The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.
Any method used for determining the location of and relative distances between genes on a chromosome.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Established cell cultures that have the potential to propagate indefinitely.
Process of classifying cells of the immune system based on structural and functional differences. The process is commonly used to analyze and sort T-lymphocytes into subsets based on CD antigens by the technique of flow cytometry.
Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.
An individual in which both alleles at a given locus are identical.
An individual having different alleles at one or more loci regarding a specific character.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Biochemical identification of mutational changes in a nucleotide sequence.
Proteins found in any species of bacterium.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
Histochemical localization of immunoreactive substances using labeled antibodies as reagents.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.
Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
All of the processes involved in increasing CELL NUMBER including CELL DIVISION.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.
Genotypic differences observed among individuals in a population.
Mice bearing mutant genes which are phenotypically expressed in the animals.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
Genes whose loss of function or gain of function MUTATION leads to the death of the carrier prior to maturity. They may be essential genes (GENES, ESSENTIAL) required for viability, or genes which cause a block of function of an essential gene at a time when the essential gene function is required for viability.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Cell changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm, and other attributes conferring the ability to invade, metastasize, and kill.
Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.
Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A cell line derived from cultured tumor cells.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
The functional hereditary units of BACTERIA.
The movement of cells from one location to another. Distinguish from CYTOKINESIS which is the process of dividing the CYTOPLASM of a cell.
Elements of limited time intervals, contributing to particular results or situations.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Genes that influence the PHENOTYPE only in the homozygous state.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
Transport proteins that carry specific substances in the blood or across cell membranes.
A characteristic symptom complex.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.
The functional hereditary units of FUNGI.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
Proteins found in any species of fungus.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Differentiation antigens residing on mammalian leukocytes. CD stands for cluster of differentiation, which refers to groups of monoclonal antibodies that show similar reactivity with certain subpopulations of antigens of a particular lineage or differentiation stage. The subpopulations of antigens are also known by the same CD designation.
An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.
A species of nematode that is widely used in biological, biochemical, and genetic studies.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
Genetic loci associated with a QUANTITATIVE TRAIT.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.
The development of anatomical structures to create the form of a single- or multi-cell organism. Morphogenesis provides form changes of a part, parts, or the whole organism.
Relatively undifferentiated cells that retain the ability to divide and proliferate throughout postnatal life to provide progenitor cells that can differentiate into specialized cells.
Lymphocytes responsible for cell-mediated immunity. Two types have been identified - cytotoxic (T-LYMPHOCYTES, CYTOTOXIC) and helper T-lymphocytes (T-LYMPHOCYTES, HELPER-INDUCER). They are formed when lymphocytes circulate through the THYMUS GLAND and differentiate to thymocytes. When exposed to an antigen, they divide rapidly and produce large numbers of new T cells sensitized to that antigen.
The integration of exogenous DNA into the genome of an organism at sites where its expression can be suitably controlled. This integration occurs as a result of homologous recombination.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.
Congenital absence of or defects in structures of the eye; may also be hereditary.
A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The functional hereditary units of PLANTS.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
Genetically identical individuals developed from brother and sister matings which have been carried out for twenty or more generations, or by parent x offspring matings carried out with certain restrictions. All animals within an inbred strain trace back to a common ancestor in the twentieth generation.
Genes that have a suppressor allele or suppressor mutation (SUPPRESSION, GENETIC) which cancels the effect of a previous mutation, enabling the wild-type phenotype to be maintained or partially restored. For example, amber suppressors cancel the effect of an AMBER NONSENSE MUTATION.
Techniques to alter a gene sequence that result in an inactivated gene, or one in which the expression can be inactivated at a chosen time during development to study the loss of function of a gene.
The functional hereditary units of INSECTS.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Morphologic alteration of small B LYMPHOCYTES or T LYMPHOCYTES in culture into large blast-like cells able to synthesize DNA and RNA and to divide mitotically. It is induced by INTERLEUKINS; MITOGENS such as PHYTOHEMAGGLUTININS, and by specific ANTIGENS. It may also occur in vivo as in GRAFT REJECTION.
A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
The relationships of groups of organisms as reflected by their genetic makeup.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability.
A group of genetically identical cells all descended from a single common ancestral cell by mitosis in eukaryotes or by binary fission in prokaryotes. Clone cells also include populations of recombinant DNA molecules all carrying the same inserted sequence. (From King & Stansfield, Dictionary of Genetics, 4th ed)
Coloration or discoloration of a part by a pigment.
The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.
Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
Adherence of cells to surfaces or to other cells.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Glycoproteins found on the membrane or surface of cells.
The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.
Proteins from the nematode species CAENORHABDITIS ELEGANS. The proteins from this species are the subject of scientific interest in the area of multicellular organism MORPHOGENESIS.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.
Measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc.
A critical subpopulation of T-lymphocytes involved in the induction of most immunological functions. The HIV virus has selective tropism for the T4 cell which expresses the CD4 phenotypic marker, a receptor for HIV. In fact, the key element in the profound immunosuppression seen in HIV infection is the depletion of this subset of T-lymphocytes.
The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)
Test for tissue antigen using either a direct method, by conjugation of antibody with fluorescent dye (FLUORESCENT ANTIBODY TECHNIQUE, DIRECT) or an indirect method, by formation of antigen-antibody complex which is then labeled with fluorescein-conjugated anti-immunoglobulin antibody (FLUORESCENT ANTIBODY TECHNIQUE, INDIRECT). The tissue is then examined by fluorescence microscopy.
The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Proteins obtained from the ZEBRAFISH. Many of the proteins in this species have been the subject of studies involving basic embryological development (EMBRYOLOGY).
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
A group of enzymes that catalyzes the phosphorylation of serine or threonine residues in proteins, with ATP or other nucleotides as phosphate donors.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.
The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.
The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.
Eukaryotic cell line obtained in a quiescent or stationary phase which undergoes conversion to a state of unregulated growth in culture, resembling an in vitro tumor. It occurs spontaneously or through interaction with viruses, oncogenes, radiation, or drugs/chemicals.
Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)
Actual loss of portion of a chromosome.
Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.
Proteins prepared by recombinant DNA technology.
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
A classification of T-lymphocytes, especially into helper/inducer, suppressor/effector, and cytotoxic subsets, based on structurally or functionally different populations of cells.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Filamentous proteins that are the main constituent of the thin filaments of muscle fibers. The filaments (known also as filamentous or F-actin) can be dissociated into their globular subunits; each subunit is composed of a single polypeptide 375 amino acids long. This is known as globular or G-actin. In conjunction with MYOSINS, actin is responsible for the contraction and relaxation of muscle.
Ability of neoplasms to infiltrate and actively destroy surrounding tissue.
The percent frequency with which a dominant or homozygous recessive gene or gene combination manifests itself in the phenotype of the carriers. (From Glossary of Genetics, 5th ed)
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
Color of hair or fur.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Wormlike or grublike stage, following the egg in the life cycle of insects, worms, and other metamorphosing animals.
The decrease in the cell's ability to proliferate with the passing of time. Each cell is programmed for a certain number of cell divisions and at the end of that time proliferation halts. The cell enters a quiescent state after which it experiences CELL DEATH via the process of APOPTOSIS.
The processes occurring in early development that direct morphogenesis. They specify the body plan ensuring that cells will proceed to differentiate, grow, and diversify in size and shape at the correct relative positions. Included are axial patterning, segmentation, compartment specification, limb position, organ boundary patterning, blood vessel patterning, etc.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
The gradual irreversible changes in structure and function of an organism that occur as a result of the passage of time.
Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.
Diminished or failed response of an organism, disease or tissue to the intended effectiveness of a chemical or drug. It should be differentiated from DRUG TOLERANCE which is the progressive diminution of the susceptibility of a human or animal to the effects of a drug, as a result of continued administration.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
The organ of sight constituting a pair of globular organs made up of a three-layered roughly spherical structure specialized for receiving and responding to light.
Congenital structural deformities, malformations, or other abnormalities of the cranium and facial bones.
Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.
Methods for maintaining or growing CELLS in vitro.
Calcium-dependent cell adhesion proteins. They are important in the formation of ADHERENS JUNCTIONS between cells. Cadherins are classified by their distinct immunological and tissue specificities, either by letters (E- for epithelial, N- for neural, and P- for placental cadherins) or by numbers (cadherin-12 or N-cadherin 2 for brain-cadherin). Cadherins promote cell adhesion via a homophilic mechanism as in the construction of tissues and of the whole animal body.
Antigens on surfaces of cells, including infectious or foreign cells or viruses. They are usually protein-containing groups on cell membranes or walls and may be isolated.
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
The reproductive organs of plants.
Lymphoid cells concerned with humoral immunity. They are short-lived cells resembling bursa-derived lymphocytes of birds in their production of immunoglobulin upon appropriate stimulation.

Mapping of the homothallic genes, HM alpha and HMa, in Saccharomyces yeasts. (1/63708)

Two of the three homothallic genes, HM alpha and HMa, showed direct linkage to the mating-type locus at approximately 73 and 98 strans (57 and 65 centimorgans [cM], respectively, whereas, the other, HO, showed no linkage to 25 standard markers distributed over 17 chromosomes including the mating-type locus. To determine whether the HM alpha and HMa loci located on the left or right side of the mating-type locus, equations for three factor analysis of three linked genes were derived. Tetrad data were collected and were compared with expected values by chi 2 statistics. Calculations indicated that the HM alpha gene is probably located on the right arm at 95 strans (65 cM) from the centromere and the HMa locus at approximately 90 strans (64 cM) on the left arm of chromosome III.  (+info)

Sulfhydryl compounds in melanocytes of yellow (Ay/a), nonagouti (a/a), and agouti (A/A) mice. (2/63708)

CLEFFMANN (1953, 1963a,b) has reported that yellow but not black melanocytes of agouti (A/A) rabbits contained reducing sulfhydryl compounds. We have attempted to repeat CLEFFMANN's observations in mouse melanocytes of the lethal yellow (Ay/a), nonagouti (a/a) and agouti (A/A) genotypes. Our results contradict those of CLEFFMANN and reveal that yellow and black melanocytes, regardless of genotype, possess equivalent amounts of histochemically detectable sulfhydryl compounds. These results do not support the hypothesis that agouti-locus genes act by controlling the sulfhydryl metabolism of pigment cells.  (+info)

Regulation of body length and male tail ray pattern formation of Caenorhabditis elegans by a member of TGF-beta family. (3/63708)

We have identified a new member of the TGF-beta superfamily, CET-1, from Caenorhabditis elegans, which is expressed in the ventral nerve cord and other neurons. cet-1 null mutants have shortened bodies and male tail abnormal phenotype resembling sma mutants, suggesting cet-1, sma-2, sma-3 and sma-4 share a common pathway. Overexpression experiments demonstrated that cet-1 function requires wild-type sma genes. Interestingly, CET-1 appears to affect body length in a dose-dependent manner. Heterozygotes for cet-1 displayed body lengths ranging between null mutant and wild type, and overexpression of CET-1 in wild-type worms elongated body length close to lon mutants. In male sensory ray patterning, lack of cet-1 function results in ray fusions. Epistasis analysis revealed that mab-21 lies downstream and is negatively regulated by the cet-1/sma pathway in the male tail. Our results show that cet-1 controls diverse biological processes during C. elegans development probably through different target genes.  (+info)

Identification of sonic hedgehog as a candidate gene responsible for the polydactylous mouse mutant Sasquatch. (4/63708)

The mouse mutants of the hemimelia-luxate group (lx, lu, lst, Dh, Xt, and the more recently identified Hx, Xpl and Rim4; [1] [2] [3] [4] [5]) have in common preaxial polydactyly and longbone abnormalities. Associated with the duplication of digits are changes in the regulation of development of the anterior limb bud resulting in ectopic expression of signalling components such as Sonic hedgehog (Shh) and fibroblast growth factor-4 (Fgf4), but little is known about the molecular causes of this misregulation. We generated, by a transgene insertion event, a new member of this group of mutants, Sasquatch (Ssq), which disrupted aspects of both anteroposterior (AP) and dorsoventral (DV) patterning. The mutant displayed preaxial polydactyly in the hindlimbs of heterozygous embryos, and in both hindlimbs and forelimbs of homozygotes. The Shh, Fgf4, Fgf8, Hoxd12 and Hoxd13 genes were all ectopically expressed in the anterior region of affected limb buds. The insertion site was found to lie close to the Shh locus. Furthermore, expression from the transgene reporter has come under the control of a regulatory element that directs a pattern mirroring the endogenous expression pattern of Shh in limbs. In abnormal limbs, both Shh and the reporter were ectopically induced in the anterior region, whereas in normal limbs the reporter and Shh were restricted to the zone of polarising activity (ZPA). These data strongly suggest that Ssq is caused by direct interference with the cis regulation of the Shh gene.  (+info)

