Information

25.10: Glossary: S - Biology

25.10: Glossary: S - Biology


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25.10: Glossary: S

Glossary

Active site The part of protein that must be maintained in a specific shape if the protein is to be functional.

Allele One of two copies of a gene.

Amino acid A peptide the basic building block of proteins.

Amplicon Replicated target molecules created by polymerase chain reaction or other nucleic acid amplification methods.

Amplification Increasing the number of copies of a desired DNA segment. The amplified regions are called amplicons.

Aneuploid cell A cell having a chromosome number that differs from the normal chromosome number for the species by a small number of chromosomes.

Annealing Spontaneous alignment of two single DNA strands to form a double helix.

Antibody A protein molecule, produced by the immune system, that recognizes a particular substance and binds to it.

Anticodon A nucleotide triplet in a tRNA molecule that aligns with a particular codon in mRNA under the influence of the ribosome so that the amino acid carried by the tRNA is inserted in a growing protein chain.

Antiparallel A term used to describe the opposite orientations of the two strands of a DNA double helix the 5’ end of one strand aligns with the 3’ end of the other strand.

Avidin A protein that specifically binds to biotin with usually high affinity.

Autoradiography The exposure of roentgenographic film to a blot or membrane containing a radiolabeled probe, used to locate the labeled probe

Bacteriophage A virus that infects bacteria

Base One nucleotide consisting of a nucleoside, pentose sugar and triphosphate building blocks for either DNA or RNA

Base analog A chemical whose molecular structure mimics that of a DNA base because of the mimicry, the analog may act as a mutagen.

Base pair (bp) One pair of complementary nucleotides (e.g. adenine to thymine or guanine to cytosine) on opposite sides of the duplex strands

Cell cycle The set of events that take place in the divisions of mitotic cells. The cell cycle oscillates between mitosis (M phase) and interphase. Interphase can be subdivided in order into G1, S phase and G2. DNA synthesis takes place during S phase. The length of the cell cycle is regulated through a special option in G1, in which G1 cells can enter a resting phase call G0

Chromosome Structure of DNA and associated proteins that contain the hereditary material within the cell. Genes are organized in linear arrangement in the chromosome.

Cistron Segments of DNA corresponding to one polypeptide chain, plus transcriptional start and stops signs.

Cloning The process of generating a large number of identical DNA fragments, typically to produce a probe for a specific gene.

Codominance The situation in which a heterozygote shows the phenotypic effects of both alleles.

Codon A sequence of three nucleotides that specifies a particular amino acid

Competent Able to take up exogenous DNA and thereby be transformed.

Complementarity The specific binding of adenine to thymidine (or uracil in RNA) and cytosine to guanine on opposite strands of DNA or RNA.

Complementary DNA or Copy DNA(cDNA) DNA generated form mRNA by the use of reverse transcriptase.

Complementary RNA Synthetic RNA produced by transcription from a specific DNA single-stranded template.

Complementation The production of a wild-type phenotype when two different mutations are combined in a diploid or a heterokaryon.

Cosmid A genetically engineered construct containing sites from lambda phage that allow for insertion of large pieces of DNA (30-50 kb). Recombinant cosmids can then be replicated in bacterial hosts.

Degenerate code A genetic code in which some amino acids may be encoded by more than one codon each.

Degradation Due to physical shearing or exposure to endogenous or exogenously added nucleases, DNA and RNA can become hydrolyzed or degraded to the oligonucleotide or single-nucleotide level.

Denaturation The process of making double-stranded DNA single stranded.

Dideoxy sequencing A method of DNA sequencing in which dideoxynucleotide triphosphates (ddNTPs) are used in the growing oligonucleotide chains synthesized from the DNA template, thereby terminating elongation.

DNA Deoxyribonucleic acid

DNAase Deoxyribonuclease, an endonuclease that randomly hydrolyzes (nicks) DNA at single sites on either strand of the DNA

DNA ligase An enzyme that covalently joins two pieces of double stranded DNA.

DNA polymerase The enzymes(s) that make DNA by the addition of bases to the end of the replicating DNA strand.Also has an editing function that can repair nicked DNA by removal of old nucleotides and replacement with new (e.g. labelled) nucleotides.

Dominant allele An allele that expresses its phenotypic effect even when heterozygous with a recessive allele thus if A is a dominant over a, then A/A and A/a have the same phenotype.

Dominant phenotype The phenotype of a genotype containing the dominant allele the parental phenotype that is expressed in a heterozygote.

Dot (slot) blot The immobilization of DNA or RNA to a sample spot (slot) on a filter that will be subsequently probed by hybridization. Usually many samples are applied, each to a different location on the same filter, for mass screening.

ds Double stranded

End-labeling The incorporation of nucleotides at the 5‘ end of a strand of DNA by the use of specific enzymes as one means of making labeled probes.

Endonuclease Enzyme that hydrolyzes dsDNA at internal locations

Enhancer A regulatory sequence that can elevate levels of transcription from an adjacent promoter. Many tissue-specific enhancers can determine patterns of gene expression in higher eukaryotes. Enhancers can act on promoters over many tens of kilobases of DNA and be 5’ or 3’ to the promoter that they regulate. Generally they are on the same chromosome.

Ethidium bromide A chemical dye that intercalates between the bases in DNA and causes DNA to fluoresce when illuminated with ultraviolet light.

