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Questions related from John Tainer
A Liquid–liquid phase condensate (LLPC) results from de-mixing into two distinct liquid phases, with different concentrations of macromolecular solutes. This process is thermodynamically-driven...
24 March 2022 2,363 0 View
Non-B DNA has impacts on cell biology and genome fidelity. Yet it is important to test if non-B DNA is being formed in cells. G-quad structure being among the stable forms of non-B DNA what...
18 March 2021 7,524 1 View
AF2 may most strongly impact experimental determination of protein structure by multiple methods with possible benefits and negative impacts over time. Some areas may need to quickly pivot or...
14 December 2020 6,247 5 View
We are examining structures of non-B-DNA such as DNA or DNA-RNA G quadruplex and would like to test if these occur in cells using antibodies. I know some G guadruplex antobides exist but we are...
21 September 2018 4,806 7 View
re there specific stains and fluorescent methods to detect dsDNA in the cytoplasm of cells? Are these quantitative? What are the best controls and methods to validate dsDNA in cytoplasm?
16 October 2017 724 1 View
Oxygen metabolism is key to eukaryotic life and important for signaling as well as metabolism. Yet, ROS are linked to cancer and aging as well as inflammation. There is also a possible link...
27 December 2014 9,020 5 View
I am interested in input and suggestions on what features make a productive and informative conference for you. Also in choosing a meeting, do you want to present your work, seek collaborators,...
22 December 2014 8,065 11 View
Nucleic acid enzymes and binding proteins expressed in E. coli can have bound RNA as well as DNA. Are there specific methods for removing RNA versus DNA?
18 December 2014 703 6 View
Are there some detergents that often help solubilize proteins for purification etc that can be completely removed efficiently afterwards?
18 December 2014 543 7 View
I am interested in doing biophysical studies and want minimal heterogeneity in terms of the number of proteins within a given nanodisc.
18 December 2014 2,952 2 View
Cultivated rice, wheat, soybeans, and corn are genetically altered by mutation of their wild counterparts far more than any existing GM plants. Yet the public fears GM plants and there seem to be...
28 December 2013 3,008 4 View
The EU has put together some impressive collaborative scientific research programs but these EU programs end without the ability to renew after 5 years. In the U.S. collaborative research projects...
14 December 2013 7,799 0 View
Thinking of shells as a biomineralization process to make shaped CaCO3 that is useful not only for providing mechanical strength and overall structure for sea creatures but also for human tools...
13 December 2013 3,443 3 View
We are increasingly learning more about rocky planets including Mars and gathering information about extremophiles and about what to look for in considering life outside of the Earth. What can you...
13 December 2013 8,674 12 View
Cancer therapy can be initially successful with the elimination of the primary tumor causing remission for a number of years and then return with therapeutic resistance. Does resistance usually...
13 December 2013 6,911 11 View
When someone invents PCR or integrated circuits it is clear that many economic opportunities are created implying leaders create opportunities for their scientific colleagues. In this view,...
10 December 2013 6,304 4 View
We have had problems disrupting microbial membranes and separating the membrane proteins for purifications and then also preserving activities of large membrane protein complexes. With more...
27 November 2013 4,919 30 View
Is metastasis something that every cancer cell can and will do at some point or are there genetic mutations or epigenetic changes are results in metastasis?
24 November 2013 271 8 View
In an interesting development for health supplements, a company has developed a test to allow people to decide if supplements may be improving their health. The company has produced a measuring...
23 November 2013 4,654 2 View
Some cells seem to produce cancers more frequently than others. There are > 200 distinct human cell types; do all of these produce cancers under some circumstances? If not what is special about...
23 November 2013 6,280 39 View
According to SciAM “the waste produced by coal plants is actually more radioactive than that generated by their nuclear counterparts. In fact, the fly ash emitted by a power plant—a by-product...
22 November 2013 6,852 16 View
Although some efforts in biology, such as the Protein Structure initiative successfully encouraged group efforts, there is considerable pressure for many researchers to compete for grants, papers,...
25 October 2013 2,581 4 View
I am interested in structural biology of DNA damage responses. Histone H2AX is a marker for DNA damage in the nucleus but I am unsure about good markers for DNA damage in the mitochondria.
25 October 2013 8,547 6 View
Does it seem water might be essential to life or are there other liquids that could reasonably be considered?
