Genetics

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25 Removing PCR inhibitors POST-extraction?
By Joshua Thia · University of Canterbury

Dr (Mrs.) Kamalakshi · Government of Tamil Nadu

PCR inhibitors can be removed by adding more of DNA polymerase or DNA template may be diluted or add additives to the PCR r eaction like BSA or Beta... [more]

PCR inhibitors can be removed by adding more of DNA polymerase or DNA template may be diluted or add additives to the PCR r eaction like BSA or Betaine or NaOH treatment or addition of Aluminium Ammonium Phosphate or separation step prior to PCR with Centricon-100 or Micro -100 filters.

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1 Is there any work being done on application of nanotechnology in evolutionary genetics
By Spandan Pandya

Elias Oziolor · Baylor University

yes there are several studies going on in aquatic toxicology testing adaptation and nanomaterials. look into CEINT, which is a group from Duke Univers... [more]

yes there are several studies going on in aquatic toxicology testing adaptation and nanomaterials. look into CEINT, which is a group from Duke University that deals with Nano research and they have a lot of evo integrated in it. hope that helps

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4 difference between HLA Allele frequency and HLA phenotype frequency
By Stanley Meribe · Kumamoto University

Stanley Meribe · Kumamoto University

Ok, I got the drift now. Thanks

Ok, I got the drift now. Thanks

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2 Can anyone tell me an effective in vivo way of permanently deactivating efflux pumps in an organism?
By Bamidele Odumosu · University of Ibadan

Yuji Morita · Aichi Gakuin University

What does "in vivo" mean in this situation?

What does "in vivo" mean in this situation?

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4 Can anyone please suggest me a pattern recognition software to identify the 3'UTR regions?
By Amruta Mhashilkar · University of South Florida

Shirin Mirlohi · Shahrekord University

I've used Dr. Cohen's method before and it works perfectly :) good luck

I've used Dr. Cohen's method before and it works perfectly :) good luck

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10 Can anybody suggest literature/ protocol/ data analysis that can help me understand transcriptome studies?
By Amruta Mhashilkar · University of South Florida

Amruta Mhashilkar · University of South Florida

That is wonderful everyone. Thank you so much. I appreciate the help.

That is wonderful everyone. Thank you so much. I appreciate the help.

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17 Does anyone have an e-book about bioinformatics ? How can i find it ?
By Najmeh Ahangari · Hormozgan University of Medical Sciences

Feyzollah Hashemi Gorji · Shahid Beheshti University of Medical Sciences

Bioinformatics for Dummies is translated to Persian. Publisher: Khane Zistshenasi Iran

Bioinformatics for Dummies is translated to Persian. Publisher: Khane Zistshenasi Iran

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5 SNP validation by Haploview
By Sergey Kolomeychuk · Russian Academy of Sciences

Yamunah Devi Apalasamy · University of Malaya

You can refer to PLINK format

You can refer to PLINK format

http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/input-file-formats-0 ×
Input File Formats | Broad Institute of MIT and Harvard

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4 Whats your view;opinion about "A transcriptomic hourglass in plant embryogenesis"
By Md. Nasir Ahmed · University of Development Alternative

Karl Brown · Centre for Eye Research Australia

I'm unsure why the exclamation marks follow Darwinian evolution. Developmental biology, and by extension all biology, is best understood through the l... [more]

I'm unsure why the exclamation marks follow Darwinian evolution. Developmental biology, and by extension all biology, is best understood through the lens of evolution and Darwin's theory is an excepted foundation stone of the biology field.

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50 Can anyone please explain what I have to do exactly to avoid primer dimer?
By Biswajit Bose · North Eastern Hill University

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7 Transient Eye colour
By Marc Inberg · University of Western Sydney

John Fingert · University of Iowa

Sounds most like subjective differences in your judgement of the color and/or changes in the lighting. If you take pictures under controlled conditi... [more]

Sounds most like subjective differences in your judgement of the color and/or changes in the lighting. If you take pictures under controlled conditions I imagine your eye color will be unchanged.

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7 How does one deal with diploid sequence data?
By Joshua Thia · University of Canterbury

Julie Hebert · University of Maryland, College Park

Oops, sorry I missed that. I don't know about that genus or family, but I know many plants have multiple ITS sequences in their genome.