Euploid A cell having any number of complete chromosome sets or an individual composed of such cells.

Exon The portion of a gene that is actually translated into protein. [Eukaryotic genes only.]

Exonuclease Enzyme that hydrolyzes ss or ds NA from the ends

Fingerprint The characteristic spot pattern produced by electrophoresis of the polypeptide fragments obtained through denaturation of a particular protein by a proteolytic enzyme.

FISH Fluorescent in situ hybridization. In situ (in the physical location) hybridization using a probe coupled to a fluorescent molecule.

Frame-shift mutation The insertion or deletion of a nucleotide pair or pairs, causing a disruption of the translational reading frame.

Functional genomics The study of patterns of gene expression and interaction in the genome as a whole.

Gene A sequence of nucleotides that code for a protein product.

Gene dose The number of copies of a particular gene present in the genome.

Gene locus The specific place on a chromosome where a gene is located.

Gene therapy The correction of a genetic deficiency in a cell by the addition of new DNA with or without its insertion into the genome.

Genetic code The set of correspondences between nucleotide pair triplets in DNA and amino acids in proteins.

Genetics The study of genes.

Genome The complete set of hereditary factors of an organism, contained in the chromosome.

Genomic library Collection of DNA fragments (library) whose sum represents the entire genomic DNA of an organism.

Genotype The specific genes that are present in an individual they may or may not be expressed.

Germ line The cell lineage in a multi-tissued eukaryote from which the gametes derive.

Growth factor Signaling molecules, usually secreted polypeptides, that induce cell division in cells receiving theses signals. Signals can be autocrine (self derived), paracrine (from another cell but local in origin), endocrine (from a distant cell/organ) or neurocrine (from nerve cells).

Haploid A cell having one chromosome set or an organism composed of such cells.

Heteroduplex A DNA double helix formed by annealing single strands of a heteroduplex DNA.

Heterozygote An individual having a heterozygous gene pair.

Homology Similarity between two distinct genes in their nucleotide sequence.

Hybridization The process of complementary base pairing between two single strands of DNA, DNA and RNA, or sense and anti-sense RNA.

Inhibitor As it pertains to DNA manipulation in vitro, contamination in the preparation or sample can inhibit the biochemical processes involved in the manipulation, generally polymerases. Can be endogenous (from the sample matrix) or exogenous.

In situ hybridization Use of labeled DNA or RNA probes to localize complementary sequences within a cell.
Intron A portion of a gene not translated into protein, even though it is transcribed into RNA. A splicing event removes it from the primary RNA transcript leaving only the exons in the mRNA. [Eukaryotes only.]

Inverted repeat sequence A sequence found in identical form, but inverted. Commonly found in transposons and viruses.

Kilobase (kb) Unit of 1000 base pairs of DNA or 1000 bases of RNA.

Labeling The process of marking a DNA molecule using radioactive or non-radioactive labels.

Ligase An enzyme that can rejoin a broken phosphodiester bond in a nucleic acid.

Ligase chain reaction (LCR) An in vitro nucleic acid amplification method that uses DNA ligase, an enzyme that joins two pieces of DNA together.

Lagging strand In DNA replication, the strand that is synthesized apparently in the 3’ to 5’ direction, by ligating short fragments synthesized individually in the 5’ to 3’ direction. The short fragments called Okazaki fragments are primed using snRNAs.

Locus The site on the chromosome where a gene is located.

Missense mutation A mutation that alters a codon so that it encodes a different amino acid.
mtDNa Mitochondria DNA.

Mutation The process that produces a gene or a chromosomal set differing from the wild type.

Nick translation A means of incorporating labelled nucleotides into a segment of nucleic acid by displacing random nicks (introduced by DNAase) through the use of DNA polymerase.

Nonsense codon A codon for which no normal tRNA molecule exists the presence of a nonsense codon causes termination of translation (ending of the polypeptide chain). The three nonsense codons are called amber, ocher, and opal.

Nonsense mutation A mutation that alters a gene so as to produce a nonsense codon.

Northern blot RNA immobilized on a solid support after separation according to size by electrophoresis.

Nucleotide (nt) The structural unit of nucleic acid consisting of phosphate, sugar and purine or pyrimidine base.

N-Terminus and C-Terminus The two ends of a protein/polypeptide chain. Protein sequences are given N?C in direction.

Oligonucleotide A short (10-100 nt) stretch of ssDNA usually prepared by a series of chemical reaction following a known sequence.

Oncogene A type of gene associated with cancer production.

Operon A set of adjacent structural genes (prokaryotic) whose mRNA is synthesized in one piece, plus the adjacent regulatory signals that affect transcription of the structural genes. Regulation can be postive (turn it on when needed) or negative (keep it off until needed).

ORF (open reading frame) A section of a sequenced piece of DNA that begins with a start codon and ends with a stop codon it is presumed to be the coding sequence of a gene.

Phenotype The form or expression taken by some character or gene in a specific individual. Genotype is not always reflected in the phenotype.

Point mutation A mutation that can be mapped to one specific locus.

Polymerase chain reaction (PCR) Enzymatic technique to create multiple copies of one sequence of DNA

Plasmid A small, circular, extrachromosomal, self-replicating piece of DNA found in some bacteria (e.g. pBR322). Used in cloning (cloning plasmid = vector).

Poly(A)tail A string of adenine nucleotides added to mRNA after transcription.

