186 results match your criteria underpinned phenotype

Formulation of a decision support tool incorporating both genetic and non-genetic effects to rank young growing cattle on expected market value.

Animal 2021 Feb 18;15(2):100077. Epub 2020 Dec 18.

Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland. Electronic address:

While breeding indexes exist globally to identify candidate parents of the next generation, fewer tools exist that provide guidance on the expected monetary value of young animals. The objective of the present study was therefore to develop the framework for a cattle decision-support tool which incorporates both the genetic and non-genetic information of an animal and, in doing so, better predict the potential market value of an animal, whatever the age. Two novel monetary indexes were constructed and their predictive ability of carcass value was compared to that of the Irish national Terminal breeding index, typical of other terminal indexes used globally. Read More

View Article and Full-Text PDF
February 2021

Dirty Fish Versus Squeaky Clean Mice: Dissecting Interspecies Differences Between Animal Models of Interferonopathy.

Front Immunol 2020 15;11:623650. Epub 2021 Jan 15.

The Bateson Centre, Institute of Neuroscience, Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom.

Autoimmune and autoinflammatory diseases are rare but often devastating disorders, underpinned by abnormal immune function. While some autoimmune disorders are thought to be triggered by a burden of infection throughout life, others are thought to be genetic in origin. Among these heritable disorders are the type I interferonopathies, including the rare Mendelian childhood-onset encephalitis Aicardi-Goutières syndrome. Read More

View Article and Full-Text PDF
January 2021

A Genetics-First Approach to Dissecting the Heterogeneity of Autism: Phenotypic Comparison of Autism Risk Copy Number Variants.

Am J Psychiatry 2021 01;178(1):77-86

MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom (Chawner, Doherty, Anney, Moss, Hall, Owen, van den Bree); Cardiff University Centre for Human Developmental Science, School of Psychology, Cardiff University, Cardiff, United Kingdom (Chawner); Department of Psychology, Syracuse University, Syracuse, N.Y. (Antshel); Department of Psychiatry and Behavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (Bearden, Kushan); Departments of Psychiatry and Behavioral Sciences, University of Washington, Seattle (Bernier); Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York (Chung); Center for Autism Research, Children's Hospital of Philadelphia (Clements, Miller, Schultz); Department of Psychology, University of Pennsylvania, Philadelphia (Clements); South West London and St. George's Mental Health National Health Service Foundation Trust, London (Curran); University Children's Hospital, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Serbia (Cuturilo); Department of Psychiatry, Brain Center, University Medical Center Utrecht, the Netherlands (Fiksinski, Vorstman); Clinical Genetics Research Program, Centre for Addiction and Mental Health, and the Dalglish Family 22q Clinic for 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network, Toronto (Fiksinski); Department of Psychiatry, Trinity College Dublin, Ireland (Gallagher); Department of Pediatrics, Baylor College of Medicine, Houston (Goin-Kochel); Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia (Gur); Department of Psychiatry, Neurodevelopment and Psychosis Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Gur); Department of Child and Adolescent Psychiatry, Children's Hospital of Philadelphia (Gur, Schultz); Developmental Medicine, Children's Hospital Boston/Harvard Medical School, Boston (Hanson); Department of Pediatrics, University of Montreal (Jacquemont, Maillard); Centre de recherche, Centre Hospitalier Universitaire Sainte Justine, Montreal (Jacquemont); Department of Psychiatry and Behavioral Sciences, State University of New York at Upstate Medical University, Syracuse (Kates); Service des Troubles du Spectre de l'Autisme et Apparentés, Lausanne University Hospital, Lausanne, Switzerland (Maillard); Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia (McDonald-McGinn); 22q and You Center, Children's Hospital of Philadelphia (McDonald-McGinn); Department of Pediatrics, University of Pennsylvania, Philadelphia (McDonald-McGinn, Schultz); Clinic for Psychiatry, Clinical Center of Serbia, Faculty of Medicine, University of Belgrade, Serbia (Mihaljevic); Institute of Mental Health, Belgrade, Serbia, Faculty of Medicine, University of Belgrade, Serbia (Pejovic-Milovancevic); Simons Foundation, New York (Green-Snyder); Program in Genetics and Genome Biology, SickKids Research Institute, Toronto (Vorstman); Department of Psychiatry, Hospital for Sick Children, University of Toronto (Vorstman); Department of Pediatrics, Seattle Children's Hospital, Seattle (Wenger); and Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom (Hall, Owen, van den Bree).

