The document provides guidelines for gene nomenclature in nematodes. It establishes that WormBase will curate and supervise gene naming for nematodes other than C. elegans to maximize consistency. Gene naming should follow C. elegans principles as much as possible. For genes with clear C. elegans homologs, the same name should be used with a species prefix. New names may be assigned for non-homologous genes after consulting WormBase. Forward genetic studies in other nematodes should also follow these principles when possible.
A complete set of chromosomes/genes inherited as a unit from one parent called genome. The entire genetic complement of a living organism.
The total amount of genetic information in the chromosomes of an organism, including its genes and DNA sequences. The genome of eukaryotes is made up of a single, haploid set of chromosomes that is contained in the nucleus of every cell and exists in two copies in the chromosomes of all cells except reproductive and red blood cells. The human genome is made up of about 35,000 genes.
Thermophilic fungi can thrive in temperatures extending up to 62°C (.pdfinfo824691
Thermophilic fungi can thrive in temperatures extending up to 62°C (143°F). As the only
representatives of eukaryotic organisms that can grow at such extreme temperatures, the
thermophilic fungi are valuable experimental systems for investigators. Although widespread in
terrestrial habitats, they have remained underexplored compared to thermophilic species of
bacteria.
You are most interested in the molecular details of DNA replication in a newly isolated
thermophilic fungus you have maintained in your laboratory. You are anxious to identify its
DNA replicator sequence.
You intend to use the same method utilized by researchers studying both prokaryotic and
eukaryotic DNA replication to identify sequences that can serve as replicator. Describe in detail
the screen you would use to identify potential DNA replicator sequences. Use pictures to
illustrate if necessary, but include text to explain.
Solution
DNA replicator sequences are the sequences where DNA replication starts. These are also called
Autonomous Replicative sequences (ARS). For a genetic screen to work, there are two methods:
i) Auxotrophic strains: strains that can not grow on a particular media
ii) Reporter assays: strains containg a reporter gene like beta-galactosidase or GFP
In this particular assay we need to use auxotrophic strains because replication is associated with
survival and not with protein expression. So, firstly, we will do random mutagenesis and select
for the strains that do not grow in absence of a crucial nutrient (For eg: Uracil). One can obtain
this mutant strain by replica plating the newly obtained irradiated fungus (having random
mutations) on nutrient rich media and media lacking uracil. The colonies that do not grow on
media lacking uracil can be taken for further analysis. Complementary assay will help to identify
the gene responsible for this mutation. Let us assume it is Ura.
Now we will generate overlapping restriction fragments of the genome of this fungus by using
different restriction enzymes (atleast two) for a brief period of time. These fragments can be
cloned in a shuttle vector (plasmid) alongwith the wild type gene Ura that was identified in the
complementary assay but having no replicative sequence of its own. So when the cell divides,
the plasmid can not replicate with the cell unless it has an external ARS. However, if the
restriction fragment cloned with Ura has ARS in it, then this plasmid can replicate along with the
cell and will get distributed equally among the daughter cells. As the original cells do not have
gene Ura to make Uracil, the cells containing the plasmid having ARS only can replicate and
form colonies. Now these plasmids can be sequenced to find out the sequences and the most
common sequences in various plasmids of the surviving colonies can be termed as ARS in that
particular species. The accuracy of the sequence obtained will depend upon the median lengths
of DNA sequences obtained while restriction digestion and fals.
A complete set of chromosomes/genes inherited as a unit from one parent called genome. The entire genetic complement of a living organism.
The total amount of genetic information in the chromosomes of an organism, including its genes and DNA sequences. The genome of eukaryotes is made up of a single, haploid set of chromosomes that is contained in the nucleus of every cell and exists in two copies in the chromosomes of all cells except reproductive and red blood cells. The human genome is made up of about 35,000 genes.
Thermophilic fungi can thrive in temperatures extending up to 62°C (.pdfinfo824691
Thermophilic fungi can thrive in temperatures extending up to 62°C (143°F). As the only
representatives of eukaryotic organisms that can grow at such extreme temperatures, the
thermophilic fungi are valuable experimental systems for investigators. Although widespread in
terrestrial habitats, they have remained underexplored compared to thermophilic species of
bacteria.
You are most interested in the molecular details of DNA replication in a newly isolated
thermophilic fungus you have maintained in your laboratory. You are anxious to identify its
DNA replicator sequence.
You intend to use the same method utilized by researchers studying both prokaryotic and
eukaryotic DNA replication to identify sequences that can serve as replicator. Describe in detail
the screen you would use to identify potential DNA replicator sequences. Use pictures to
illustrate if necessary, but include text to explain.
