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Questions related from Luigi Marongiu
I have prepared a suspension of bacteria and phages. I attempted to filter it using 0.2 μm filters with a vacuum pump, but the filtrate remained unclear; in fact, bacteria were present in it (as...
2 weeks ago 5,278 2 View
It is common knowledge that Gram-negative bacteria possess an internal membrane and an outer membrane, which contains lipopolysaccharide (LPS), as well as a periplasm that contains peptidoglycan....
4 weeks ago 2,521 2 View
I need to run a series of genetic expression assays using RT-qPCR. I will use housekeeping gene to normalize the output of the genes of interest. Shall I normalize the experiment in some...
last month 5,339 1 View
I would like to make pellets of phages. The protocol seems easy enough for instance this one from YouTube https://youtu.be/detP_viS6BA?si=62rHDL2sXe8TVQU0 However I don't get any pellet. For...
01 August 2025 7,361 3 View
I would like to check the morphology of bacteria under the microscope, but the microscope is in a clean room, thus I cannot bring bacteria alive there. Is there a method to kill the bacteria...
15 July 2025 4,481 3 View
Hello, I have a filter disc with a porosity of 0.2 um. Can I obtain a porosity of 0.1 um by combining two of them in series (one on top of the other)? Would that be a bit like the HEPA filters,...
01 July 2025 2,644 2 View
I have placed E. coli in a medium supplemented with a specific sugar and observed evidence of membrane impairment. How can I determine whether the sugar has changed the osmolarity of the medium?...
03 June 2025 4,196 1 View
Hello, I tried to prepare some samples for scanning electron microscopy (SEM) of viruses. To ensure the presence of viruses on the slides. I have placed a drop of 50 ul of suspensionion titrated...
29 May 2025 1,357 3 View
When I need to desing primers for a given target, located for instance at position `2057241..2058593`, I simply tell the primer design software to focus the primer search within positions...
17 May 2025 5,990 4 View
Hello, I tried to stain some phages with SYBR green I (Roth) to do some epigenetic analysis. The phages were from a commercial source, and I stained 500 uL of it with 5 uL SYBR green for 15 min in...
01 May 2025 8,441 2 View
I have a minimal medium for bacteria. I would like to buffer the pH. How much PBS should I add? Thank you
15 April 2025 2,971 1 View
Hello, I would like to analyze quantitative PCR (qPCR) data using R rather than proprietary softwares. I can see there are several packages out there, but mostly they perform relative...
10 April 2025 4,473 0 View
I am planning to produce some recombinant proteins with a His-tag in an E. coli system. I am also planning to purify the proteins by affinity chromatography followed by dialysis. Do I need to run...
20 February 2025 1,602 4 View
Hello, I have a suspension of viruses (phages, specifically). How can I obtain a pellet of viruses? The point is that I need to wash the viruses and concentrate them like with bacteria. But I...
12 February 2025 2,758 2 View
I have some cells marked with a plasmid producing luciferin/luciferase. If I check the cells for their luminosity, I get very little signal. In fact people use specific camera that get images...
26 November 2024 1,030 3 View
Is Academica Press (https://www.academicapress.com/) a legit (not vanity or predatory) publisher? Is it any better than Nova? What makes me suspicious is that their email ends with 'gmail' and...
12 November 2024 3,490 2 View
I have bought bacteria transfected with a bioluminescent plasmid (https://www.addgene.org/search/catalog/plasmids/?q=54630). The plasmid is supposedly constitutively active, and the luciferase...
09 October 2024 3,290 1 View
I would like to enumerate phages by flow cytometry. One standard method is given by Brussaard (DOI: 10.1007/978-1-60327-164-6_11), where the capsid is first loose allowing SYBR green to stain the...
06 October 2024 4,673 0 View
Hello, I suspect that a molecule I am using is causing bacteria to experience osmotic shock. What chemical properties should I look for to compare this capability with those of other substances?...
07 August 2024 1,533 1 View
I would like to investigate the surface of bacteria using electron microscopy to assess changes in specific conditions. Is there an established protocol for that? Thank you.
16 July 2024 2,440 2 View
Is there an established protocol to measure the permeability of bacterial membranes? Thank you
01 July 2024 7,089 3 View
I have a set of bacteria that I stained with fluorescent dyes to check for viability. The protocol suggests to place 5 ul of the suspension on a slide, cover with a cover glass, and observe on a...
