Animal Genetics - Science topic

I am planning on inducing a young cohort of mice with tamoxifen between the age range of P21 to P28 (3-4 weeks). I was planning on using the calculations that I have used for adult mice (>8 weeks). Those calculations being tamoxifen dissolved in corn oil at a concentration of 20mg/mL and then injecting at a dose of 75mg (tamoxifen)/kg (bodyweight). These being the suggested calculations from Jackson Labs. Will I be okay to administer to the same concentration and dose at this age range?

is there any ways that i can find genome similarity of an organism without whole genome sequencing ,like using maths formulas or experimental progress ?

Maybe impossible to discern yet, an Egyptian plover can maybe clean a Crocodile's mouth without getting eaten.

No mutation can change an animal into a human and no gene is completely known to manifest into a trait.

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I am relatively new to the genetics field and am curious if their is an established way of representing BAC transgenic mouse models. I know that a homozygous knockout trangenic model is expressed -/- etc. I was just curious if there is a correct notation for the addition of a BAC in a mouse model. Thank you.

Would you please let me to know about the methods for measurement of medullation and Kemp % on animal? My problem is that the wool sampling and sending to laboratory is not possible. So I would like to verify the possibility of a method to measure Kemp/medullation % in wool rapidly on the animal. I know "Benzene test" (attached file) for distinguishing of Kemp fibers, but Benzene is a risky material. Furthermore the use of portable OFDA in our situation is not possible.

Is there safe substance similar to benzene that has the similar optical refractive index ? Which safe liquid can be found that has a light refractive index similar to wool? (1.54). Sincerely,

Who agrees with me that maybe technically I am over 100 Western European? How? Why? “I am over 100% Western European when all the max possible Western European blood percentages of my ethnicity estimate are added together and the highest possibilities of the other ethnicities are subtracted then I become over 100% Western European. Factors contributing to that genetic paradox are that I have a high mutational load(exemplified by my autism). And that the Southeast Asian Ethnicity is more Neanderthal than the European one”(Ohnemus 2023).

Supporting Sources:

Outcome depends on the type of food it takes right ? So if a cow consumes Genetically modified grass rather than normal will the quality of milk increase? And can we observe any changes in the behaviour ?

Dear experts: are all substrains of Bown Norway (BN) derived from the same strain? The most readily available strain is BN/Crl, but the reference genome is built on BN/NHsdMcwi. I was wondering if it's possible that those 2 strains were separately derived from the wild but both happened to be "brown norway".

Thank you!!

" In stark contrast to classical theory, the total heritable variance in a trait can be larger than the phenotypic variance in the trait, Var(TBV) > Var(P)..... In that case, a population contains a heritable variance which is greater than the observed phenotypic variance. Social interactions, therefore, result in hidden heritable variation ".( In book : Julius van der Werf et al. 2009 Adaptation and Fitness in Animal Populations - Page 116 )

Can Piter Bijama's sentence in the book be interpreted in this way: If in the formula heritability, genetic variance is greater than phenotypic variance, the heritability would be greater than one.!

Can we arrive at true breeding values (TBVs) from average progeny performances, or would they still be estimated breeding values (EBVs)? Can true breeding values be found at all from retrospective phenotypic data (no genotypic data) of the animal?

"The development and validation of a medium density SNP genotyping assay in Shrimp" is a research proposal I'm currently working on. Given the restricted budget allotted (9,600 USD) to the project, I'd like to know ahead of time how much it might probably cost me.

Strictly going by the amount of research that has been done in the diapause phase (dauer) of C. elegans, which aspect (recovery, maintenance, entry) has received maximum attention.

In Europe (in France and Germany at least), there is a new cultural-political position suggesting there were no human races … Not really … only as a delusion… as a constructed deception originating from the early modern times of beginning colonialism. – So not whites, no blacks (in former times: “negros” – sorry, I apologize for this), no yellow or Mongolian race, no Eskimos and so on.

The traditionalists in Europe still oppose this position and complain about a new ideological war with the progressive activists, who try for instance to make jobs dependent on compliance to the no-race-concept.

I would be especially interested in the opinions of coloured people and of non-Westerners. (But this is not meant as an exclusion … So all are invited (independent of any external traits) …).

I have a database of snp genotypes analyzed with an Affimetryx platform I want to analyze with a reference genome, however I find obvious differences between Btau8 / UMD3.1.1 or ARS-UCD1.2, I must work with the latter that has been updated or keep me with UMD3.1.1?

