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molecular & cellular overview
Q: Do you see any
profound intellectual ideas taking shape in this post- genome era?
(put to David Botstein (Professor and Chairman, Dept. of Genetics, Stanford
Univ., US) in an interview on the Incyte Genomics website )
Dr. Botstein:
Finding guide to terms in these
glossaries Biology term
index
Biology for non-biologists: Basic
genetics & genomics
alternative splicing:
The production of two or more distinct mRNAs from RNA transcripts having the same sequence via differences in splicing (by the choice of different exons).
Mouse Genome Informatics http://www.informatics.jax.org/glossary/alternative_splicing Recent genome- wide analyses of alternative splicing indicate that 40- 60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Here we review these recent results from bioinformatics studies, assess their reliability and consider the impact of alternative splicing on biological functions. Although the 'big picture' of alternative splicing that is emerging from genomics is exciting, there are many challenges. High- throughput experimental verification of alternative splice forms, functional characterization, and regulation of alternative splicing are key directions for research.
B. Modrek, C. Lee, "A genomic view of alternative splicing" Nature Genetics30 (1) :13- 19, Jan.
2002 Gene definitions
apoptosis:
One
of the two mechanisms by which CELL DEATH occurs (the other being the pathological
process of NECROSIS). 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. [MeSH, 1993] If
someone could figure out how to make fat cells undergo apoptosis (without
harmful side effects) they could make a bundle. Related term: programmed
cell death. Cell biology
glossary
biomolecules:
An organic molecule, part of a living organism.
Includes proteins, DNA, RNA. Biomolecules glossary
codon:
The sequence of three consecutive nucleotides that occurs in
mRNA which directs the incorporation of a specific amino acid into a
protein or represents the starting or termination signals of
protein synthesis. IUPAC Biotech, IUPAC Medicinal Chemistry
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
MeSH, 1991 Sequences,
DNA & beyond glossary
combinatorial biology:
Involves genetic manipulation of bacteria
and fungi that produce complex natural products. This technology includes
construction of large libraries of recombinant microbes capable of generating
novel organic molecules and engineering secondary metabolite biosynthetic
pathways to modify valuable biologically active microbial metabolites.
ASB [Am Soc. Biomechanics] Newsletter, June 1998 http://asb-biomech.org/newsletter/V11N1/guest.html
Biomaterials & bioengineering glossary
expression:
The cellular production
of the protein encoded by a particular
gene. The process includes
transcription of DNA, processing of the resulting mRNA product and its
translation into an active protein. N.B. A recombinant gene inserted
into a host cell by means of a vector is said to be expressed if the synthesis
of the encoded polypeptide can be demonstrated. IUPAC Bioinorganic,
IUPAC Compendium
A description as to how a gene demonstrates
a phenotype. This can range from production of a mRNA to a disease.
If a disease gene carrier shows signs of the disease gene, then that gene
is expressed. Note that an individual must carry the disease gene
and be penetrant for it before the term expression is utilized. [NHLBI]
Narrower terms gene expression, protein expression. Expression
glossary
Gene OntologyTM (GO): The goal of the Gene
OntologyTM Consortium is to produce a dynamic controlled vocabulary that can be applied to all
eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
http://www.geneontology.org/
Functional genomics glossary
genes, human:
At the 2000 Cold
Spring Harbor Genome conference [May 10-14] "one of the hotly debated topics
was the number of human genes. This has been estimated at anything from
35,000 to 150,000. Considering the spread of opinion, the only way to resolve
was to get people to bet on it … This led to an interesting debate on the
definition of a gene … and how to assess that number. A gene is a set of
connected transcripts. A transcript is a set of exons via transcription
followed (optionally) by pre- mRNA splicing. Two transcripts are connected
if they share at least part of one exon in the genomic coordinates. At
least one transcript must be expressed outside of the nucleus and one transcript
must encode a protein. "Genesweep" Ensembl, European Bioinformatics
Institute, UK http://www.ensembl.org/Genesweep/
With the publication of the Human Genome Project draft sequence
in Feb. 2001 we learned that the number of genes (about 30,000) seems to
be many fewer than expected, but the number of proteins per gene, with
alternative splicing (two to three, instead of one) is greater. More
surprises seem sure to be in store. Gene Definitions
gene nomenclature, human:
The Human Gene Nomenclature Committee (HGNC)
is part of the Human Genome Organization
(HUGO), and has established official, unique nomenclature for human genes. If a
gene lacks official nomenclature, the research community is encouraged to use
the Nomenclature Committee web form to submit a proposed gene symbol and name. Guidelines for
naming are provided.