Solution
DNA replicator sequences are the sequences where DNA replication starts. These are also called
Autonomous Replicative sequences (ARS). For a genetic screen to work, there are two methods:
i) Auxotrophic strains: strains that can not grow on a particular media
ii) Reporter assays: strains containg a reporter gene like beta-galactosidase or GFP
In this particular assay we need to use auxotrophic strains because replication is associated with
survival and not with protein expression. So, firstly, we will do random mutagenesis and select
for the strains that do not grow in absence of a crucial nutrient (For eg: Uracil). One can obtain
this mutant strain by replica plating the newly obtained irradiated fungus (having random
mutations) on nutrient rich media and media lacking uracil. The colonies that do not grow on
media lacking uracil can be taken for further analysis. Complementary assay will help to identify
the gene responsible for this mutation. Let us assume it is Ura.
Now we will generate overlapping restriction fragments of the genome of this fungus by using
different restriction enzymes (atleast two) for a brief period of time. These fragments can be
cloned in a shuttle vector (plasmid) alongwith the wild type gene Ura that was identified in the
complementary assay but having no replicative sequence of its own. So when the cell divides,
the plasmid can not replicate with the cell unless it has an external ARS. However, if the
restriction fragment cloned with Ura has ARS in it, then this plasmid can replicate along with the
cell and will get distributed equally among the daughter cells. As the original cells do not have
gene Ura to make Uracil, the cells containing the plasmid having ARS only can replicate and
form colonies. Now these plasmids can be sequenced to find out the sequences and the most
common sequences in various plasmids of the surviving colonies can be termed as ARS in that
particular species. The accuracy of the sequence obtained will depend upon the median lengths
of DNA sequences obtained while restriction digestion and fals.
Biology questions Please answer all of themTrue or false. If fals.pdfxlynettalampleyxc
Biology questions: Please answer all of them
True or false. If false then state correct answer
1. The frequency of crossing over decreases with the distance seperating genes on a
chromosome.
2. Codominant alleles are expressed equally.
3. Under normal rules of domininace, if two diffferent alleles are present, the dominant allele is
expressed.
4. A mutagen is a substance that causes a change in DNA.
Multiple Choice questions:
5. A DNA nucleotide does not contain A. adenine B. thymine C. uracil
6. Human blood type is determined by A. codominant alleles B. a dominant alleles C. multiple
alleles D. sex-linked genes
7. People who carry genetic disorders (carriers) are A. codominant alleles B. thymine C. uracil
D. cytosine
8. A method to trace the inheritance of a trait over many generations is called a A. carrier tree B.
pedigree C. phenotype D. genotype
9. The insertion or deletion of a single base pair of DNA results in a A. missense mutation B.
nonsense mutation C. duplication mutation D. frameshift mutation
10. Gregor Mendel called the generation created by crossbreeding the parental generation the A.
second parental generation B. cross filial generation C. duplication mutation D. frameshift
mutation.
11. A recessive trait is expressed only in a individual who is A. heterozygous B. homozygous C.
haploid D. polygenic
12. A tall pea plant (TT) and a tall pea plant (Tt) have the same A. alleles B. phenotype C.
genotype D. filial type
13. The faliure of homolougus chromosomes to seperate properly during meiosis is calles A.
nondisjunction B. disjunction C. zygote faliure D. telomere faliure
14. Watson and Crick\'s model of DNA replication is called A. conservation B. semiconservative
C. transcription D. translation
15. Pea plants usually reproduce by A. self-pollination B. cross-pollination C. teste-crossing D.
cloning
16. The pairs of alleles in an organism\'s genetic makeup are called A. phenptype B. genotype C.
parental type D. filial type
Solution
False: As the distance between two gene increases frequency of crossing over between them a
also increases. True : In co dominance both allele are expressed equally True: Cross between
plant having allele TT with plant having allele Tt will show dominant phenotype having
genotype Tt True: Mutation is any sudden change in gene/ DNA that can lead to alteration in
normal genetic make up of an organism False: DNA contain adenine , guanine , cytosine and
thymine; Uracil is present in RNA Co-dominant alleles Pedigree: Change in genetic make up
over generation can be seen in pedigree Missense mutation: Insertion or deletion can lead to
missense mutation First generation b. Homozygous B.Phenotype Non disjunction: is the failure
of homologous chromosome on sister chromatin to separate during cell division
b.Semiconservative model in which one strand is old and another new A. Mendel choose plant
which can do self pollination B.Genotype.
Presentation 6: Vibrio parahaemolyticus: genome plasticity, mobile genetic el...ExternalEvents
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The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
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• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
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Nomenclature of plant parasitic nematodes
1. Curation and supervision
An accepted system of gene nomenclature was established for the nematode Caenorhabditis elegans in
the nineteen seventies.