17 June 2024 9,491 1 View
I would like to transfect bacteria with some plasmids. However, the bacteria are not competent but either isolated from the environment or purchased reference strains. Can I transfect these...
17 June 2024 9,482 6 View
After performing statistical analysis, there is the need to report the p-values in the text. Is there an accepted (published) stratification range? For instance, is 0.04 'slightly' significant?...
29 May 2024 7,821 3 View
I used Microscale thermophoresis(MST, from Nanotemper) to determine the constant of dissociation (Kd) between a protein (20 nM) and a ligand (1:2 serial dilution from 50 μM to 1.5 nM). I ran the...
05 May 2024 2,151 0 View
I would like to track in real time the growth of bacteria using fluorescent miscoscopy. I remember there was at least one plasmid that could be used: transfected bacteria would emit a red or green...
30 April 2024 7,129 3 View
Hello, I would like to take some publication-quality pictures of organoids. What magnification shall I use? Do I need a 60x or is a 40x enough? Thank you
16 April 2024 8,567 1 View
Hello, I think I am using a 5 mL pipette that is contaminated with bacteria. Nothing serious, just the usual environmental microbes. The problem is that the tips for the 5 mL pipette are without...
08 April 2024 6,816 1 View
I am running a bacterial culture and reading the bacterial density on a spectrophotometer at 600 nm. I blanked with the culture medium and also ran a tube without inoculation as a control. After...
26 March 2024 7,554 3 View
I sequenced some bacterial genomes and obtained consensus fasta from the original fastq after aligning against a reference genome. I now would like to create a comparative map (AKA, I reckon,...
21 March 2024 6,085 0 View
Hello, I have measured the optical density at 600 nm of a bacterial suspension. I got a value of 1.65. I then diluted the suspension 1:10 in medium and got a measurement of 0.144. What would be...
15 March 2024 2,614 1 View
Hello, I am quantifying bacteria exposed or not to a certain chemical at specific time points. How can I compute the results in a relative manner? That is: what is the formula for a ∆∆Ct analysis...
11 March 2024 6,362 4 View
Hello, I would like to enumerate phages using flow cytometry as reported in these articles: DOI: 10.1128/AEM.70.3.1506-1513.2004 DOI: 10.1007/978-1-60327-164-6_11...
01 March 2024 349 2 View
I would like to follow the growth of bacteria with life-cell microscopy. I reckon I will need a 100x objective, but since these are immersion lenses, how can I follow several colonies in the same...
15 February 2024 4,212 4 View
Are there phage preparations for phage therapy against Yersinia enterocolitica? Maybe from Georgia? Thanks
19 December 2023 2,737 3 View
I would like to differentiate the presence of Escherichia coli K-12 in my samples by qPCR. In particular I would like to discriminate between K-12 and HB101. The problem is that these two strains...
19 December 2023 2,228 2 View
I have seen there are some papers where they used optical microscopy to visualise bacterial growth in real time even just with contrast field. The magnification used was 100x and the microscope...
15 December 2023 747 0 View
In the literature there is a lot of talk about the Firmicutes/Bacteroidetes ratio. But is there a paper that actualklky lists what species actually belong to these phyla? Thank you
14 October 2023 7,259 1 View
In the paper "Pharmacokinetics and metabolism of N-[N-[3-(3-hydroxy-4-methoxyphenyl) propyl]-α-aspartyl]-L-phenylalanine 1-methyl ester..." (Food Chem Toxicol. 2011 Nov;49 Suppl 1:S8-29) is...
04 October 2023 6,822 2 View
Hello is a standard 1.5 mL tube made of polypropylene transparent to UV-A light? Thank you
02 October 2023 5,989 1 View
In this interesting chapter (Tools for Comparison of Bacterial Genomes ) there is a list of bioinformatic tools that can be used for the analysis of bacterial genomes, particularly MUMmer, Genome...
01 October 2023 5,956 2 View
Hello, in the 1940s, Max Delbruck and Salvador Luria worked with some phages that they called alpha, delta, and gamma. Then they decided to change the names to 'T' with a number that is still in...
23 September 2023 7,966 1 View
I am following this paper (DOI: 10.1128/AEM.02895-10) to run a PCR that could differentiate between live and dead bacteria. The method is based on propidium monoazide (PMA), which enters the dead...