(09/20/07)
SNP FAQ Archives
https://www.ncbi.nlm.nih.gov/books/NBK44416/
Nomenclature,
genes & beyond
genetic maps:
The value of the genetic map is that an inherited
disease can be located on the map by following the inheritance of
a DNA marker present in affected individuals (but absent in unaffected
individuals), even though the molecular basis of the disease may not yet
be understood nor the responsible gene identified. Genetic maps have been
used to find the exact chromosomal location of several important disease
genes, including cystic fibrosis, sickle cell disease, Tay- Sachs disease,
fragile X syndrome, and myotonic dystrophy. Primer on Molecular
Genetics, Oak Ridge National Lab, US
https://web.ornl.gov/sci/techresources/Human_Genome/publicat/primer2001/primer.pdf
Can be cytogenetic, linkage, or physical maps.
Starting genetic maps is easier than finishing them. Maps-
genomic & genetic glossary
genomic DNA gDNA:
The entire length of DNA, including non coding regions. (Sometimes called gDNA.)
CHI
Bioinformatics report
DNA which includes exons and introns, coding and noncoding regions. Compare with
cDNA DNA Glossary
glycomics:
Glycans
are complex, making it hard to exploit their therapeutic possibilities. However,
promising new tools and methodologies are available to tackle the most pressing
questions, such as: How to purify the glycoproteins? How to analyze the
“sticky” substance? What is necessary to get more information on the
compound, its structure and binding specificities? After deciding on a target
compound - what are the next steps? What are the weaknesses and strengths of
analytical tools used? How can you compare various methods? And finally, how do
you turn your investment in glycoproteins and carbohydrates into a success story
Glycosciences glossary
housekeeping genes:
In theory, expressed in all genes. Contrast with luxury
genes. Genes that encode housekeeping proteins. Specific housekeeping genes can be used to normalize
gene expression data. Not usually the
gene of greatest interest for functional studies. Gene
categories glossary
hypothetical protein:
Many of the
gene products of completely sequenced organisms are "hypothetical" –
they cannot be related to any previously characterized proteins – and so
are of completely unknown function. ... As each [completely sequenced]
organism’s genome is analyzed about one third of the observed open reading
frames (ORFs), although conserved among several organisms, encode for
"hypothetical‘ proteins. E Eisenstein et al "Biological function made crystal
clear – annotation of hypothetical proteins via structural genomics" Current
Opinion in Biotechnology 11(1): 25-30 Feb. 2000 Protein
categories glossary
induced pluripotent stem cells IPS: A
type of pluripotent stem cell, similar to an embryonic stem cell, formed
by the introduction of certain embryonic genes into a somatic cell. Stem
Cell Glossary https://stemcells.nih.gov/glossary.htm#ips
Stem cell
glossary
luxury genes:
Specialized genes with specific functions. Compare with housekeeping
genes. Gene categories
model organisms: Model organisms are of key importance in both creating
databases of gene sequences for homology searching, and as platforms for investigating the biology of genes of interest. Over the last few years, the use - and sophistication - of such models has increased substantially. Findings from the recent publications by the
Human Genome Project and Celera Genomics support that homology between human and animal- model genes and proteins is significant, particularly among vertebrate species. Still, the conservation of genes and genetic
pathways between humans and invertebrate organisms is great enough that some of these organisms
have become critical model systems. Related terms: knockdown, knockin, knockout Model
& other organisms glossary
modular biology:
Leland H. Hartwell, et. al. From Molecular to Modular
Cell Biology, Nature 402 (suppl)., C47-C52, 1999
https://www.nature.com/articles/35011540
https://en.wikipedia.org/wiki/Modularity_(biology))
pharmacophore:
The ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response. Does not represent a real molecule or a real association of functional groups, but a purely abstract concept that accounts for the common molecular interaction capacities of a group of compounds towards their target structure. Can be considered as the largest common denominator shared by a set of active molecules.
