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Questions related from Luigi Marongiu
Hello I am running a PCR to quantify bacteria (namely Escherichia coli). I would like to count only live cells and I have seen there are several protocols that employe chemical dying of the death...
31 July 2023 7,237 3 View
Hello, I would like to report the relative expression of genes, measured by qPCR, using relative quantification. The answer would be along the line "Cell X expresses gene Y Z-fold more than the...
14 July 2023 4,582 0 View
Hello, what carbohydrates are not used by Escherichia coli for its metabolism? Thank you
17 April 2023 8,254 3 View
Some experiments measured the effect of particular chemicals on the infectivity of lytic phages in terms of influence on the PFU/mL counts. For example, the reduction of PFU/mL of exposed phages...
12 April 2023 3,534 6 View
Hello, I have bought some mitomycin C in powder. On the instructions, it is said first to dilute the powder in a few drops of ethanol, then in the solvent of choice. But there are many options....
26 February 2023 7,236 1 View
Hello, is there a calculator that computes the energy released in a chemical reaction given the reagents and the products. That is: If I have a molecule A, B and C, with A being the reagent and...
30 January 2023 8,835 7 View
Hello, I have generated a docking model using SwissDock (http://www.swissdock.ch/). The results include a ViewDock object with several entries, each with a different tridimensional position and...
15 January 2023 8,860 0 View
Hello, The high-end journals Nature and Cell not only publish top-quality research but also very catchy schematic figures, for instance, those on infection Trained immunity: a tool for reducing...
09 May 2022 5,230 5 View
While NPS3 (including the protease PLpro) and NSP5 (protease Mpro) are essential to cleave the polyprotein precursor that generates the replicative-transcriptase complex (RTC), are these proteases...
02 April 2022 7,644 2 View
Hello, I tried to get the sequences of the variants for SARS-CoV-2. I can find what should be 'alpha' that is the "NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,...
13 December 2021 3,754 10 View
Hello, some papers report the density of bacteria in the whole colon. For instance, both O’Hara et al., EMBO reports 2006;7(7):688 and Sender et al., Plos Biol 2016;14(8):e1002533 give 1011...
07 December 2021 3,712 2 View
I am performing a systematic review of the literature and the data is stored as a table including the fields: DISEASE, VIRUS, TISSUE, ASSAY. I made a random effect model for each of the first...
22 October 2021 2,700 5 View
In several models of phage infection there is the term 'lysis rate' (η). What is the procedure for the experimental methods for measuring it? I could find nothing on PubMed. Also, is there a list...
24 June 2021 9,640 4 View
I have seen that some equation sets have an explicit way of defining the substrate consumption whereas others have an implicit way. I would like to know how to convert the former into the...
23 June 2021 2,165 3 View
Hello, is it possible to generate anaerobic conditions for growing bacteria without buying those ready-made bags sold by, for instance, ThermoFisher? That is, instead of buying the bags can I use...
07 March 2021 1,813 6 View
If phages (bacterium-eating viruses) prowl on bacteria, are there bacteria (or other micro-organisms) that hunt phages for food? They are rich in proteins anyway... Are there studies on this...
23 February 2021 4,105 9 View
Hello, there are some molecules that bind to double-stranded DNA; for instance, SYBR green and some antibodies. Are there more examples? Thank you
26 January 2021 7,733 4 View
Hello, I would like to hybridize a probe and an anti-probe (ssDNA oligonucleotides) in a reaction vessel. What would be the best buffer to use? and the temperature of annealing? Thank you
07 December 2020 4,247 0 View
I diluted ethyl-carbodiimide hydrochloride (EDAC) powder in water to 1 M and stored it at -20 °C. I am using a 10 mM solution as a working solution and I keep it at room temperature. Would the...
07 September 2020 4,451 3 View
Is there a simple (that is one that requires few and not very exotic reagents) chemical reaction to "activate" or "functionalize" the polystyrene of a simple microtitre plate? In other words, I...
07 September 2020 371 3 View
Hello, I have obtained the following Shannon indices from a trio of samples: 27.73 (healthy tissues), 24.55 (primary colon tumor), and 1.20 (metastatic tissues). The indices have been obtained...
31 August 2020 5,650 1 View
Hello, what is the correct molarity of a stop solution for a peroxidase using o-Phenylenediamine dihydrochloride (OPD)? I am getting all sorts of molarities, from fractional up to 3 M according to...
02 July 2020 3,875 1 View
In the work of Cleo Anastassopoulou et al. "Data-based analysis, modeling and forecasting of the COVID-19 outbreak" (Plos One 15(3):e0230405), the authors extracted the parameters α, β, and γ...
02 July 2020 4,150 0 View
Hello, when was recorded the first case of COVID-19 outside the Chinese region of Hubei? The first case was reported on the city of Wuhan on the 31/12/19 -- although other sources said that...
24 May 2020 7,402 7 View
Hello, is there a repository of the basic characteristics of bacteria, such as maximum growth rate? In the works related to the modelling of bacterial growth, the parameters requested are always...
26 February 2020 5,609 2 View
Hello, I did the PCR (long-range, target ~5 Kb) that is shown in the attached file. The lanes are: 1. ladder 2. target (plasmid purified from E. coli after transfection), 50 ng/uL corresponding to...
19 February 2020 6,990 3 View
Is it possible to grow different bacteria in a fermenter/chemostat under common conditions? I have a panel of bacteria, some anaerobic, some microaerophilic, some requires Columbia blood agar,...
21 August 2019 2,568 8 View
Hello, from this website (http://phage.org/names/2000/) it is possible to determine the genera targeted by a family of bacteriophages, for instance the phage species DS96 , H24 , M35 , P3 , P9 ,...
01 July 2019 7,723 8 View
I'd like to know the features of single stranded RNA molecules such as diameter and charge, but I can't find any experiment on the subject. There are some works on dsRNA and hairpins, but nothing...
15 July 2016 9,456 2 View
I am trying to set a model using the pcrfit() function of the R's qpcRpackage. I have defined a dataframe with 45 cycles (rows) and 4readings (columns) derived from a TaqMan qPCR with...
16 March 2015 7,362 3 View
PCR is a very powerful tool but also has some drawbacks. In particular, the need for a thermal cycler is a major limitation if you have to buy it upfront (as in a newly established laboratory)....
01 January 1970 9,293 3 View
Hello, in the literature, the studies based on the next-generation sequencing analysis of microbes are called "microbiome studies". On Wikipedia, the microbiome is defined as: "the microorganisms...
01 January 1970 328 6 View
Hello, there are several books about the life of Louis Pasteur. Is there a biography that contextualizes his life and works in the Germ Theory and its acceptance? For instance, I have found one...
01 January 1970 7,064 8 View
Hello, most of the grant calls I have found (especially those from the UE) are based on medical issues (cancer, etc). But if one wanted to carry out just general microbiology (for instance...
01 January 1970 4,694 2 View
Hello, is there a good book that talks about the difference between Darwin and Lamarck, also in the light of modern studies on epigenetics? Thank you
01 January 1970 4,983 1 View