Hematopoietic stem-cell transplantation for the treatment of severe combined immunodeficiency. (5/63708)

BACKGROUND: Since 1968 it has been known that bone marrow transplantation can ameliorate severe combined immunodeficiency, but data on the long-term efficacy of this treatment are limited. We prospectively studied immunologic function in 89 consecutive infants with severe combined immunodeficiency who received hematopoietic stem-cell transplants at Duke University Medical Center between May 1982 and September 1998. METHODS: Serum immunoglobulin levels and lymphocyte phenotypes and function were assessed and genetic analyses performed according to standard methods. Bone marrow was depleted of T cells by agglutination with soybean lectin and by sheep-erythrocyte rosetting before transplantation. RESULTS: Seventy-seven of the infants received T-cell-depleted, HLA-haploidentical parental marrow, and 12 received HLA-identical marrow from a related donor; 3 of the recipients of haploidentical marrow also received placental-blood transplants from unrelated donors. Except for two patients who received placental blood, none of the recipients received chemotherapy before transplantation or prophylaxis against graft-versus-host disease. Of the 89 infants, 72 (81 percent) were still alive 3 months to 16.5 years after transplantation, including all of the 12 who received HLA-identical marrow, 60 of the 77 (78 percent) who were given haploidentical marrow, and 2 of the 3 (67 percent) who received both haploidentical marrow and placental blood. T-cell function became normal within two weeks after transplantation in the patients who received unfractionated HLA-identical marrow but usually not until three to four months after transplantation in those who received T-cell-depleted marrow. At the time of the most recent evaluation, all but 4 of the 72 survivors had normal T-cell function, and all the T cells in their blood were of donor origin. B-cell function remained abnormal in many of the recipients of haploidentical marrow. In 26 children (5 recipients of HLA-identical marrow and 21 recipients of haploidentical marrow) between 2 percent and 100 percent of B cells were of donor origin. Forty-five of the 72 children were receiving intravenous immune globulin. CONCLUSIONS: Transplantation of marrow from a related donor is a life-saving and life-sustaining treatment for patients with any type of severe combined immunodeficiency, even when there is no HLA-identical donor.  (+info)

Phenotypic analysis of human glioma cells expressing the MMAC1 tumor suppressor phosphatase. (6/63708)

MMAC1, also known as PTEN or TEP-1, was recently identified as a gene commonly mutated in a variety of human neoplasias. Sequence analysis revealed that MMAC1 harbored sequences similar to those found in several protein phosphatases. Subsequent studies demonstrated that MMAC1 possessed in vitro enzymatic activity similar to that exhibited by dual specificity phosphatases. To characterize the potential cellular functions of MMAC1, we expressed wild-type and several mutant variants of MMAC1 in the human glioma cell line, U373, that lacks endogenous expression. While expression of wild-type MMAC1 in these cells significantly reduced their growth rate and saturation density, expression of enzymatically inactive MMAC1 significantly enhanced growth in soft agar. Our observations indicate that while wild-type MMAC1 exhibits activities compatible with its proposed role as a tumor suppressor, cellular expression of MMAC1 containing mutations in the catalytic domain may yield protein products that enhance transformation characteristics.  (+info)

The role of RBF in the introduction of G1 regulation during Drosophila embryogenesis. (7/63708)

The first appearance of G1 during Drosophila embryogenesis, at cell cycle 17, is accompanied by the down-regulation of E2F-dependent transcription. Mutant alleles of rbf were generated and analyzed to determine the role of RBF in this process. Embryos lacking both maternal and zygotic RBF products show constitutive expression of PCNA and RNR2, two E2F-regulated genes, indicating that RBF is required for their transcriptional repression. Despite the ubiquitous expression of E2F target genes, most epidermal cells enter G1 normally. Rather than pausing in G1 until the appropriate time for cell cycle progression, many of these cells enter an ectopic S-phase. These results indicate that the repression of E2F target genes by RBF is necessary for the maintenance but not the initiation of a G1 phase. The phenotype of RBF-deficient embryos suggests that rbf has a function that is complementary to the roles of dacapo and fizzy-related in the introduction of G1 during Drosophila embryogenesis.  (+info)

JunB is essential for mammalian placentation. (8/63708)

Lack of JunB, an immediate early gene product and member of the AP-1 transcription factor family causes embryonic lethality between E8.5 and E10.0. Although mutant embryos are severely retarded in growth and development, cellular proliferation is apparently not impaired. Retardation and embryonic death are caused by the inability of JunB-deficient embryos to establish proper vascular interactions with the maternal circulation due to multiple defects in extra-embryonic tissues. The onset of the phenotypic defects correlates well with high expression of junB in wild-type extra-embryonic tissues. In trophoblasts, the lack of JunB causes a deregulation of proliferin, matrix metalloproteinase-9 (MMP-9) and urokinase plasminogen activator (uPA) gene expression, resulting in a defective neovascularization of the decidua. As a result of downregulation of the VEGF-receptor 1 (flt-1), blood vessels in the yolk sac mesoderm appeared dilated. Mutant embryos which escape these initial defects finally die from a non-vascularized placental labyrinth. Injection of junB-/- embryonic stem (ES) cells into tetraploid wild-type blastocysts resulted in a partial rescue, in which the ES cell-derived fetuses were no longer growth retarded and displayed a normal placental labyrinth. Therefore, JunB appears to be involved in multiple signaling pathways regulating genes involved in the establishment of a proper feto-maternal circulatory system.  (+info)

