBP on neurons was basicity-dependent because the binding was...

High-density 3-D coordinate data of avian and non-avian dinosaur endocasts

Akinobu Watanabe, Amy Balanoff, Paul Gignac, M. Eugenia Gold & Mark Norell
How do large and unique brains evolve? Historically, comparative neuroanatomical studies have attributed the evolutionary genesis of highly encephalized brains to deviations along, as well as from, conserved scaling relationships among brain regions. However, the relative contributions of these concerted (integrated) and mosaic (modular) processes as drivers of brain evolution remain unclear, especially in non-mammalian groups. While proportional brain sizes have been the predominant metric used to characterize brain morphology to date, we perform a...

Data from: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa

Lin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, V. Gaurav Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski … & Frans P. M. Cremers
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post...

Data from: Safety and immunogenicity of the Na-GST-1 hookworm vaccine in Brazilian and American adults

Amar Jariwala, Anna Yakovleva, Carlos Geraldo Fraga, David J. Diemert, Doreen Campbell, Frederico Talles, Guangzhao Li, Janaína Freire, Jeffrey Bethony, Jill Brelsford, Jin Peng, Maria Flávia Gazzinelli, Maria Victoria Periago, Maria Elena Bottazzi, Martin Enk, Peter Hotez, Robert Hamilton, Rodrigo Correa-Oliveira, Shannon Grahek & Vanderson Valente
Necator americanus Glutathione-S-Transferase-1 (Na-GST-1) plays a role in the digestion of host hemoglobin by adult N. americanus hookworms. Vaccination of laboratory animals with recombinant Na-GST-1 is associated with significant protection from challenge infection. Recombinant Na-GST-1 was expressed in Pichia pastoris and adsorbed to aluminum hydroxide adjuvant (Alhydrogel) according to current Good Manufacturing Practice. Two Phase 1 trials were conducted in 142 healthy adult volunteers in the United States and Brazil, first in hookworm-naïve individuals and...

Data from: Long-lasting vocal plasticity in adult marmoset monkeys

Lingyun Zhao, Bahar Boroumand Rad & Xiaoqin Wang
Humans exhibit a high level of vocal plasticity in speech production which allows us to acquire both native and foreign languages, dialects and adapt to local accents in social communication. In comparison, non-human primates exhibit limited vocal plasticity, especially in adulthood, which would limit their ability to adapt to different social and environmental contexts in vocal communication. Here we quantitatively examined the ability of adult common marmosets (Callithrix jacchus), a highly vocal New World primate...

Data from: Lysine-14 acetylation of histone H3 in chromatin confers resistance to the deacetylase and demethylase activities of an epigenetic silencing complex

Mingxuan Wu, Dawn Hayward, Jay H. Kalin, Yun Song, John W.R. Schwabe, Philip A. Cole & John WR Schwabe
The core CoREST complex (LHC) contains histone deacetylase HDAC1 and histone demethylase LSD1 held together by the scaffold protein CoREST. Here we analyze the purified LHC with modified peptide and reconstituted semisynthetic mononucleosome substrates. LHC demethylase activity toward methyl-Lys4 in histone H3 is strongly inhibited by H3 Lys14 acetylation, and this appears to be an intrinsic property of the LSD1 subunit. Moreover, the deacetylase selectivity of LHC unexpectedly shows a marked preference for H3 acetyl-Lys9...

Data from: Neural correlates of domain-specific cognitive decline: the ARIC-NCS study

Andrea Lauren Christman Schneider, Matthew L Senjem, Aozhou Wu, Alden Gross, David S. Knopman, Jeffrey L Gunter, Christopher G Schwarz, Tom H. Mosley, Rebecca F. Gottesman, A. Richey Sharrett & Clifford R. Jack
Objective: To evaluate the association of cognitive declines in the domains of memory, language, and executive function with brain gray matter (GM) volume in old age. Methods: Prospective study of 1,846 participants in the Atherosclerosis Risk in Communities (ARIC) study who underwent 3T brain MRI scans in 2011-2013. Participants were categorized by cognitive domain performance trajectory over the prior 20 years (cut-point to define decline: 20th percentile). Associations between GM volume and cognitive declines were...

Data from: High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo

Guanghan Meng, Yajie Liang, Sarah Sarsfield, Wan-Chen Jiang, Rongwen Lu, Joshua Tate Dudman, Yeka Aponte & Na Ji
Optical imaging has become a powerful tool for studying brains in vivo. The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning...

Data from: Assessment of lung function in successfully treated Tuberculosis reveals high burden of ventilatory defects and COPD

Akshay Gupte
Background: Burden, phenotype and risk-factors of lung function defects in successfully treated tuberculosis cases are unclear. Methods: We performed spirometry with bronchodilators in new drug-sensitive adult (>18 years) pulmonary tuberculosis cases during the 12 months following successful treatment in India. Airflow obstruction was defined as pre-bronchodilator FEV1/FVC<5th percentile of Global Lung Initiative mixed-ethnicity reference (lower limit of normal [LLN]). Chronic obstructive pulmonary disease (COPD) was defined as post-bronchodilator FEV1/FVC Methods: We performed spirometry with bronchodilators...

Data from: HIV testing in a South African emergency department: a missed opportunity

Bhakti Hansoti, David Stead, Andy Parrish, Steven J. Reynolds, Andrew D. Redd, Madeleine M. Whalen, Nomzamo Mvandaba & Thomas C. Quinn
Background: South Africa (SA) has the highest burden of HIV infection in the world. Even though HIV testing is mandated in all hospital-based facilities in SA, it is rarely implemented in the emergency department (ED). EDs are episodic care centers that provide care to large volumes of undifferentiated patients for short periods of time, and may treat undiagnosed HIV-infected patients not captured through standard clinic based screenings. Methods and Findings: In this prospective study, we...

