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Questions related from John Tainer
We have used DOT to dock DNA to proteins but increasingly need to examine computational models for RNA docking onto proteins. Would appreciate advice and examples where this has proven successful.
11 November 2019 7,927 4 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...
09 September 2018 6,466 7 View
I am intersted in measuring the impact of specific enzymes and their inactivating mutations on genome instability and on the mutation burden in human cells and cancers. I want experiment ways to...
07 July 2018 2,370 0 View
Many institutions are limiting travel and meeting attendance with the idea of saving money. Yet, I think meetings always save research money for me. I find that when I attend meetings the...
11 November 2017 2,244 4 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?
10 October 2017 5,329 1 View
Since the use of journal impact factors as frequently used to evaluate researh quality has been criticised for many reaons, might it be useful to devise mertics based upon a given author's impact....
12 December 2016 2,036 3 View
I have a protein that binds DNA bubbles and that I think is a dimer on DNA. I do not know if one or two subunits bind to DNA. I would like to cross-link subunits adjacent to DNA (bound) to see...
08 August 2016 1,560 2 View
With decreased funding for scientific research there is a compelling need to make the most efficient progress possible without sacrificing rigor or impact. I would value hearing what you have...
08 August 2016 6,176 2 View
We largely teach students and then ask them questions that we taught them how to answer. In science and many other areas of life, one wishes to address and answer questions where you have not...
07 July 2016 6,619 2 View
Are there breakthroughs in structural, mechanistic, and predictive knowledge of macromolecules expected form cro-EM that are likley to major impacts on synthetic biology, medicine, and the bioeconomy?
12 December 2015 8,716 0 View
We are working on enzyme engineering to convert methane to alcohols. As part of this process we wish to measure methane binding to various enzymes and would benefit from suggestions as to what has...
01 January 2015 9,411 4 View
The recent Science paper by C. Tomasetti and Vogelstein B. uses analyses of cancer risk and stem cell divisions to argue that many cancers, such as pancreatic cancer, are just bad luck and...
01 January 2015 3,575 13 View
According to the National Cancer Institute, the FDA has approved two types of vaccines to prevent cancer: vaccines against the hepatitis B virus, which can cause liver cancer, and vaccines against...
01 January 2015 6,543 7 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?
12 December 2014 4,911 7 View
Issues have been raised about peer review, open access, costs, reviewer bias and quality, fairness, and efficiency among other things. If you could change just one thing about research...
12 December 2014 4,389 3 View
In thinking about training of postdocs with less resources, I am interested in hearing what are the most value parts of the postdoc experience, what works well, etc as seen from the perspective of...
12 December 2014 8,888 3 View
The concepts published on the hallmarks of cancer (Hanahan D, Weinberg RA, The hallmarks of cancer Cell. 2000 Jan 7;100(1):57-70) and its update (Hanahan D, Weinberg RA, Hallmarks of cancer: the...
12 December 2014 9,919 24 View
It seems that we are increasingly learning more about cancer mechanisms and what things make useful and long-term therapeutic strategies work and fail to work. What can we say now that we would...
12 December 2014 6,651 2 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,...
12 December 2014 3,190 12 View
I am interested in doing biophysical studies and want minimal heterogeneity in terms of the number of proteins within a given nanodisc.
12 December 2014 698 2 View
Crystallography provides information of enormous general and long-lasting value to researchers across many fields. The data as well as the resulting structures are generally deposited for access...
12 December 2014 6,645 4 View
Are there some detergents that often help solubilize proteins for purification etc that can be completely removed efficiently afterwards?
12 December 2014 2,365 7 View
Are there near term benefits that we should be better harvesting? How do we move ahead effectively with sequence data?
12 December 2014 5,977 2 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...
12 December 2014 3,839 6 View
Is the problem with US research an “erroneous assumption of never-ending rapid growth in biomedical science” as noted by Alberts B, Kirschner MW, Tilghman S, Varmus H. Rescuing US biomedical...
12 December 2014 4,765 7 View
Would intelligence provide advantages to plants or not? If so, is it too energetically costly or why has it not evolved? Could we make plants smart with synthetic biology?
01 January 2014 8,779 2 View
Dinoflagellates use flagella to move through the water. Although land plants are restricted by their roots, I find it interesting that plants have not evolved systems for movement at least in the...
01 January 2014 904 2 View
Will it be more about data deposition, blogs and internet postings, self-publication to peers as in earlier periods, or the classic society journals? Will journals stay the same or change?
01 January 2014 7,725 7 View
What types of cancers seem to be successfully treated by chemotherapy? Are there cancers where chemotherapy is rarely successful? I am wondering is there are emerging insights into cancer cell...
01 January 2014 2,403 10 View
There is great interest in improving access to publications but access to primary data is a larger problem in my view with the increasing number of active researchers producing results that might...
12 December 2013 5,800 4 View
Many open access internet journals are being created and charge the authors for the cost of publication. So they shift the cost of scientific publishing from institutional subscriptions to...
