95 Questions 138 Answers 0 Followers
Questions related from Yijie Daniel Deng
Unculturable bacteria represent the majority of the microbial world. There are also many bacterial pathogens are very hard to grow in vitro. What are some possible ways to grow those...
09 September 2016 507 3 View
During DNA transformation experiments, we sometimes see a few false positive transformants ---- bacterial colonies that carry no any insert plasmids or DNA fragments but can still grow on...
08 August 2016 3,805 5 View
Genetic manipulation is easier in some model bacteria such E. coli and B. subtilis. However, we need to study many medical and environment related bacteria isolates. What experiencedo you have to...
05 May 2016 2,289 2 View
There are some reports on reducing CO2 into fuel chemicals but the efficiency is quite low. What do you think is the limiting factor of CO2 reduction? We have to identify the rate-limiting factor...
02 February 2016 1,201 6 View
Many proteins are oxygen-sensitive. If I want a lot of those proteins, is there any solution to express and isolate those proteins without loss of their activity?
09 September 2015 4,875 5 View
Thermo-stable proteins are of great industrial importance. Say, I want to increase the stability of a protein by raising its optimal temp from 50 to 70°C. It is relatively easy to create a...
07 July 2015 9,969 7 View
Thermophilic bacteria grow under high temperature but the problem is that many coenzymes (NADPH, NADH) are not very stable under high temperature. What mechanisms do those bacteria use to deal...
05 May 2015 2,959 4 View
I am looking for some good academic conference for bioenergy, biofuels and biotechnology field. It would be best if the conference is in the US.
04 April 2015 4,792 0 View
Cell-free systems utilize the key enzymes (may need coenzymes/ATP) involved in biochemical reactions/pathways to synthesize desired products in vitro. With the complexity significantly reduced,...
04 April 2015 362 6 View
Many enzymes in biochem pathways are in complex form, such as ATP synthase, some fatty acids synthase, enzyme complexes in electron transport chains. How do those proteins expressed in cells? Are...
03 March 2015 9,903 8 View
Both aerobic and anaerobic bacteria need to have ETC to synthesize ATP. While aerobic bacteria use oxygen as the terminal electron acceptor, anaerobic bacteria use other substrates as the electron...
03 March 2015 2,542 13 View
Protein complexes perform essential functions in cells. Fatty acid synthase in human is a protein complex made of multiple proteins. RuBisCO is another protein complex. They are composed of...
03 March 2015 8,345 4 View
Cells have complex metabolic pathways that are characterized by linear or cyclic routes. For example, glycolysis is linear but TCA is cyclic. There are many cyclic pathways like pentose phosphate...
03 March 2015 1,808 6 View
Comparing those expression hosts, they all have pros and cons. I know that it all depends on what proteins we are going to express. However, Is there general rule on how to chose a good expression...
03 March 2015 4,253 13 View
I am isolating bacteria degrading lignin on agar plate. I found one bacteria turn the lignin plate into dark quickly while the bacteria do not turn TSA or LB plate into dark. What is the...
02 February 2015 905 3 View
I am working on B subtilis. I want to put a whole gene cassette (promoter-gene-terminator) into an integration vector so that my cassette is flanked by amyE gene that I am going to insert into. I...
01 January 2015 2,707 14 View
I tied transforming B. subtilis with a plasmid containing ermR and plated them on erythromycin agar plates. After incubation at 37 overnight, I found the bacteria are spreading over whole plates,...
12 December 2014 4,295 11 View
Usually enzymes are soluble in water, but I am interested some enzymes that function in fatty acids?
12 December 2014 9,384 7 View
Say, I get a DNA sequence from a bacteria genome. I can get the RNA transcript in the bacteria. I want to know whether the DNA is responsible for coding a non-coding RNA. What should I do to test...
10 October 2014 5,800 3 View
The RBS calculator has been used to predict protein expression in various bacteria or to design RBS sequences for a desired expression level. Do you have any experience about this tool? RBS...
10 October 2014 970 12 View
GFP is a good reporter that can be tagged at the N- or C-termini, or even in the middle of a protein. What is the rationale for the different tagging strategies?
10 October 2014 1,288 10 View
I wonder some principles to tell the zeta potential of a material such as glass, cotton, paper or plastic. Are they positively or negatively charged in water? Why ?
09 September 2014 3,957 13 View
I want to design an artificial metabolic pathway in bacteria or just using responsible enzymes to produce certain products such as H2 or other biofuels. Where can I start with? Do you have some...
