Questions tagged [lab-techniques]

Questions relating to protocols, procedures, and good practice when using laboratory equipment.

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How do I go about detecting cfu and subsequently, log10, for colonies which are uncountable or zero?

All of my Miles Misra dilution series either have an uncountable colony count or are zero. I'm not sure how to go about picking a dilution series to find the cfu for. Do I omit these results for my ...
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Guided tour through history of Biology experiments

Is anyone aware of list of pivotal Biology experiments; similar to https://en.wikipedia.org/wiki/List_of_experiments - but a little more guided? Might be slightly ambitious; but looking to build my ...
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Can we prepare for pandemics by predicting highly-probable mutations and by synthesising viruses in lab before they occur in nature? [closed]

I am excited about synthetic biology https://academic.oup.com/synbio and bioinformatincs. Apparently, not all mutations (and combination of them) in viruses and bacteria are equally probably. But can ...
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qPCR to detect viral load

In an experiment qPCR was used to determine viral load. Alongside this conventional PCR was also performed and ran on an agarose gel. However I do not understand why both methods would have been used, ...
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How do you sanitize blood for use in a BSL-1 lab?

I do research in a BSL-1 (biosafety level 1) lab, though I have access to a BSL-2 lab if needed (though very inconveniently). I'm doing medical research with the goal of identifying biomarkers for ...
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Using a magnetic stirrer as a makeshift shaking incubator?

I'm working in my high school's lab and need to culture bacteria in a broth culture. More specifically, I'm trying to harvest Bacillus endospores with the exhaustion method published in "Molecular ...
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How does SDS-PAGE separate based on mass?

If $F=qE =ma$ then $\frac{m}{q}a=E$, and in SDS-PAGE electric field and mass-to-charge ratio is all approximated to be constant for all proteins. Thus, all proteins must migrate with a constant ...
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How to choose an assay for detecting virulence factors?

When looking for a protein of interest, an ELISA is being administered. I read this article about the different types of ELISAs and the advantages/disadvantages. However, I am conflicted about ...
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Using autoclaved store-bought distilled water for labwork?

I'm a high school student who's working on a molecular biology project in my school's lab. I need pure water for making culture media, buffers, running a BCA protein assay, running digests, cleaning ...
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RNA product storage in isopropyl alcohol

I have an issue. I isolated RNA from cortex a few days ago. For isolation of RNA i used this procedure: I homogenizised my sample (mouse cortex) with Trizol. Then to the sample add chloroform, shooke ...
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Minimum amount of RNA for cDNA conversion and qPCR

I searched several protocols for reverse transcription of RNA and all suggest using RNA concentrations of 1ug. Could a lower amount result in inferior transcript representation and therefore decreased ...
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What is the most durable electronic pipette?

We have a routine task of pipetting substance concentration series in triplicate on cell cultures under a laminar hood. To speed up the process, we use an electronic pipette in the repetitive ...
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Are controls needed for urine cultures?

If testing for bacteria (gram-negative) in a urine culture, are negative or positive cultures needed? I could not find anything that says controls are needed unless results seem to be contaminated. ...
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Lab technique to distinguish between single stranded and double stranded DNA?

What lab techniques exist to differentiate between single-strand and double-stranded DNA?
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Why spin live fruit flies in centrifuge?

I was reading this article about the evolution of monarch butterflies’ resistance to cardiac glycosides: These Butterflies Evolved to Eat Poison. How Could That Have Happened? And this passage made ...
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Bacterial Growth Formula

What are the units of $N$: the colonies of bacteria or the viable cell count? This is in regards to the bacterial growth formula used during serial dilutions, $$ N =N(0) e^{kt} \quad . $$
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Autoclaving media Question

1.When I autoclave media should I close the cap tightly or slightly? I put all tools in plastic bag when I autoclave, should I close slightly the plastic and when it finish I close tightly the ...
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How can I improve efficiency of Ecoli transformation?

I am an intern in biology institute. I have a 17.3kbp plasmid need to transform to Ecoli. But I have tried many time but have no or very few colony on LB plate. I know large plasmid have less ...
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How does a heat-ratio sap flow sensor work and how invasive is it?

The Gizmodo article Undead Tree Stump Is Being Kept Alive by Neighboring Trees says: Leuzinger and Bader stumbled upon the stump while out for a hike. The woody stub caught their eye because callus ...
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Alternatives to Matrigel in chick aortic arch assay

When conducting a chick embryo aortic arch assay in order to see angiogenesis inhibition properties of various substances(originally in powder form but soluble in water or ethanol) is it possible to ...
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what are best methods for mrsa screening in hospital?

methods for screening MRSA are based on PCR (mecA detection) and MRSA latex test and culture. I need to know sensitive, specific and cost-effective methods for diagnosis MRSA infection on one work day ...
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Why do protein solutions have to be alkalised in biuret test?

I’ve read that CuSO4 solution reacts with peptide bonds that connect amino acids to create a violet colour, but the instructions always tell me to add NaOH solution to the protein solution before I ...
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Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
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56 views

Preparing sample for SDS PAGE

I have more than 10 cell lysate samples (70 µL each) whose concentration varies from 1.9 mg/mL to 4.8 mg/mL. I have 5X and 2X SDS sample buffers. I would like to prepare SDS PAGE samples in such a way ...
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I did an agar gel electrophoresis but I could not see DNA, why? [closed]

After performing a PCR, I ran the products (700 bp) in an agar gel electrophoresis along with a Genedirex ladder (100 bp), but the transilluminator did not reveal them.
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How do I homogenise a small pellet of 10 to 50 cells within less than 50 µL?