The application of conventional approaches in animal breeding ( selection and mating systems ) achieved very good results to improve the production traits of animals in the past and still working, far of the applications of molecular in the laboratories, what the molecular economic achievements in animal production.

Thank you for sharing your ideas

I am a little bit confused about how to calculate reliability for EBV of each animal using the BLUPF90 program; taking into account repeated measures data, contemporary groups, and removing parent average effects. I think some programs of BLUPF90 family, such as ACCF90 and BLUPF90test, can compute the reliability directly through a few commands. How could I get them? May someone suggest me some ideas in order to create a script for that kind of analysis?

Cross-species sequence comparison is doing normally in sequence analysing. However, is it necessary or effective of doing corrections of the query sequence with the subject sequence when identifying an unknown species?

What is the underlying basis of correcting nucleotide mismatches of a query sequence?

As mentioned before, i am interested to write a research paper in the field of poultry/broiler chicks, respectively in major of Animal Genetics and Reproduction, so i will be highly appreciated if someone come up with a great title for me.

I have tried to calculate genetic parameters using only Microsoft Excel ..

please tell me about an easy to understand application for calculating genetic parameters if I want to publish scopus articles at least Q3?

I am thinking to investigate the roles of a specific gene during the embryonic development stages in a crab species. I was just wondering to ask about the possibility of gene knock-down or over-expression before hatching in aquatic animals.

Dose any have some experience regarding the drug/chemical/RNAi delivery into eggs in any aquatic animals?

Hi Everyone,

I have a list of 2000 SNPs (chicken)and require to find close genes to all these 2000 SNPs.

I used to do that one by one in a small set of SNPs by using org.Gg.eg.DB, BiocManager, Entrezquery, and chicken database in R, but that way is most time-consuming.

It is appreciative, if anyone suggests to me a reasonable and practical way to do so.

Frankly, I have a hitch here and I need your constructive comments or suggestions.

Thanks in advance

Normally dN/dS ratios are calculated and interpreted as below one negative selection, above 1 is positive selection and 1 means neutral selection. How to interpret dS/dN ratios? Programs like SNAP provides dS/dN graphs and ratios.

For example:   

Averages of all pairwise comparisons: ds = 0.1678, dn = 0.4090, ds/dn = 0.4072, ps/pn = 0.4707

Please see image as well.

Can somebody explains it in simple words as I am not much familiar with this?

A while ago the website of Qvotek went offline, and their supplies haven't been open for ordering.

We were using their custom 5 micron micropipettes/needles/tips for microinjections in zebra fish larvae. Is there any good alternative available?

For context, our lab is working with a ROSA-tomato reporter line (strain B6.Cg-Gt(ROSA)26Sor<tm14(CAG-tdTomato)Hze>/ J) that we have crossed to several Cre mice for the purpose of identifying specific neuronal populations. While crossing these reporter mice into Cre lines appears to present no apparent problems for them, when we have attempted to cross them into additional lines (i.e. knockout or flox lines) in order to identify specific cells with the reporter (that say have receptor X knocked out as well) we've started to notice that over time the mice begin to develop bright pink pigmentation in their skin (i.e. bright pink paws, tails, feet, ears, etc). When we go to collect brains from these animals for physiological or histological experiments, we also notice that their brains are also bright pink! This has become problematic, as trying to identify specific cells in slices from these animals brains has been hampered by the presence of the reporter (to a lesser extent) in all the surrounding cells in the neural tissue.

I was wondering if anyone has ever experienced a similar problem if they have worked with this reporter strain in the past, and if they have any suggestions or details on how they tackled this issue when breeding up mice within this reporter line.

I am working on a project involving parthenogenesis in crested geckos (Correlophus ciliatus), and I plan on comparing genes- particularly STRs- in samples from the eggs, the potential parents, and previous records (via GenBank, etc), to each other. However, I do not know how to successfully isolate DNA from a very early embryo in a shelled reptile egg. I will likely have to do this, because all the previous parthenogenic eggs from my geckos have failed long before complete development. Please excuse my phrasing, this is not a subject I have much experience in yet.

I'm studying the polymorphism of a microsatellite related productive performance in 4 goat breeds and I would like to represent the distances between them according to its polymorphism (alleles and genotypes), which method is the most appropriate: PCoA, dendrogram,...? . Thank you in advance

What do you think is the best genetic marker to define species?

In our genetic marker's world, what do you think is the best one to describe species, 12S, 16S, 18S, 28S, COI, COII, COIII, ITS1, ITS2 or Cytb?