12 September 2023 5,668 9 View
I am trying to build a cheap chemostat to generate pilot data. I am following this paper: DOI: 10.21769/BioProtoc.3813 (www.bio-protocol.org/e3813). In the paper, they used an air pump to generate...
08 September 2023 2,441 0 View
Hello, There are several studies regarding the quantification of chemicals by chromatography and/or mass spectrometry in urine samples. Would the same techniques work in stools (faeces)? Or one...
05 September 2023 8,499 3 View
Hello I have sequenced a clone of bacteria. I got the fastq files back. What is the procedure for the assembly? What are the differences with human re-sequencing? Specifically, how can I account...
04 September 2023 6,352 2 View
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 7,324 3 View
Hello, I have two time-series, A and B; what test can I apply to check if they differ? I could compare the values between A and B at specific time points; for instance, is there a difference...
16 July 2023 3,472 7 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 4,653 0 View
Hello, when is the light measurement taking place in qPCR? during the annealing or during the extension? Thank you
30 May 2023 8,512 3 View
To have a sure positive control for a PCR, I have ordered an oligo containing the cognate sequences of the primers (20 nt each) separated by 150 of random DNA; before and after the binding sites,...
16 May 2023 5,627 3 View
I would like to quantify Escherichia coli K-12 by qPCR, discriminating it from other coli and bacteria. I have found this primer set on DOI: 10.1128/aem.61.11.4135-4139.1995 but on my hands...
13 May 2023 3,178 4 View
Hello, what carbohydrates are not used by Escherichia coli for its metabolism? Thank you
17 April 2023 8,331 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 3,591 6 View
I would like to compare the growth of bacteria exposed to a particular chemical to that of something that does not affect their growth. Since I am using the non-exposed at all bacteria to...
12 April 2023 3,706 1 View
Hello, I applied exploratory factor analysis with network analysis to data from healthy and diseased patients. The analysis shows different clusters of parameters; some are similar in both groups,...
10 March 2023 2,333 2 View
Hello, I would like to study the induction of bacteriophages; thus, I will need a strain of lysogenic bacteria (let's say E. coli) that will produce phages upon induction and another strain...
01 March 2023 1,458 2 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 7,297 1 View
Hello, I have used mitomycin C (0.5 μg/mL) to induce prophages in Escherichia coli K-12. After 24 h exposure, I filtrated an aliquot of the suspension and placed a drop of the filtrate on a colony...
26 February 2023 3,006 4 View
Hello, I am modeling bacterial growth using a logistic growth function: X' = μX(1-N/κ), where B' is the increment in bacterial population, μ the specific growth rate, N the total bacterial...
06 February 2023 3,510 2 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 8,920 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 8,929 0 View
Hello, it is reported that the sweetener stevia is not metabolized by animals, and it is, therefore, a non-nutritive sweetener. However, some bacteria can degrade it; specifically, Bacteroides...
29 November 2022 8,605 0 View
Hello, is there a value (and a reference) for the growth rate MU of Salmonella enterica (preferably serovar Typhimurium ATCC 14028S)? Thank you
04 September 2022 5,985 1 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 5,303 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 7,698 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 3,821 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 3,773 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 2,770 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 9,751 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 2,251 3 View
Hello, Is it possible to calculate the carrying capacity K of an environment based on the composition of the environment, or is K an empirical parameter? For instance, if I consider the...
10 June 2021 9,794 4 View
Hello, I am curious about the growth of bacterial consortia, namely pathogens among commnesals. I have found several publications reporting the experimental growth or the model of single bacteria...
06 June 2021 8,622 3 View
In the literature it is reported that stem cells are present in the basal layer of the epithelium, then they migrate and differentiate. But how many stem cells are there? It is the whole bottom...
19 May 2021 7,303 3 View
I have read on Reich and Regauer, Int J Gyn Pathol 2016;36:71 that there are cervical cancers not associated with HPV and these are characterized by being thin (max 9 cell layers), without LSIL...
18 May 2021 4,521 4 View
Hello, is there a simple method for the wet activation of polystyrene using Potassium Hydroxide or Sodium Hydroxide? For activation, I intend the addition of Carboxylic group COOH to the surface...