Polycistronic mRNA An mRNA that encodes more than one protein (prokaryotes and viruses).

Polymorphism The occurrence in a population of several phenotypic forms associated with alleles of one gene or homologs of one chromosome

Primer A short single-stranded DNA or RNA that can act as a start site for 3’ chain growth when bound to a single-stranded template.

Probe A fragment or sequence of ssDNA, dsDNA or RNA that will be hybridized to a complementary sequence of nucleotides in another single-strand nucleic acid (target). Probes are labeled in some what to make the reaction visible.

Promoter A regulator region a short distance from the 5’ end (transcription start site) of a gene that acts as the binding site for RNA polymerase.

Reading frame The codon sequence that is determined by reading nucleotides in groups of three from some specific start codon.

Recombinant DNA The DNA molecule produced from inserting DNA from one organism into another piece of DNA by using genetic engineering techniques.

Regulatory genes Genes that have roles in turning on or off the transcription of other genes.

Replication The process of making DNA.

Replication fork The point at which the two strands of DNA are separated to allow replication of each strand.

Restriction enzyme Another name for restriction endonuclease.

Reverse Transcriptase An enzyme capable of synthesizing ssDNA from RNA. From retroviruses.

Ribosomal RNA (rRNA) A class of RNA molecules that have an integral role in ribosome structure and function.

RNA Ribonucleic acid, the single stranded nucleic acid of three types mRNA (messenger RNA), tRNA (transfer RNA) and rRNA (ribosomal RNA)

RNA polymerase A DNA directed RNA polymerase that creates a strand of RNA complementary to one strand of the dsDNA template.

RNases Ubiquitous enzymes that degrade RNA

Sequencing A method that determines the actual sequence of the nucleotide bases in DNA or protein.

Signal sequence The N-terminal sequence of a secreted protein, which is required for transport through the cell membrane.

Southern blot DNA that has been separated by gel electrophoresis, transferred from the gel to an immobile support (e.g. nitrocellulose or nylon), and bonded onto the support in single-stranded form ready for hybridization
ss Single stranded

Staggered cuts The cleavage of two opposite strands of duplex DNA at points near one another.

Streptavidin A bacterial form of avidin that has a slightly stronger affinity for biotin than does avidin form egg white.

Stringency The conditions of hybridization that increase the base-pairing of binding between two single strand portions of nucleic acid.

Supercoil A closed, double-stranded DNA molecule that is twisted on itself.

Target nucleic acid DNA or RNA to be hybridized with the labelled probe.

Tissue-specific gene expression The expression of a gene in a specific and reproducible subset of tissues and cells during the development of a higher eukaryote.

Transcription The process of producing an RNA copy from a DNA template.

Translation The production of protein from messenger RNA.

Uracil-N-glycosylase An enzyme that digests DNA that was replicated using dUTP instead of dTTP and is used to prevent amplicon carry over contamination.

Vector A plasmid, bacteriophage, cosmid or virus that carries foreign DNA into a host organism.

Western blot Proteins that have been separated by acrylamid electrophoresis, transferred and immobilized onto a solid support, then probed with labelled antibody.


25.10: Glossary: S - Biology

The degrees of Master of Arts and Doctor of Philosophy are offered in English Language and Literature.

Candidates for the M.A. in English may complete the program as either part-time or full-time students. Candidates for the Ph.D. in English must be in attendance as full-time students for at least three semesters of the program.

Admission to the Ph.D. in English is limited and competitive. Applicants should have a Master&rsquos degree in English or its equivalent from a recognized university and should have an outstanding academic record.

All candidates will be required to complete 15 credit hours in graduate courses. These courses will be selected by the candidate in consultation with the candidate&rsquos Supervisory Committee.

While candidates will normally be free to choose graduate courses of interest to them, it will be a primary responsibility of their Supervisory Committees to ensure that any serious deficiencies in their record of previous courses, graduate and undergraduate, are remedied, particularly in the area of proposed thesis research.

Candidates who have not previously taken English 7003 or its equivalent will take English 7003, which will count as one of the required courses for the Ph.D. Students who have taken English 7003 or its equivalent before entering the Ph.D. program must still complete 15 credit hours.

Candidates who have not completed English 4900 or English 5900 or an equivalent course will be required to complete English 5900, which will not count as one of the required courses for the Ph.D. The course will be graded &ldquopass&rdquo or &ldquofail&rdquo. As in other graduate courses a grade of 65B or above is considered a pass.

Candidates must submit a thesis proposal which includes a statement of topic, a working title, a plan of research, and a preliminary bibliography. The thesis proposal should be approved by the Supervisory Committee and submitted to the departmental Graduate Studies Committee for its approval before the Comprehensive Examination and before the end of the fifth semester. The departmental Graduate Studies Committee shall return the thesis proposal to the candidate no later than one month after receiving it.

Reading knowledge of a second language will be required of all candidates. Reading knowledge is defined as a minimum B grade in a second-year language course taken within the previous five years, a passing grade in an approved second-language course for graduate students, or performance satisfactory to the Department in an arranged reading proficiency test (in which a dictionary may be used).

The language requirement should be completed before the Comprehensive Examination is taken.

The second language will normally be French. In exceptional circumstances, and on the recommendation of the Supervisory Committee and the departmental Graduate Studies Committee, a language other than French may be substituted.