This system has been refined and consistently used by the many laboratories engaged in active C.
elegans research.
Increasing amounts of genomic and genetic information have become available for other nematode
species.
Draft complete genome sequences have been generated for several of these other nematodes, some of
which are being curated by WormBase.
For these organisms, gene naming will also be supervised by WormBase, in order to maximize
consistency with C. elegans
It is recommended that nomenclature in general should follow the principles used for C. elegans, as far
as possible.
2. How to Register a New Gene Class or Gene Name
Species Prefixes
To unambiguously specify the nematode species-of-origin, a 3-letter standard prefix and
hyphen can be added to the gene name
Prefixes so far used include:
Cel- = Caenorhabditis elegans
Cbr- = Caenorhabditis briggsae
Cbn- = Caenorhabditis brenneri
Cjp- = Caenorhabditis japonica
Hba- = Heterorhabditis bacteriophora
Oti- = Oscheius tipulae
Ppa- = Pristionchus pacificus
Cre- = Caenorhabditis remanei
3. Gene naming: Homologous Genes
Genes predicted from whole genome sequences in other nematode species will, in most
cases, have identifiable close homologs in C. elegans, for which approved names
already exist. In these cases, the same name should be used as in C. elegans, with the
relevant species identifier.
Possible Scenarios
One-to-one: Where one gene in C. elegans corresponds to a single gene in another
nematode species, ortholog naming can be applied automatically. e.g. thoc-1 in C.
elegans has a C. briggsae ortholog, Cbr-thoc-1.
One-to-many: Where one gene in C. elegans is related to multiple genes (paralogs) in
another nematode species, these paralogs can be named using additional decimal
numbers. e.g. thoc-3 in C. elegans has two C. briggsae paralogs, Cbr-thoc-3.1 and Cbr-
thoc-3.2.
4. Gene naming cont….
Many-to-one: Where multiple genes exist in C. elegans, but only a single gene in
another nematode species, either the most closely similar, or the lowest numbered
C. elegans gene, be used to name the single gene, as appropriate
Many-to-many: Where multiple closely related genes can be identified in both
species, but the phylogenetic relationships of the two sets are complex, new gene
numbers can be assigned to the set of genes in the other nematode species, after
consultation with genenames@wormbase.org.
In cases where a standard gene name has not yet been assigned in C. elegans, the
gene can be referred to using the cosmid.number identifier for the C. elegans
gene, preceded by a species prefix. e.g. the ortholog of C. elegans W01B11.3 in
Heterorhabditis bacteriophora can be referred to as Hba-W01B11.3. However, in
such cases it will usually be both feasible and desirable to assign a standard name
to the C. elegans gene as well, at the same time.
5. Gene naming cont….
Non-homologous Genes
It is expected that many genes in other nematode species will lack obvious close
homologs in C. elegans, because of loss or substantial divergence during the
evolution of C. elegans.
These genes can be given new gene numbers, if they belong to an identifiable
named class in C. elegans, or else new gene name classes can be established for
them.
In either case, assignment of an approved name should be made after consultation
with genenames@wormbase.org.
6. Gene naming
Forward Genetics
A significant amount of mutation-based forward genetic analysis is being pursued in
nematodes other than C. elegans, in particular using other species of Caenorhabditis (C.
briggsae, C. remanei, C. brenneri and others), as well as species of Oscheius and
Pristionchus.
It is expected that most, but not all, of the mutationally-defined genes discovered in these
species will prove to have orthologs with equivalent or similar function in C. elegans,
and hence that standard genetic names will have been approved already. Several
situations can arise:
7. Forward Genetics
1. where the molecular identity is known and orthology is obvious, it is recommended that
the C. elegans name be used, with the appropriate species identifier prefix. e.g. Ppa-mab-5
is the Pristionchus pacificus ortholog of C. elegans mab-5.
2. In cases where the molecular identity is not initially known, but the mutant phenotype
corresponds to a known C. elegans mutant phenotype, it is recommended that the mutant
gene be temporarily defined using the relevant gene class name and the mutation number, in
parentheses. e.g. mutation s1270 isolated in C. briggsae confers an uncoordinated
phenotype, so the gene is temporarily called unc(s1270) or Cbr-unc(s1270).
Once the molecular identity becomes known, the gene can be given an approved unc-
number, using the number of the C. elegans ortholog (if this exists) or a new number (if
there is no suitable C. elegans ortholog).
8. Forward Genetics
In cases where the molecular identity is unknown and the mutant phenotype does
not correspond to a known C. elegans mutant phenotype, a new gene class name
can be established, following consultation with genenames@wormbase.org in
order to ensure that the new name is available and appropriate. e.g. cov =
Competence and/or centering Of Vulva abnormal.
