82 Questions 115 Answers 0 Followers
Questions related from Yijie Daniel Deng
Several G- bacteria including Salmonella Typhimurium and E coli, have been engineered to treat cancers. One of the main things been found is that those bacteria can specifically colonize tumor...
31 October 2019 6,337 2 View
By knowing the mechanism and determining factors, we will know how to increase the transformation efficiency in microbes.
21 February 2017 2,969 4 View
We can easily get tons of 16S rRNA sequence data for microbial communities by next-gen sequencing techniques with primers (eg., V3 to V4). If we want to compare whether bacterial communities are...
19 October 2015 3,321 7 View
Mechanic force (like shaking or running flow) influences bacterial biofilm formation and alter biofilm structure. Do you think the change of biofilm structure is a mere result of interactions...
15 October 2015 8,072 2 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?
25 September 2015 8,784 4 View
Autotrophic bacteria are able to fix CO2 by chemical energy or light. Cyanobacteria and Microalgae doing photosynthesis require sun light. But I am more interesting in microbes that fix CO2...
08 August 2015 338 3 View
People are using both tissue culture treated plates ( more hydrophilic) and non-treated plates (hydrophobic) for bacterial biofilm formation assays. Is there a big difference? Which one is better...
25 June 2015 4,333 10 View
Many new materials and new pathways have been developed to improve the efficiency of artificial photosynthesis (AP) and to produce useful chemicals. Any conceptual or technical breakthrough in...
07 June 2015 2,867 3 View
The efficiency of water splitting into H2 and O2 is not very high. The efficiency means the ratio of energy in H2 (usually the heat released after burning) to electrical energy input. What is the...
06 June 2015 2,964 2 View
Nitrogenase is the key enzyme responsible from nitrogen fixation. However, this enzyme is oxygen-sensitive and its activity is irreversibly inhibited by oxygen. It is said that a few bacteria have...
27 April 2015 3,968 3 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...
30 March 2015 2,342 12 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...
28 March 2015 8,929 3 View
High fidelity DNA polymerases like "Phusion" have 3'--5' exonuclease activity. What DNA type do they degrade, ssDNA , dsDNA or both? What is the optimal temperate for them, RT, 37 or higher?
09 February 2015 5,562 7 View
Bacteria like E. coli synthesize fatty acids through a repeat extension with malonyl-ACP and adding 2 carbon at a time. Once the fatty acid chain reaches a certain number, usually palmitoyl-CPA...
02 January 2015 2,227 3 View
Why do we sometimes have bad breath? Some bacteria are responsible for bad breath in our mouth. How do they co-exist in our mouth?
27 December 2014 9,849 2 View
Methicilin-resistant S. aureus were originally resistant to Methicilin but later on develop resistance to many other antibiotics. Similarly, vancomycin resistant Enterococci (VRE) also develop...
18 December 2014 1,914 6 View
People usually make glycerol stock and store at -80 freezer. Do you remove salts before making the glycerol stock?
03 December 2014 4,430 4 View
People commonly use methanol, sometimes ethanol and acetonitile to elute microbial extracts from absorbent resin. Which solvent is better and why? What are the pros and cons?
26 November 2014 2,606 1 View
I got a hundred of marine bacteria strains and want to get the microbial extracts from those bacterial cultures to screen some potential compounds with antimicrobial activity. What culture media...
25 November 2014 6,151 2 View
Drug-resistant bacteria pose a great threat to the public but also to the researchers who are working on them. Do you have any experience dealing with those super-bugs when working on them? How do...
31 October 2014 6,612 12 View
Generally, mRNA secondary structures like hairpin, loop, stem will cause interference with the translation of protein. Given a DNA or RNA sequence, the secondary structure can be predicted and...
14 October 2014 4,205 3 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?
03 October 2014 8,602 9 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 ?
18 September 2014 8,206 12 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...
15 September 2014 1,294 5 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...
27 August 2014 4,549 5 View
Agar plates amended with substrates (eg, CMC, casein) can be used to screen for bacteria producing active enzymes such as proteinases and cellulases. Similarity, inhibition zone in Burkholder agar...
13 August 2014 617 8 View
Most research on Bacillus biofilm such as strain 3610 focus on pellicle biofilm formed at liquid-air interface. I wonder whether Bacillus biofilm can form robust biofilm in submerged surface. One...
