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17

First, a note on spelling. Both "ortholog" and "orthologue" are correct, one is the American and the other the British spelling. The same is true for homolog and paralog. On to the biology. Homology is the blanket term, both ortho- and paralogs are homologs. So, when in doubt use "homologs". However: Orthologs are homologous genes that are the result of a ...


13

3. is right thing to do. You can mention in the introduction that "Campylobacter fetus, which was previously known as Vibrio fetus [Ref] ........." You should not use the old name anywhere again (also for the sake of consistency), once you have made it clear that the species was renamed, in the Introduction. I don't think there is any written convention ...


9

Lactobacillus sanfranciscensis first shows up in pubmed in Gänzle et al. (1998). They reference Trüper and De'Clari (1997) for the name Lactobacillus sanfranciscensis. The latter say: As none of them makes sense in the nominative apposition construction, we hereby correct these names to forms that are in agreement with Rule 12c as follows. ... ...


9

I don't know if these are his earliest descriptions but Darwin did describe several species of Planaria, such as Planaria vaginuloides, P. oceania, plus a new genus, Diplanaria in 1844. Darwin, C. R. 1844. Brief descriptions of several terrestrial planariæ, and of some remarkable marine species, with an account of their habits. Annals and Magazine of ...


8

Both orthologs and paralogs are types of homologs, that is, they denote genes that derive from the same ancestral sequence. Orthologs are corresponding genes in different lineages and are a result of speciation, whereas paralogs result from a gene duplication. This often has important implications: while orthologs often fulfill the same role, paralogs tend ...


8

The term "polymorphism" itself is more generally defined as "the quality or state of existing in or assuming different forms" (Merriam-Webster dictionary). So I guess semantically, it would be correct to say that there is polymorphism in a gene that can occur in different allelic variants, or polymorphism in phenotype because of variant traits (such as ...


8

I don't have a definitive answer, but I suspect Hymenoptera is "just a name," albeit a name that has lasted through the phylogenetic nomenclature revolution. Hymenoptera was erected by Linnaeus in the 10th edition of Systema Naturae (1758). The description of Hymenoptera (membrane wing; p. 553 [hope your Latin is better than mine]) follows that of ...


8

Those describe the genotype of an animal (or plant, virus etc.). The nomenclature can be very varied and domain-specific, but for those two examples: $dt^{sz}$ is a Syrian golden hamster model with a spontaneous mutation (i.e. occurred during breeding, without specific human intervention) which gives predisposition to seizures. They are described in this ...


8

The name is derived from the sugar which is bound to the base. For RNA it is Ribose (that why it is called ribonucleic acid) and for DNA it is Deoxyribose (hence the name deoxynucleic acid). The deoxyribose is missing an OH-group at positition 2 of the sugar ring, the name literally means "without oxygen". See the image below (from here) for further ...


7

I've discovered that searching for Darwin on the Encyclopedia of Life (EOL) appears to prioritise in its search results those species named by Darwin rather than for him. The first page of results includes many barnacle species (as noted by 3cat). The first five species are: Amphibalanus amphitrite (Striped Barnacle) Megabalanus coccopoma (Titan Acorn ...


6

I went to the Yeastbank website at Weihenstephan for some info. The keyword here is "Stamm," which is German for stem, clade, clan, or strain. So, I would take this to mean that the 34/70 is an isolate (#70) of strain 34. Two of 34/70's strengths, according to the link above are it makes clean beer and gives a pleasant taste profile due to its low yeast-like ...


6

There are different unrelated plants called "pepper" in English. Black pepper (species of the Piper genus), as indicated by Chris, is not related to tomato and doesn't "look alike". I guess the OP meant actually a different plant (Capsicum genus), to which the common bell pepper (Capsicum annuum) belongs. This one is similar to tomato and they both belong ...


6

All breeds of dogs are members of the same (sub) species: Canis lupus familiaris. "Breeds" of dogs are not scientific designations but are collections of traits recognized as unique by different breeding organizations. As such, certain breeds are recognized as unique in some organizations do not exist in others (see here for examples).


5

It seems like your question might contain two separate and linked issues, both of which are perhaps equally confusing and equally interesting. They're both really discussion questions in a sense, but they've also both been dealt with in the literature in thoughtful ways, so here's a stab at an "answer". Issue One: how does your species concept deal with ...