High-throughput phenotyping of seeds is the assessment of seed morphometry to aid in the prediction of yield, tolerance, resistance, and development of seeds in various environmental conditions. The paper focuses on the application of 3D graphics to image processing as a means to conduct seed phenotyping better. The paper proposes two algorithms - similar in the outcome, but different in implementation. The algorithms perform image processing on a variety of seeds such as wheat, soy, sorghum, rough rice, white rice, and canola to arrive at their morphometric estimations. In the area of static image processing, addressed are at least three common yet significant problems of seed clusters on images, skewed images, and poor image quality. As a means to address the problems, we propose the use of low-cost physical components. The algorithms provide the estimated count, area, perimeter, length, and width of seeds within an image.. Keyphrases: 3D graphics, high-throughput phenotyping, image ...
Introduction: Functional movement disorders (FMD) refer to a group of movement disorders that present with clinical characteristics incongruent to those due to established pathophysiologic processes, as for example in the case of neurodegeneration or lesions. The aim of this study was to assess clinical features that contribute to the specific phenotypic presentations and disease course of FMD.Methods: The study consisted of 100 patients with FMD treated at Clinic for Neurology, Clinical Center of Serbia, who were longitudinally observed. Comprehensive clinical and psychiatric assessment was performed at the baseline, when initial FMD phenotype was defined. Follow-up assessment of phenotypic pattern over the time and clinical course was done after 3.2 ± 2.5 years at average.Results: We showed that 48% of FMD patients were prone to changes of phenotypic pattern during the disease course. Dystonia had tendency to remains as single and unchanged phenotype over the time (68.2%), while patients initially
Genomic selection (GS) and high-throughput phenotyping (HTP) have great potential to increase the efficiency of wheat, Triticum aestivum L., breeding programs. GS is the use of markers covering the whole genome for selection. With GS, reviewed by Lorenz et al. (2011), a training set that has been phenotyped and genotyped is used to calibrate a prediction model, which is then used predict the breeding values of a test set of genotyped selection candidates. This enables indirect selection for quantitative traits prior to phenotyping. Genomic selection has already been implemented in dairy cattle breeding to increase rates of genetic gain (Pryce and Daetwyler 2012), and simulation studies have demonstrated that GS can increase rates of genetic gain in crop plants (Bernardo and Yu 2007; Wong and Bernardo 2008; Heffner et al. 2010). In contrast to GS, HTP is the use of remote and proximal sensing to measure a large number of phenotypes across time and space at low cost and with less labor ...
In this dissertation we expose the results of two research conducted using high-throughput phenotyping techniques with the aim of discovery the genetic bases underling drought adaptive traits in maize and durum wheat. In the first study, we used a maize Introgression Library (IL) derived from the cross between Gaspé Flint (an early flowering Canadian landrace) and B73 (an elite genetics reference line) which was previously shown to segregate for phenology and seminal root architecture (SRA). The IL was phenotypically evaluated in the high-throughput platform PhenoArch (INRA, Montpellier), for large-scale automated imagery and evapotranspiration measurements of potted plants in controlled environment, under well-watered and water-deficit conditions. Biomass accumulation for each plant was estimated by software and model-assisted imaging analysis. Several QTLs were detected (Dunnet test p-value , 0.05) for biomass accumulation and water-use efficiency (WUE) on chr. 1, 2, 3, 4, 7, 8, and 9). In ...
High-throughput phenotyping has opened whole new perspectives for crop improvement and better understanding of quantitative traits in plants. Generation of loss-of-function and gain-of-function plant
Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word phenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as phenomics.[12][13] Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness.[14] Phenomics forms a large part of the Human Genome Project[15]. Phenomics has widespread applications in the agricultural industry. With an exponentially growing population and inconsistent weather patterns due to global warming, it has become increasingly difficult to cultivate enough crops to support the worlds population. Advantageous genomic variations, like drought and heat resistance, can be identified through the use of phenomics to create more durable GMOs.[16][17]. Phenomics is also a crucial stepping stone towards personalized ...
In field and laboratory studies of birds, positive associations between male phenotype and success at obtaining extra-pair copulations or extra pair fertilizations are often interpreted as providing evidence that females are using extra-pair copulations to obtain indirect benefits for their offspring, either through genes for increased viability, or for a fisherian mating advantage. I describe a simple model, in which functional fertility (the success of ejaculates in fertilizing eggs) covaries with male phenotype, which can explain the observed associations equally well. Under such a model, females pursue extra-pair copulations as insurance against the functional infertility of their mate, and obtain only direct benefits for themselves in their current reproductive event. Several studies of birds suggest that a relation between male phenotype and functional fertility is often likely to exist and that there are many potential causes of functional infertility. Non-manipulative field studies are unlikely
Autor: Müller, Oliver et al.; Genre: Zeitschriftenartikel; Im Druck veröffentlicht: 2004; Keywords: bioorganic chemistry • combinatorial chemistry • library screening • medicinal chemistry • signal transduction; Titel: Identification of potent Ras signaling inhibitors by pathway-selective phenotype-based screening
Abstract Motivation Determining the relative contributions of functional genetic categories is fundamental to understanding the genetic etiology of complex human traits and diseases. Here, we present Annotation Informed-MiXeR, a likelihood-based method for estimating the number of variants influencing a phenotype and their effect sizes across different functional annotation categories of the genome using summary statistics from genome-wide association studies. Results Extensive simulations demonstrate that the model is valid for a broad range of genetic architectures. The model suggests that complex human phenotypes substantially differ in the number of causal variants, their localization in the genome and their effect sizes. Specifically, the exons of protein-coding genes harbor more than 90% of variants influencing type 2 diabetes and inflammatory bowel disease, making them good candidates for whole-exome studies. In contrast, <10% of the causal variants for schizophrenia, bipolar disorder ...
The Mammalian Phenotype (MP) Ontology is a community effort to provide standard terms for annotating phenotypic data. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated phenotype data at MGI are provided in Term Detail reports.
The Mammalian Phenotype (MP) Ontology is a community effort to provide standard terms for annotating phenotypic data. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated phenotype data at MGI are provided in Term Detail reports.
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environment-friendly way becomes increasingly important. Therefore, rice research community needs to share resources to better understand functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants.|br| We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93,000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the database at Taiwan Rice Insertional Mutants Database (|br| Detailed analyses of
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environment-friendly way becomes increasingly important. Therefore, rice research community needs to share resources to better understand functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants.|br| We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93,000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the database at Taiwan Rice Insertional Mutants Database (|br| Detailed analyses of
Purpose : Age-related macular degeneration (AMD) is a multifactorial disease with a highly variable phenotypic presentation. Recently, a Genome-Wide Association Study identified 52 single nucleotide polymorphisms (SNPs) that showed an association with AMD. These genetic variants may represent different pathways involved in AMD pathogenesis and contribute to the variability of the phenotype. We performed a Deep Phenotype Association Study (DeePAS) in Age-Related Eye Disease Study 2 (AREDS2) to identify variants that are related to specific AMD and non-AMD phenotypes. Methods : Genotyping information of the 52 GWAS SNPs was available for 1826 AREDS2 participants. AREDS2 participants have had detailed phenotyping for AMD characteristics and have been assessed for phenotypes related to other retinal disease, cataract, cardiovascular disease, neurological disease, cognitive function, gastro-intestinal and endocrine disease, nutrient serum levels and other. In total, we distinguished 138 phenotypes. ...
TY - JOUR. T1 - Age-related M1/M2 phenotype changes in circulating monocytes from healthy/unhealthy individuals. AU - Costantini, Andrea. AU - Viola, Nadia. AU - Berretta, Antonella. AU - Galeazzi, Roberta. AU - Matacchione, Giulia. AU - Sabbatinelli, Jacopo. AU - Storci, Gianluca. AU - De Matteis, Serena. AU - Butini, Luca. AU - Rippo, Maria Rita. AU - Procopio, Antonio Domenico. AU - Caraceni, Daniele. AU - Antonicelli, Roberto. AU - Olivieri, Fabiola. AU - Bonafè, Massimiliano. PY - 2018/6/1. Y1 - 2018/6/1. N2 - Macrophage polarization is a candidate biomarker of disease-related inflammatory status, but its modulation during aging has not been investigated. To do this, the M1/M2 profile was assessed by CD80/CD163 gating in classical (CD14++CD16-), intermediate (CD14++CD16+), and non-classical (CD14lowCD16+) monocytes from 31 healthy subjects (CTRs) of different ages. Cytofluorimetric analysis showed a significantly different CD80/CD163 distribution in the three subsets, as more than 80% of ...
This study had three objectives: (1) to determine the degree to which within-source genetic variation and genetic correlations differ among elevational sources of Douglas-fir [Pseudotsuga menziesii (Mirb). Franco var. menziesii]; (2) to ascertain the degree to which phenotypic stability differs among and within elevational sources; and (3) to compare the relationships among four measures of stability (variance, regression slope coefficient, deviation from regression and ecovalence). To accomplish the objectives seeds were collected from 10 parent trees in three populations from each of three elevations. Nine traits were measured on two-year-old seedlings grown in four test environments that factorially combined heated and unheated air and soil. Results support the hypothesis that the magnitude of within-source genetic variation is homogeneous among elevations. However1 genetic correlations between growth and phenological traits varied by elevation. For example, increased height was positively ...
Polyphyly of the genus Canoparmelia- uncovering incongruences between phenotype-based classification and molecular phylogeny within lichenized Ascomycota (Parmeliaceae)
The mechanisms by which adaptive phenotypes spread within an evolving population after their emergence are understood fairly well. Much less is known about the factors that influence the evolutionary accessibility of such phenotypes, a pre-requisite for their emergence in a population. Here, we investigate the influence of environmental quality on the accessibility of adaptive phenotypes of Escherichia colis central metabolic network. We used an established flux-balance model of metabolism as the basis for a genotype-phenotype map (GPM). We quantified the effects of seven qualitatively different environments (corresponding to both carbohydrate and gluconeogenic metabolic substrates) on the structure of this GPM. We found that the GPM has a more rugged structure in qualitatively poorer environments, suggesting that adaptive phenotypes could be intrinsically less accessible in such environments. Nevertheless, on average approximately 74% of the genotype can be altered by neutral drift, in the ...
Autor: Dauwe, R. et al.; Genre: Zeitschriftenartikel; Im Druck veröffentlicht: 2007; Keywords: metabolomics|br/|transcriptomics|br/|ccr|br/|cad|br/|oligolignol|br/|cinnamyl-alcohol-dehydrogenase|br/|ammonia-lyase gene|br/|transgenic tobacco|br/|down-regulation|br/|arabidopsis-thaliana|br/|o-methyltransferase|br/|coa reductase|br/|phenylpropanoid metabolism|br/|chlorophyll fluorescence|br/|transcriptome analysis; Titel: Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration
When ordering genetic testing or triaging candidate variants in exome and genome sequencing studies, it is critical to generate and test a comprehensive list of candidate genes that succinctly describe the complete and objective phenotypic features of disease. Significant efforts have been made to curate gene:disease associations both in academic research and commercial genetic testing laboratory settings. However, many of these valuable resources exist as islands and must be used independently, generating static, single-resource gene:disease association lists. Here we describe genepanel.iobio ( an easy to use, free and open-source web tool for generating disease- and phenotype-associated gene lists from multiple gene:disease association resources, including the NCBI Genetic Testing Registry (GTR), Phenolyzer, and the Human Phenotype Ontology (HPO). We demonstrate the utility of genepanel.iobio by applying it to complex, rare and undiagnosed disease cases that had reached a
THAP1 mutations have been shown to be the cause of DYT6. A number of different mutation types and locations in the THAP1 gene have been associated with a range of severity and dystonia phenotypes, but, as yet, it has been difficult to identify clear genotype phenotype patterns. Here, we screened the THAP1 gene in a further series of dystonia cases and evaluated the mutation pathogenicity in this series as well as previously reported mutations to investigate possible phenotype-genotype correlations. THAP1 mutations have been identified throughout the coding region of the gene, with the greatest concentration of variants localized to the THAP1 domain. In the additional cases analyzed here, a further two mutations were found. No obvious, indisputable genotype-phenotype correlation emerged from these data. However, we managed to find a correlation between the pathogenicity of mutations, distribution, and age of onset of dystonia. THAP1 mutations are an important cause of dystonia, but, as yet, no ...
An ontology of anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The Xenopus Phenotype Ontology represents and standardizes anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The XPO is being designed primarily to support phenotype curation in Xenbase, the model organism database for Xenopus, and to facilitate mappings between frog phenotypes and human disease ...