13 August 2014 5,433 4 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?...
01 August 2014 2,482 9 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...
01 August 2014 8,833 3 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...
29 July 2014 2,671 8 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...
11 July 2014 9,843 19 View
Though it has been studied for a long time, many issues still limit the performance of microbial fuel cells, including low power output and efficiency. How do you think is the potential and the...
26 June 2014 1,037 12 View
In bacteria biofilm, a lot of bacteria become metabolically dormant while some are still actively growing. How do you separate them?
16 May 2014 282 12 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?
12 May 2014 1,881 2 View
Human guts are inhabited by trillions of bacteria. However this is not a random selection. Why is it that only some bacteria are able to stably colonize our gut while others cannot? What is the...
09 May 2014 5,796 6 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 7,047 3 View
I designed a kanamycin resistance cassette (up-kan-down, about 3 kb) and want to knock out the EPS operon in B subtilis. I didn't get any transformants on kanamycin plates (10 ug/ml kan), while...
05 May 2014 466 2 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....
30 April 2014 342 5 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...
22 April 2014 2,278 33 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?
31 March 2014 1,309 5 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...
27 March 2014 1,712 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.
25 March 2014 449 4 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...
20 March 2014 7,460 31 View
E coli is one the the fastest growers. They multiply every 20 min under optimal condition. How can we genetically engineer a bacteria that can grow as fast as possible? If so, do you think there...
18 March 2014 8,169 7 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?
16 March 2014 6,822 17 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...
11 March 2014 1,772 11 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...
04 March 2014 7,470 4 View
In order to ensure the survival of their own population, bacteria must develop some strategies to differentiate their own species from other bacteria. One strategy might include the production of...
25 February 2014 5,203 5 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?
03 February 2014 2,239 4 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...
27 January 2014 6,882 4 View
I am going to test the algeacidal activity of bacteria. I am going to use both bacteria suspension and supernatant. What are simple ways to measure the effect?
15 January 2014 3,303 5 View
I want to clone cellulase into my host bacteria. Ideally, I want non-complex cellulase that is free from cell rather than cell-associated. I need to know the source of cellulolytic bacteria. Can I...
10 December 2013 7,037 1 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...
04 December 2013 5,684 4 View
I need to engineer strains of Vibrio and Bacillus with heterogeneous cellulase and make them grow on cellulose. I want to control the plasmid number in each bacteria and compare their...
18 November 2013 6,673 0 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...
16 October 2013 5,489 21 View
Let's say, I have sequence data of bacterial communities from multiple samples, I want to find out what bacteria are either negatively or positively associate with other bacteria. What software or...
09 October 2013 7,893 4 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?
01 October 2013 1,340 13 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...
05 September 2013 2,747 4 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...
28 August 2013 3,947 3 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....
26 July 2013 4,502 12 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...
19 July 2013 8,597 4 View
Such as public-available database or government agencies.
10 July 2013 9,628 16 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 2,413 87 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...
02 July 2013 8,707 9 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...
28 June 2013 10,153 25 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...
22 June 2013 9,863 7 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...
20 June 2013 4,131 5 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...
16 June 2013 9,390 32 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...
15 June 2013 2,396 1 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...
13 June 2013 1,139 49 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...
05 June 2013 9,570 3 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?
03 June 2013 2,401 8 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...
23 May 2013 5,008 4 View
I mean whether the possibility is higher for closer related bacteria species to have similar functions / activities in term of their capability of producing functional proteins or metabolite...
08 May 2013 1,679 1 View
I want to test whether the AI-2 produced by bacteria A impact the growth of bacteria B. I want to extract AI-2 but remove proteins, sugars and others from culture broth that might also stimulate...
13 March 2013 2,182 8 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....
28 January 2013 8,135 4 View
I grow my bacteria in a define culture medium (C-limited) in 96-well plates. I tried TTC assay, but it doesn't seem to work well. I have to add extra glucose to intensify the reaction and the red...
16 January 2013 6,556 10 View
I want to count bacteria from biofilm with DNA probes and study bacterial interactions in biofilm.
28 December 2012 2,522 14 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 6,373 3 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 1,561 5 View
Many important drugs are produced as secondary metabolites by microbes. Why are secondary metabolites mainly produced in the stationary phase where nutrients become scarce? How can we increase the...
01 January 1970 6,569 5 View
iGEM has a collection of many ribosomal binding sites (RBS) at varying strength. eg, BBa_B0030, B0031, B0032, and BBa-J61100-J61150. On the other hand, RBS calculator (...
01 January 1970 8,393 5 View