12 April 2021 851 5 View
Hello, I would like ot prepare Eosin Methylene Blue (EMB) agar but I don't have the following: Dipotassium phosphate (K2HPO4) Lactose. Can I use something else instead of Dipotassium...
10 March 2021 6,444 5 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 1,874 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 4,170 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 7,931 4 View
Although phages are highly variable in sequence and lack a common marker, is there, anyway, a kind of pan-PCR to quantify the total phage load in a sample? Perhaps a common integrase? A...
07 January 2021 7,134 4 View
There are several papers describing the intestinal mucosa but very little is reported for the vaginal and cervical mucosae. Is there scientific literature describing these mucosae? Are bacteria...
01 January 2021 664 2 View
Hello, the formula to calculate the number of individuals given the initial population size is: Nₜ = rᵗN₀ where Nₜ is the number of individuals at time t, N₀ is the initial number of individuals...
20 December 2020 1,895 3 View
Hello, it is possible to determine the initial population of, let's say, bacteria given a measure at a later time? Let's say I use the logistic growth model: dN/dt = rN(1-N/K) and let's assume I...
10 December 2020 5,067 0 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 4,428 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 4,668 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 560 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 5,844 1 View
Hello, I would like to cultivate fecal bacteria, not for diagnostic purposes but for an ecological study. Thus, I am not interested so much in the pathogenic species but the normal commensal...
23 August 2020 5,797 6 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 4,113 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 4,399 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 7,457 7 View
Hello, in many papers, the basic reproduction number (R0) is calculated via SIR or similar models such as SIRD or SEIRD. The main parameters of these models are alpha = infection rate beta =...
05 May 2020 4,746 0 View
Hello, when was the lockdown/quarantine law applied in China and when was lifted? I understand it was applied on the 29 January 2020 and lifted after 76 days, that is on the 14 April. Is that...
28 April 2020 7,924 8 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 5,795 2 View
Hello, If I wanted to simulate the flow rate present in the human intestine, what rate should I set in a chemostat? A standard value I have is 0.05 h^-1 (I assume mL/h) but would that be correct?...
25 February 2020 9,182 0 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 7,177 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 2,698 8 View
Hello, is it difficult to grow Fusobacterium nucleatum? Does it grow in liquid medium? Is there some particular requirement that makes this bacterium different from other? Is it slow to grow? I...
12 August 2019 6,294 2 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 7,780 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 9,520 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 7,424 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 9,372 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 409 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 7,135 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 4,750 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 5,042 1 View
There is a wide collection of bacteriophages in the colon targeting a plethora of bacteria. Pathogens are mostly similar to the bacteria present in the colon, just the former have more virulence...
01 January 1970 215 1 View
Hello, I am looking for Julia programmers to collaborate on a project for modeling bacterial populations. The project will involve solving ODEs and interactive plots. The workload will not be...
01 January 1970 8,045 0 View
Max Delbruck, Emory Ellis, and Salvador Luria asserted that the plaque-forming unit (PFU) is a spot where a single bacterium has been infected by at least one phage. The phages liberated by the...
01 January 1970 7,296 2 View
I received an invitation to join Sigma Xi, a Scientific Research Honor Society (https://en.wikipedia.org/wiki/Sigma_Xi). The membership is about 140 euro/year. Is this society legit? Is it worth...
01 January 1970 10,042 1 View
In the paper that introduced TRANSDUCTION (J Bacteriol. 1952 Nov;64(5):679-99.), Lederberg and his student Zinder reported that S. typhimurium "LT-22 is lysogenic for a virus active on LT-2. This...
01 January 1970 5,629 3 View
I am looking for a small-scale (0.2-1.0 L) parallel (4-8 chambers) chemostat to grow bacteria. I got a couple of quotes but the price is over 100K. Is there a professional set (I mean not...
01 January 1970 2,913 0 View
Hello, I have found a couple of papers showing how certain molecules reduce the infectivity of phages. They only report a reduction in the density of the host For instance, there was a 3 log10...
01 January 1970 7,832 0 View
Hello, are there some software that can determine the characteristics of specific molecules? For instance, what is the physical difference between water and methane? Or between benzene and...
01 January 1970 8,533 0 View
There are several publishers of scientific books that are classified as vanity press, such as LAMBERT and NOVA. So, what if I wanted to publish a legitimate book but couldn't compete with the...
01 January 1970 4,919 3 View