09 September 2014 8,093 6 View
Mathematic models are often seen in biology papers such as evolutionary biology. As a biologist, sometimes it is hard to read those complex formula and equations. How would you do with the...
09 September 2014 8,597 4 View
RNase is stable even by autoclave. What is the mechanism for its heat stability? Can we engineer some other proteins with this kind of stability?
09 September 2014 9,831 5 View
I isolated Bacillus strains from soil by heat shock method. I want to make sure how many my isolates are belong to the species Bacillus subtilis. Do you know some specific targets for PCR test?...
08 August 2014 5,944 10 View
A lot of mutation methods are PCR-based and the mutations in vectors are then transferred to host cells. Are there any ways to mutate a plasmid in the bacteria in vivo? I want to make random...
08 August 2014 2,626 7 View
I am working with bacteriophage SPP1 to do transduction with Bacillus subtilis. I wonder how specific this SPP 1 phage to host bacteria? Does it work with any strains of B. subtilis or only some...
08 August 2014 9,669 3 View
We are always fighting with bacterial pathogens. However, the speed of discovering a new antibiotic is much slower than that of bacteria developing a resistance gene to that new antibiotic. What...
07 July 2014 593 20 View
I am working with a lot of bacterial isolates from the environment. I've already sequenced them and many are from different species. I try best to keep them pure and not mixed-up during my...
07 July 2014 1,032 9 View
Creativity is essential to research. Brainstroming and mind-mapping are sometimes very useful to generate creative ideas. Do you find any good tools for this job?
06 June 2014 7,583 7 View
Some bacteria have very high species diversification with various phenotypes and genotypes. For example, Bacillus subtilis have a lot of subspecies and strains carrying different properties such...
05 May 2014 3,902 3 View
In bacteria biofilm, a lot of bacteria become metabolically dormant while some are still actively growing. How do you separate them?
05 May 2014 4,017 13 View
I want to over-express one operon within a bacterium. The operon has about 10 genes, each 1 kb in size. How can I design the expression system?
05 May 2014 6,721 2 View
We can make lots of modification on 3' or 5' of the DNA oligonucleoties. Say, I add a modification group to 3' of oligonucleotide (such as thiol, amino, biotin, phosphate, or a fluorophore) ....
04 April 2014 1,070 9 View
As many might notice from news, fraud and misconduct in science are becoming serious issues in recent years. Does scientific misconduct relate to disciplines? What discipline do you think is more...
04 April 2014 7,800 10 View
Transduction by phage is a useful technique in bacterial genetic engineering. It is usually done between certain strains within the same bacteria species. What is the rule for choosing donor...
04 April 2014 8,271 1 View
I knocked GFP into Bacillus at amyE locus but found results were interesting. Most successful transformants carrying Spectinomycin marker lose their ability to degrade starch. This was expected....
04 April 2014 2,500 6 View
We have been developing and using solar energy for a long time. What limits the large scale use of solar energy fuels? What are the technical problems we need to address before it can support a...
04 April 2014 6,340 34 View
It was discovered almost 100 years ago and we still see only a few applications. One of the main problems is the low power output. Can we really address this bottleneck? Do you have any ideas?
04 April 2014 9,387 10 View
I want to make sure why or why not.
04 April 2014 3,938 2 View
Drug-resistant bacteria are a big problem in clinics. As bacteria gain resistance genes much faster than do we develop a new antibiotic, one solution is to use bacteriophage to specifically kill...
03 March 2014 464 11 View
For transformation of foreign DNA, E. coli prefer circular plasmid while Bacillus subtilis get higher transformation efficiency with linearized plasmid. What is the reason for that?
03 March 2014 8,273 18 View
I want to insert a reporter gene (eg, GFP) right after a promoter on a plasmid by overlap PCR. However, this method will add some non-coding spacer sequences (~20bp) in between the promoter and...
03 March 2014 3,489 6 View
Usually, bacteria have multiple copies of 16S rRNA genes and also for some other functional genes. But most of the genes seem to exist in single copy in the chromosome. What is the reason for...
03 March 2014 4,782 26 View
Two integration methods are widely used: single and double crossover. Before I chose which one to use, I want to make sure the advantages and disadvantages of them.
03 March 2014 8,837 5 View
Inducible antibiotic resistance genes might give bacteria better fitness, while some bacteria constitutively express resistance genes. How are resistance genes regulated? Why some are inducible...