The Supervisory Committee may also require a demonstrated reading knowledge of an additional language (other than French or the substituted language) if such knowledge is deemed necessary for the student&rsquos research interests.

The Ph.D. Comprehensive Examination in English is a written examination prepared by the candidate&rsquos Comprehensive Examination Committee.

In accordance with General Regulation Comprehensive Examinations, Ph.D. Comprehensive Examination, the candidate&rsquos Comprehensive Examination Committee will include the Head (or the Head&rsquos delegate, usually the Graduate Coordinator), the candidate&rsquos supervisor, and three other members of the Department.

The written examination shall consist of three parts: a four-hour examination in the student&rsquos area of concentration and two three-hour examinations in two other specified areas. In accordance with General Regulation Comprehensive Examinations, Ph.D. Comprehensive Examination, the examination shall take place before the end of the seventh semester.

Candidates will be graded &ldquopass with distinction&rdquo, &ldquopass&rdquo, &ldquore-examination&rdquo, or &ldquofail&rdquo, in accordance with General Regulation Comprehensive Examinations, Ph.D. Comprehensive Examination, 4. Candidates who are marked for &ldquore-examination&rdquo will be re-examined in the area or areas in which the Comprehensive Examination Committee has determined that the candidate's performance is deficient. The nature of this re-examination (and whether it will be written or oral) is left to the discretion of the Comprehensive Examination Committee.

A selection of the following graduate courses will be offered to meet the requirements of candidates, as far as the resources of the Department will allow.

Since it is impossible to list in detail the many topics that may from time to time be offered, the titles below refer only to the major periods and general subject areas in which specific courses may be available. The content and approach in specific courses will vary according to the research interests of students and faculty involved in the course. Students should consult the Department's annual Graduate Student Guide (or the Graduate Co-ordinator) for detailed descriptions of specific course offerings. Normally, no fewer than 30 credit hours in graduate courses are offered in any given academic year.

English 5900 cannot be counted as one of the required graduate courses in any program.

All students will normally take English 7003 - Trends in Contemporary Literary Theory, usually in their first semester.

Students who took graduate courses in English at Memorial before 1997 should consult with the Department before selecting further courses.


25.10: Glossary: S - Biology

The self-sufficient nature of some bacterial cytochromes P450 makes them attractive biocatalysts as they do not require a redox partner protein for catalysis.

The self-sufficient class VII is the first full length multidomain P450 for which the 3D structure has been solved.

Many self-sufficient P450s are present in extremophiles in polluted sites, suggesting a high stability in extreme conditions, which is an advantage for biocatalysts and bioremediation purposes.

Protein engineering has successfully targeted self-sufficient P450s: the reductase domain can supply electrons to other enzymes in chimeric fusion proteins, whereas the P450 domain can be designed for high activity and selectivity.

Semi-rational and random mutagenesis have created variants with improved catalytic efficiency towards substrates of biotechnological interest that are converted in high value chemicals.

Members of class VII cytochromes P450 are catalytically self-sufficient enzymes containing a phthalate dioxygenase reductase-like domain fused to the P450 catalytic domain. Among these, CYP116B46 is the first enzyme for which the 3D structure of the whole polypeptide chain has been solved, shedding light on the interaction between its domains, which is crucial for catalysis. Most of these enzymes have been isolated from extremophiles or detoxifying bacteria that can carry out regio- and enantioselective oxidation of compounds of biotechnological interest. Protein engineering has generated mutants that can perform challenging organic reactions such as the anti-Markovnikov alkene oxidation. This potential, combined with the detailed 3D structure, forms the basis for further directed evolution studies aimed at widening their biotechnological exploitation.


S phase

The next phase of the trial consists of vaccinating Ebola workers on the front lines.

“A guy drives up in a 2008 Mercedes, brand new,” Harry S. Connelly Jr. says in the video, according to the Times.

“Personal hotspots can get speeds of up to 60 Mb/s down, whereas hotel Wi-Fi can be as slow as 1.5 Mb/s,” Sesar said.

In our headlong quest for a legally perfect society, we don’t take the time to take stock of what‘s been created so far.

The families announced along with it that they had entered a “phase of silence” surrounding the details of the new deal.

But between the phase of schooling and the phase of adult learning there is an intermediate stage.

Ajoutez cecy, s'il vous plaist, la grande difficult qu'il y a de tirer d'eux les mots mesmes qu'ils ont.

Neantmoins le vieil Membertou, pere du malade, conceut asss l'affaire, et me promit qu'on s'arresteroit tout ce que j'en dirois.

En effet un soir, sa femme et enfans l'abandonnerent entierement, et s'en allerent cabaner ailleurs, pensant que c'en estoit vuid.

Mrs. S. said she was familiar with it from having heard Thomas's orchestra play it in New York.


Glossary

Action area means all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action.

Applicant refers to any person, as defined in section 3(13) of the Act, who requires formal approval or authorization from a Federal agency as a prerequisite to conducting the action.

Biodiversity - The variety of life and its processes, including the variety of living organisms, the genetic differences among them, and the communities and ecosystems in which they occur.

Biological assessment refers to the information prepared by or under the direction of the Federal agency concerning listed and proposed species and designated and proposed critical habitat that may be present in the action area and the evaluation potential effects of the action on such species and habitat.