12 December 2013 3,488 7 View
Funding has hit new lows and many of us are not surviving. Many colleagues have lost jobs or moved to other countries. What are you doing to keep going? Do you have suggestions that might provide...
12 December 2013 9,008 8 View
After separating membrane proteins from the membrane environment, we are seeking robust and efficient ways to exchange detergents for X-ray scattering structural experiments. Are sizing columns or...
12 December 2013 792 1 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...
12 December 2013 5,491 4 View
For some journals reviewers can see other reviewer comments once theirs are submitted, and I think this is useful and should be something journals are encouraged to do. I find that having me as a...
12 December 2013 6,505 7 View
Considering the large investment in cancer research what do you see as some of the emerging home runs? Are some areas particularly exciting to you currently? Where is cancer research going during...
12 December 2013 4,949 5 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...
12 December 2013 2,002 12 View
We wish to purify proteins that may be modified and in complexes in as few steps as possible for structural studies.
12 December 2013 5,004 37 View
The world may be shifting toward a bioeconomy with current drivers viewed as three foundational technologies: genetic engineering, DNA sequencing, and automated high-throughput manipulations of...
12 December 2013 2,923 9 View
The peer review system is old. Eliminating peer review has been suggested to save time and money, see http://www.stat.cmu.edu/~larry/Peer-Review.pdf . I believe that despite being imperfect, as...
12 December 2013 5,462 84 View
The quality of life in modern society depends heavily upon advances from science and technology that are now largely taken for granted. Yet, recent cuts to research across the western world may...
11 November 2013 4,320 4 View
The U.S. NIH government and DOE National Labs were the envy of the world before high priorities for weapons, war, and low taxes and very low priorities for science eroded excellence and efficiency...
11 November 2013 2,275 2 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?
11 November 2013 1,979 8 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...
11 November 2013 4,284 41 View
Are there specific therapeutic advantages or disadvantages to killing cancer cells by apoptosis versus necrosis or autophagy and how important are microRNAs in regulating these processes?
11 November 2013 6,835 94 View
At the Mesoscale or the middle area spanning macromolecules to tissues, reactions are relatively slow (
11 November 2013 6,577 7 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...
11 November 2013 4,326 18 View
Tumor necrosis factor-related apoptosis inducing ligand (TRAIL) was proposed to have exciting potential to kill a wide variety of tumor cells with little effect on normal cells. Evidence suggested...
11 November 2013 3,387 8 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...
11 November 2013 9,554 31 View
Does it seem water might be essential to life or are there other liquids that could reasonably be considered?
10 October 2013 9,336 17 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...
10 October 2013 2,282 2 View
Can you provide practical or empirical ways to distinguish cancer cells from other cells in general or does this depend upon specific types of cancer cells? What is known and not known well enough...
10 October 2013 4,836 47 View
Human nitric oxide synthases (~1400 residues with 5 co-factors) can be expressed in E. coli to produce mg amounts by using low temperature expression. Is this truly unusual or something that can...
10 October 2013 4,372 13 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?
10 October 2013 4,532 12 View
So far we know life uses H with C, N, O, P, S with Na, K, Mg, and Ca plus the transition metal ions Mn, Fe, Co, Ni, Cu, Zn, and Mo with Se and B plus halides Cl and I. These elements fall in...
10 October 2013 2,375 3 View
Is creativity an innate talent or something we can and should be teaching along with technique?
10 October 2013 6,302 3 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...
10 October 2013 7,778 4 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...
10 October 2013 7,245 10 View
Optogenetics tools, such as fusions of light-absorbing domains with protein 'effector' domains, should in principle allow light to be used to control protein expression in bacteria and archaea. Is...
10 October 2013 5,400 4 View
We can currently only study earth life. So one means to examine how feasible life may be elsewhere and what it might look like in terms of signatures is to test how many parameters need to be...
10 October 2013 7,202 12 View
Albert Szent-Györgyi wrote: "Discovery consists of seeing what everybody has seen and thinking what nobody has thought." How might we increase the value of our scientific efforts? Is it about...
10 October 2013 9,707 4 View
Several years ago we tried in vitro expression and were successful only at the level of seeing bands on a silver-stained gel when we wanted big Coomassie bands that indicated expression levels...
10 October 2013 3,698 4 View
DNA enzymes and binding proteins expressed in E. coli often have bound DNA or RNA that can be troublesome to remove completely for biochemical experiments and crystallizations.
10 October 2013 5,447 47 View
Impact factors can be a negative distraction from quality and science because they can be economic drivers for some scientific journals and researchers. Yet scientific impacts are often only...
09 September 2013 4,788 8 View
As we learn more from the cancer genome project and therapeutic strategies that provide long-term benefits, what types of targets might allow us to do better? Many successful cancer therapies...
09 September 2013 9,972 6 View
I see synchrotrons as exemplary investments in science for areas such as structural biology, medicine, and materials science where collaborative efforts coupled with invested government funding...
09 September 2013 9,434 3 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.
08 August 2013 8,277 13 View