TY - JOUR. T1 - Lentivirus delivery of IL-10 to promote and sustain macrophage polarization towards an anti-inflammatory phenotype. AU - Boehler, R. M.. AU - Kuo, R.. AU - Shin, S.. AU - Goodman, A. G.. AU - Pilecki, M. A.. AU - Leonard, J. N.. AU - Shea, L. D.. PY - 2014/6. Y1 - 2014/6. N2 - Gene delivery from biomaterials can create an environment that promotes and guides tissue formation. However, the immune response induced upon biomaterial implantation can be detrimental to tissue regeneration. Macrophages play a central role in mediating early phases of this response, and functional polarization of macrophages towards M1 (inflammatory) or M2 (anti-inflammatory) phenotypes may bias the local immune state at the implant site. Since gene delivery from biomaterial scaffolds can confer transgene expression in macrophages in vivo, we investigated whether transduction of macrophages with an IL-10 encoding lentivirus can (1) induce macrophage polarization toward an M2 phenotype even in an ...
Epigenetic phenomena, such as DNA methylation, histone modifications, changes in chromatin structure or effects of non coding RNAs, affect gene expression and thus are expected to have important effects on phenotypes. The phenotypic diversity of a population is the result of both genetic and epigenetic variations, with epigenetics accounting for a portion of the variability of complex traits that is linked to interactions with the environment [1, 2]. The real contribution of epigenetics to phenotypic variation remains to be evaluated, but it is an attractive new path in animal breeding that might help to explain the missing causality of complex traits [3]. In recent years, a growing number of studies have shown that epigenetic information can be transmitted across generations. In particular, the intergenerational transmission of DNA methylation and the influence of epigenetic marks on phenotype variability has been clearly established in plants [4]. These phenomena could also partly explain the ...
The Annual Meeting of the UK Plant Phenomics Network will take place 13:00-16:00 on Friday 8th April, at the Sutton Bonington campus of the University of Nottingham. (This meeting follows directly after the UKPPN root phenotyping workshop).
Phenotype prediction from genome-wide association studies: application to smoking behaviors. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains
Until further notice, in response to COVID-19, I-Share requesting and Statewide Library Delivery are temporarily suspended, and I-Share library materials will not be considered overdue.. As of June 24, 2020, the I-Share catalog and your local library catalog have moved to a new system! This catalog is no longer being updated and you cannot request or renew materials here; it will be retired on Oct. 30, 2020. Please visit to find the new URL to access the new library catalog system. ...
Functional mannose-binding lectin (f-MBL) plays an important role in the innate neonatal immune system. We studied the origin of f-MBL in umbilical cord blood (UCB) by measuring maternal MBL (n=47), collected before elective cesarean section, and neo
Regulation of alveolar epithelial cell phenotypes in fetal sheep: roles of cortisol and lung expansion.: Our aim was to determine whether cortisols effect on a
However, environmental changes during early development may result in the selected trajectory becoming inappropriate, resulting in adverse effects on health. This paradox generates doubts about whether the thrifty phenotype is adaptive for human offspring. Thus, the thrifty phenotype should be considered as the capacity of all offspring to respond to environmental cues during early ontogenetic development. It has been suggested that the thrifty phenotype is the consequence of three unlike adaptive processes: maternal effects, niche construction and developmental plasticity, which all are influenced by the brain. While developmental plasticity demonstrates an adaptation by the offspring, niche construction and parental effects are result of parental selections rather than offspring fitness. Therefore, the thrifty phenotype can be described as a manipulation of offspring phenotype for the benefit of maternal fitness. The information that enters offspring phenotype during early development mirror ...
Enormous progress in mapping complex traits in humans has been made in the last 5 yr. There has been early success for prevalent diseases with complex phenotypes. These studies have demonstrated clearly that, while complex traits differ in their underlying genetic architectures, for many common disorders the predominant pattern is that of many loci, individually with small effects on phenotype. For some traits, loci of large effect have been identified. For almost all complex traits studied in humans, the sum of the identified genetic effects comprises only a portion, generally less than half, of the estimated trait heritability. A variety of hypotheses have been proposed to explain why this might be the case, including untested rare variants, and gene-gene and gene-environment interaction. Effort is currently being directed toward implementation of novel analytic approaches and testing rare variants for association with complex traits using imputed variants from the publicly available 1000 ...
This study focuses on the participants of the Long Life Family Study to elucidate whether biogenetic mechanisms underlying relationships among heritable complex phenotypes in parents function in the same way for the same phenotypes in their children. Our results reveal 3 characteristic groups of relationships among phenotypes in parents and children. One group composed of 3 pairs of phenotypes confirms that associations among some phenotypes can be explained by the same biogenetic mechanisms working in parents and children. Two other groups including 9 phenotype pairs show that this is not a common rule. Our findings suggest that biogenetic mechanisms underlying relationships among different phenotypes, even if they are causally related, can function differently in successive generations or in different age groups of biologically related individuals. The results suggest that the role of aging-related processes in changing environment may be conceptually underestimated in current genetic ...
71.31% of tested genes with null mutations on a B6N genetic background have a phenotype association to embryonic lethality prior to organogenesis (251/352) ...
Human Phenotype Ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
Human Phenotype Ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
Improving efficiency of disease diagnosis based on phenotype ontology is a critical yet challenging research area. Recently, Human Phenotype Ontology (HPO)-based semantic similarity has been affectively and widely used to identify causative genes and diseases. However, current phenotype similarity measurements just consider the annotations and hierarchy structure of HPO, neglecting the definition description of phenotype terms. In this paper, we propose a novel phenotype similarity measurement, termed as DisPheno, which adequately incorporates the definition of phenotype terms in addition to HPO structure and annotations to measure the similarity between phenotype terms. DisPheno also integrates phenotype term associations into phenotype-set similarity measurement using gene and disease annotations of phenotype terms. Compared with five existing state-of-the-art methods, DisPheno shows great performance in HPO-based phenotype semantic similarity measurement and improves the efficiency of disease
From cell senescence to age-related diseases: differential mechanisms of action of senescence-associated secretory phenotypes - Age-associated diseases;Cell senescence;Differential expression;Senescence-associated secretory phenotypes (SASP);
Human Phenotype Ontology:HP:0000212,MedGen:C0017567,Human Phenotype Ontology:HP:0000316,MedGen:CN000296,Human Phenotype Ontology:HP:0000821,MedGen:C0020676,Human Phenotype Ontology:HP:0001382,MedGen:C1844820,Human Phenotype Ontology:HP:0001636,MedGen:CN001489,Human Phenotype Ontology:HP:0002019,MedGen:C0009806,Human Phenotype Ontology:HP:0004322,MedGen:C0349588,Human Phenotype Ontology:HP:0012471,MedGen:C1836543,MeSH:C536914,MedGen:C0238462,Orphanet:ORPHA1332,SNOMED CT:255032005,MeSH:D013964,MedGen:C0040136,MeSH:D018761,MedGen:C0025267,OMIM:131100,Orphanet:ORPHA652,SNOMED CT:30664006,MeSH:D018813,MedGen:C0025268,OMIM:171400,Orphanet:ORPHA247698,SNOMED CT:61808009,MeSH:D018814,MedGen:C0025269,OMIM:162300,Orphanet:ORPHA247709,SNOMED CT:6153000,SNOMED CT:61530001,MedGen:C0031511,OMIM:171300,MedGen:C1833929,MedGen:C1970712,OMIM:610755,Orphanet:ORPHA276152,MedGen:CN073359,Orphanet:ORPHA653,SNOMED CT:61808009,MedGen:CN169374,MedGen: ...
Candida dubliniensis is closely related to Candida albicans, a major causative agent of candidiasis, and is primarily associated with oral colonization and infection in human immunodeficiency virus (HIV)-positive patients. Despite the high similarity of genomic and phenotypic features between the two species, C. dubliniensis is much less virulent and less prevalent than C. albicans. The ability to change morphological phenotypes is a striking feature of Candida species and is linked to virulence. In this study, we report a novel phenotype, the gray phenotype, in C. dubliniensis. Together with the previously reported white and opaque cell types, the gray phenotype forms a tristable phenotypic switching system in C. dubliniensis that is similar to the white-gray-opaque tristable switching system in C. albicans. Gray cells of C. dubliniensis are similar to their counterparts in C. albicans in terms of several biological aspects including cellular morphology, mating competence, and genetic ...
Typical Rett syndrome (RTT) is a pediatric disorder caused by loss-of-function mutations in the methyl-CpG binding protein 2 (MECP2) gene. The demonstrated reversibility of RTT-like phenotypes in mice suggests that MECP2 gene replacement is a potential therapeutic option in patients. We report improvements in survival and phenotypic severity in Mecp2-null male mice after neonatal intracranial delivery of a single-stranded (ss) AAV9/chicken β-actin (CBA)-MECP2 vector. Median survival was 16.6 weeks for MECP2-treated versus 9.3 weeks for green fluorescent protein (GFP)-treated mice. ssAAV9/CBA-MECP2-treated mice also showed significant improvement in the phenotype severity score, in locomotor function, and in exploratory activity, as well as a normalization of neuronal nuclear volume in transduced cells. Wild-type (WT) mice receiving neonatal injections of the same ssAAV9/CBA-MECP2 vector did not show any significant deficits, suggesting a tolerance for modest MeCP2 overexpression. To test a ...
TY - JOUR. T1 - Molecular phenotyping of HCS-2/8 cells as an in vitro model of human chondrocytes. AU - Saas, J.. AU - Lindauer, K.. AU - Bau, B.. AU - Takigawa, M.. AU - Aigner, Thomas. N1 - Funding Information: Funding sources: This work was supported by the BMBF (grant 01GG9824) and Aventis Pharma Deutschland GmbH. Funding Information: This work was supported by the BMBF (grant 01GG9824) and Aventis Pharma Deutschland GmbH. We are grateful to Drs M.B. Goldring (Boston) and J. Block (Chicago) for the chondrocyte cell lines C28I2 and C28a4 as well as AG and SG. The SW1353 chondrosarcoma cell line was obtained by ATCC (Manassas, Virginia, USA).. PY - 2004/11. Y1 - 2004/11. N2 - Objective: Cultures of primary articular chondrocytes for studying chondrocyte biology are notoriously difficult to handle. One alternative is the use of chondrocytic cell lines. Because the HCS-2/8 cells are the most widely used cell line in cartilage research, we investigated the molecular phenotype of these cells by ...
TY - JOUR. T1 - Phenotype severity in the bladder exstrophy-epispadias complex. T2 - Analysis of genetic and nongenetic contributing factors in 441 families from North America and Europe. AU - Reutter, Heiko. AU - Boyadjiev, Simeon A.. AU - Gambhir, Lisa. AU - Ebert, Anne Karoline. AU - Rösch, Wolfgang H.. AU - Stein, Raimund. AU - Schröder, Annette. AU - Boemers, Thomas M.. AU - Bartels, Enrika. AU - Vogt, Hannes. AU - Utsch, Boris. AU - Müller, Martin. AU - Detlefsen, Birte. AU - Zwink, Nadine. AU - Rogenhofer, Sebastian. AU - Gobet, Rita. AU - Beckers, Goedele M A. AU - Bökenkamp, Arend. AU - Kajbafzadeh, Abdol Mohammad. AU - Jaureguizar, Enrique. AU - Draaken, Markus. AU - Lakshmanan, Yegappan. AU - Gearhart, John Phillip. AU - Ludwig, Michael. AU - Nöthen, Markus M.. AU - Jenetzky, Ekkehart. PY - 2011/11. Y1 - 2011/11. N2 - Objective: To identify genetic and nongenetic risk factors that contribute to the severity of the bladder exstrophy-epispadias complex (BEEC). Study design: ...
Metabolic variations occur during normal pregnancy to provide the growing fetus with a supply of nutrients required for its development and to ensure the health of the woman during gestation. Mass spectrometry-based metabolomics was employed to study the metabolic phenotype variations in the maternal plasma that are induced by pregnancy in each of its three trimesters. Nontargeted metabolomics analysis showed that pregnancy significantly altered the profile of metabolites in maternal plasma. The levels of six metabolites were found to change significantly throughout pregnancy, with related metabolic pathway variations observed in biopterin metabolism, phospholipid metabolism, amino acid derivatives, and fatty acid oxidation. In particular, there was a pronounced elevation of dihydrobiopterin (BH2), a compound produced in the synthesis of dopa, dopamine, norepinephrine, and epinephrine, in the second trimester, whereas it was markedly decreased in the third trimester. The turnover of BH2 and tryptophan
TY - JOUR. T1 - Genotype/Phenotype Correlations in Tuberous Sclerosis Complex. AU - Curatolo, Paolo. AU - Moavero, Romina. AU - Roberto, Denis. AU - Graziola, Federica. PY - 2015/12/1. Y1 - 2015/12/1. N2 - Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by the development of widespread hamartomatous lesions in various organs, including brain, skin, kidneys, heart, and eyes. Central nervous system is almost invariably involved, with up to 85% of patients presenting with epilepsy, and at least half of patients having intellectual disability or other neuropsychiatric disorders including autism spectrum disorder. TSC is caused by the mutation in one of the 2 genes TSC1, at 9q34, and TSC2, at 16p13.3. They respectively encode for hamartin and tuberin, which form an intracellular complex inhibiting the mammalian target of rapamycin. Mammalian target of rapamycin overactivation following the genetic defect determines the cell growth and proliferation responsible for ...
TY - JOUR. T1 - Interferon regulatory factor 3 plays an anti-inflammatory role in microglia by activating the PI3K/Akt pathway. AU - Tarassishin, Leonid. AU - Suh, Hyeon Sook. AU - Lee, Sunhee C.. PY - 2011/12/30. Y1 - 2011/12/30. N2 - Background: Microglia are the principal cells involved in the innate immune response in the CNS. Activated microglia produce a number of proinflammatory cytokines implicated in neurotoxicity but they also are a major source of anti-inflammatory cytokines, antiviral proteins and growth factors. Therefore, an immune therapy aiming at suppressing the proinflammatory phenotype while enhancing the anti-inflammatory, growth promoting phenotype would be of great benefit. In the current study, we tested the hypothesis that interferon regulatory factor 3 (IRF3), a transcription factor required for the induction of IFNβ following TLR3 or TLR4 activation, is critical to the microglial phenotype change from proinflammatory to anti-inflammatory, and that this phenotype change ...
Neurobehavioral phenotype in Prader-Willi syndrome.: The focus of this article is on the lifetime development of people with Prader-Willi syndrome (PWS) and spe