Biological opinion is the document that states the opinion of the U.S. Fish and Wildlife Service as to whether or not the Federal action is likely to jeopardize the continued existence of listed species or result in the destruction or adverse modification of critical habitat.

Candidate species - Plants and animals that have been studied and the Service has concluded that they should be proposed for addition to the Federal endangered and threatened species list. These species have formerly been referred to as category 1 candidate species. From the February 28, 1996 Federal Register, page 7597: "those species for which the Service has on file sufficient information on biological vulnerability and threat(s) to support issuance of a proposed rule to list but issuance of the proposed rule is precluded."

Category 1 candidate species - A term no longer in use, having been replaced by the term "candidate species" which uses the same definition.

Category 2 candidate species - A term no longer in use. Previously referred to species for which the Service had some indication that listing as threatened or endangered might be warranted, but there were insufficient data available to justify a proposal to list them.

Category 3 candidate species - A term no longer in use. Previously referred to species which once were category 1 or 2 candidate species, but for which subsequent data indicated that listing as threatened or endangered was not appropriate.

CITES - The 1973 Convention on International Trade in Endangered Species of Wild Fauna and Flora, restricting international commerce between participating nations for plant and animal species believed to be harmed by trade.

Common name - The nonscientific name of an animal or plant most widely used and accepted by the scientific community.

Conference is a process which involves informal discussions between a Federal agency and the U.S. Fish and Wildlife Service under section 7(a)(4) of the Act regarding the impact of an action on proposed species or proposed critical habitat and recommendations to minimize or avoid the adverse effects.

Conservation - From section 3(3) of the Federal Endangered Species Act: "The terms "conserve," "conserving," and "conservation" mean to use and the use of all methods and procedures which are necessary to bring any endangered species or threatened species to the point at which the measures provided under this Act are no longer necessary. Such methods and procedures include, but are not limited to, all activities associated with scientific resources management such as research, census, law enforcement, habitat acquisition and maintenance, propagation, live trapping, and transportation, and, in the extraordinary case where population pressures within a given ecosystem cannot be otherwise relieved, may include regulated taking."

Consultation - All Federal agencies must consult with the U.S. Fish and Wildlife Service when any activity permitted, funded, or conducted by that agency may affect a listed species or designated critical habitat.

Critical habitat - Specific geographic areas, whether occupied by listed species or not, that are determined to be essential for the conservation and management of listed species, and that have been formally described in the Federal Register.

Delist - The process of removing an animal or plant from the list of Endangered and Threatened Wildlife and Plants.

Designated non-Federal representative refers to a person designated by the Federal agency as its representative to conduct informal consultation and/or to prepare any biological assessment.

Distinct population segment - If it satisfies the criteria specified in the February 7, 1996, Federal Register, pages 4722-4725, a portion of a vertebrate (i.e., animals with a backbone) species or subspecies can be listed. The criteria require it to be readily separable from the rest of its species and to be biologically and ecologically significant. Such a portion of a species or subspecies is called a distinct population segment.

Ecosystem - Dynamic and interrelating complex of plant and animal communities and their associated nonliving (e.g. physical and chemical) environment.

Ecosystem Approach - Protecting or restoring the function, structure, and species composition of an ecosystem, recognizing that all components are interrelated.

Endangered - The classification provided to an animal or plant in danger of extinction within the foreseeable future throughout all or a significant portion of its range.

Endangered Species Act of 1973, as amended - Federal legislation intended to provide a means whereby the ecosystems upon which endangered and threatened species depend may be conserved, and provide programs for the conservation of those species, thus preventing extinction of native plants and animals.

Endangered species permit - A document issued by the Service under authority of Section 10 allowing an action otherwise prohibited under Section 9 of the Endangered Species Act.

Endemic species - A species native and confined to a certain region having comparatively restricted distribution.

Extinct species - A species no longer in existence.

Extirpated species - A species no longer surviving in regions that were once part of their range.

Federal action agency - Any department or agency of the United States proposing to authorize, fund, or carry out an action under existing authorities.

Formal consultation is a process between the U.S. Fish and Wildlife Service and the Federal agency that commences with the Federal agency's written request for consultation under section 7(a)(2) of the Act and concludes with the Service's issuance of the biological opinion under section 7(b)(3) of the Act.

Habitat - The location where a particular taxon of plant or animal lives and its surroundings (both living and nonliving) and includes the presence of a group of particular environmental conditions surrounding an organism including air, water, soil, mineral elements, moisture, temperature, and topography.

Habitat Conservation Plan (HCP) - A plan which outlines ways of maintaining, enhancing, and protecting a given habitat type needed to protect species. The plan usually includes measures to minimize impacts, and might include provisions for permanently protecting land, restoring habitat, and relocating plants or animals to another area. An HCP is required before an incidental take permit may be issued.

Harm - An act which actually kills or injures wildlife. Such acts may include significant habitat modification or degradation when it actually kills or injures wildlife by significantly impairing essential behavioral patterns including breeding, feeding, or sheltering.

Historic range - Those geographic areas the species was known or believed to occupy in the past.

Implementation schedule - An outline of actions, with responsible parties, estimated costs and timeframes, for meeting the recovery objectives described in the species recovery plan.

Incidental take - Take that results from, but is not the purpose of, carrying out an otherwise lawful activity.