Objective: Certain copy number variants (CNVs) greatly increase the risk of autism. The authors conducted a genetics-first study to investigate whether heterogeneity in the clinical presentation of autism is underpinned by specific genotype-phenotype relationships.

Methods: This international study included 547 individuals (mean age, 12. Read More

View Article and Full-Text PDF
January 2021

Elevated Circulatory Levels of Microparticles Are Associated to Lung Fibrosis and Vasculopathy During Systemic Sclerosis.

Front Immunol 2020 23;11:532177. Epub 2020 Oct 23.

University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, Bordeaux, France.

Background: Microparticles (MPs) are vesicular structures that derive from multiple cellular sources. MPs play important roles in intercellular communication, regulation of cell signaling or initiation of enzymatic processes. While MPs were characterized in Systemic Sclerosis (SSc) patients, their contribution to SSc pathogenesis remains unknown. Read More

View Article and Full-Text PDF
October 2020

Defense Response in Brazilian Honey Bees (Apis mellifera scutellata × spp.) Is Underpinned by Complex Patterns of Admixture.

Genome Biol Evol 2020 08;12(8):1367-1377

Department of Biology, Faculty of Sciences, York University, Toronto, Canada.

In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage honey bee subspecies). The resulting cross-African hybrid honey bees (AHBs)-escaped from their enclosure and spread through the Americas. Read More

View Article and Full-Text PDF

Macrophage polarisation associated with atherosclerosis differentially affects their capacity to handle lipids.

Atherosclerosis 2020 07 10;305:10-18. Epub 2020 Jun 10.

Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK. Electronic address:

Background And Aims: Lipid-rich foam cell macrophages drive atherosclerosis via several mechanisms, including inflammation, lipid uptake, lipid deposition and plaque vulnerability. The atheroma environment shapes macrophage function and phenotype; anti-inflammatory macrophages improve plaque stability while pro-inflammatory macrophages promote rupture. Current evidence suggests a variety of macrophage phenotypes occur in atherosclerotic plaques with local lipids, cytokines, oxidised phospholipids and pathogenic stimuli altering their phenotype. Read More

View Article and Full-Text PDF

Focus on the heterogeneity of amyotrophic lateral sclerosis.

Amyotroph Lateral Scler Frontotemporal Degener 2020 11 25;21(7-8):485-495. Epub 2020 Jun 25.

Mario Negri-ALS Study Group, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy.

The clinical manifestations of amyotrophic lateral sclerosis (ALS) are variable in terms of age at disease onset, site of onset, progression of symptoms, motor neuron involvement, and the occurrence of cognitive and behavioral changes. Genetic background is a key determinant of the ALS phenotype. The mortality of the disease also varies with the ancestral origin of the affected population and environmental factors are likely to be associated with ALS at least within some cohorts. Read More

View Article and Full-Text PDF
November 2020

Circulating BPIFB4 Levels Associate With and Influence the Abundance of Reparative Monocytes and Macrophages in Long Living Individuals.

Front Immunol 2020 29;11:1034. Epub 2020 May 29.

Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy.

Long-Living Individuals (LLIs) delay aging and are less prone to chronic inflammatory reactions. Whether a distinct monocytes and macrophages repertoire is involved in such a characteristic remains unknown. Previous studies from our group have shown high levels of the host defense BPI Fold Containing Family B Member 4 (BPIFB4) protein in the peripheral blood of LLIs. Read More

View Article and Full-Text PDF

Neuroanatomical underpinnings of autism symptomatology in carriers and non-carriers of the 22q11.2 microdeletion.

Mol Autism 2020 06 8;11(1):46. Epub 2020 Jun 8.

Department of Forensic and Neurodevelopmental Sciences, and the Sackler Institute for Translational Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, UK.

Background: A crucial step to understanding the mechanistic underpinnings of autism spectrum disorder (ASD), is to examine if the biological underpinnings of ASD in genetic high-risk conditions, like 22q11.2 deletion syndrome (22q11.2DS), are similar to those in idiopathic illness. Read More

View Article and Full-Text PDF

Transcriptome changes underlie alterations in behavioral traits in different types of chicken.

J Anim Sci 2020 Jun;98(6)

Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.