TY - JOUR. T1 - Improving the diagnostic yield of exome-sequencing by predicting gene-phenotype associations using large-scale gene expression analysis. AU - Deelen, Patrick. AU - van Dam, Sipko. AU - Herkert, Johanna C. AU - Karjalainen, Juha M. AU - Brugge, Harm. AU - Abbott, Kristin M. AU - van Diemen, Cleo C. AU - van der Zwaag, Paul A. AU - Gerkes, Erica H. AU - Zonneveld-Huijssoon, Evelien. AU - Boer-Bergsma, Jelkje J. AU - Folkertsma, Pytrik. AU - Gillett, Tessa. AU - van der Velde, K Joeri. AU - Kanninga, Roan. AU - van den Akker, Peter C. AU - Jan, Sabrina Z. AU - Hoorntje, Edgar T. AU - Te Rijdt, Wouter P. AU - Vos, Yvonne J. AU - Jongbloed, Jan D H. AU - van Ravenswaaij-Arts, Conny M A. AU - Sinke, Richard. AU - Sikkema-Raddatz, Birgit. AU - Kerstjens-Frederikse, Wilhelmina S. AU - Swertz, Morris A. AU - Franke, Lude. PY - 2019/6/28. Y1 - 2019/6/28. N2 - The diagnostic yield of exome and genome sequencing remains low (8-70%), due to incomplete knowledge on the genes that cause ...
TY - JOUR. T1 - Genetically predicted body mass index and Alzheimers disease-related phenotypes in three large samples. T2 - Mendelian randomization analyses. AU - Adult Changes in Thought Study Investigators. AU - Religious Orders Study/Memory and Aging Project Investigators. AU - Alzheimers Disease Genetics Consortium. AU - Mukherjee, Shubhabrata. AU - Walter, Stefan. AU - Kauwe, John S K. AU - Saykin, Andrew J.. AU - Bennett, David A.. AU - Larson, Eric B.. AU - Crane, Paul K.. AU - Glymour, M. Maria. AU - Albert, Marilyn S.. AU - Albin, Roger L.. AU - Apostolova, Liana G.. AU - Arnold, Steven E.. AU - Asthana, Sanjay. AU - Atwood, Craig S.. AU - Baldwin, Clinton T.. AU - Barber, Robert C.. AU - Barmada, Michael M.. AU - Barnes, Lisa L.. AU - Beach, Thomas G.. AU - Becker, James T.. AU - Beecham, Gary W.. AU - Beekly, Duane. AU - Bigio, Eileen H.. AU - Bird, Thomas D.. AU - Blacker, Deborah. AU - Boeve, Bradley F.. AU - Bowen, James D.. AU - Boxer, Adam. AU - Burke, James R.. AU - Buxbaum, ...
As the human genome project approaches completion, the challenge for mammalian geneticists is to develop approaches for the systematic determination of mammalian gene function. Mouse mutagenesis will be a key element of studies of gene function. Phenotype-driven approaches using the chemical mutagen ethylnitrosourea (ENU) represent a potentially efficient route for the generation of large numbers of mutant mice that can be screened for novel phenotypes. The advantage of this approach is that, in assessing gene function, no a priori assumptions are made about the genes involved in any pathway. Phenotype-driven mutagenesis is thus an effective method for the identification of novel genes and pathways. We have undertaken a genome-wide, phenotype-driven screen for dominant mutations in the mouse. We generated and screened over 26,000 mice, and recovered some 500 new mouse mutants. Our work, along with the programme reported in the accompanying paper, has led to a substantial increase in the mouse mutant
Now that genome-wide association studies (GWAS) are dominating the landscape of genetic research on neuropsychiatric syndromes, investigators are being faced with complexity on an unprecedented scale. It is now clear that phenomics, the systematic study of phenotypes on a genome-wide scale, comprise …
Bergmann glia (Bg) respond to the early postnatal Purkinje cell (Pc) death in Lurcher (Lc) mutant mouse cerebellum by down-regulating expression of the enzyme glycerol-3-phosphate dehydrogenase (GPDH). To determine whether glial GPDH expression requires the continued presence of Pcs in adults, we us …
Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in
Genome-scale metabolic models (GEMs) allow predicting metabolic phenotypes from limited data on uptake and secretion fluxes by defining the space of all the feasible solutions and excluding physio-chemically and biologically unfeasible behaviors. The integration of additional biological information in genome-scale models, e.g., transcriptomic or proteomic profiles, has the potential to improve phenotype prediction accuracy. This is particularly important for metabolic engineering applications where more accurate model predictions can translate to more reliable model-based strain design. Here we present a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO) model of Bacillus subtilis, which uses publicly available proteomic data and enzyme kinetic parameters for central carbon (CC) metabolic reactions to constrain the flux solution space. This model allows more accurate prediction of the flux distribution and growth rate of wild-type and single-gene/operon deletion strains compared to a
Chitosan (C), alginate-crosslinked chitosan (CA), and pectin-crosslinked chitosan (CP) were covalently bonded to Ti-6Al-4V surfaces and tested for their biocompatibility. Compared to the clinically treated Ti-6Al-4V surface (Ti64), C, CA, and CP, had higher contact angles and promoted higher cell proliferation, type I collagen deposition, and mineralization after two weeks (all p|0.05). Cells on C, CA, and CP expressed more alkaline phosphatase (ALP) activity compared to those on Ti64 (p|0.05). The swelling ratios and drug release efficacies of CA and CP were significantly higher and lower, respectively, than those of C (both p|0.05). Only cells on CA expressed ALP activity after three weeks of culture. Generally speaking, crosslinking with alginate and pectin changed surface wettability as well as the swelling and drug release properties of the chitosan coatings. Cells on the coatings had higher proliferation, type I collagen deposition, and degree of mineralization compared to those on Ti64.
TY - JOUR. T1 - The ER-positive / PgR-negative breast cancer phenotype is not associated with mutations within the DNA binding domain. AU - Fuqua, Suzanne A.W.. AU - Allred, D. Craig. AU - Elledge, Richard M.. AU - Krieg, Shelly L.. AU - Benedix, Margaret G.. AU - Nawaz, Zafar. AU - OMalley, Bert W.. AU - Greene, Geoffrey L.. AU - McGuire, William L.. N1 - Copyright: Copyright 2007 Elsevier B.V., All rights reserved.. PY - 1993/1. Y1 - 1993/1. N2 - We have used in vitro DNA binding assays as a measure of estrogen receptor (ER) function in human breast tumors. We found that the majority of ER+ (25 ER+/progesterone receptor [PgR]+, and 25 ER+/PgR-) tumors we examined were capable of binding consensus estrogen response element (ERE) oligonucleotides in this assay system. We found significant proteolytic activity in many of the tumors such that protease inhibitors were found to be essential during the preparation of tumor extracts. We next applied direct sequence analysis of the ER DNA binding ...
Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy.s profile, publications, research topics, and co-authors
Multi-Minicore DiseaseSearching for Boundaries: Phenotype Analysis of 38 Cases Ana Ferreiro, MD,* Brigitte Estournet, MD, Danielle Chateau, MSci,* Norma B. Romero,
TY - JOUR. T1 - Berberine inhibits myofibroblast differentiation in nasal polyp-derived fibroblasts via the p38 pathway. AU - Moon, You Mi. AU - Park, Il Ho. AU - Cho, Jung Sun. AU - Um, Ji Young. AU - Kim, Tae-Hoon. AU - Lee, Heung Man. PY - 2013/1/1. Y1 - 2013/1/1. N2 - The purposes of this study were to determine whether berberine has any effect on phenotype changes and extracellular matrix (ECM) production in nasal polyp-derived fibroblasts (NPDFs) and to investigate the underlying molecular mechanism. NPDFs were pre-treated with berberine prior to induction by transforming growth factor (TGF)-β1. The expression of α-smooth muscle actin (SMA) and collagen type I mRNA was determined by a reverse transcription-polymerase chain reaction, and the expression of α-SMA protein and collagen type I was determined by western blotting and/or immunofluorescent staining. The total soluble collagen production was analysed by the SirCol collagen assay. The expression of several signaling molecules of ...
Motor symptoms in Huntingtons Disease (HD) are commonly assessed by the Unified Huntingtons Disease Rating Scale-Total Motor Score (UHDRS-TMS). However, the UHDRS-TMS is limited by interrater variability, its categorical nature, and insensitivity in premanifest subjects. More objective and quantitative measures of motor phenotype may complement the use of the UHDRS-TMS as outcome measure and increase the power and sensitivity of clinical trials. Deficits in tongue protrusion are well acknowledged in HD and constitute a subitem of the UHDRS-TMS. We, therefore, investigated whether objective and quantitative assessment of tongue protrusion forces (TPF) provides measures that (1) correlate to the severity of motor phenotype detected in the UHDRS-TMS in symptomatic HD, (2) detect a motor phenotype in premanifest HD gene-carriers, and (3) exhibit a correlation to the genotype as assessed by a disease burden score (based on CAG-repeat length and age). Using a precalibrated force transducer, the ...
Guolian Kang,(St. Jude Childrens Research Hospital). 2018.06.27 9:00-10:00,N219. 【Abstract】Genome-wide association studies (GWAS) have been successful in the last decades to identify common variants associated with common or rare diseases. Study designs most commonly used for GWAS are based on a primary outcome including the case-control study (CC) for studying a common disease or extreme phenotype sequencing design (EPS) for studying an ordinal or continuous phenotype, such as the well-known National Heart, Lung, and Blood Institute Exome Sequencing Project. Besides the primary outcome, extensive data on secondary phenotypes (SP) that may correlate and share the common genetic variants with the primary outcomes are available. Although na?ve methods for GWAS could be applied to analyze the secondary phenotypes, they lead to biased risk estimates if there is correlation between the primary outcome and secondary phenotype. This is resulted from the fact that the GWAS samples selected ...
Epigenetic regulation of gene expression is a developing field of study with many potential therapeutic applications. Chromatin remodeling is necessary for proper mammalian development, and misregulation of this process is associated with many human diseases. Three mechanisms by which chromatin structure is modified include methylation of the DNA, covalent modification of histone tails, and repositioning of nucleosomes by ATP dependant chromatin remodeling enzymes. To further increase our knowledge of the mechanisms and proteins involved in the modification of chromatin structure I undertook two projects; the role of DNA methylation in the regulation of human β-globin gene expression, and analysis of the Chd6 ATPase-/- mouse. Methylation status of the human β-globin gene promoters correlates with the expression pattern of the individual genes. However an extensive locus wide analysis of the methylation pattern in primary human tissue has not been performed. We used bisulfite sequencing to ...
Epigenetic regulation of gene expression is a developing field of study with many potential therapeutic applications. Chromatin remodeling is necessary for proper mammalian development, and misregulation of this process is associated with many human diseases. Three mechanisms by which chromatin structure is modified include methylation of the DNA, covalent modification of histone tails, and repositioning of nucleosomes by ATP dependant chromatin remodeling enzymes. To further increase our knowledge of the mechanisms and proteins involved in the modification of chromatin structure I undertook two projects; the role of DNA methylation in the regulation of human β-globin gene expression, and analysis of the Chd6 ATPase-/- mouse. Methylation status of the human β-globin gene promoters correlates with the expression pattern of the individual genes. However an extensive locus wide analysis of the methylation pattern in primary human tissue has not been performed. We used bisulfite sequencing to ...
For example, there is 70% penetrance if only 700 individuals express red phenotype out of 1,000 HairredHairred individuals. If penetrance of a phenotype is not 100%, then it has reduced penetrance. Mechanisms of reduced penetrance are not always clear. Expressivity is another important concept in describing genotype-phenotype correlation. Expressivity describes the severity of a phenotype among individuals with the same genotype. For example, if a condition has variable expressivity then one individual might have mild symptoms while another might have severe symptoms (although they have the same genotype). If a trait has constant expressivity then individuals with the same genotype will have the same degree of symptoms.. Mechanisms of variable expressivity are not always clear. Although there is typically a clear genotype-phenotype correlation that associates a specific allele with a specific phenotype, this link is frequently muddled. Even individuals with identical genotypes can have different ...
Islet leukocytic infiltration (insulitis) is first obvious at around 4 weeks of age in the NOD mouse - a model for human type 1 diabetes (T1D). The molecular events that lead to insulitis and initiate autoimmune diabetes are poorly understood. Since TID is caused by numerous genes, we hypothesized that multiple molecular pathways are altered and interact to initiate this disease. We evaluated the molecular phenotype (mRNA and protein expression) and molecular networks of ex vivo unfractionated spleen leukocytes from 2 and 4 week-old NOD mice in comparison to two control strains. Analysis of the global gene expression profiles and hierarchical clustering revealed that the majority (∼90%) of the differentially expressed genes in NOD mice were repressed. Furthermore, analysis using a modern suite of multiple bioinformatics approaches identified abnormal molecular pathways that can be divided broadly into 2 categories: metabolic pathways, which were predominant at 2 weeks, and immune response pathways,
We initially established ENU mutagenesis conditions for the rat in setting up gene-driven knockout technology using target-selected mutagenesis (Smits et al. 2004). However, the same F1 animals are also suited for forward genetic, phenotype-driven approaches. Indeed, several phenotypes caused by dominant mutations were readily identified in our experiments (Smits et al. 2004) as well as by others (Zan et al. 2003). Gould and colleagues (Zan et al. 2003) identified 74 visually aberrant mutants in a screen for dominant phenotypes in nearly 5000 F1 progeny from ENU-treated Sprague Dawley rats. About half of them were found to be fertile and to inherit the phenotype. Here, we describe a small-scale study on recessive phenotypes after ENU mutagenesis in the rat and the subsequent cloning of the mutated gene using a novel SNP mapping panel. Although the SNP mapping panel is of relatively low density and specifically designed for mapping crosses between Wistar and Brown Norway, it can easily be adapted ...
Amyotrophic lateral sclerosis (ALS) is a disease of variable severity in terms of speed of progression of the disease course. We found a similar variability in disease onset and progression of 2 familial ALS mouse strains, despite the fact that they carry the same transgene copy number and express the same amount of mutant SOD1G93A messenger RNA and protein in the central nervous system. Comparative analysis of 2 SOD1G93A mouse strains highlights differences associated with the disease severity that are unrelated to the degree of motor neuron loss but that appear to promote early dysfunction of these cells linked to protein aggregation. Features of fast progressing phenotype are (1) abundant protein aggregates containing mutant SOD1 and multiple chaperones; (2) low basal expression of the chaperone alpha-B-crystallin (CRYAB) and β5 subunits of proteasome; and (3) downregulation of proteasome subunit expression at disease onset. In contrast, high levels of functional chaperones such as ...