Hello,

I have some small secreted proteins which have the ability to move from plant to fungi. As they can move between plant and fungi, I assume these small secreted proteins have some domains responsible for their movement such as export and import domains. I am planning to generate a series of deletion constructs to identify domains that are responsible for protein movement. What might be the good experimental strategy to identify the domains? Is there any good system or experimental strategy that I can use for quick testing of my deletion constructs?

Thanks in advance

When working with eDNA we sometimes face some contamination, and it may lead to false-positive or negative, and I think if some of these cases, it creates a problem, or it may be interpreted as a grown on robustness, cause if we are using universal approach, we should be capable of finding any DNA sequences, like human DNA contamination, so what do you think about it?

I am completing my Master's in Biology on small mammal research (Sorex shrews) in Washington State. I am looking for a reliable lab in the US to send tail clips/liver samples to, to sequence the mitochondrial cytochrome b gene. I am hoping to use this to verify species and analyze relatedness between populations. Any advice is greatly appreciated!

If the virus is detected in serological and molecular tests is it interpreted as potentially zoonotic?

If I have data of performance of chickens, biochemical analysis, egg production traits How calculate genetic correlation and phenotypic correlation?

Dear my professors and colleagues,

I prepare a review about use biotechnology and molecular marker at poultry breeding.

I want your help.

need help on finding biomarker for F1 hybrid and backcross of a fish species

How to calculate PIC Polymorphism information content?

How to calculate heterozygosity ?

What happened to this pigeon's wing feathers?

Is it a genetically problem? Or a dietary deficiency?

What is your suggestion for treatment?

-It's sisters and brothers show this appearance too.

Scientists rush to treat diseases with Gene Therapy: It must be good for Humanity, surely?

Eg: Cystic Fibrosis

But creating a method of delivery for genetic material may bring all the psychopaths out to play: could the delivery of genetic material be weaponised by errant regimes? Viral vectors may be an ideal weapon of mass destruction

Modern science demands that we publish all our methodology in great detail. But whose eyes are falling upon this research and should we not be thinking of a way to better control the flow of potentially catastrophic information?

Or is it too late? Pandora's Box...

' Most people were silent. I remembered the line from the Hindu scripture, the Bhagavad Gita; Vishnu is trying to persuade the Prince that he should do his duty and, to impress him, takes on his multi-armed form and says, 'Now I am become Death, the destroyer of worlds.'

J. Robert Oppenheimer - Wikipedia'

'Father of the Atom Bomb'

Research proposal in Animal Genetics and Breeding.

Hello researchers

all of us know, that we need a special protocol to extract DNA from frozen blood other than protocol which used to extract DNA from fresh blood .

the question is : .what are the specific changes in blood properties that obligate us to use a special protocol to extract its DNA.

best regard

I am aware that several genetic nomenclatures exist for specific groups of organisms. Unfortunatelly, such nomenclature is not available for my group (diatoms, microalgae, protists)and I did not find any general genetic nomenclature.

From what I read it seems there is a consensus among geneticists to distinguish between name formats of proteins (non-italicised) and corresponding genes (italicised; e.g. COI vs. COI). I have suspicion that this is often written incorrectly in taxonomy papers. Seems to me that most people write even protein-coding genes entirely non-italicised. Anyway, a letter coming for part of the gene/protein (lets call it sufix here for convenience) should be non-italicised (e.g. rbcL, psbA). Question is, shouldn’t „I“ sufix in „COI“ also be non-italicised because it also stays for the part of the gene/protein? Then when I refer to certain subregions of these genes and I define them as "COI-5P" and "rbcL-3P" (see postscript) then these „-5P“ and „-3P“ sufices should probably also be non-italicised, right? Following this logic it seems that these genes should be correctly written this way: COI-5P, rbcL-3P.

Yet another chapter are ribosomal genes which are written non-italicised as far as I have seen. It is true that it is easy to distinguish gene (LSU rDNA) and the product (LSU rRNA) if written in full. However, as short forms (just LSU or SSU) are often used in papers (also non-italicised) I guess it would be beneficial to distinguish product and the gene in the same way as in protein-coding genes. So I would prefer to write them this way to keep the same format as in protein-coding genes regardless of product type (protein vs. RNA): LSU rDNA and SSU rDNA, in short LSU and SSU (btw I would prefer to entirely avoid short forms here), and when speaking about products then LSU and SSU. I did not find anything in nomenclatures about genes encoding another product than proteins so I do not know. What is your opinion?