Data from: An enigmatic new ungulate-like mammal from the early Eocene of India

Shawn Zack, Kenneth Rose, Luke Holbrook, Kishor Kumar, Rajendra Rana & Thierry Smith
We report on a new genus and species of herbivorous mammal, Pahelia mysteriosa, from the early Eocene Cambay Shale Formation, Tadkeshwar Lignite Mine, Gujarat, India. The new taxon, approximately the size of a small phenacodontid (e.g., Ectocion parvus), is represented by three mandibular fragments, the most complete of which documents nearly the entire symphysis and mandibular body plus P3-M3. Pahelia has incipiently selenolophodont molars with strong exodaenodonty, absent paraconids, weak but distinct entolophids, and prominent...

Glucose transporter expression and regulation following a fast in the ruby-throated hummingbird, Archilochus colubris

Raafay Syed Ali, Morag F. Dick, Saad Muhammad, Dylan Sarver, Lily Hou, G. William Wong & Kenneth C. Welch
Hummingbirds, subsisting almost exclusively on nectar sugar, face extreme challenges to blood sugar regulation. The capacity for transmembrane sugar transport is mediated by the activity of facilitative glucose transporters (GLUTs) and their localisation to the plasma membrane (PM). In this study, we determined the relative protein abundance of GLUT1, GLUT2, GLUT3, and GLUT5 via immunoblot using custom antibodies in whole-tissue and PM fractions of flight-muscle, heart, and liver of ruby-throated hummingbirds (Archilochus colubris). GLUTs examined...

Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi

Gaik Tamazian, Pavel Dobrynin, Anna Zhuk, Daria Zhernakova, Polina Perelman, Natalia Serdyukova, Alexander Graphodatsky, Aleksey Komissarov, Sergei Kliver, Nikolay Cherkasov, Alan Scott, David Mohr, Klaus-Peter Koepfli, Stephen O'Brien & Ksenia Krasheninnikova
The Puma lineage within the family Felidae consists of three species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of two species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome...

Large mitochondrial DNA deletions in HIV sensory neuropathy

Ricardo Roda, David Bargiela, Weiran Chen, Ken Perry, Ronald J. Ellis, David B. Clifford, Ajay Bharti, Asha Kallianpur, Michelli F Oliveira, Monica M. Diaz, Leah H. Rubin, Christina Gavegnano, Justin C. McArthur, Ahmet Hoke & Michael Polydefkis
Objective: The primary objective of this study was to evaluate the correlation of large mitochondrial DNA deletions in skin samples of people with HIV with measure of neuropathy and prior exposure to therapy. We hypothesized that deletions would be associated with the presence of neuropathy. As secondary objectives we determined the correlation of deletion burden with demographic data and neuropathy measures. Methods: In this retrospective cohort study we measured the accumulation of large mtDNA deletions...

Data from: The tetrapod fauna of the upper Permian Naobaogou Formation of China: a new species of Elginia (Parareptilia, Pareiasauria)

Jun Liu & Gabriel S. Bever
The pareiasaur fossil record in China is poor compared to that of Russia or South Africa. A new pareiasaur specimen is here reported from the upper Permian Naobaogou Formation of the Daqing Mountains, Nei Mongol, China. It is recognized as a new species of Elginia, a taxon otherwise known only from the upper Permian Cutties Hillock Sandstone of Scotland. Diagnostic features include a moderately developed cheek flange; prominent otic notch (formed between squamosal and quadratojugal...

Data from: ATN profiles among cognitively normal individuals and longitudinal cognitive outcomes

Anja Soldan, Corinne Pettigrew, Anne M. Fagan, Suzanne E. Schindler, Abhay Moghekar, Christopher Fowler, Qiao-Xin Li, Steven J. Collins, Cynthia M. Carlsson, Sanjay Asthana, Colin L. Masters, Sterling Johnson, John C. Morris, Marilyn Albert & Alden L. Gross
Objective. The amyloid/tau/neurodegeneration (ATN) research framework for Alzheimer’s disease (AD) was proposed to organize AD biomarkers and to stage AD across its preclinical and symptomatic phases. Applying this framework requires a large number of participants since the framework envisions eight biomarker profiles. This study examined the long-term cognitive trajectories of individuals with normal cognition at baseline and distinct ATN profiles. Methods. Pooling data across four cohort studies, 814 cognitively normal participants (mean baseline age=59·6 years)...

Data from: Autoimmune encephalitis: a costly condition

Jesse Cohen, Javier Sotoca, Shikha Gandhi, Anusha K. Yeshokumar, Eliza Gordon-Lipkin, Romergryko G. Geocadin, Kevin D. Frick, John C. Probasco & Arun Venkatesan
Objective: To assess the inpatient hospitalization burden and costs of patients with autoimmune encephalitis (AE) at a tertiary care institution. Methods: Adult inpatients with AE were identified retrospectively from July 1, 2005 – June 30, 2015. Demographic and clinical data were collected and analyzed. Billing data were compared to that of patients with herpes simplex encephalitis (HSE). Charges were adjusted for inflation. Results: Of 244 admissions for encephalitis reviewed, 63 patients met criteria for probable...

Registration Year

  • 2021
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Resource Types

  • Dataset
    27

Affiliations

  • Johns Hopkins University School of Medicine
    27
  • University of California, San Diego
    2
  • National Institutes of Health
    2
  • Harvard Medical School
    2
  • Institute of Vertebrate Paleontology and Paleoanthropology
    1
  • Emory University School of Medicine
    1
  • Howard Hughes Medical Institute
    1
  • Zhejiang University
    1
  • Stanford University
    1
  • National Institute on Drug Abuse
    1