In recent decades, artificial selection has contributed greatly to meeting the demands for animal meat, eggs, and milk. However, it has also resulted in changes in behavior, metabolic and digestive function, and alterations in tissue development, including the brain and skeleton. Our study aimed to profile the behavioral traits and transcriptome pattern of chickens (broilers, layers, and dual-purpose breeds) in response to artificial selection. Read More

View Article and Full-Text PDF

Remodeling of light and dark zone follicular dendritic cells governs germinal center responses.

Nat Immunol 2020 06 18;21(6):649-659. Epub 2020 May 18.

Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland.

Efficient generation of germinal center (GC) responses requires directed movement of B cells between distinct microenvironments underpinned by specialized B cell-interacting reticular cells (BRCs). How BRCs are reprogrammed to cater to the developing GC remains unclear, and studying this process is largely hindered by incomplete resolution of the cellular composition of the B cell follicle. Here we used genetic targeting of Cxcl13-expressing cells to define the molecular identity of the BRC landscape. Read More

View Article and Full-Text PDF

ICGEC: a comparative method for measuring epigenetic conservation of genes via the integrated signal from multiple histone modifications between cell types.

BMC Genomics 2020 May 12;21(1):356. Epub 2020 May 12.

College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.

Background: Histone post-translational modifications play crucial roles in epigenetic regulation of gene expression and are known to be associated with the phenotypic differences of different cell types. Therefore, it is of fundamental importance to dissect the genes and pathways involved in such a phenotypic variation at the level of epigenetics. However, the existing comparative approaches are largely based on the differences, especially the absolute difference in the levels of individual histone modifications of genes under contrasting conditions. Read More

View Article and Full-Text PDF

Identification of CTNNB1-PLAG1 gene rearrangement in a patient with pulmonary pleomorphic adenoma.

Virchows Arch 2020 Nov 19;477(5):739-742. Epub 2020 Apr 19.

Department of Human Pathology, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.

Pulmonary pleomorphic adenoma (PA) is a rare salivary gland-type neoplasm, which predominantly occurs in the proximal airway. Rearrangement of the pleomorphic adenoma gene 1 (PLAG1) is the most frequent genetic event in PAs of salivary glands. However, whether pulmonary PA also harbors PLAG1 rearrangement has not been elucidated. Read More

View Article and Full-Text PDF
November 2020

Genetics of congenital hypogonadotropic hypogonadism: peculiarities and phenotype of an oligogenic disease.

Hum Genet 2021 Jan 21;140(1):77-111. Epub 2020 Mar 21.

Department of Clinical Sciences and Community Health, University of Milan, 20100, Milan, Italy.

A genetic basis of congenital isolated hypogonadotropic hypogonadism (CHH) can be defined in almost 50% of cases, albeit not necessarily the complete genetic basis. Next-generation sequencing (NGS) techniques have led to the discovery of a great number of loci, each of which has illuminated our understanding of human gonadotropin-releasing hormone (GnRH) neurons, either in respect of their embryonic development or their neuroendocrine regulation as the "pilot light" of human reproduction. However, because each new gene linked to CHH only seems to underpin another small percentage of total patient cases, we are still far from achieving a comprehensive understanding of the genetic basis of CHH. Read More

View Article and Full-Text PDF
January 2021

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera).

Mol Biol Evol 2020 07;37(7):1964-1978

Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand.

Phenotypic plasticity, the ability of an organism to alter its phenotype in response to an environmental cue, facilitates rapid adaptation to changing environments. Plastic changes in morphology and behavior are underpinned by widespread gene expression changes. However, it is unknown if, or how, genomes are structured to ensure these robust responses. Read More

View Article and Full-Text PDF

To compete or defend: linking functional trait variation with life-history tradeoffs in a foundation tree species.

Oecologia 2020 Apr 14;192(4):893-907. Epub 2020 Feb 14.

Department of Entomology, University of Wisconsin-Madison, Madison, WI, 53706, USA.

Although chemical deterrents to herbivory often exact costs in terms of plant growth, the manner in which those costs arise, and their physiological relationship to other functional traits, remain unclear. In the absence of appreciable herbivory, we examined interrelationships among chemical defense levels and other foliar functional traits (e.g. Read More

View Article and Full-Text PDF

Syntrophy via Interspecies H Transfer between and Underlies Their Global Cooccurrence in the Human Gut.

mBio 2020 02 4;11(1). Epub 2020 Feb 4.

Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany

Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family and the archaeal family cooccur and are enriched in individuals with a lean, compared to an obese, body mass index (BMI). Whether these association patterns reflect interactions between metabolic partners, as well as whether these associations play a role in the lean host phenotype with which they associate, remains to be ascertained. Here, we validated previously reported cooccurrence patterns of the two families and their association with a lean BMI with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Read More

View Article and Full-Text PDF
February 2020

Chromatin remodeling dysfunction extends the etiological spectrum of schizophrenia: a case report.

BMC Med Genet 2020 01 8;21(1):10. Epub 2020 Jan 8.

Institut Neuromyogène, métabolisme énergétique et développement durable, CNRS UMR 5310, INSERM U1217, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.

Background: The role of deleterious copy number variations in schizophrenia is well established while data regarding pathogenic variations remain scarce. We report for the first time a case of schizophrenia in a child with a pathogenic mutation of the chromodomain helicase DNA binding protein 2 (CHD2) gene.

Case Presentation: The proband was the second child of unrelated parents. Read More

View Article and Full-Text PDF
January 2020

Recent advances in understanding the phenotypes of osteoarthritis.

F1000Res 2019 12;8. Epub 2019 Dec 12.

Division of Internal Medicine & Dermatology, Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands.

Recent research in the field of osteoarthritis (OA) has focused on understanding the underlying molecular and clinical phenotypes of the disease. This narrative review article focuses on recent advances in our understanding of the phenotypes of OA and proposes that the disease represents a diversity of clinical phenotypes that are underpinned by a number of molecular mechanisms, which may be shared by several phenotypes and targeted more specifically for therapeutic purposes. The clinical phenotypes of OA supposedly have different underlying etiologies and pathogenic pathways and they progress at different rates. Read More

View Article and Full-Text PDF
January 2020

Inflammatory responses to a pathogenic West Nile virus strain.

BMC Infect Dis 2019 Oct 29;19(1):912. Epub 2019 Oct 29.

Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, Australia.

Background: West Nile virus (WNV) circulates across Australia and was referred to historically as Kunjin virus (WNV). WNV has been considered more benign than other WNV strains circulating globally. In 2011, a more virulent form of the virus emerged during an outbreak of equine arboviral disease in Australia. Read More

View Article and Full-Text PDF
October 2019

A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight.

Fang-Ge Li Hui Li

BMC Genomics 2019 Oct 23;20(1):771. Epub 2019 Oct 23.

Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, 150030, People's Republic of China.

Background: The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms. Read More

View Article and Full-Text PDF
October 2019

Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection.

Front Plant Sci 2019 1;10:1195. Epub 2019 Oct 1.

Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Tulln, Austria.

Winter hardiness is a major constraint for autumn sown crops in temperate regions, and thus an important breeding goal in the development of new winter wheat varieties. Winter hardiness is though influenced by many environmental factors rendering phenotypic selection under field conditions a difficult task due to irregular occurrence or absence of winter damage in field trials. Controlled frost tolerance tests in growth chamber experiments are, on the other hand, even with few genotypes, often costly and laborious, which makes a genomic breeding strategy for early generation selection an attractive alternative. Read More

View Article and Full-Text PDF
October 2019

Infection by the castrating parasitic nematode Sphaerularia bombi changes gene expression in Bombus terrestris bumblebee queens.

Insect Mol Biol 2020 04 21;29(2):170-182. Epub 2019 Oct 21.

Centre of Ecology, Evolution and Behaviour, Department of Biological Sciences, Royal Holloway University of London, Egham, UK.

Parasitism can result in dramatic changes in host phenotype, which are themselves underpinned by genes and their expression. Understanding how hosts respond at the molecular level to parasites can therefore reveal the molecular architecture of an altered host phenotype. The entomoparasitic nematode Sphaerularia bombi is a parasite of bumblebee (Bombus) hosts where it induces complex behavioural changes and host castration. Read More

View Article and Full-Text PDF

Histologic spectrum of polymorphous adenocarcinoma of the salivary gland harbor genetic alterations affecting PRKD genes.

Mod Pathol 2020 01 6;33(1):65-73. Epub 2019 Sep 6.

Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Polymorphous adenocarcinoma (PAC) and cribriform adenocarcinoma of (minor) salivary gland (CASG) are salivary gland tumors with overlapping spectrum of morphology. Whether these represent distinct entities or a histologic spectrum of the same tumor remains contentious. PACs harbor recurrent PRKD1 E710D hotspot mutations in >70% of cases, whereas 80% of CASGs display rearrangements involving PRKD1, PRKD2, or PRKD3 (PRKD1/2/3). Read More

View Article and Full-Text PDF
January 2020

Genome-wide identification, expression and functional analysis of Populus xylogen-like genes.

Plant Sci 2019 Oct 15;287:110191. Epub 2019 Jul 15.

School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China. Electronic address:

As an extracellular arabinogalactan protein (AGP) containing a non-specific lipid transfer protein (nsLTP) domain, xylogen mediates the local intercellular communication required for tracheary element (TE) differentiation in Zinnia cell culture. Although XYLP (xylogen-like protein) gene families have been reported in Arabidopsis and rice, no comprehensive analysis has been performed in woody plants. In this work, 31 XYLP genes in five phylogenetic groups were identified from Populus trichocarpa genome and a comprehensive bioinformatic analysis including gene and protein structures, chromosomal locations and duplication events were conducted. Read More

View Article and Full-Text PDF
October 2019

Atypical EEG in autism spectrum disorder: Comparing a dimensional and a categorical approach.

J Abnorm Psychol 2019 Jul 10;128(5):442-452. Epub 2019 Jun 10.

Sheffield Autism Research Lab.

Myriad studies have found group differences in neural dynamics between people with and without autism spectrum disorder (ASD). However, the extent to which variation in neural dynamics is related to variation in the autism phenotype across the population is not known. Here we measured behavioral characteristics of autism alongside intertrial phase coherence (ITC) and multiscale entropy (MSE) computed from EEG in order to address this question. Read More

View Article and Full-Text PDF

Genomic landscape of lymphoepithelioma-like hepatocellular carcinoma.

J Pathol 2019 10 18;249(2):166-172. Epub 2019 Jul 18.

Department of Anatomical and Cellular Pathology, Sir YK Pao Centre for Cancer, Hong Kong SAR, PR China.

Lymphoepithelioma-like hepatocellular carcinoma (LEL-HCC) is a distinct variant of HCC that is characterized by dense tumor-infiltrating lymphocytes (TILs). Patients with LEL-HCC also show better clinical outcomes compared to conventional HCC (c-HCC), which is commonly presented with low TIL. Emerging evidence has begun to highlight tumor-intrinsic genetic abnormalities in the tumor-host immune interfaces. Read More

View Article and Full-Text PDF
October 2019

Habituation underpins preference for mates with novel phenotypes in the guppy.

Proc Biol Sci 2019 05;286(1902):20190435

Department of Biological Science, Florida State University , Tallahassee, FL , USA.

Populations harbour enormous genetic diversity in ecologically important traits. Understanding the processes that maintain this variation is a long-standing challenge in evolutionary biology. Recent evidence indicates that a mating preference for novel sexual signals can be a powerful force maintaining genetic diversity. Read More

View Article and Full-Text PDF

Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice.

Vet Pathol 2019 09 6;56(5):799-806. Epub 2019 May 6.

3 The Jackson Laboratory, Bar Harbor, ME, USA.

During a screen for vascular phenotypes in aged laboratory mice, a unique discrete phenotype of hyaline arteriolosclerosis of the intertubular arteries and arterioles of the testes was identified in several inbred strains. Lesions were limited to the testes and did not occur as part of any renal, systemic, or pulmonary arteriopathy or vasculitis phenotype. There was no evidence of systemic or pulmonary hypertension, and lesions did not occur in ovaries of females. Read More

View Article and Full-Text PDF
September 2019

Additive Traits Lead to Feeding Advantage and Reproductive Isolation, Promoting Homoploid Hybrid Speciation.

Mol Biol Evol 2019 08;36(8):1671-1685

Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa.

Speciation through homoploid hybridization (HHS) is considered extremely rare in animals. This is mainly because the establishment of reproductive isolation as a product of hybridization is uncommon. Additionally, many traits are underpinned by polygeny and/or incomplete dominance, where the hybrid phenotype is an additive blend of parental characteristics. Read More

View Article and Full-Text PDF