PS: Just to be sure what genes and their parts I am dealing with: COI = gene encoding Cytochrome c oxidase subunit I; COI-5P = 5' region of the mitochondrial gene encoding Cytochrome c oxidase subunit I (distinguished by specific primer pair in my manuscript); ITS rDNA, nuclear gene Internal Transcribed Spacer; LSU rDNA, nuclear gene encoding large-ribosomal subunit; psbA, plastid gene encoding Photosystem II protein D1; rbcL, plastid gene encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase; rbcL-3P, 3' region of rbcL; SSU rDNA, nuclear gene encoding small-ribosomal subunit; UPA, Universal Plastid Amplicon; V4 SSU rDNA, subregion of SSU rDNA.

Cloning and transgenic animal

I am doing a study and we looked at the tongue of Obese and Lean Zucker rats over a period of 3 months. The tongue is known to have increased fat as the rats gain weight/age. I did a microarray of the tongues from baseline, one month, two month, and three month. There are a number of genes associated with Collagen that signficantly decrease over time, including Col1a1, Col3a1, Col1a2, etc. Does anyone know why this is? I thought that there would be increased in these genes over time.

Hi, I am asking about the maximum period of time which the blood sample still fresh and can be used for the RNA extraction, from the collection to the analysis procedure?

Thank you

Which universal/ housekeeping genes I can use to find presence of any animal origin (as contaminant) in animal feed samples (by PCR/Real Time PCR)? Kindly suggest its the primer probe sequences.

I want to look at the level of gene flow / migration between fish populations sampled at 10 km intervals within a river system to see if there is a link between genetic and morphological variation between the populations. I'm using microsatellite loci and the fish have only been present in the system for 40-60 generations.

I was intending on using BayesAss as its meant for contemporary migration, but fear that it will only look at <5 generations.

Which program should I use - Migrate, IMA, BayesAss? Any advice would be appreciated.

I have breed seven Rat, all of them has given birth but after 14th day I have observed that one female rat eating her own baby. What is the reason behind this kind of cannibalism? Is it possible can we read this behavior through any kind of molecular analysis?

Any suggestions? 

Dear all,

I'm currently working on mammal genomes. I had received Illumina NGS data and decided to use QDD (on Windows) to fish out microsatellites for PCR primer design. I've encountered some problems and hopefully someone can help me up here.

1. By following the instructions in http://net.imbe.fr/~emeglecz/qdd_installation.html, I've downloaded Active Perl, BLAST+, ClustalW and Primer3. For Primer3, should I downloaded version 2.3.7 (the C code), version 4.0.0 (Web Interfaces - Primer3 Web) or 2.3.6 (Web Interfaces - Primer3Plus)?

2. Can I use the raw data from NGS (paired ends reads, 1GB) as the input file for Pipe1 in QDD?

3. I've tried the above and my laptop is still working on Pipe2 after 12 hours. How long will Pipe2 and Pipe 3 take for a sample size 1GB?

4. Anyone has a detail workflow for using QDD on Windows to design PCR primers?

Thank you in advance for helping.

Great Day

I am looking for a reference in which a single gene mutant having weak phenotype when combined with another single gene mutant having strong phenotype of the relative trait, result in a weaker phenotype.

For example, a single mutant plant with extremely dawarf phenotype when combined with another single mutant with slightly dawarf phenotype, gave a slight dawarf double mutant phenotype. Please share if you know any reference in plants or animals. Thanks

Hi every body

I am going to optimize the Cas9 gene in Grainthat is why, looking for the right tool for this purpose

How can i access data sets for cattle genetic diversity studies using molecular microsatellite markers, especially for cattle breeds in Sub-Saharan Africa. I need to compare with my own results that i found using ISAG/FAO recommended markers

There are very few animals with polyploidy like salamanders. Why is it that polyploidy is so uncommon in animals? On the other hand, there are numerous examples of polyploid plants. If it is something to do with the gene dosage, how does it not affect plants?

I'm looking for additional information (frequency, distribution, etc) about a congenital Abnormality in goat's udder callled weeping teats. 

Regards,

Stefano

I'm trying to evaluate the cost-benefit of working with this model in the lab.

i want to search some gene associated with plumage colour and shank colour of native chicken. its happy to receive answers. 

I am researching the SNPs simple and cheap protocols, methods to apply on animal genetic resources?

We did a study on a free-ranging population of this species, in which we tested whether spatial associations (2 adult deer within 25 m of each other) varied with several factors such as season, home range overlap, genetic relatedness, and sex, age and disease status of pairs of deer.  

Relatedness was not a good predictor of spatial associations. 

Pairwise relatedness measures were estimated in SPAGeDi version 1.4 (Hardy & Vekemans 2002) using the estimator by Queller & Goodnight (1989).

