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14

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 ...


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. ... ...


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 ...


6

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 ...


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 ...


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 ...


4

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 ...


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

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

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

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 ...


3

In theory, your idea seems reasonable, but I can see at least to problems with implementing it. First, the situation is complicated by the fact that genes often carry out multiple functions, and a single label is often insufficient to annotate the complete functional repertoire of a gene. @MichaelKuhn made an excellent point with regards to the evolution of ...


3

I've found a rough answer myself: The globe of the eye, or bulbus oculi, is the eyeball apart from its appendages http://en.wikipedia.org/wiki/Globe_%28human_eye%29 ... the orbit is the cavity or socket of the skull in which the eye and its appendages are situated. "Orbit" can refer to the bony socket, or it can also be used to imply the ...


3

From Wikipedia: Some biologists refer to wholly syncytial organisms as "acellular" because their bodies contain multiple nuclei which are not separated by cell walls. As Albano pointed out, "cell walls" should probably be "cell membranes". Paramecium and some types of amoeba like the Chaos genus have multiple nuclei so they fall under this definition.


3

I am not sure why you say there is no information... a quick Google search returned a few interesting pages... In this paper: Progress in Metabolic Engineering of Saccharomyces cerevisiae - Nevoigt, Microbiol Mol Biol Rev. 2008 the author says: The identification of the entire genomic sequence of a commonly used lager brewer's yeast strain, i.e., ...


2

You can think of a genetic network as a network of interacting genes, turning each other on and off based on complex relationships and external stimuli. A genetic network is typically characterized in terms of graph theory--connectivity, density, etc. The term genetic architecture, on the other hand, typically refers to a trait or phenotype and the ...


2

The easiest way to understand this, in my opinion, is to think in social insects. In the ants, for example, there are polymorphisms, since the workers don't have the same phenotype as the queen or the soldiers. Also, one could argue that the whole colony is a massive metaorganism or superorganism, formed by the summation of all the individual ants. As in an ...


2

Apparently I asked too soon. Summarizing my recent findings, I conclude that adrenaline is the better term. To be more explicit, here is why: The US National Library of Medicine recommends “epinephrine”, this is however mainly due to historical reasons (adrenaline used to be a trademark name in the USA). This quite comprehensive paper on the issue ...


2

The boney component of the anatomical orbit*strong text* (in lay terms the eye socket) is the area bordered by the zygomatic, frontal, maxilla, sphenoid, palatine, lacrimal and ethmoid bones. The use of the word orbit (red) in orbitofrontal cortex refers to the positioning of this part of the frontal cortex (green) being directly behind the orbit: ...


2

This is actually already done in some contexts. For instance: yeast (a fungus) is a pretty extensively studied organism, and this means that there are a vast number of yeast strains which are know/used by biologists. Many of these strains are referred to simply by an alphanumeric string rather than a "verbal" name. (some examples in link 1) This is also ...


1

Its fairly common for a gene to have multiple names. I cant say for certain, but Jax and GeneCards also lists them as being synonymous so I would say its safe to say they are the same http://www.informatics.jax.org/marker/MGI:1289288 http://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC52A2 Edit in reply to comment: In higher level Eukaryotes the vast ...


1

According to A Source-Book of Biological Names and Terms by Jaeger, the appropriate terms are the simple, obvious ones: "Geographical" for place-derived names and "Personal" for person-derived names.



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