Oops, sorry I missed that. I don't know about that genus or family, but I know many plants have multiple ITS sequences in their genome.

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1 Help~why after floral dip with Agrobacterium in 5%sucrose and 0.05% Silwet L 77 solution, my Arabdopsis plant died on the next day??
By Rui Wang · Northwest A & F University

Suchismita Roy · Jawaharlal Nehru University

use less dosage of silwet..0.01%

use less dosage of silwet..0.01%

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11 Does anyone have experience with the Two step PCR amplicon approach?
By John Leonard · Texas A&M University - Kingsville

John Leonard · Texas A&M University - Kingsville

Thanks for the help. I'm waiting for a quote from our genomics lab for library preparation. If the cost is relatively low I may just PCR amplify my ... [more]

Thanks for the help. I'm waiting for a quote from our genomics lab for library preparation. If the cost is relatively low I may just PCR amplify my amplicons and send them to the lab for library preparation and multiplexing. If it is too expensive, I will want to create the libraries myself. One other concern that I had is how to quantify the DNA in these samples. Has anyone had any experience with this?

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5 Is the MAO gene really responsible for violent actions?
By Nahi Yaseen · Iraqi Centre for Cancer & Medical Genetics Research

Avinash Veerappa

Its believe that MAO is involved in anti-social and violent behaviour. MAO has something to do with neurotransmission. It is the same genetic associat... [more]

Its believe that MAO is involved in anti-social and violent behaviour. MAO has something to do with neurotransmission. It is the same genetic association studies which has validated it.

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23 Statistics software (free, user-friendly interface, and easy)? do you have suggestions?
By Ahmed Hussien · University of Milan

Eli Araujo-Jnr · University of Cambridge

My colleagues and I use R studio as a GUI for R. It's very good.

My colleagues and I use R studio as a GUI for R. It's very good.

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5 How much genetics is done with algae communities?
By Jay Yang · Singer Instruments

David Mitchell · State University of New York Upstate Medical University

Sorry for the late reply, I just saw this post. We use a yeast tetrad dissection scope, but the probe has a rounded end (flame-generated) rather than... [more]

Sorry for the late reply, I just saw this post. We use a yeast tetrad dissection scope, but the probe has a rounded end (flame-generated) rather than a flat end. Tetrad products are moved across the surface of the plate with the probe gently touching the surface, and the cell(s) trapped in the liquid around the probe tip. By streaking the mating mix in a square on the dissection plate, you can dissect 40-50 tetrads/plate in about an hour. Of course, sometimes you get 8 products instead of 4...

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1 As you know, RBCs do not have any HLA molecules, so how do these cells protect themselves from the NK killing activities?
By Alireza Rafiei · Mazandaran University of Medical Sciences

Sabiha Anis · Sindh Institute of Urology and Transplantation

RBC's do not have MHC class I molecules to engage inhibitory receptors of NK cells and also do not express receptors that engage NK activating recepto... [more]

RBC's do not have MHC class I molecules to engage inhibitory receptors of NK cells and also do not express receptors that engage NK activating receptors. In erythroblastosus fetalis , RBC lysis is via ADCC in which antibodies binding to RBC antigens bind to Fc receptors on NK cells mediating lysis. Hope this is explains the reason.

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4 I have evaluated an amino acid substitution Ala698Thr in a COL3A1 protein by MUpro software. Is it good for this job?
By Francesca Cortini · Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico

Shubhandra Tripathi · University of Allahabad

For amino acid substitution in a protein, CUPSAT server is also a good one.....

For amino acid substitution in a protein, CUPSAT server is also a good one.....

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9 What does it mean for a population to have a "substantial genetic structure"?
By Cora Romanow · The University of Winnipeg

Joachim Mergeay · Research Institute for Nature and Forest

Indeed, the degree of the structure within and among populations depends on the difference between the observed frequencies and the expected frequenci... [more]