IUPAC Medicinal Chemistry Drug targets glossary
post-translational modifications:
Proteins once synthesized on the ribosomes, are subject to a multitude of modification steps. They are cleaved (thus eliminating signal sequences, transit or pro- peptides and initiator methionines); many simple chemical groups can be attached to them … as well as some more complex molecules, such as sugars and lipes. Finally they can be internally or externally cross- linked. More than a hundred different types of post- translational modifications are currently known (Aug. 1999) and many more are yet to be discovered. The
complexity due to all these modifications is compounded by the high level of diversity that
alternative splicing can produce at the level of sequence. Thus the number of different
protein molecules expressed by the
human genome is probably closer to a million than to the hundred thousand generally considered by genome scientists.
The SWISS-PROT protein sequence
database and its supplement TrEMBL in 2000
Amos
Bairoch*
Rolf
Apweiler
Nucleic Acids Research 28
(1): 45-48
http://nar.oxfordjournals.org/content/28/1/45.full?ref=klasshop.com
Proteins glossary
protein structure:
Given that proteins carry out their functions
as three- dimensional structures (e.g., that determine the active sites
of enzymes and the ligand- binding sites of receptors), a greater ability
to work with three- dimensional structures and to look for similarities
in these structures (between the products of different genes) is expected
to yield improved functional information. CHI Functional
Genomics report Protein
structure glossary
RNAi
RNA interference: RNA interference (RNAi) has
been a continually evolving area of research. Discovered primarily as a
technique for gene silencing, RNAi has now emerged as a screening tool for
target identification and validation in early drug discovery. Since establishing
its presence as a screening tool, RNAi is now looking to make an impact in the
therapeutic arena. Several RNAi-based compounds are already in various stages of
clinical testing. Although still in its infancy, RNAi therapeutics are making
rapid progress in the clinic, learning from mistakes made in the past by other
gene therapy approaches.
RNA glossary
SNP Single
Nucleotide Polymorphism:
A point
mutation that occurs in greater than 1% of the population. May serve
as hereditary markers if they are either within a gene or regulatory
region or associated with a gene. Occur every 100-300 bases.
Narrower terms: SNPs
anonymous SNPs, cSNPs, candidate SNP, pSNP, rSNP, synonymous SNP. Related terms
idiomorphism SNPs
& other genetic variations glossary
systems biology:
Researchers
at ISB seek to understand not only each constituent of a biological network but
also how all of a network’s constituents function together. They use
cutting-edge technologies to gather as much information as they can about a
biological system. They then use this information to build mathematical and
graphical models that account for the behavior of the system. They test these
models by gathering additional data, often by perturbing a system through
genetic or environmental changes. In this way, they build an understanding of
biological systems that can be used, for example, to explore what goes wrong
when a biological system becomes diseased and how to treat or prevent that
disease. ISB Institute for Systems biology
http://www.systemsbiology.org/about-systems-biology.
Bioinformatics
glossary
IUPAC definitions are
reprinted with the permission of the International Union of Pure and Applied
Chemistry.
Evolving terminology for emerging
technologies
Suggestions? Comments? Questions?
Mary Chitty MSLS mchitty@healthtech.com
Last revised
September 18, 2018
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Yes. In my mind, the most profound thing - in
terms of the really big picture- is what I think of as the grand unification
of biology. It is no longer debatable that all organisms are in one giant
taxonomic group. There is no fundamental difference between prokaryotes and
eukaryotes that is at the level of the difference between chemistry and
physics or between a sun and a planet. Nothing like that is true. Until quite
recently, many, many of my colleagues believed that difference existed. The
corollary is that what you learn about one organism
is likely to impact, and very possibly explain, phenomena in another organism.
You see that in the literature every day now. ... That is a very big deal. http://www.incyte.com/3_0browser/dbotstein_10_00/question_05.shtml
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