22 October 2013 2,505 17 View
We are doing protein mutagenesis to alter methane binding and wish to robustly measure methane binding affinity. All suggestions welcome
21 October 2013 4,591 2 View
We are working on the structural biology of FEN1 complexes and mutants, but would like to test activities in vivo in fission or budding yeast or other model systems. Which cell systems make sense...
21 October 2013 6,716 3 View
The software I have used in the past did not allow us to include moveable non-bound substrate ligands and attach them (pseudo-covalently) to the end of some adjacent residue. Then the problem is...
20 October 2013 756 1 View
The CRISPR-associated endonuclease Cas9 was derived from the bacterium Streptococcus pyogenes, but the technology seems to be used more for eukaryotic gene targeting than microbial. How well does...
15 October 2013 3,140 9 View
Human cells primarily use NHEJ for repairing DNA double-strand break (DSBs), but microbial systems primarily use homologous recombination for DSB repair. Are there bacteria and archaea with strong...
13 October 2013 6,566 3 View
For repair of DNA double strand breaks (DSBs) by homologous recombination, ATP dependent DNA strand exchange takes place whereby a template strand invades base-paired strands of homologous DNA...
13 October 2013 10,002 4 View
Given that viruses are typically classified as non-living, where are useful places to make the distinction between information storage and life?
08 October 2013 3,328 10 View
Prof. Michael Yaffe’s article (http://stke.sciencemag.org/cgi/reprint/sigtrans;6/269/pe13.pdf) about the scientific drunk and lamppost defines an addiction to extensive sequencing data despite the...
07 October 2013 7,061 2 View
I am interested in studying organisms dependent on alkaline (high) pH values > pH 9 that can be grown in the lab and ideally have available DNA sequence information and be thermophiles.
05 October 2013 1,951 5 View
Over the long term, life sciences will provide the basis for substantial numbers of improved jobs and economic progress. Biotechnology provides economic value over the shorter term and is more...
03 October 2013 7,687 3 View
Astrobiology concerns the study of the origin, evolution, distribution, and future of life in the cosmos. Where should we be most usefully putting our efforts for studies on earth and elsewhere?
03 October 2013 9,207 12 View
Space missions are expensive and we have a lot of valuable information from prior missions. How might we leverage this to ask questions about the possibility of life and what to look for...
02 October 2013 2,186 4 View
Electronics and computing created economic opportunities and provided solutions to multiple problems. With the rate of DNA sequencing increasing faster than data storage or computer speed, I...
29 September 2013 8,291 2 View
With advances in technologies it seems reasonable to consider how structural results might positively impact cell biology and medicine and what we might do to improve the impact.
24 August 2013 1,500 12 View
Solving the protein structure prediction problem by AlphaFold2(AF2) from sequence seems at its core a game-changing breakthrough. Major areas of biology and biophysics will thrive and others may...
01 January 1970 7,987 8 View
Controversial pre-publication results suggest SARS-CoV-2 RNAs may be reverse transcribed in human cells by reverse transcriptase (RT) from LINE-1 elements, integrated into the cell genome, and...
01 January 1970 920 5 View
bioRxiv, which is operated by Cold Spring Harbor Laboratory, provides a free online archive and distribution service for unpublished preprints in the life sciences. Authors can post unreviewed...
01 January 1970 8,271 1 View
This advance from the machine learning method AlphaFold totally stopped me in my tracks. To me it seems that many things will change in how we do research and what research we do. Many biological...
01 January 1970 6,014 9 View
In terms of meeting length my impression is that if one travels several hours or more to a conference site, then 3 or 4 days is good since the length justifies the travel time. For zoom...
01 January 1970 6,621 6 View
Basic knowledge of DNA Damage Reponses (DDR) and their functional integration with the therapeutically relevant immune responses are fundamentally advancing cancer biology and medicine. The 7th...
01 January 1970 9,833 1 View
We face huge medical, security, agricultural, and environmental problems likely to cause wars, hunger, and disease if not faced with our best science and logic. Yet, in an increasing number of...
01 January 1970 2,040 7 View
To interject some reality into current U.S. government actions on NIH research overhead, I seriously doubt there are any biomedical research efforts of any useful quality in the US that could...
01 January 1970 1,476 7 View