Since pharmacogenetic clinical recommendations are based on phenotype, the assignment of phenotype based on genotype is an important aspect to clinical implementation and reporting of different inferred phenotypes across laboratories and guidelines has created considerable confusion and inconsistencies in recommendations. To maximize the utility of pharmacogenetic test results, it is desirable to standardize the phenotype prediction from genotype data. The purpose of this project was to determine consensus among CYP2D6 experts as to the definitions used to assign CYP2D6 phenotype based on genotype.. ...
hi ml-stat-talks a reminder that barbara engelhardt is speaking tomorrow. she does top notch research at the intersection of graphical models and computational biology. best dave ---------- Forwarded message ---------- From: David Mimno ,mimno at, Date: Sun, Sep 18, 2011 at 8:55 PM Subject: [Ml-stat-talks] Wed 9/21: Barbara Englehardt on genome-wide associations To: ml-stat-talks at For our first ML talk of the year, we have Barbara Englehardt from Duke. The talk will be this Wednesday (9/21) at 12:30 in CS 402. Title: Genome-wide associations studies with complex phenotypes: How statistics can help Abstract: Genome-wide association studies (GWAS), or studies to identify genetic variants that are associated with a particular phenotype or disease, can be performed trivially using available software given sufficient numbers of individuals and simple quantitative or case-control phenotypes. However, when the phenotype of interest is complex (e.g., ...
PURPOSE: Mutations in murine and human versions of an ancestrally related gene usually result in similar phenotypes. However, interspecies differences exist, and in the case of two forkhead transcription factor genes (FOXC1 and FOXC2), these differences include corneal or anterior segment phenotypes, respectively. This study was undertaken to determine whether such discrepancies provide an opportunity for identifying novel human-murine ocular phenotypes. METHODS: Four pedigrees with early-onset glaucoma phenotypes secondary to segmental chromosomal duplications or deletions encompassing FOXC1 and 18 individuals from 9 FOXC2 mutation pedigrees underwent detailed ocular phenotyping. Subsequently, mice with mutations in Foxc1 or a related forkhead gene, Foxe3, were assessed for features of the human phenotypes. RESULTS: A significant increase in central corneal thickness was present in affected individuals from the segmental duplication pedigrees compared with their unaffected relatives (mean
Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r(2) | 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial
In order to identify the function of genes, the consortium uses a series of response (ABR) test conducted at 14 weeks of age. Hearing is assessed at five frequencies - 6kHz, 12kHz, 18kHz, 24kHz and 30kHz - as well as a broadband click stimulus. Increased thresholds are indicative of abnormal hearing. Abnormalities in adult ear morphology are recorded as part of the Combined SHIRPA and Dysmorphology (CSD) protocol, which includes a response to a click box test (absence is indicative of a strong hearing deficit) and visual inspection for behavioural signs that may indicate vestibular dysfunction e.g. head bobbing or circling. ...
Unique metabolic biomarkers specific to lung cancer were found through metabolic phenotyping of blood plasma by proton nuclear magnetic resonance (H-NMR), enabling diagnosis of both early-stage and late-stage disease.
Background: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.Results: We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits
article{7193339, abstract = {We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor a) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER+ or ER-) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER-tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.}, author = {Dunning, Alison M and Michailidou, Kyriaki and Kuchenbaecker, Karoline B and Thompson, Deborah and French, Juliet D and Beesley, Jonathan and Healey, Catherine S and Kar, Siddhartha and Pooley, Karen A and Lopez-Knowles, Elena and Dicks, Ed ...
We have identified DIAPH1 as a novel candidate gene for dominant MTP and sensorineural hearing loss by analysis of the largest ever assembled collection of cases with previously uncharacterized BPD. Essential to this discovery was the annotation of the characteristics of the cases with HPO terms for hematologic features and phenotypes in other organ systems, and then statistical analysis to identify similarities in HPO terms between cases. We have previously shown that cluster analysis of HPO terms within a large BPD case collection enabled identification of causal variants in ACTN1 and MYH9 that have been associated with MTP.7,9 However, the statistical evidence supporting DIAPH1 as a candidate gene could only be obtained by applying a novel similarity regression method to the phenotype and genotype data.19 Specifically, similarity regression revealed a hitherto unidentified association between a characteristic phenotype that was ontologically similar for 2 unrelated index cases and the shared ...
TY - JOUR. T1 - Phenotype harmonization and cross-study collaboration in GWAS consortia. T2 - The GENEVA experience. AU - Bennett, Siiri N.. AU - Caporaso, Neil. AU - Fitzpatrick, Annette L.. AU - Agrawal, Arpana. AU - Barnes, Kathleen. AU - Boyd, Heather A.. AU - Cornelis, Marilyn C.. AU - Hansel, Nadia N.. AU - Heiss, Gerardo. AU - Heit, John A.. AU - Kang, Jae Hee. AU - Kittner, Steven J.. AU - Kraft, Peter. AU - Lowe, William. AU - Marazita, Mary L.. AU - Monroe, Kristine R.. AU - Pasquale, Louis R.. AU - Ramos, Erin M.. AU - van Dam, Rob M.. AU - Udren, Jenna. AU - Williams, Kayleen. PY - 2011/4. Y1 - 2011/4. N2 - Genome-wide association study (GWAS) consortia and collaborations formed to detect genetic loci for common phenotypes or investigate gene-environment (GE) interactions are increasingly common. While these consortia effectively increase sample size, phenotype heterogeneity across studies represents a major obstacle that limits successful identification of these associations. ...
Fingerprint Dive into the research topics of Mac-1-negative B-1b phenotype of natural antibody-producing cells, including those responding to Galα1,3Gal epitopes α1,3-galactosyltransferase-deficient mice. Together they form a unique fingerprint. ...
TY - JOUR. T1 - Dark brown is the more virulent of the switch phenotypes of Candida glabrata. AU - Srikantha, Thyagaraja. AU - Daniels, Karla J.. AU - Wu, Wei. AU - Lockhart, Shawn R.. AU - Yi, Song. AU - Sahni, Nidhi. AU - Ma, Ning. AU - Soll, David R.. PY - 2008. Y1 - 2008. N2 - Candida glabrata undergoes reversible, high-frequency core switching between phenotypes that include dark brown (DB), light brown (LB) and white (Wh). These phenotypes in turn can switch to the irregular wrinkle (IWr) phenotype. Natural isolates, however, express predominantly the DB phenotype, leading to the hypothesis that it has a colonization advantage over the other switch phenotypes. Using the mouse model of systemic infection, results are presented which support this hypothesis. DB has an advantage over other switch phenotypes in colonizing the two major target organs in the mouse model, the spleen and liver. A time-course study reveals that colonization of the major target organs occurs very rapidly (within 2 ...
Cancer clinical outcome prediction using gene expression profiles has been proposed by the field of translational bioinformatics for better diagnostics, prognostics, and further therapeutics [1]. Somatic mutations and regulation abnormalities in a tumor cell cause substantial gene expression changes [2]. Expression of oncogenes or tumor suppressor genes promotes the malignant phenotype of cancer cells or inhibits cell division, development, or survival of cancer cell [2]. Thus, DNA microarray technologies have been widely used to predict clinical phenotypes such as stage, grade, metastatic status, recurrence, and patient survival in several cancers [3-5]. In terms of translational bioinformatics, accurate phenotype prediction based on the molecular signature can be used clinically to choose the best of several available therapies for a cancer patient.. However, clinical phenotype prediction based on gene expression profiles can vary between independent data sets [6, 7]. One possible explanation ...
This was the front page of this project wiki from June 1, 2007 to July 31, 2011, while it was funded (under the title of this page) by NSF grant BDI,nowiki>-,/nowiki>0641025. ==Linking Evolution to Genomics Using Phenotype Ontologies== [[Image:NESCent Logo.png,right]] ===About this project=== What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach this question due to a lack of computational tools that allow researchers to integrate developmental genetic and comparative morphological/anatomical data. [[Image:Ctol Logo.jpg,right]] [[Image:Zfinlogo.png,left]] We are addressing this by developing a database of evolutionarily variable morphological characters for a large clade of fishes (the Ostariophysi) and connecting this database to the large collection of mutant phenotypes in the [ ZFIN database], the central database of the zebrafish model organism community. The evolutionary and mutant ...
Rise and fall of phenotype frequency[edit]. Melanism has appeared in the European and North American peppered moth populations ... Much more is known about the subsequent fall in phenotype frequency, as it has been measured by lepidopterists using moth traps ... From around 1962 to the present, the phenotype frequency of carbonaria has steadily fallen in line with cleaner air around ... He thus showed that the melanic phenotype was important to the survival of peppered moths in such a habitat. Kettlewell ...
The current hypothesis for the evolution of the saber-toothed phenotype, made possible by Batollnes-1, is that this phenotype ... so the evolutionary history of the saber-toothed phenotype, a phenotype affecting craniomandibular, cervical forelimb and ... Evolutionary history and origin of phenotype[edit]. Until the recent discovery of the Late Miocene fossil depository known as ... They provide further morphological evidence for the importance of speed in the evolution of the saber-toothed phenotype.[23] ...
Age related conditions and phenotypes[edit]. Horvath co-authored the first articles demonstrating that DNA methylation age ...
Extension phenotypes[edit]. *E/E (+/+, E+/E+, EE/EE) wildtype, homozygous dominant. Visually, such horses are black, seal brown ... Dun phenotypes[edit]. *D/D (+/+, D+/D+) wildtype, homozygous dominant. Visually, the horse may be bay dun, grullo, red dun, ... Agouti phenotypes[edit]. *A/A wildtype, homozygous. Visually, the horse may be bay, buckskin, bay dun, amber champagne, and so ... Champagne phenotypes[edit]. *ch/ch (N/N) wildtype, homozygous recessive. Visually, the horse may be any color other than the ...
Phenotype characteristics[edit]. Both breeds are easily identifiable by their phenotypic characteristics.[1] There are no ... A microsatellite study on the genetic distance between Suri and Huacaya phenotypes in Peruvian alpaca (Vicugna pacos). ...
Partial EMT or a hybrid E/M phenotype[edit]. Not all cells undergo a complete EMT, i.e. losing their cell-cell adhesion and ... phenotype are endowed with special properties such as collective cell migration.[50][87][88][89][90][91][92][93] Two ... In vertebrates, epithelium and mesenchyme are the basic tissue phenotypes. During embryonic development, migratory neural crest ... an alliance against the epithelial phenotype?". Nature Reviews Cancer. 7 (6): 415-428. doi:10.1038/nrc2131. hdl:10261/81769. ...
Extended phenotype. *my website. *My photos on flickr. *I plus a bit here and tweet here ...
Lineage and antigenic phenotype[edit]. These have been established by classic work by Raff et al. in early 1980s on Rat optic ... Astrocytes that have been pushed into a reactive phenotype (termed astrogliosis, defined by upregulation of GFAP expression, a ...
Mcph1 knockout mouse phenotype Characteristic. Phenotype Homozygote viability. Normal Fertility. Abnormal Body weight. Normal ...
Prmt5 knockout mouse phenotype Characteristic. Phenotype Homozygote viability. Abnormal Recessive lethal study. Abnormal ...
The recent definition of genotype-phenotype correlations allows prediction of the clinical evolution of the disease in most ... cases.[40][53] Genotype-phenotype correlations have been reported also for the severity of thrombocytopenia, platelet size, and ... "Mutation spectrum and genotype-phenotype correlations in a large French cohort of MYH9-Related Disorders". Molecular Genetics ... "MYH9-related disease: a novel prognostic model to predict the clinical evolution of the disease based on genotype-phenotype ...
Pnpt1 knockout mouse phenotype Characteristic. Phenotype Homozygote viability. Abnormal Recessive lethal study. Abnormal ...
... knockout mouse phenotype Characteristic. Phenotype All data available at.[7][12] ...
... knockout mouse phenotype. Characteristic. Phenotype. Homozygote viability. Normal. Fertility. Normal. Body weight. Normal ...
Optn knockout mouse phenotype Characteristic. Phenotype Homozygote viability. Normal Fertility. Normal Body weight. Normal ...
GAP43 is also haploinsufficient for the cortical phenotypes and the severity of the axon targeting phenotype is directly ... "Deletion of chromosome 3q proximal region gives rise to a variable phenotype". Clinical Genetics. 53 (3): 220-2. doi:10.1111/j. ...
Phenotype. Body. Born any color, progressively lightens with age until completely white, flea-bitten form may develop red hairs ... Dark skin distinguishes the grey phenotype from that of pink-skinned cremello and white horses.. ...
Suppose that the phenotypes of AA and Aa are indistinguishable, i.e., there is complete dominance. Assuming that the Hardy- ... This data is from E.B. Ford (1971) on the Scarlet tiger moth, for which the phenotypes of a sample of the population were ... The phenotype distribution from Table 3 above will be used to compute Hardy's initial genotype distribution. Note that the p ... Genotype-phenotype distinction is assumed to be negligibly small. The null hypothesis is that the population is in Hardy- ...
Phenotype[edit]. Main article: Phenotype. Any given gene will usually cause an observable change in an organism, known as the ... Conversely, some phenotypes could be the result of multiple genotypes. The genotype is commonly mixed up with the phenotype ... Genotype and phenotype are not always directly correlated. Some genes only express a given phenotype in certain environmental ... phenotype) of that cell/organism/individual.[2] Genotype is one of three factors that determine phenotype, the other two being ...
Dawkins, Richard (1999). The extended phenotype: the long reach of the gene (Revised with new afterword and further reading ed ... The Extended Phenotype (1982), in which he describes natural selection as "the process whereby replicators out-propagate each ... The Extended Phenotype. Oxford: Oxford University Press. 1982. ISBN 978-0-19-288051-2. .. ... With his book The Extended Phenotype (1982), he introduced into evolutionary biology the influential concept that the ...
Just as all researched human behavioural phenotypes are influenced by genes (i.e., are heritable), all such phenotypes are also ... is the phenotype, g. {\displaystyle g}. is the effect of genes, ϵ. {\displaystyle \epsilon }. is the effect of the environment ... 2013). Behavioral Genetics of the Mouse: Genetics of Behavioral Phenotypes. Cambridge Handbooks in Behavioral Genetics. 1. ... of variation in the phenotype.[3] This fact has been discovered primarily through genome-wide association studies of complex ...