Incidental take permit - A permit issued under Section 10 of the Federal Endangered Species Act to private parties undertaking otherwise lawful projects that might result in the take of an endangered or threatened species. Application for an incidental take permit is subject to certain requirements, including preparation by the permit applicant of a conservation plan, generally known as a "Habitat Conservation Plan" or "HCP."

Incidental take statement - If a Federal action is reasonably certain to cause incidental take, but will not jeopardize listed species or destroy or adversely modify critical habitat, U.S. Fish and Wildlife Service provides an incidental take statement (ITS) with its biological opinion. The ITS specifies the amount or extent of take that the Service anticipates and includes reasonable and prudent measures (RPM) to minimize the effects of the take and terms and conditions that implement the RPMs. Any taking which is subject of an ITS and that is in compliance with its terms and conditions is not a prohibited taking under the Act.

Informal consultation is an optional process that includes all discussions, correspondence, etc., between U.S. Fish and Wildlife Service and the Federal agency or the designated non-Federal representative prior to formal consultation, if required. Informal consultation includes any form of communication between the Federal action agency, applicant, or designated non-Federal representative and the Service to determine if listed species are likely to occur in the action area and, if so, how the action may affect the species. During information consultation, agencies and the Service may modify projects or identify acceptable alternatives that may avoid adverse effects to listed species, which could preclude the need for formal consultation.

Jeopardize the continued existence of means to engage in an action that reasonably would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species.

Lead region - The Fish and Wildlife Service Region that coordinates actions taken to assess the status of a species and, if appropriate, to propose the species for listing and to complete the final listing rule. After listing, the lead region would coordinate actions to conserve the species and to delist the species if and when it is recovered.

Lead office - The field office that has been given the responsibility for coordinating all or most actions taken to study, propose, list, conserve, and delist a species within the boundaries of Region 3. If Region 3 is the lead region for a particular species, the lead office has these responsibilities over the entire range of that species.

Listed species - A species, subspecies, or distinct vertebrate population segment that has been added to the Federal lists of Endangered and Threatened Wildlife and Plants as they appear in sections 17.11 and 17.12 of Title 50 of the Code of Federal Regulations (50 CFR 17.11 and 17.12).

Listing - The formal process through which the Service adds species to the Federal List of Endangered and Threatened Wildlife and Plants.

Listing priority - A number from 1 to 12 indicating the relative urgency for listing plants or animals as threatened or endangered. The criteria used to assign this number reflect the magnitude and immediacy of threat to the species, as well as the relative distinctiveness or isolation of the genetic material they possess. This latter criterion is applied by giving a higher priority number to species which are the only remaining species in their genus, and a lower priority number to subspecies and varieties. These listing priorities are described in detail in the Federal Register on September 21, 1983, as pages 43098-43105.

Not likely to jeopardize biological opinion - A U.S. Fish and Wildlife Service biological opinion that articulates the Service&rsquos determination that a Federal agency action is not likely to jeopardize the continued existence of any listed species.

Petition (Listing) - A formal request, with the support of adequate biological data, suggesting that a species, with the support of adequate biological data, be listed, reclassified, or delisted, or that critical habitat be revised for a listed species. See also Region 3 Guidance for Potential Petitioners

Propose - The formal process of publishing a proposed Federal regulation in the Federal Register and establishing a comment period for public input into the decision-making process. Plants and animals must be proposed for listing as threatened or endangered species, and the resulting public comments must be analyzed, before the Service can make a final decision.

Proposed species - Any species of fish, wildlife, or plant that is proposed in the Federal Register to be listed under Section 4 of the Endangered Species Act.

Range - The geographic area a species is known or believed to occupy.

Reauthorization - A term referring to periodic action taken by Congress to reauthorize the Endangered Species Act. By reauthorizing an act, Congress extends it and may also amend it.

Reclassify - The process of changing a species' official threatened or endangered classification.

Recovery - The process by which the decline of an endangered or threatened species is arrested or reversed, or threats to its survival neutralized so that its long-term survival in nature can be ensured.

Recovery implementation strategy - The Recovery Implementation Strategy (RIS), is a short-term, flexible operational recovery document focused on how, when, and with whom the recovery actions in a recovery plan will be implemented.

Recovery outline - The first Service recovery document provided for a listed species. While very brief, the document serves to direct recovery efforts pending the completion of the species' recovery plan.

Recovery permit - Permits issued under Section 10(a)(1)(A) of the Federal Endangered Species Act for scientific research and other activities benefitting the recovery of Federally listed species.

Recovery plan - Recovery plans provide a road map with detailed site-specific management actions for private, Tribal, federal, and state cooperation in conserving listed species and their ecosystems. A recovery plan provides guidance on how best to help listed species achieve recovery, but it is not a regulatory document.

Recovery priority - A number, ranging from a high of 1C to a low of 18, whereby priorities to listed species and recovery tasks are assigned. The criteria on which the recovery priority number is based are degree of threat, recovery potential, taxonomic distinctiveness, and presence of an actual or imminent conflict between the species and development activities.

Scientific name - A formal, Latinized name applied to a taxonomic group of animals or plants. A species' scientific name is a two-part combination consisting of the name of the genus, followed by a species name. For example, the scientific name of gray bat is Myotis grisescens. If a species has been further divided into subspecies, a third part is added to the scientific name. The Ozark big-eared bat is Plecotus townsendii ingens. "Ingens" distinguishes the Ozark subspecies from other subspecies of the big-eared bat.

