The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA.

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124 views

Extending a small fragment of DNA

Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence? For example, I want a 1 ...
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1answer
32 views

T7 vs pBAD promoter strength

How do pBAD and T7 promoter strengths compare when pBAD is induced under conditions which would lead to its highest strength? Are there any papers that compare the two inducible promoter systems?
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1answer
26 views

Does mechanotransduction of cells play a role in the biocompatibility of titanium?

What exactly is mechanotransduction as the information varies between sources. Some sources indicate that mechanotransduction is the underlying principle where cells pull on the surface they grow on ...
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1answer
48 views

probe amplification in MLPA

I'm reading an article about MLPA (Multiplex ligation-dependent probe amplification) and I got stuck on this sentence: The advantage of splitting the probe into two parts is that only the ...
6
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0answers
134 views

Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
4
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0answers
115 views

At what rate do chromosomal rearrangements occur?

How often does chromosomal rearrangements occur? i.e. what is the rate of chromosomal rearrangements? I am interested about these kind of chromosomal rearrangements that are passed on to the ...
3
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0answers
33 views

Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
3
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0answers
42 views

Should gene therapy safety protocol include isolation?

In the case of a gene therapy trial where viral vectors are used to deliver genes into mammalian cells, including humans, should biosafety and ethical protocols include isolation of the patient as a ...
3
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0answers
45 views

What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?

In the Miller–Urey experiment they produced several amino acids. I'm not sure if there were other similar experiments that got further. ...
3
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0answers
31 views

Gibson assembly - primer design with A and T rich regions

I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: ...
3
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0answers
65 views

Inbreeding Coefficient and Coefficient of Relationship

Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$: $$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} ...
3
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0answers
150 views

What metabolic processes do dormant and ungerminated seeds carry out?

What metabolic processes does a dormant embryo in a seed carry out? Seeds will not germinate, either because of a lack of favourable conditions, seed hibernation, or because of a genetically ...
2
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0answers
45 views

PCR that worked previously is now only showing primer dimers and a smear on gel

PCR amplification of a promoter sequence for gel extraction worked beautifully using Phusion HF enzyme with GC (higher error but less picky) buffer. However, DNA concentration from the gel extraction ...
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0answers
35 views

Do The Traces Genetic Diseases Remain in families?

I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. ...
2
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0answers
59 views

CRISPR Knock in

Using the CRISPR/Cas9 technology, it is possible that after inducing a DSB with the Cas9 endonuclease guided with an RNA designed by the user and using a template DNA, get a desired Knock-In (KI) by ...
2
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0answers
41 views

Question about mutation of multiple nuclei?

If an organism with multiple nuclei, such as the slime mold Physarum polycephalum, was to be exposed to a mutagen, such as 5-bromouracil, what would be the effect (besides death)? Especially if ...
2
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0answers
30 views

Is it reasonable to assume that RNA polymerase would bind preferentially to the promoter of the long allele of the SERT gene?

I'm trying to come up with an idea for a school project (a hypothetical research study). I'm looking at depression and the serotonin transporter gene, which is highly expressed in the human ...
2
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0answers
228 views

What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)

What tests could be run to test the purity and type of HCG? We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide ...
2
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0answers
307 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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0answers
14 views

Does any specific property decide which DNA strand acts as leading strand template?

Of the two strands of DNA, the one that unwinds in the 3' to 5' direction constitutes the leading strand template, with the other strand of course acting as the lagging strand template. Is there any ...
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0answers
25 views

UV light-induced mutagenesis during gel extraction

this is a very short question I did not find the answer for online, neither on this nor other fora. At the beginning of my cloning protocol, I extracted the band with the sequence of interest directly ...
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0answers
10 views

Mosaic segregation in C. elegans

How can mosaic segregation be used in C. elegans? Can it tell us where a given gene is expressed, or needs to be expressed for worm survival?
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0answers
26 views

Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes

In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as ...
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81 views

What type of point mutation and chromosomal mutation cause Albinism in humans?

First of all, I know that OCA1 (Oculocutaneous Albinism Type 1) is autosomal recessive which means that both parents-who are unaffected-have to pass down one copy of a mutated gene in order to ...
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0answers
31 views

Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription. Does this mean no new proteins are made during what can be 20% of a cell's life? ...
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0answers
24 views

Degenerate primer designing software

Can any one provide online free degenerate primer designing software. I have tried couple of them like CODEHOP is one where BLOCK formatting step finding difficulty, can anyone help me out....
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0answers
38 views

“Signal Advance”: Unsure of meaning or contextual use

I am reading through Recombinant DNA; Genes and Genomes - A Short Course - Third Edition by James D. Watson, et. al. and I came across this paragraph in the discussion about discrete factors of ...
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0answers
35 views

Can genes be expressed sequentially?