I have a problem with declumping/ homogenising bacterial cells in small volumes (10 to 50 µL). I know that I can get all of my cells out of the tube, but they are still stuck together and won't form ...
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Re-stain slice using a different secondary antibody?

I stained a free-floating ~300uM brian slice using 4 different 1º antibodies (rabbit, chick, mouse, rat). For the mouse primary, I mistakenly used an Alexa-350 secondary, when I should have used 594. ...
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How to isolate a high proportion of available helminth ova from animal faeces/feces without damaging them?

I need to isolate large numbers (tens to hundreds of thousands) of cat (and later dog) hookworm ova from cat/dog faeces. I have a centrifuge, and various sieves with pore sizes of 20, 63, 75, 106, ...
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How to supply oxygen to a culture vessel?

I'm reading this paper: https://www.jstage.jst.go.jp/article/jpsa/51/3/51_0130043/_pdf From day 17 of the culture period until hatching, pure oxygen was supplied at a flow rate of approximately 500 ...
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Why both forward and reverse primer are added in asymmetric PCR?

If the purpose of Asymmetric PCR is to amplify single targeted strand of dsDNA then instead of adding just one primer for targeted strand why do we add both forward and reverse primer? Upon addition ...
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Does the preservation fluid (ethanol or formaldehyde) leach heavy metals from mollusc tissue?

In a thread on researchgate, the concern was raised that long term exposure to unbuffered preservation fluids such as ethanol or formaldehyde may leach heavy metals from biological samples due to a ...
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What is the fastest way to crystallise lysozyme (for student course)?

High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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Double Digestion with Restriction Enzymes Using Different Buffers

I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site ...
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1answer
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Must I HPLC-purify my PCR Primers for amplicon sequencing with PacBio SMRT?

I would like to order some primers for amplicon sequencing. I am using universal tag primers (unusually long 30-mers recommended by PacBio for SMRT, both F&R) + barcodes (16-mers). The resulting ...
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Is it normal to see yeast cells stacked in the Z axis when counting yeast?

I just got started with yeast cell counting and was surprised to observe yeast cells that are at different z axis depths at 400x. That is, by adjusting the focus (not the x/y stage) I can make some ...
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1answer
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How to confirm secondary structure formation of Precursor miRNA on gel?

I want to fold precursor-miRNA into its secondary structure and then confirm it on gel. At first, I heat it in annealing buffer at 95°C for 5 minutes and cool down slowly. Then I run it on gel but the ...
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157 views

Killing microorganisms on agar plates?

If I grow microorganisms on agar plates and I expose them to UV light. How exactly will I know that the microorganisms have been killed? I was watching a video that showed spots in the petri dish ...
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1answer
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How many cells should be seeded for passaging?

Do you count cells when you passage them? I found that many people will according to a ratio (maybe 1:2 or 1:3,etc.) to subpackage. It is so indistinct! What is the optimal seedling density or ...
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1answer
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Improving DNA quality and yield from stool samples

I prepared genomic DNA from pig stools but the concentration was very low — about 3~4 ng/µl, when I measured it using nanodrop. The A260/A280 and ...
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Why pellet and resuspend E. coli for plasmid prep

For maxipreps, cant you just add all the stuff that would be in P1 (RNase A, EDTA) then just add P2? Because if we pellet cells then resuspend theres got to be a reason, right? Is it slats and other ...
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1answer
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Why electroporator need a cuvette?

I have never obtain an Electroporator for my home-lab. Because it's very expensive, I'm trying to create a diy cheap version for myself. In all commercial design, I see that we need to put the sample ...
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1answer
137 views

How to perform cell biology research without lab affiliation [closed]

Related to this question, I am wondering just generally how one can do cell biology research without being part of an already well-established University laboratory. I am not doing this myself but am ...
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110 views

How does the OD correlate with the number of algae cells?

My research team and I are using a spectrometer to measure the OD of an algae sample. We are trying to answer the question "Is there a correlation between OD and the number of algae cells?" What ...
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Why do Petri dish lids not fit?

I understand that they are generally "vented", but why such a poor fit? For the batch I bought, the lid and container don't even recognizably go together (like 1/2" difference in diameter). The wind ...
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What kind of sieve does one use to extract meiofauna?

Suppose I have a core of sediment, and I want to extract the meiofauna from it, in order to study these organisms. According to the sources I could find, this involves using a very fine (e.g. 45 μm) ...
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DNA preservation at room temperature

I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in ...
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Why Cerebrospinal fluid is not heated for VDRL?

For performing VDRL of serum , we heat serum to inactivate complement proteins which may otherwise interfere , but why don't we do same for CSF even though it too has complement proteins in it? Is it ...
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How is the role of ethylene in ripening demonstrated in biology (or agriculture) education?

I want to know what are some typical experiments performed in the course of biology education (or possibly in applied biology education e.g. agricutlure education) to prove to the students (or have ...
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When in Ampicillin degraded (gone) in liquid TB-media? Concerns about selectivity

Question: Specifically regarding Ampicillin; When growing cells in TB (terrific broth) for protein expression - when should I expect the ampicillin to be gone due to degradation by b-lactamases? (and ...
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Using distilled water on sterile swab for collecting microbes on solid surfaces

I was wondering if it is acceptable to use distilled water on a sterile swab for the collection of microbes on a solid surface. - in this case, Salmonella and Shigella.

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