5

In this context, "trait reservoir" refers to the set of all possible alleles for all the different genes in the organism. The more different alleles the organism has, the more possible genotypes it might have. The Nature paper might have referred specifically to the set of known allelic variants.


5

Let me clarify my answer since it is lower quality than people may like. To answer the question, my friend is a horticulist and has given a more detailed answer. Subspecies is the most generic, taxonomically-defined term one rank order lower than species. The subspecies (either an individual subspecies, or collective group of subspecies) are defined to be ...


5

Linkage disequilibrium (LD) occurs when there is a non-random association or correlation between genotypes. Note I used the word correlation; this is a quantitative trait. Some genotypes may well correlate perfectly (R=1), i.e. they are always inherited together. Others may not be in 'perfect' linkage (e.g. R=0.9), but are still considered to be in LD ...


5

This is a question of chemical nomenclature and the principle source for this is the IUPAC (IUBMB in case of biological molecules; but not in this case). You can find all hetero-ring nomenclature references on the IUPAC web site: http://www.acdlabs.com/iupac/nomenclature/ http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm (I'm skipping the actual ...


5

Initial letters of the names of the amino acids were chosen where there was no ambiguity. There are six such cases: cysteine, histidine. isoleucine, methionine, serine and valine. All the other amino acids share the initial letters A, G, L, P or T, so arbitrary assignments were made. These letters were assigned to the most frequently occurring ...


5

There is a useful set of links to nomenclature guidelines for all of the main genetic systems at this Wikipedia page. Personally, I think that the Saccharomyces cerevisiae system works best: it manages to cover dominant and recessive alleles of a gene, the name of the protein, how to refer to a related phenotype, and the use of a parallel convention for the ...


5

The correct latin nomenclature is Sander vitreus, with the genus capitalized and the species name in lowercase. This is known as binomial nomenclature. Carl Linnaeus chose to use a two-word naming system [...] binomial nomenclature scheme, using only the genus name and the specific name or epithet which together form the whole name of the species. For ...


5

These strings are specific genotypes of these animals. They often denominate mutations or transgenes. For the hamster $dt^{sz}$ stands for dystopic, the sz comes from the first denomination of this symptoms as seizure. See here for a brief explanation. For the mouse you have both alleles named: Rgs9-cre is a transgene, + in this context always stands for ...


5

All the different breeds of dogs - from Irish setters to greyhounds - are all part of the same species, canis lupus familiaris. The common, domesticated dog is actually a subspecies of the grey wolf. The different breeds do have different genetic characteristics (just as humans have, say, different eye or hair colors), but they're a all one and the same. The ...


4

That's a good question, and honestly, the nomenclature for genes and their coded proteins is somewhat abused in scientific literature. For example, when referring to microbes (like E. coli), gene names are all lowercase (eg, lacZ). The problem of protein names is compounded when the protein name is (often) an abbreviation. With respect to myc, it can refer ...


4

The Biology Project from the University of Arizona provides the best explanation of Dr. Margaret Oakley Dayhoff's logic for the non-obvious single letter AA abbreviations: Glutamine ~ Q-tamine therefore, Q


4

Neurotransmitters were classically the most specific in terms of demands on experimental demonstration (thus, the so-called "classical neurotransmitter") but the chief role of neurotransmitter is direct neuron-to-neuron communication via the synaptic cleft in which the post-synaptic neuron has channels that readily engage the neurotransmitter. Classical ...


4

This isn't a case of gene splicing causing different protein variants. In the studies that identified these two functions (GHB sensitivity and riboflavin transport), they were using DNA derived from mRNA (cDNA), which means what was being expressed in their experiments did not have introns, so there was no chance for alternative splicing. This gene has a ...


4

Many gene names are descriptive, e.g. DRD1: dopamine receptor D1, TOP2A: DNA topoisomerase 2-alpha, or PTGS1: prostaglandin G/H synthase 1. These are examples of genes that have a clearly defined main function. The genes you listed are involved in development, and there describing the function of a gene becomes much more difficult. E.g. sonic hedgehog is ...


4

According to my Henderson's Dictionary of Biological Terms, dry weight is The weight or mass of organic matter or soil after removal of water by heating to constant weight. So yes, your definition is correct and it is also applicable to cells. The dry weight of cells is the weight left when their water content has been removed by heating.


4

Orbitofrontal cortex: the area of the cerebral cortex located at the base of the frontal lobes above the orbits (or eye sockets), involved especially in social and emotional behaviour.



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