03 March 2014 1,436 32 View
CRISPR-Cas is a new gene editing technique with high target-specificity. It has successful applications in gene knock-out/in/down in many Eukaryota organisms including zebra fish, fruit fly, mouse...
03 March 2014 5,369 4 View
Many research labs have both PhD students and postdocs. For principal investigators, what does a postdoc in your lab mean to you? What is your expectation of those postdocs?
03 March 2014 943 6 View
Quorum sensing (QS) in bacteria regulates their gene expression in a population-density dependent manner, which controls population behaviors. Once the population reach a high density and so do...
03 March 2014 7,961 2 View
We call something "life" that is able to survive and reproduce (at least, potentially). Why has life the tendency to reproduce or survive? Does it happen by chance? What controls this phenomenon?...
02 February 2014 1,034 69 View
Quorum sensing (QS) acts in microbes through a population-density dependent manner and is important in bacterial communication and interactions. While our gut harbors an extremely high density of...
02 February 2014 6,627 6 View
I want to use bacteria Vibrio to express an enzyme that need to be secreted into medium. What are some good vectors for that purpose?
02 February 2014 8,234 5 View
Do you think evolution is still gong on in human? If so, what are we going to be like after hundreds of thousands of years if we still exist somewhere in this universe?
02 February 2014 5,685 8 View
From great philosophers in ancient Greek to the age of Renaissance, age of Enlightment to the 21st century, our knowledge has accumulated exponentially, especially during the past 50 years. We...
02 February 2014 1,959 9 View
Different bacteria can produce pigments of different colors. What is the purpose for bacteria doing so? Does it happen just by chance? One thing I know is that some pigments have antibiotic...
02 February 2014 9,087 34 View
Many options are available. From your experience, what choice is the most efficient tool for gene knockout in bacteria, considering the time consumption, robustness of protocols, availability of...
01 January 2014 2,005 14 View
Let's say, I amplified a gene from a unknown bacteria and want to determine whether this gene located in plasmids or chromosome.
01 January 2014 3,533 8 View
I am going to compare bacterial genomes to find structure of some interesting genes and design primers for the target genes.
01 January 2014 4,834 5 View
Biofilm-based techniques have been used for decades in wastewater treatment plants. Many ideas have been made to explain the process, such as condensed bacteria in biofilm, higher enzyme...
01 January 2014 9,623 5 View
Many techniques have been developed to treat wastewater, including nanoparticle-based, biofilm-based techniques and maybe many others. What is needed for the future study? How well do we know...
01 January 2014 1,228 29 View
Using cyanobacteria to produce hydrogen seems to be a good idea for future energy alternative. People have been working on this for many years. What do you think is biggest problem need to address...
12 December 2013 7,637 9 View
With new DNA sequencing techniques, we can sequence almost any kind of samples with microbes in and get a good idea of the structure and composition of the microbial communities. That is nothing...
12 December 2013 4,172 5 View
I want to express an enzyme in host bacteria (E. coli), but I need to make sure the copy number of the plasmid in a single host cell.
11 November 2013 5,840 8 View
I want to control bacteria growth at a gradient density to confirm whether the antibiotic production is density-dependent. But I don't want possible effects of culture medium during growth. For...
11 November 2013 5,140 3 View
It is noted that in microbial world many behaviors of microbes are associated with their population density. For example, some antibiotic productions, biofilm formation or enzyme productions are...
10 October 2013 587 1 View
When dealing with non-normally distributed data, can we do nonparametric analysis or transform the original data to normally distributed if possible and then do parametric analysis? For example, I...
10 October 2013 2,999 33 View
I have a data set of pairwise interactions (present / absent) among 50 bacteria and I want to visualize their interactions in a network. What can I do? What program or software do you think I can use?
10 October 2013 3,760 14 View
For experiments dealing with bacterial cultures or cell line, people usually grow a strain of bacteria or cell from one culture stock. If I grow a bacteria in 3 containers (eg, flasks) from the...
10 October 2013 7,888 22 View
To profile a bacterial community, we can do pyrosequencing of 16S rRNA genes (the DNA). We can also extract the rRNA and do cDNA sequencing. We assume that the rRNA sequencing measures the active...
09 September 2013 3,332 5 View
Molecular tools allow us to measure the diversity and also abundance of some functional genes, such as nitrogen fixation genes(nif H), ammonia oxidation genes (amo B) etc. For the gene diversity...
