Dory's Biology Questions Thread

[GenesForLife]

Endo = inside , genous = originating, transposition = or genetic transposition, a mutation in which a chromosomal segment is transferred to a new position on the same or another chromosome.

Oh right, old Barbaria Mcklinglock (sp?) figured that shit up with corn, IIRC. Something with their melanin, or colour. I don't remember exactly how she did it. I just remember it being termed "transposable elements". Not "endegonous transposition"...kinda confused me.

Transposons/transposable elements, are genomic regions or jumping genes, the process is transposition.

Basically Dory, RNAi goes like this, say you introduce double stranded RNA into the cell

wtf, RNA can be double-stranded? Since when???

A little logical step from secondary structures in RNA such as tRNA , Dory, if complementary nucleotides in a single strand can bind together , producing loops, the same chemistry can hold two single strands of RNA together, it is base pairing again, of course, just to provide evidential support to that logical extrapolation, I post this

http://en.wikipedia.org/wiki/Double-str ... NA_viruses

Double-stranded (ds) RNA viruses are a diverse group of viruses that vary widely in host range (humans, animals, plants, fungi, and bacteria), genome segment number (one to twelve), and virion organization (T-number, capsid layers, or turrets). Members of this group include the rotaviruses, known globally as a common cause of gastroenteritis in young children, and bluetongue virus, an economically important pathogen of cattle and sheep.
Viruses with dsRNA genomes are currently grouped into six families: Reoviridae, Birnaviridae, Totiviridae, Partitiviridae, Hypoviridae, and Cystoviridae. Of these six families, the Reoviridae is the largest and most diverse in terms of host range.
In recent years virus particle assembly, virus-cell interactions, and viral pathogenesis, approaches for the development of novel antiviral strategies and/or agents can be designed.[1]

an enzyme called Dicer slices it up into shorter fragments, this then binds to an enzyme complex called the RNA Induced Silencing Complex, or RISC, which then separates the fragments into a single stranded, bound version, the complex can then bind to complementary mRNA and cleave it, thus blocking expression of the gene which produced the mRNA.

So it has to go through all this complex stages to become a sort of molecular knife that cleaves mRNA's?

This is the pathway for dsRNA to begin to cleave mRNA... if there are antisense RNA transcripts, they bind to mRNA and trigger cleavage in just one enzyme mediated step, therefore it is also possible to silence gene expression by just introducing/ inducing the production of the antisense nucleic acid sequences. I've worked with antisense sequence design in the past, and RNAi design for a particular gene, and can show you how to do that for any given gene.

PS - sense sequence - the sequence on the mRNA that produces a protein, antisense sequence is the one complementary to that.

sense + antisense = double stranded entity.

[Berthold]

On the peopling of the Americas, I can recommend this book.

Also interesting is Monte Verde.

However, beware of crackpottery, of which there is a lot around in this field of research.

[Dory]

Ah...so tRNA is considered double-stranded as well?

if complementary nucleotides in a single strand can bind together , producing loops, the same chemistry can hold two single strands of RNA together, it is base pairing again, of course, just to provide evidential support to that logical extrapolation, I post this

Extrapolation...you just can't say that word and not be right

This is the pathway for dsRNA to begin to cleave mRNA... if there are antisense RNA transcripts, they bind to mRNA and trigger cleavage in just one enzyme mediated step, therefore it is also possible to silence gene expression by just introducing/ inducing the production of the antisense nucleic acid sequences. I've worked with antisense sequence design in the past, and RNAi design for a particular gene, and can show you how to do that for any given gene.

PS - sense sequence - the sequence on the mRNA that produces a protein, antisense sequence is the one complementary to that.

sense + antisense = double stranded entity.

Antisense makes a lot more sense as a gene silencer than all that complex mumbo jumbo with Dicer, silencing complexes, fragments and shit! Even for molecular biology that's too much molecular biology.

[GenesForLife]

Ah...so tRNA is considered double-stranded as well?

Nope, all I was saying is that the same chemistry that results in base pairing within the single strand of tRNA to result in portions that resemble double stranded portions is the same thing that can hold two ssRNA strands to form dsRNA

if complementary nucleotides in a single strand can bind together , producing loops, the same chemistry can hold two single strands of RNA together, it is base pairing again, of course, just to provide evidential support to that logical extrapolation, I post this

Extrapolation...you just can't say that word and not be right

This is the pathway for dsRNA to begin to cleave mRNA... if there are antisense RNA transcripts, they bind to mRNA and trigger cleavage in just one enzyme mediated step, therefore it is also possible to silence gene expression by just introducing/ inducing the production of the antisense nucleic acid sequences. I've worked with antisense sequence design in the past, and RNAi design for a particular gene, and can show you how to do that for any given gene.

PS - sense sequence - the sequence on the mRNA that produces a protein, antisense sequence is the one complementary to that.

sense + antisense = double stranded entity.

Antisense makes a lot more sense as a gene silencer than all that complex mumbo jumbo with Dicer, silencing complexes, fragments and shit! Even for molecular biology that's too much molecular biology.

Yup, but RNAi is an important natural mechanism used for regulating gene expression, it was first discovered and studied in C.elegans, and it won Fire and Mello a Nobel, practically speaking, from a biotechie's POV, antisense is better than RNAi.

[Dory]

Nope, all I was saying is that the same chemistry that results in base pairing within the single strand of tRNA to result in portions that resemble double stranded portions is the same thing that can hold two ssRNA strands to form dsRNA

Agreed.