Scientific take permit - A type of recovery permit authorized under Section 10 allowing for research pertaining to species recovery such as taking blood samples from a peregrine falcon for genetic analysis, or conducting surveys of freshwater mussel beds to determine species status and distribution.

Section 4 - The section of the Endangered Species Act that deals with listing and recovery of species, and designation of critical habitat.

Section 4(d) rule - A special regulation developed by the Service under authority of Section 4(d) modifying the normal protective regulations for a particular threatened species when it is determined that such a rule is necessary and advisable to provide for the conservation of that species.

Section 6 - The section of the Endangered Species Act that authorizes the Service to provide financial assistance to States through cooperative agreements supporting the conservation of endangered and threatened species.

Section 7 - The section of the Endangered Species Act (ESA) that requires all Federal agencies, in consultation with and with the assistance of the Service, to insure that their actions are not likely to jeopardize the continued existence of listed species or to result in the destruction or adverse modification of critical habitat. This section also requires federal agencies to use their authorities to carry out programs to conserve listed species – again, in consultation with and with the assistance of the Service.

Section 9 - The section of the Endangered Species Act that deals with prohibited actions, including the import and export, take, possession of illegally taken species, transport, or sale of endangered or threatened species.

Section 10 - The section of the Endangered Species Act that lays out the guidelines under which a permit may be issued to authorize activities prohibited by Section 9, such as take of endangered or threatened species.

Species - From Section 3(15) of the Federal Endangered Species Act: "The term 'species' includes any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature." A population of individuals that are more or less alike, and that are able to breed and produce fertile offspring under natural conditions.

Species Status Assessment (SSA) - An SSA is a focused, repeatable, and rigorous assessment of a species' ability to maintain self-sustaining populations over time. This assessment is based on the best available scientific and commercial information regarding life history, biology, and consideration of current and future vulnerabilities. The result is a single document that delivers foundational science for informing all ESA decisions, including listing determinations, consultations, grant allocations, permitting, and recovery planning.

Take - From Section 3(18) of the Federal Endangered Species Act: "The term 'take' means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct."

Threatened - The term “threatened species” means any species which is likely to become an endangered species within the foreseeable future throughout all or a significant portion of its range - - as defined in the Endangered Species Act.


25.10: Glossary: S - Biology

How much does a bald eagle weigh?
Weight varies depending on latitude and gender. Generally, males weigh approximately 25% less than females from the same area. The average weight of a female bald eagle is 10-14 pounds, however there exists great variation depending on where an eagle is from. Southern bald eagles tend to be smaller than those in northern parts of their range. For example in Alaska, females might weigh up to 18 pounds, whereas eagles in Florida can weigh as little as 7-8 pounds.

How much does a golden eagle weigh?
Weight varies depending on latitude and gender. Generally, males weigh approximately 25% less than females from the same area. The average weight of a female is between 10 and 15 pounds.

What is a bald eagle’s wingspan?
The average wingspan ranges from 6 to 7.5 feet (182cm-229cm).
Wingspan of an eagle depends on overall size. Eagles in northern parts of their range tend to be larger overall, including a larger wingspan.

What is a golden eagle’s wingspan?
The average wingspan of a golden eagle is 6 to 7.5 feet (182cm-229cm).
Wingspan of an eagle depends on overall size. Eagles in northern parts of their range tend to be larger overall, including a larger wingspan.

What is the length of a bald eagle?
Size varies with geography and gender with females being larger than males and northern birds being larger than southern birds. The average female bald eagle is 35 to 38 inches (89cm-96.5 cm) in length and is approximately 25% larger than the male.

What is the length of a golden eagle?
Size varies with geography and gender with females being larger than males and northern birds being larger than southern birds. The average golden eagle’s body length is between 33 and 38 inches (84cm-96.5 cm).

How far can an eagle turn its head?
An eagle can rotate its head approximately 180 degrees in each direction. Eagles have 14 cervical vertebrae allowing for greater rotation than humans who have just 7 cervical vertebrae and can typically rotate just 70-90 degrees in either direction.

Do eagles beaks and talons grow?
Yes. Eagles’ beaks and talons are made of keratin (like human finger nails). Normal use in the wild keeps them the proper length. In captivity, talons and beaks are coped (trimmed) regularly to ensure the health of the bird.

How long do eagles live?
In the wild, an eagle that makes it to adulthood might live 20-25 years. 70-80% of eagles die before they reach adulthood at five years of age. In captivity, eagles are known to live much longer 40+ and up to 50 years, due to a controlled environment, nutrient rich diet and veterinary care.

Legends of eagles rejuvenating and living another 30+ years by going through a painful rebirthing process are purely mythical.

Do eagles have teeth?
No. They use their sharp beak and strong neck muscles to rip their food into pieces small enough to swallow.

How much do eagle bones weigh?
Eagles have hollow bones the entire skeleton of an adult eagle is generally estimated to be 5-6% of the body weight.

How large is an eagle’s stomach?
An eagle’s stomach is quite small, about the size of a walnut. However, eagles can eat up to 1/3 of their own body weight in food. They have an area called the crop to store food, allowing them to survive without finding new food everyday.

Taxonomy
Scientific names are two word designations of genus and species. The genus is capitalized, while the species name is lowercase. Scientific names are italicized. Common names can vary by region.