9. SPECIFIC NAMES DERIVED FROM HOST NAMES
A parasite named after its hosts should be given the specific (not the
generic) name of its host; this name should be treated as a substantive in
the genitive case.
For example, Hemicaloosia americana is a species from India named
after its host : Agave americana. H. americana is to be spelled H.
amencanae.
Many authors use the generic name of the host. It would not serve the
stability of nomenclature to change these names and they will be
accepted as proposed.
10. SPECIFIC NAMES DERIVED FROM
GEOGRAPHICAL NAMES
Nothocriconema sanctus-francisci van den Berg & Heyns, 1977, must be
corrected by deletion of a hyphen (Art. 26), and should be written in the
genitive case as N. sanctifrancisci.
Scutellonema imphalus Sultan & Jairajpuri, 1979, from the town of Imphal,
India, is treated as an adjective. It should be spelled S. imphalum
11. SPECIFIC NAMES FORMED FROM MODERN PERSONAL NAMES
Aphelenchoides franklini Singh, 1969, from the name of Dr Mary Franklin, is corrected
to A. franklinae. Cosaglenchus rafiqus Siddiqui & Khan, 1983 is corrected to C. rafiqi
(Recommendation 31 A; see also D Ill).
ERRORS IN TARJAN AND HOPPER'S BOOK
The specific names listed in Tarjan and Hopper (1974) are sometimes spelled with an
ending different from that in the original publication. These discrepancies occurred when
a taxon is better known in a genus different from the original genus, and with a different
gender.
For example the species named Tylenchus balsamophilus Throne, 1926, in the original
description was spelled T. balsamophila in Tarjan and Hopper's book, probably because
it is now Anguina balsamophila. In the computerized datafile, the spelling has been
reverted to that of the original author,
12. ERRORS IN TARJAN AND HOPPER'S BOOK
Other typographical errors in Tarjan and Hoppe(1974) include
Anguillonema erenati for A. crenati.
Aphelenchoides eradicatus for A. eradicitus
These incorrect subsequent spellings have no status in nomenclature (Art. 33, b).
Another incorrect subsequent spelling was made when Bajaj and Bhatti (1979)
transferred Basiroides longimatricalis Kazachenko, 1975 to Basiria under the
specific name Basiria leptolongimatricalis. The correct new combination is
Basiria longimatricalis (Kazachenko) Bajaj & Bhatti.
13. Common Names of Major Phytonematodes of
Horticultural Crops
Anguina spp.: Seed and leaf gall
nematode
A. agrostis : Bent grass
nematode
Aphelenchoides spp.: Bud and
leaf nematode, foliar nematode
A. besseyi : Rice white-tip
nematode, strawberry bud
nematode, summer crimp,
summer dwarf nematode
A. fragariae : Spring crimp
nematode, spring dwarf
nematode, strawberry bud
nematode
A. ritzemabosi :
Chrysanthemum foliar
nematode
Bursaphelenchus cocophilus :
Coconut palm nematode, red ring
nematode
Bursaphelenchus xylophilus :
Pinewood nematode
Cacopaurus pestis : Walnut nematode
C. cacti : Cactus cyst nematode
Criconema / Criconemoides : Ring
nematode
Ditylenchus destructor : Potato rot
nematode
D. dipsaci : Stem and bulb nematode,
alfalfa stem nematode
Dolichodorus spp.: Awl nematode
Globodera pallida : Pale/white
potato cyst nematode
G. rostochiensis : Golden nematode,
golden potato cyst nematode
14. Cont….
Helicotylenchus multicinctus :
Banana spiral nematode, spiral
nematode
Hemicriconemoides spp.: False
sheath nematode
Hemicycliophora spp.: Sheath
nematode
Heterodera carotae : Carrot cyst
nematode
H. cruciferae : Cabbage cyst
nematode
H. cyperi : Nutgrass cyst nematode
H. fici : Fig cyst nematode
H. goettingiana : Pea cyst nematode
H. schachtii : Sugar beet cyst
nematode
Hoplolaimus spp.: Lance nematode
Longidorus spp.: Needle nematode
Meloidodera spp.: Cystoid nematode
Meloidogyne spp.: Root-knot nematode
M. carolinensis : Blueberry root-knot
nematode
M. exigua : Coffee root-knot nematode
M. graminis : Grass root-knot nematode
M. hapla : Northern root-knot nematode
M. incognita : Southern root-knot
nematode
M. javanica : Javanese root-knot
nematode
M. konaensis : Kona coffee root-knot
nematode
M. lusitanica : Olive root-knot nematode
M. megatyla : Pine root-knot nematode
M. nataliei : Michigan grape root-knot
nematode