09 September 2013 2,633 5 View
Why do microbes in our gut form a certain structure? Why do not they overgrow? Are there some limiting factors of their growth? Such as the source of C, N and P, oxygen availability, host immune...
08 August 2013 4,627 4 View
It has been found that there is an abundance of archaea in soil, sea floor and sediment. What are the ecological functions that archaea are playing in these ecosystems? Are they doing the same...
08 August 2013 6,347 5 View
We now have very powerful tools that allow us to answer complicated ecological questions that we could not answer before. What is the ultimate goal for microbial ecology studies? How can people...
08 August 2013 7,267 6 View
I am measuring DNA concentration by using a fluorescent dye called Gelgreen on 96-well plates. Does the incubation time affect DNA measurement? Because I found some problems with the standard...
07 July 2013 8,540 10 View
To get good PCR yield and reduce non-specific products, how much DNA template is generally used and how many cycles do you usually run for a PCR?
07 July 2013 9,374 89 View
It seems that the smaller the size of an organism, the greater number of it in the environment. For example, bacteria is tiny, but the number of it is huge. Virus is even smaller, but its number...
07 July 2013 10,018 5 View
Although next-generation sequencing allows characterizing microbial communities on a very large data scale, it is still difficult to profile all rare microbial species from environmental samples....
07 July 2013 4,410 13 View
Bacteria and fungi have been genetically modified to produce recombinant proteins, vaccines, pharmaceuticals, materials, fuels, etc. Finally, the reconstructed organisms will be put to large-scale...
06 June 2013 8,770 8 View
Microbes often form consortia performing material processing and cycling in the environment. Cooperation and interaction occur within those consortia. We can use microbial consortia to do work...
06 June 2013 8,800 6 View
It is often a problem when using 16S rRNA bacterial universal primer sets (eg., 341F/531R and 515F/806R) to amplify bacterial community DNA. I almost always get PCR products for negative...
06 June 2013 4,810 33 View
Bacteria have different sensitivity to their or others' autoinducers. When those chemical signals reach a certain centration, the population start to behave in a concerted way, by expressing some...
06 June 2013 6,482 1 View
Microbial ecologists often apply diversity indices from the macro world (eg., animals or plants) to the microbial world. If you get certain numbers from calculations, what do those indices really...
06 June 2013 2,489 28 View
Most papers present mean value for their samples though some present median value. What is the difference?
06 June 2013 2,912 6 View
I wonder why some labs are very productive and doing good science while others not. Do good labs have some patterns or structures that others can follow? To run a good research lab, what should we...
06 June 2013 1,491 47 View
It is widely noticed that microbial consortia have the potential to enhance the degradation and conversion of lignocellulosic biomass. What are the underlying mechanisms?
06 June 2013 4,718 9 View
The concentration dynamics of quorum sensing molecules such as AHL during bacterial growth; when do bacteria start to produce QS compounds? When is the QS compound consumed by bacteria? Does the...
06 June 2013 914 3 View
I was lucky to isolate a strange bacterium from salt marsh detritus. Its 16S rRNA gene sequence (~1350 bp I got) only shares ~ 90% similarity to those of Tunicatimonas and Porifericola which are...
06 June 2013 1,403 4 View
How can Congo red dye stain cellulose fiber? What are the interactions between the dye and fiber?
05 May 2013 7,862 4 View
How do non-complexed cellulases recognize and bind to cellulose? How is cellulose hydrolysis by cellulases possible? What interactions occur between enzymes and the substrate? Those are some of...
05 May 2013 2,139 5 View
Restrictive endonucleases and ligases are critical tool enzymes for DNA manipulation and genetic engineering. If you have similar tool enzymes for protein manipulation and engineering, it will be...
05 May 2013 6,842 1 View
Bacterial 16s rRNA gene is the most widely used molecular marker to study the diversity of microbial communities. However, multiple primer sets have being used in different combinations to target...
04 April 2013 7,111 6 View
Lignocellulose degradation is a key process in both the biofuel production and the carbon cycling in environment. For this reason, intensive studies in this field have been going on for long time....
01 January 2013 5,845 5 View
Many enzymes require coenzymes (NADH, NADPH, CoA, TPP, etc) to catalyze biochemical reactions, such as redox reactions. Does an Enzyme bind to substrate and coenzyme at the same time or bind to...
01 January 1970 3,822 5 View
Gut microbiota play significant roles in human health. With the help of Next-gen sequencing, we know much about the compositions of bacteria in the gut but little is known about their activities....
01 January 1970 2,731 3 View