Indeed, the degree of the structure within and among populations depends on the difference between the observed frequencies and the expected frequencies given a random distribution within and among your forests (actually, given the expected distribution under Hardy-Weinberg equilibrium allele frequencies). So your redwood example is correct: one population may have a stronger structure than another (in this case we're talking F-IS), because is has a stronger deviation from the expected distribution of alleles than expected under this Hardy-Weinberg equilibrium than the other population. You can also say that there is strong structure among your redwood populations, when the allele frequencies are very different when comparing multiple forest stands (this is F-ST). Typically, allele frequencies are used to determine population genetic structure, and this is typically called "neutral" population genetics. You can also estimate structure at actual phenotypic traits under selection, if you know the traits are largely heritable. Typically, one determines then the Q-ST: structure at quantitative traits. Typically, Qst - Fst comparisons are used to prove differences in (responses to) selection among populations (Q) in the light of neutral processes (which are measured by the fixation index F). Excellent lecture notes on basic popgen are given by Michael Whitlock on his page: http://www.zoology.ubc.ca/~whitlock/bio434/434LectureNotes.pdf . In case you're looking for a good textbook on population genetics, I strongly recommend this one http://www.blackwellpublishing.com/hamiltongenetics/

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Question:
Open GSEA analyses?
I am trying to use the gene set enrichment desktop version which I have downloaded from the Broad's web site. I will run a GSEA analysis with a contin... [more]

I am trying to use the gene set enrichment desktop version which I have downloaded from the Broad's web site. I will run a GSEA analysis with a continuous phenotype label but the program keeps giving me the error: "numMarkers: 100 cannot be larger than dataset size: 98". Am I choosing the wrong parameters or the format of the input data is wrong?

By Kerem Mert Şenses · Bilkent University

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3 Holliday junction prepartion and visualization?
By Amandeep Singh · Indian Institute of Science

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Question:
Open Gender plasticity and Epigenetics (wrt Botany): Does anyone know of a substantial review on the topic?
I would greatly appreciate a nudge in the right direction. I keep ending up in the land of metazoa grasping around for some metaphyta!

I would greatly appreciate a nudge in the right direction. I keep ending up in the land of metazoa grasping around for some metaphyta!

By Cora Romanow · The University of Winnipeg

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8 What is the reason for getting a poor yield of dsRNA for gene silencing experiments after in vitro transcription process?
By Bharat Bhusan Patnaik · Chonnam National University

Bharat Bhusan Patnaik · Chonnam National University

Hello, Let me answer your more pertinent questions- 1-dsDNA concentration taken into IVT reaction- 0.380 microgram/microlitre, dsRNA yield after pool... [more]

Hello, Let me answer your more pertinent questions- 1-dsDNA concentration taken into IVT reaction- 0.380 microgram/microlitre, dsRNA yield after pooling three separate IVT reactions- 7.92 microgram/microlitre. That's the best i have achieved. 2- dsRNA is injected to larvae of beetle once (1 microlitre injection). 3- Currently iam using about 8 micrograms of dsRNA to deplete the protein. 4- I usually observe the knockdown by RT-PCR analysis with dsRNA primer till 7-8 days after injection. 5- dsRNA will be about 350 bp (including the T7 promoter sequence). The gene is an important cellular signaling molecule in the Toll pathway of insect and is about 1172 bp. Please find the results-4 days post injection of dsRNA. LANE 1-4: L27A (housekeeping); LANE 6-9: target gene (6,7-buffer injected; 8,9- dsRNA injected) Hope it solves. Please suggest.

myD88-26.04.2013-4DAY.tif ×

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Question:
Open Is there any method to make every chromosome polarized, i.e. each end with different charge?
Human somatic cell contains 46 chromosome,every pairs of chromosome are homologous. The preparation method for chromosomal analysis still faced by man... [more]

Human somatic cell contains 46 chromosome,every pairs of chromosome are homologous. The preparation method for chromosomal analysis still faced by many difficulties, one of important obstacle is the spread of chromosomes on slides. Therefore we seek to find any approach to improve spreading of metaphases.

By Nahi Yaseen · Iraqi Centre for Cancer & Medical Genetics Research

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8 Is the Cochran Armitage Trend Test valid, if any of the counts are less than 5?
By Veera Manikandan · Christian Medical College Vellore

Veera Manikandan · Christian Medical College Vellore

thank you Santoso.

thank you Santoso.

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5 Need information on Glutaric Aciduria in Spanish.
By Maria Corena-McLeod · WSAID

Maria Corena-McLeod · WSAID

Thank you for your help. I appreciate it.

Thank you for your help. I appreciate it.

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About Genetics

Genetics is a discipline of biology, is the science of genes, heredity, and variation in living organisms.

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Genetics

Input File Formats | Broad Institute of MIT and Harvard

About Genetics

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