Relatedness was on average -0.003 ± 0.005 (±SE, SD = 0.15, range -0.4 to 0.6). 

I would like to compare these values with others generated in other mule deer populations, but I cannot find any reference!

Any guidance will be appreciated. 

Osteopetrosis is an ophthalmic disease, the scientists think two gene are implicate in the expression. We actually find a case so extreme to this anomaly, but we haven't a possibility to analyse it by molecular tools, who can help us?

I would like to know whether any individual belonging to any extinct or extant bird species is conserved in any museum or other place worldwide. Would like to know about genetic studies on this material.

Is the chance that donor vector was integrated into genome randomly high or rare?

Hi everybody, 

If a phylogenetic tree is reconstructed by maximum likelihood (ML) method, how the DNA sequences for one gene or genetic marker must overlap after alignment step ? There is a treshold to have a good phylogenetic reconstruction to respect ? If yes, can you indicate me with reference to read and learn.

Thanks you and best wishes

I used hypred package in R and constructed my base population then reference population that consists of 50 sires and 50 dams and my offspring are half sibs and full sibs. I used GBLUP method for measuring accuracy.

Will spending some months for going from 94% black 6 to 97-98% black 6 be worthwhile? And also will there be substantial difference in the glucose homeostasis then?

Do any one know the chromesome number of Lumbricus earthworms, except L. castaneus, L. festivus, L. frendi, L. rubellus and L. terrestris? Are there any species currently places in Lumbricus that has another chromosome number then 2n=36?

Hi everybody 

I want to make simulated gastric and intestinal fluid which mimic real poultry stomach and small intestine condition.

In literature the  pH values of SGF and SIF are 1.5 and 7.4, respectively.

But in poultry, pH of proventriculus and small intestine is  4.5 and 6.5, respectively.

So, pH for my SGF will be 1.5 or 4.5? how about for SIF?

with thanks

Hi there,

I'm planning some immunofluorescence where I want to dual label either BDNF or TRKB with caspase-3.  However, for the species of tissue I'm using, I need to use an antibody that hasn't been raised in rabbit, as the caspase ab we have is anti-rabbit and validated for our species.  As most antibodies for BDNF are anti-rabbit, I was wondering if measuring TRKB expression is as good an indicator of neurogenesis as BDNF, or is this only when the case when BDNF is liganding with TRKB.

Having said that, I have sourced an anti-sheep polyclonal BDNF ab but I need to validate it first but would like some advice on using TRKB from people with more expertise than myself!

Thanks in advance.

Considering the threat of extinction from interbreeding, inbreeding, cross breeding as well as the introduction of genetically and productively superior animals in line with the low input production systems in the developing world.

To describe the impact of liver, gizzard, heart, spleen, pancreas in broilers meat production.My experimental broilers were reared for 35 days. After slaughtering  offal's & glands were separately measured, but how can i compare the groups.

what are the best microsatellite markers in camel for parentage verification? and How many marker should i use to confirm relationship.

We are creating a Thy1-EGFP colony from a breeding pair (male hemizygous for Thy1-EGFP and wild-type female). My question is related to the mating for the second generation. Shall I cross one of the females positive for GFP with her father (which is hemizygous for GFP) so we can increase the proportion of homozygous mice for GFP?. Or is it better not to cross the male with its daughters?. How would it be for the third generation?

Thanks!!!

What genes are most responsible for the growth of ruminants such as goats?

I am looking for rates to calibrate my analyses, but have not found any so far. Does anyone know of any research done in this area? There appears to be plenty on mtDNA markers, microsatellites and some nuclear genes, but none on neutral nuclear markers. Any help would be much appreciated!

Hi,

I have around nine traits, which I would like to use in the animal model (estimate heritabilities and genetic, phenotypic correlations). Haven't worked with these models before, I found out that increasing number of traits in the model results in convergence problems.

Is there a way to improve the convergence (I use vce), or what would be the best design for my study, should I split the traits into several models? Perhaps if someone could give me some information on the main pitfalls when working with animal models that would be great.

Thank you.

Hello, I am currently volunteering with an association which studies fin whales in the western Mediterranean sea. Specifically, we are willing to collect fin whale's faeces to perform genetic and hormonal analyses. The faeces are a loose aggregation of particles that get attached to the holes of the net and contaminate future samples if we use it more than once (it is almost impossible to clean!). We thought of creating some sort of device that allows us to change the net everytime we collect faeces.

Does anybody know a way to avoid the faeces getting stuck on the net or have created a new one ("home-made" net) to collect faeces? Thank you! :)