Using these two antibodies, three common phenotypes were defined: Fy(a+b+), Fy(a+b-), and Fy(a-b+).[citation needed] ... The Duffy negative phenotype occurs at low frequency among whites (~3.5%) and is due to a third mutation that results in an ... The genetic basis for the Fy(a-b-) phenotype is a point mutation in the erythroid specific promoter (a T -, C mutation at ... In Grande Comore (also known as Ngazidja) the frequency of the Fy(a- b-) phenotype is 0.86.[55] ...
Further information: Phenotype § Phenotypic_variation. Sub-Saharan Africa has the most human genetic diversity and the same has ... As a result of variation in frequencies of both genetic and nongenetic risk factors, rates of disease and of such phenotypes as ... and associated phenotype, can be inherited across generations of individuals.[29] ... been shown to hold true for phenotypic variation in skull form.[36][44] Phenotype is connected to genotype through gene ...
Dawkins, Richard (1982). The Extended Phenotype. Oxford University Press. ISBN 978-0-19-286088-0.. ...
Dawkins, Richard (1982). The Extended Phenotype. Oxford: Oxford University Press. p. 2. ISBN 978-0-19-286088-0. .. ...
The Extended Phenotype (1982). *The Blind Watchmaker (1986). *River Out of Eden (1995) ...
The Extended Phenotype (1982). *The Blind Watchmaker (1986). *River Out of Eden (1995) ...
The Extended Phenotype (1982). *The Blind Watchmaker (1986). *River Out of Eden (1995) ...
The Extended Phenotype (1982). *The Blind Watchmaker (1986). *River Out of Eden (1995) ...
The Extended Phenotype (1982). *The Blind Watchmaker (1986). *River Out of Eden (1995) ...
DECIPHERING EEG PHENOTYPES ONLINE CLASS RECORDING. Instructor: Linda Walker, MHR, LCP. Whether you are new to the field of ... Phenotypes provide classification of the abnormal EEG record only and even advise on the response the brain will have to ... The phenotypes she will discuss include:. • Diffuse Slow Activity (with or without slower alpha). • Focal Abnormalities (not ... Over the four sessions, Linda Walker will discuss the EEG of the brain in terms of the phenotype model for understanding ...
Nordo-Cromagnoid phenotype,... Nordo-Cromagnoid phenotype, intelligent/Redpilled, morals, has a sustainable income. ... Im interested in classifying various European phenotypes, and its kind of fun to do. I try finding as many forums that have ...
State the main phenotypes of these African-Americans Started by Tooting Carmen, Today 01:27 AM ...
Of course genotype is not phenotype. It is not equivalent or 1:1. Still it makes some sense that where there is for example low ... But I guess in our potpourri of phenotypes the originals still shimmers through.. So you expect in Northern Germany/ North ... We know phenotypes have heavy genomic basis if not the only factor ; but as external aspect is based on a relative small number ... Of course genotype is not phenotype. It is not equivalent or 1:1. Still it makes some sense that where there is for example low ...
Associations between phenotypes of preeclampsia and thrombophilia Last post by caryn « Wed Feb 18, 640533 8:07 am ...
Associations between phenotypes of preeclampsia and thrombophilia Last post by caryn « Wed Feb 18, 640533 8:07 am ...
Thread: MAJOR RANT - Pseudo Science Cherrypicking, white obssession, racism, lack of exposure to phenotypes.. by The Lawspeaker ...
The idea of traditional eugenics is to have a healthy phenotype, while being totally ignorant about the underlying genotype.. ...
The genes that have made our phenotypes different are few and far between. The genes we all share are by far more common, and ... and change its phenotype, it does so to one particular gene and protein. Again, you may decide to focus on one particular ... and thus phenotypes, that humans have in common, or the approximately 100 s that are different from person to person? Do you ...
Germanic Online Community. Securing Freedom, Social Justice and the Germanic Leitkultur.
Using data from all participants, age emerged as the only reliably predicted phenotype. Follow-up analyses done for each age ... attempted to use individuals functional connectivity during rest in predicting individual differences in behavioral phenotypes ...
NEW: YSEQ Phenotype Predictor. Free tool to visualize phenotyping alleles.. Accepts uploads of raw data files from WGS400 and ...
NEW: YSEQ Phenotype Predictor. Free tool to visualize phenotyping alleles.. Accepts uploads of raw data files from WGS400 and ...
You have Dantes phenotype (check my latest thread). You may very well be the biggest mentalcel of all time ...
Mucosal unheroic freely: waken phenotypes. Last post by ovufazo « 21 Sep 2021 12:57 Posted in Chit chat ...
Additional acquired resistant genes could lead to pan resistant phenotype.. Explore the genetic background from two human and ...
Most likely part of the Broader Autism Phenotype (some traits).. Profile. Report. ...
Most likely part of the Broader Autism Phenotype (some traits).. Profile. Report. ...
Most likely part of the Broader Autism Phenotype (some traits).. Board index ...
Yes, as youve learnt, this phenotype is not natural and in my opinion quite cruel. ...
Yes, as youve learnt, this phenotype is not natural and in my opinion quite cruel. ...
In these four 1.5-hour session recordings, originally presented in June 2011, Linda Walker instructs participants on Alpha-Theta training to facilitate treatment of individuals struggling with recovery from substance abuse, trauma and PTSD. Furthermore, Alpha-Theta training can benefit meditation and performance enhancement. The material discussed is based on current research and her own clinical experiences. A brief synopsis of these lessons is as follows: - Lesson 1: History of alpha-theta training, theory of why it helps and contemporary research and protocols.. - Lesson 2: Leading up to starting Alpha-Theta therapy with a client; relaxation strategies; principles for induction and running an Alpha-Theta session; EEG electrode placement and montage; EEG bandwidths; induction tips; example of an alpha-theta session.. - Lesson 3: Further examples of an alpha-theta session, in terms of EEG reading and the therapeutic induction; review of Alpha-Theta training suite visual displays for monitoring ...
CONTENT: This 6-hour class presented by Linda Walker, MHR, LPC, BCN, BCB introduced licensed professionals to the measurement of heart rate variability (HRV) from an EKG signal or from peripheral blood flow (HR/BVP). The 4 x 1.5 hour lesson demonstrated a variety of convergent training strategies to produce increased heart rate variability.. ...
3.12 Discussions pertaining to physical appearance and/or phenotype that are quantitative and accompanied with structured ...
Nobody knows for sure where OG Kush comes from, but the most plausible lineage links to it being a phenotype of Chemdawg. ...
Phenotypes and Characteristics. *General Discussions *Angel Talk. *General Aquatic Discussions. *Aquarium News ...
Phenotypes and Characteristics. *General Discussions *Angel Talk. *General Aquatic Discussions. *Aquarium News ...
Septentrion replied to a thread Taxonomy/phenotype is bullshit in Anthropology It is no BS!!!! Not everybody is mixed like you ...
  • Search by «Any study term» provides results for phenotype terms through the studies having common genes knocked down. (
  • Microarray data are good phenotypes to determine the order of genes and are a good surrogate measure of cell status," said Dr. Gad Shaulsky, associate professor of molecular and human genetics at BCM. (
  • The microarray data Shaulsky and his collaborators used show that they can determine the order in which genes act in a cascade that results in a particular phenotype. (
  • Some phenotypes are controlled entirely by the individual's genes . (
  • Geneticists use easily observable phenotypes to deduce an organism's genotype, and analyze complex phenotypes to help hypothesize about how individual genes function. (
  • Many phenotypes also are determined by multiple genes . (
  • The idea of an extended phenotype refers to the expression of genes in the behavior of an organism rather than its physical composition. (
  • The goal of this big idea is to address how we predict the phenotype, the structure, function and behavior of an organism, based on what we know about its genes and environment," Olds says. (
  • In it, Dawkins extended the gene's eye view to argue that the genes that sit within an organism have an influence that reaches out beyond the visible traits in that body - the phenotype - to the wider environment, which can include other individuals. (
  • By measuring this variation and its effect on phenotype, we show that expression for specific genes may be free to vary during evolution within particular bounds. (
  • The breed purity debate goes along these lines: should a breed be based on genotype (what genes it inherited) or phenotype (appearance, despite an out-cross four generations ago) A Tabby-point Siamese is phenotypically Siamese, but because the tabby pattern was introduced from non-Siamese cats, genotype-followers consider it "not Siamese" and are worried it will pollute their purebred breeding lines. (
  • This diagram displays phenotype observables (purple squares) that are shared between the given gene (yellow circle) and other genes (gray circles) based on the number of phenotype observables shared (adjustable using the slider at the bottom). (
  • As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. (
  • The variation in genes caused by mutation generates the different phenotypes, characteristics such as animal behaviour, that allow natural selection to work. (
  • many of our genes, that's how genotype affects phenotype. (
  • We have proposed that an early step in tumor progression is the expression of a mutator phenotype resulting from mutations in genes that normally function in the maintenance of genetic stability. (
  • Larvae with these traits have a higher chance of survival when exposed to the predators, but grow more slowly than other phenotypes. (
  • Phenotype is the total observable physical traits of an individual ( organism or cell ). (
  • Still other phenotypes are entirely non-genetic, for example, a person's language or physical traits that were altered by surgery. (
  • Either way, the term phenotype includes traits or characteristics that can be made visible by some technical procedure. (
  • An intermediate phenotype describes an organism that displays a blend of the phenotypic traits that its parents expressed. (
  • An individual's phenotype refers to their observable traits, such as height or eye color. (
  • Newswise - Irvine, CA - June 1, 2021 - A new study analyzing the association between an individual's genetics (genotype) and their observable characteristics resulting from the interaction of genetics and the environment (phenotype), contributes new knowledge to the understanding of human complex traits and diseases. (
  • Gene expression patterns provide a cellular phenotype, while phenotypic traits relate to the individual subject. (
  • Phenotype refers to the traits that are actually present in the organism. (
  • This combination of traits may not be available in any existing organism or if they do exist, the mechanisms involved in the phenotype-expression may not be efficient enough to be useful. (
  • This timely text presents a comprehensive guide to genetic association, a new and rapidly expanding field that aims to elucidate how our genetic code (genotypes) influences the traits we possess (phenotypes). (
  • In genetics, the phenotype (from Greek φαινο- 'pheno', and τύπος 'type') is the set of observable characteristics or traits of an organism. (
  • The thrifty phenotype hypothesis suggests that early-life metabolic adaptations help in survival of the organism by selecting an appropriate trajectory of growth in response to environmental cues. (
  • Recently, some scientists have proposed that the thrifty phenotype prepares the organism for its likely adult environment in long term. (
  • If there is little plasticity, the phenotype of an organism can be reliably predicted from knowledge of the genotype, regardless of environmental peculiarities during development. (
  • A phenotype is said to be canalized if mutations (changes in the genome) do not noticeably affect the physical properties of the organism. (
  • The phenotype of a developing or developed organism is held to be the result of interaction between the inherited genotype (the genetic makeup of the individual), transmitted epigenetic factors (those changes in genome function that do not alter the nucleotide sequence within the DNA), and non-hereditary environmental variation . (
  • Thus, the identity of one or a few alleles of an organism does not always enable prediction of its phenotype. (
  • It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. (
  • In this instance, the organism would only show the dominant phenotype of the gene. (
  • Metabolite profiling technologies have improved to generate close to quantitative metabolomics data, which can be employed to quantitatively describe the metabolic phenotype of an organism. (
  • Sometimes, the target phenotype maybe required in combination with other phenotypes, in order to be useful, for e. g., an industrial process may require that the organism survive in an anaerobic, alcohol rich environment and be able to feed on both hexose and pentose sugars to produce ethanol. (
  • The change of perspective which Dawkins advocates is from the supposedly then orthodox view that it is the individual organism which is the beneficiary of evolutionary adaptation, to one in which the beneficiary is the extended phenotype. (
  • The genotype-phenotype distinction is drawn in genetics . (
  • These results do not negate the invaluable contributions of mouse genetics to biomedical science, but they do show that genotype-phenotype relationships cannot be reliably inferred by studying a single genetic background, and thus constitute a major challenge to the status quo. (
  • The biggest gap in biological knowledge is our inability to look at an organism's genetics and environment and predict its observable characteristics, or phenotype. (
  • In genetics, what is the difference between a genotype and phenotype? (
  • In contrast to phenotypic plasticity, the concept of genetic canalization addresses the extent to which an organism's phenotype allows conclusions about its genotype. (
  • In a narrow 'genetic' sense, the genotype defines the phenotype. (
  • An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype , and the influence of environmental factors, which may interact, further affecting phenotype. (
  • This database aims to provide a central resource to archive and display associations between genetic variation and high-throughput molecular-level phenotypes. (
  • My first book, The Revolutionary Phenotype, proposes a new theory for the emergence of life which explains how new layers of genetic code are added to the iterations of previous life forms. (
  • The Revolutionary Phenotype is essential in understanding the mechanisms for the emergence of life as well as the potential dangerous effects of genetic modifications in humans. (
  • In addition to genetic factors, a person's phenotype is also influenced by environmental factors. (
  • Genotype is the genetic makeup while phenotype is the outward physical manifestation of the genotype. (
  • Here we re-emphasize the old standpoint that the genotype-phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. (
  • Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes. (