Bald eagle (common name) – Haliaeetus leucocephalus
Haliaeetus = member of the sea or fish eagle group
leucocephalus = leuco=white, cephalus = head

Golden eagle (common name) – Aquila chrysaetos
Aquila – means eagle in Latin
chrysaetos – means golden in Greek

Eagles are members of the Accipitridae family, along with most diurnal birds of prey and old world vultures.


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The degree to which a living organism is suited to a particular environment. The more specific term, genetic fitness, refers to the relative contribution the organism of a particular genotype makes to the next generation. Those individuals exhibiting higher genetic fitness are selected for and as a result, their genetic characteristics become more prevalent within the population.

The path that energy takes through an ecosystem, from sunlight to producers, to herbivores, to carnivores. Individual food chains connect and branch to form food webs.


A glossary for stem-cell biology

Stem-cell biology is in a phase of dynamic expansion and is forming connections with a broad range of basic and applied disciplines. The field is simultaneously exposed to public and political scrutiny. A common language in the stem-cell community is an important tool for coherent exposition to these diverse audiences, not least because certain terms in the stem-cell vocabulary are used differently in other fields.

Asymmetric division Generation of distinct fates in progeny from a single mitosis. Oriented division may position daughter cells in different microenvironments or intrinsic determinants may be segregated into only one daughter. Observed in some but not all stem cells and can occur in other types of progenitor cell.

Cancer cell of origin Precancerous cell that gives rise to a cancer stem cell. May be a mutated stem cell, or a committed progenitor that has acquired self-renewal capacity through mutation.

Cancer-initiating cell General term that encompasses both cancer cell of origin and cancer stem cell.

Cancer stem cell Self-renewing cell responsible for sustaining a cancer and for producing differentiated progeny that form the bulk of the cancer. Cancer stem cells identified in leukaemias and certain solid tumours are critical therapeutic targets.

Cell replacement therapy Reconstitution of tissue by functional incorporation of transplanted stem-cell progeny. Distinct from ‘bystander’ trophic, anti-inflammatory or immunomodulatory effects of introduced cells.

Clonal analysis Investigation of properties of single cells. Essential for formal demonstration of self-renewal and potency.

Commitment Engaging in a programme leading to differentiation. For a stem cell, this means exit from self-renewal.

Embryonic stem cell Pluripotent stem-cell lines derived from early embryos before formation of the tissue germ layers.

Founder/ancestor/precursor cell General terms for cell without self-renewal ability that contributes to tissue formation. In some cases they generate tissue stem cells.

Immortal strand The hypothesis of selective retention of parental DNA strands during asymmetric self-renewal. Potential mechanism to protect stem cells from the mutations associated with replication.

In vitro stem cell Self-renewal ex vivo in cells that do not overtly behave as stem cells in vivo. Occurs due to liberation from inductive commitment signals or by creation of a synthetic stem-cell state.

Label-retaining cell Candidate for adult tissue stem cell because of slow division rate and/or immortal strand retention. Interpret with caution.

Lineage priming Promiscuous expression in stem cells of genes associated with differentiation programmes.

Long-term reconstitution Lifelong renewal of tissue by transplanted cells. The definitive assay for haematopoietic, epidermal and spermatogonial stem cells. Transplantation assay may not be appropriate for all tissues.

Niche Cellular microenvironment providing support and stimuli necessary to sustain self-renewal.

Plasticity Unproven notion that tissue stem cells may broaden potency in response to physiological demands or insults.

Potency The range of commitment options available to a cell.

Totipotent Sufficient to form entire organism. Totipotency is seen in zygote and plant meristem cells not demonstrated for any vertebrate stem cell.

Pluripotent Able to form all the body's cell lineages, including germ cells, and some or even all extraembryonic cell types. Example: embryonic stem cells.

Multipotent Can form multiple lineages that constitute an entire tissue or tissues. Example: haematopoietic stem cells.

Oligopotent Able to form two or more lineages within a tissue. Example: a neural stem cell that can create a subset of neurons in the brain.

Unipotent Forms a single lineage. Example: spermatogonial stem cells.

Progenitor cell Generic term for any dividing cell with the capacity to differentiate. Includes putative stem cells in which self-renewal has not yet been demonstrated.

Regenerative medicine Reconstruction of diseased or injured tissue by activation of endogenous cells or by cell transplantation.

Reprogramming Increase in potency. Occurs naturally in regenerative organisms (dedifferentiation). Induced experimentally in mammalian cells by nuclear transfer, cell fusion, genetic manipulation or in vitro culture.

Self-renewal Cycles of division that repeatedly generate at least one daughter equivalent to the mother cell with latent capacity for differentiation. This is the defining property of stem cells.

Stem cell A cell that can continuously produce unaltered daughters and also has the ability to produce daughter cells that have different, more restricted properties.

Stem-cell homeostasis Persistence of tissue stem-cell pool throughout life. Requires balancing symmetric self-renewal with differentiative divisions at the population level, or sustained asymmetric self-renewal.

Stemness Unproven notion that different stem cells are regulated by common genes and mechanisms.

Tissue stem cell Derived from, or resident in, a fetal or adult tissue, with potency limited to cells of that tissue. These cells sustain turnover and repair throughout life in some tissues.

Transit-amplifying cell Proliferative stem-cell progeny fated for differentiation. Initially may not be committed and may retain self-renewal.


Watch the video: Ch1 Basic Definitions pt1 (September 2022).