Yup, but RNAi is an important natural mechanism used for regulating gene expression, it was first discovered and studied in C.elegans, and it won Fire and Mello a Nobel, practically speaking, from a biotechie's POV, antisense is better than RNAi.

I've no doubt it's important, but it's too many little facts to remember, as opposed to a concept to understand.

[GenesForLife]

Yup, but RNAi is an important natural mechanism used for regulating gene expression, it was first discovered and studied in C.elegans, and it won Fire and Mello a Nobel, practically speaking, from a biotechie's POV, antisense is better than RNAi.

I've no doubt it's important, but it's too many little facts to remember, as opposed to a concept to understand.

It is simple actually, Dicer dices it into shorter double stranded fragments, RISC processes it to carry one of the strands, RISC + one of the strands cleaves complementary mRNA, that is the basic concept, as with any other concept in biology, it is simple, but the body of knowledge that comes with asking questions about it, such as where, when, what, how and why is a major scientific headache filled with the geeky goodness of intricate details.

Are you looking to study Biochemistry at the Undergraduate level, Dory?

[Dory]

Yup, but RNAi is an important natural mechanism used for regulating gene expression, it was first discovered and studied in C.elegans, and it won Fire and Mello a Nobel, practically speaking, from a biotechie's POV, antisense is better than RNAi.

I've no doubt it's important, but it's too many little facts to remember, as opposed to a concept to understand.

It is simple actually, Dicer dices it into shorter double stranded fragments, RISC processes it to carry one of the strands, RISC + one of the strands cleaves complementary mRNA, that is the basic concept, as with any other concept in biology, it is simple, but the body of knowledge that comes with asking questions about it, such as where, when, what, how and why is a major scientific headache filled with the geeky goodness of intricate details.

You're right, no doubt, but I don't feel it would benefit me to know that intricate geeky goodness as of now...I'll save my brainbox for more general biology info. I got a general biology test a week from now.

Are you looking to study Biochemistry at the Undergraduate level, Dory?

We'll see, I might just professionalize myself as paramedic before delving deep into science. Biochemistry though is definitely my scientific choice as of now.

[GenesForLife]

Good luck with your test, Dory.

[Dory]

Good luck with your test, Dory.

Thanks!

[Dory]

Say GNF, have you ever worked with selective markers or reporter genes? Can you give examples of what sort of reporter genes are used? I assume these stuff create some sort of cytological markers.

[Dory]

I think it's a trick question:

If the frequency of the autosomal recessive disease sickle cell anaemia is 1/500 in African Americans?
If the frequency of the autosomal recessive disease sickle cell anaemia is 1/500 in African Americans the chance of two unrelated and unaffected African Americans having a child affected with Sickle Cell disease is about:

a) 1/500
b) 1/128
c) 1/64
d) 1/1024

The answer to me seems to be 1/500 since this is the frequency..and there's nothing special about the parents

[GenesForLife]

Say GNF, have you ever worked with selective markers or reporter genes? Can you give examples of what sort of reporter genes are used? I assume these stuff create some sort of cytological markers.

GFL

No, I haven't worked practically with selective markers or reporter genes, as for reporter genes, mostly fluorescent proteins are employed, they create a marker for gene expression,
the idea is that you integrate the reporter gene close to the promoter you are studying, when a promoter is activated/turned on, the reporter attached to it produces a fluorescent protein that can be visualized, examples include luciferase, mCherry, mKatushka, mKate and so on and so forth for such reporter products.

An example of a palette of such proteins is this



Pretty, innit?

Selective markers involve the same mechanism, but they allow selection to be carried out based on a phenotype, these are not always linked to a particular promoter being studied/gene of interest, but they are good at telling you if something is transgenic or not, such markers can include fluorescent tags again, and antibiotic resistance markers, for instance.

And for the frequency, Dory, I think you basically have it right, the frequency is determined for the population of unrelated, unaffected parents, usually, so I'd say that the odds wouldn't change for the specified conditions.

[Dory]

Say GNF, have you ever worked with selective markers or reporter genes? Can you give examples of what sort of reporter genes are used? I assume these stuff create some sort of cytological markers.

GFL

Oops...typo! Although I think a cooler nick would be Genes ftw!

No, I haven't worked practically with selective markers or reporter genes, as for reporter genes, mostly fluorescent proteins are employed, they create a marker for gene expression,
the idea is that you integrate the reporter gene close to the promoter you are studying, when a promoter is activated/turned on, the reporter attached to it produces a fluorescent protein that can be visualized, examples include luciferase, mCherry, mKatushka, mKate and so on and so forth for such reporter products.

An example of a palette of such proteins is this



Pretty, innit?

Fucking awesome is more like it! And look it that, looks like we have protein fluorescence for nearly every damn colour.

Selective markers involve the same mechanism, but they allow selection to be carried out based on a phenotype, these are not always linked to a particular promoter being studied/gene of interest, but they are good at telling you if something is transgenic or not, such markers can include fluorescent tags again, and antibiotic resistance markers, for instance

Ohhh...gotcha. So, a reporter gene is a type of selective marker. I see.

And for the frequency, Dory, I think you basically have it right, the frequency is determined for the population of unrelated, unaffected parents, usually, so I'd say that the odds wouldn't change for the specified conditions.

Thanks for covering that up, too.



Damn you're a fountain of knowledge.

[Dory]

Genes, you should like totally open a blog or something. I'll happily help you if you got any interest to do it.

[GenesForLife]

Genes, you should like totally open a blog or something. I'll happily help you if you got any interest to do it.

I'm too lazy and will be too busy, lass, I may start a youtube channel though