  • However, before any genetic modification can take place, it is important to identify the underlying cellular subsystems responsible for the expression of the target phenotype. (
  • Mutation is modeled by diffusion, selection is modeled by differential phenotype fitness, and genetic recombination is modeled by an averaging process. (
  • Please contact us with any other questions about the Mammalian Phenotype Ontology. (
  • Paul Andersen explains how changes in the genotype of an individual can affect the phenotype. (
  • The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. (
  • The genome in which a genotype is found can affect the expression of that genotype, and the environment can affect the phenotype. (
  • If, on the other hand, the patient has failed an efavirenz-containing regimen and has a K103N mutation, which is one of the primary resistance mutations for efavirenz, the phenotype test might be reported as a '60-fold reduction in susceptbility to EFV', compared to wild-type virus. (
  • In the above example, the patient who is failing an EFV-based regimen first develops the K103N resistance mutation, and then, within a short period of time, their phenotype will also show reduced susceptibility of the patient's virus to EFV. (
  • The term "phenotype" has sometimes been incorrectly used as a shorthand for phenotypic difference from wild type , bringing the absurd statement that a mutation has no phenotype. (
  • Lastly, I will speculate on the theoretical and practical implication of a mutator phenotype in cancer and consider the possibility of cancer prevention by delay, i.e. , a reduction in mutation rates early during carcinogenesis might slow the progression of tumors. (
  • This is faulty logic, because there are almost certainly many other mutations that produce the hairless phenotype. (
  • The concept of a mutator phenotype in cancer was initially formulated (1) to account for the disparity between the rarity of mutations in normal cells and the large numbers of mutations present in a variety of human malignancies. (
  • Even two organisms with identical genotypes normally differ in their phenotypes. (
  • in many organisms these phenotypes are very different under varying environmental conditions (see ecophenotypic variation ). (
  • An incomplete dominance Punnett square is a diagram that predicts the outcome of genotype as well as phenotype in organisms. (
  • The method can compare the organismal network information from hundreds of phenotype expressing and phenotype non-expressing organisms to identify cellular subsystems that are more prone to occur in phenotype-expressing organisms than in phenotype non-expressing organisms. (
  • Another extension adds behavior to the phenotype, since behaviors are observable characteristics. (
  • A Non-interventional Nationwide Registry to Identify Indian Phenotype Characteristics in Diabetes Mellitus Patients in India. (
  • The purpose of this study is to correlate phenotype and genotype of Down syndrome patients in order to identify the biochemical reactions involved in their mental retardation and their other phenotypic characteristics. (
  • An integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. (
  • Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. (
  • Since the early proposal that genotypes and phenotypes form two fundamentally different levels of biological abstraction ( Johannsen, 1911 ), the challenge has been to understand how they articulate with each other, how genotypes map onto phenotypes. (
  • Here we reflect on the relationship between genotypes and phenotypes and we address this essay to biologists who are willing to try to challenge their current understanding of phenotypes. (
  • The terms "genotype" and "phenotype" were created by Wilhelm Johannsen in 1911. (
  • The genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces. (
  • The Cellular Phenotype database provides easy access to phenotypic data derived from high-throughput screening, facilitating data sharing and integration. (
  • A high level of plasticity means that environmental factors have a strong influence on the particular phenotype that develops. (
  • The phrase norm of reaction refers to the amplitude of variation of a phenotype produced under different environmental conditions (Mayr 2001). (
  • Phenotype, by contrast, refers to basically everything else. (
  • His bestselling books include The Selfish Gene (1976), The Extended Phenotype (1982) and its sequel The Blind Watchmaker (1986), River Out of Eden (1995), Climbing Mount Improbable (1996), Unweaving the Rainbow (1998), A Devil's Chaplain (2004), The Ancestor's Tale (2004), and The God Delusion (2007). (
  • Due to the potential volume of data, the latter option is available only if a phenotype trait was selected in the initial search. (
  • To facilitate the development of a personalized approach to the treatment of patients with major depression , this study is designed to elaborate the clinical and neurobiological phenotype of depressed patients with increased inflammation. (
  • This study examined empirical evidence related to this diagnostic shift and aimed to identify basic sensory-clinical pain phenotypes in patients with chronic local primary pain (chronic primary back pain [CBP]) and patients with chronic widespread primary pain (fibromyalgia syndrome). (
  • Combined sensory-clinical pain phenotypes of 185 patients with previous CBP and fibromyalgia syndrome diagnoses were derived by a stepwise data reduction through descriptive statistical, correlational, principal components and latent class analyses. (
  • These sensory-clinical phenotypes differed also in somatic symptoms and impairment but neither in psychopathology nor in psychosocial cofactors. (
  • [ 55 , 64 ] This study examined the diagnostic significance of sensory changes by a cluster-analytic approach to identify subgroups of patients according to sensory-clinical pain phenotypes without the comorbidity components of the Symptom Severity Scale. (
  • The "hypertriglyceridemic waist" phenotype (i.e., abdominal obesity in combination with hyper-triglyceridemia) is a clinical marker of visceral obesity. (
  • The hypertriglyceridemic-waist phenotype has been identified as a simple, easily available clinical marker of visceral obesity and related metabolic abnormalities. (
  • To advance the clinical use of precision medicine, big data cohort for genotype/phenotype research and multidisciplinary team approaches are necessary. (
  • In addition to the clinical classification of phenotypes, FTD can also be classified according to its histopathological substrate established after autopsy. (
  • This entire section is optional if a category and/or trait are selected in the phenotype selection. (
  • An organism's genotype is a major (the largest by far for morphology ) influencing factor in the development of its phenotype, but it is not the only one. (
  • The genotype-phenotype distinction should not be confused with Francis Crick 's central dogma of molecular biology , which is a statement about the directionality of molecular sequential information flowing from DNA to protein, and not the reverse. (
  • however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets. (
  • It seems pertinent now to summarize recent data and to consider the theoretical and practical implications of a molecular phenotype in cancer. (
  • dominance when AA = Aa in phenotype, A is dominant, a is recessive . (
  • Our male X-linked recessive cases show significant new phenotypes: developmental delay (without eye anomalies) in two affected half-brothers with a novel BCOR variant, and one male with high myopia, megalophthalmos, posterior embryotoxon, developmental delay, and heart and bony anomalies with a previously undescribed BCOR splice site variant. (
  • What are examples of homozygous recessive phenotype? (
  • An example of homozygous recessive phenotype would be a red-flowered pea plant. (
  • Cystic fibrosis is another homozygous recessive phenotype. (
  • Other diseases, such as Huntington's, are also expressed through the recessive phenotype. (
  • If canalization is not present, small changes in the genome have an immediate effect on the phenotype that develops. (
  • approaches that relate genome structure to phenotype. (
  • Richard Dawkins, the man who proposed the idea of the extended phenotype, argues that once the new allele was introduced, the population of birds would evolve because of the allele. (
  • Richard Dawkins' Extended Phenotype (EP) concept is as relevant now as when it was first proposed 26 years ago and is not at odds with other evolutionary explanations. (
  • The link between regulation of INO1 gene expression and the Opi − phenotype is further supported by the existence of the dominant OPI5+ mutant allele ( S wift and M c G raw 1995 ). (
  • The white-flowered pea plant expresses the dominant phenotype. (
  • When allele A is dominant over allele A', write out the parental phenotypes and genotypes. (
  • Selection acts on phenotypes because differential reproduction and survivorship depend on phenotype. (
  • The model consists of a partial differential equation for population density with respect to a continuous variable representing phenotype diversity. (
  • Phenotype " is an organism's actual observed properties, such as morphology , development , or behavior . (
  • Collectively, these findings suggest that Vmat2 heterozygotes display a depressive-like phenotype that is devoid of anxiety-like behavior. (
  • Forty-eight patients from two independent cohorts fulfilling the Canada 2003 criteria for ME/CFS were evaluated with respect to cytotoxic lymphocyte phenotype and function. (
  • CONCLUSIONS -Hp phenotype is an apparent risk factor for the development of GDM in our study population. (
  • Polygenic inheritance can be explained by additive effects of many loci: if each 'capital' allele contributes one increment to the phenotype. (
  • The data suggest that there may be an association between acetylation phenotype and colorectal carcinoma. (
  • It has been suggested that the thrifty phenotype is the consequence of three unlike adaptive processes: maternal effects, niche construction and developmental plasticity, which all are influenced by the brain. (
  • The concept of phenotypic plasticity describes the degree to which an organism's phenotype is determined by its genotype. (
  • If the basis for breed was purely about the phenotype then would it be true to say that any breed which produces variants (prick-eared Scottish Folds, tailed Manxes etc) is not strictly a breed according to this definition? (
  • Behavioral phenotypes include cognitive, personality, and behavioral patterns. (
  • Some behavioral phenotypes may characterize psychiatric disorders [5] or syndromes. (
  • I have a weird overexpression phenotype in S. pombe and I would like to link it to mutants or other overexpression. (
  • The Opi − phenotype correlates with constitutive overexpression of the INO1 gene ( H irsch and H enry 1986 ), which is responsible for de novo synthesis of inositol ( Figure 1 ) ( C ulbertson and H enry 1975 ). (
  • In contrast, a phenotype test is a measure of the ability of a single patient's virus to replicate in the presence of each ART drug. (
  • Model of dominance from enzyme activity: no copies produce no phenotype, one copy produces x amount of product and two copies produces 2x then the alleles are additive and there is no dominance (intermediate inheritance). (
  • Combinations of these alleles create genotypes, which translate to phenotypes . (
  • It is possible that an apparent genotype-phenotype relationship could be due to linkage disequilibrium with the functional SNP. (
  • RESEARCH DESIGN AND METHODS -From consecutive Caucasian pregnant women ( n = 250) referred for oral glucose tolerance testing, the Hp phenotype was determined. (
  • Alternatively, complete HIVDB phenotype datasets may be downloaded here . (
  • Common laboratory hallmark in all phenotypes is the reduced glucose level in cerebrospinal fluid with lowered CSF-to-blood glucose ratio. (
  • Significance of distribution and odds ratios (ORs) associated with Hp phenotype were calculated for women with GDM ( n = 110) and women with normal glucose tolerance ( n = 140). (
  • Our study aimed to assess the association between the hyper-triglyceridemic-waist phenotype in early pregnancy and glucose intolerance in later pregnancy. (
  • 8 , 9 It is defined as the simultaneous presence of abdominal obesity (i.e., a waist girth greater than 85 cm in women or greater than 90 cm in men) and hypertriglyceridemia (i.e., a triglyceride concentration ≥ 2 mmol/L). The aim of our study was to document the association between the presence of the hypertriglyceridemic-waist phenotype in early pregnancy and impaired glucose tolerance in later pregnancy. (
  • To correlate imaging and pathological phenotype with genotype to the ends described above. (
  • In all cases, the phenotype results from the genotype, i.e. usually a structural change will occur first, and soon thereafter a phenotypic change will result. (
  • Taken together, these results indicate that jacalin, by exerting a proinflammatory activity, can direct macrophages to an antitumor phenotype. (
  • These studies are based on the assumption that observed genotype-phenotype relationships will generalize to humans, implying that the results would at least generalize to other inbred mouse strains. (
  • Studies that use PhenX (consensus measures for Phenotypes and eXposures) measures benefit from the ability to perform cross-study analyses to increase statistical power and to replicate results. (
  • The opi1 mutant o ver p roduces and excretes i nositol into the growth medium in the absence of inositol and choline (Opi − phenotype). (
  • Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. (
  • Here we show that in the 2.7% and 1.8% of patients with advanced-stage cancer and germline pathogenic or somatic loss-of-function alterations in BRCA1/2 , respectively, selective pressure for biallelic inactivation, zygosity-dependent phenotype penetrance, and sensitivity to PARP inhibition were observed only in tumour types associated with increased heritable cancer risk in BRCA1/2 carriers (BRCA-associated cancer types). (
  • OBJECTIVE To determine plasma apolipoprotein A-IV (apoA-IV) levels and phenotype distribution in non-insulin-dependent diabetes mellitus (NIDDM) patients and to analyze the influence of apoA-IV phenotype on lipid profiles in NIDDM. (
  • The potential protective lipid profile (characterized by increased HDL and HDL 2 cholesterol levels) linked with apoA-IV-1-2 phenotype in control subjects is no longer found in NIDDM patients. (
  • Sulfamethazine acetylation phenotype was determined in 49 patients with cancer of the colon or rectum, 41 old, and 45 young control subjects. (
  • As a consequence of racial intermixture during the colonial era, phenotype in the contemporary Mexican-origin population ranges on a continuum from those who appear white to those who have dark skin, indigenous facial features, and shorter height than average. (
  • In view of the extended phenotype, we suggest a new term of X-linked BCOR -related syndrome. (
  • MASS phenotype is a medical disorder similar to Marfan syndrome . (
  • Given that the interactions between tumor cells and TAMs involve several players, a better understanding of the function and regulation of TAMs is crucial to interfere with their differentiation in attempts to skew TAM polarization into cells with a proinflammatory antitumor phenotype. (
  • Cite this: Association of Interactions Between Mammographic Density Phenotypes and Established Risk Factors With Breast Cancer Risk, by Tumor Subtype and Menopausal Status - Medscape - Jan 01, 2021. (