As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
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0answers
28 views

recombination between DNA segments question

In the diagram shown above, segments A and C are copies of a repeated DNA sequence, flanking a unique stretch shown as B. A and C are in an inverted orientation relative to each other, as indicated ...
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0answers
106 views

mutations induced by transposons

Question: In contrast to chemically-induced mutations, mutations induced by transposons are more likely to ... be lethal de dominant be stable revert to wild types be a gain of function The ...
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0answers
48 views

How does intron retention make the alternative transcript non-coding?

I faced with a non-coding transcript that specified as one the isoform of BIN1. It sounds that this isoform generated as a result of alternative splicing with a intron retained; am I right? However, ...
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0answers
28 views

Is a Ribonuclease Inhibitor protein the only mechanism employed by the human cell to protect cellular RNA from degradation by endoribonuclease?

Are there any other methods of protection for cellular RNA from degradation by endonuclease (specifically the Pancreatic Ribonuclease RNase II (Eosinophil-derived neurotoxin) and RNase III (Eosinophil ...
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0answers
136 views

Recommend any Molecular lab LIMS (Laboratory Information Management System)

We are looking to develop or customize a LIMS for our molecular lab. Do you know of a LIMS that you've used in a molecular lab before, or one that could be used. Thanks for the help (Edit) Some of ...
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0answers
20 views

How to engineer chromosomal duplications?

Specific genetic engineering of chromosomal aberrations like deletions, inversions and translocations are doable by using the CRISPR/Cas system or the other programmable nuclease systems. Insertions ...
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0answers
58 views

What genetic distance model should be used when calculating genetic differences in Arelquin?

I'm using Arelquin to look at the genetic structure between a number of different populations. I want to compare the populations by producing pairwise FST values, however I don't know what model for ...
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0answers
72 views

Loss in DNA band size extracted from polyacrylamide gel

I'm using cDNA AFLP teq.. I extracted 670 bp band from polyacrylamide (urea) gel and I have amplified with PCR but on agarose gel it stops at nearly 350 bp.it happened for most of other bands before. ...
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0answers
26 views

Linkage disequilibrium D sign

Linkage disequilibrium D equals D=x11−p1⋅q1 where: Haplotype > Frequency A1B1 > x11 A1B2 > x12 A2B1 > x21 A2B2 > x22 and Allele Frequency A1 > ...
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0answers
43 views

Assembling DNA fragments with ~10kb overlap in vitro

Let's say I have two fragments of bacterial DNA (~50kb in length each) that overlap on the ends by roughly ~10kb; the overlap sequences are unknown. I would like to assemble these into longer ...
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0answers
39 views

Study case of the inheritance system of Oenothera

I've been told some interesting facts about oenothera. Apparently in this species some lineages have been through some translocations and in results to these translocations and in consequence, some ...
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0answers
55 views

Transduction with P1 lysate prepared from strain that is proC::Tn10

If I do a transduction with a P1 lysate prepared from a strain that is pro*C*::Tn10 and the recipient is wild type, will all my recombinants be ProC- and Tet resistant since the Tn10 is in the proC ...
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0answers
21 views

How do expression levels change along lineages?

Is there any general trend between gene expression levels (or transcription levels) and cell lineages? For example, I would naively expect that stem cells express less genes as they have the ability ...
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0answers
22 views

How does epigenetics affect the birth conditions via alcohol?

Recent study has shown that epigenetics can play role in male-caused infertility and it cites for example studies which showed an enhancing of silent genes when drinking alcohol. Since the study ...
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0answers
13 views

Developing cDNA for RDT

Eukaryotic genes cannot be inserted in prokaryotic hosts for making recombinant proteins, since eukaryotic genes are split genes and their hnRNA must first be processed to functional mRNA before ...
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0answers
19 views

What is the highest number of genes expressed under one T7 promoter?

What is the highest number of genes expressed under one T7 promoter? Also, what is the longest polycistronic mRNA? I am interested in the context of heterologously expressing biosynthetic gene ...
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0answers
49 views

mutant and variant differentiation

Can anyone clearly differentiate between a variant and a mutant in genetics. I am confusing these terms a bit, as the evolutionary aspect also comes to my mind.
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0answers
27 views

Do any gaps in DNA during cell division (meiosis in particular) lead to crossover?

I have some gaps in the knowledge abour crossover. I know, that crossover is connected with reparation process. I'd like to know if all gaps in chromosomes lead to crossover (reparation based on 2d ...
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0answers
23 views

Amplified Fragment Lenth Polymorphism (AFLP) primers

I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome. For example, in the ...
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0answers
7 views

Double stranded breaks in E. coli

What could be a possible reason why no enzymes have been found that make double stranded breaks in the RecBCD pathway?
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0answers
49 views

Why is dsDNA nuclease activity by CRISPR/Cas9 only shown indirectly?

In Jinek et al., the authors show nuclease activity of their CRISPR/Cas9 system using the so-called Surveyor assay method. This assay recognizes small mismatches in dsDNA which are introduced by error ...
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21 views

Stable transfection

I need to achieve stable transfection of a pCI-Neo plasmid into the genome of a mouse embryo. The most common way to achieve stable transfection is through positive selection, however positive ...