Science topics: Cell BiologyMethods
Science topic
Methods - Science topic
A platform to address questions regarding methods and development of new methods.
Questions related to Methods
For H202 radical scavenging assay. How to prepare 75 uM hydrogen peroxide from 30% H2O2 solution ? Thanks in advance.
Dear all,
I am trying to find a list of journals that publish method papers. I know a few, like Nature Methods, but I would like to have an updated list to have an overview. I could not find anything.
Any help is appreciated!
Ivan
Is there any particular advantage, other than the smaller insert size, to expressing an shRNA rather than a microRNA primary transcript when using a lentiviral delivery system?
I am trying to revive my cells and I don't know what they're being affected by. I have thoroughly cleaned every corner of the culture room and incubator; done all possible cleaning practices to avoid all possible sources of contamination. Now my cells are not adhering to the surfaces of the plates. They become rounded and are floating in the media. What additional techniques can I try to establish my culture? I don't know whether it is some biological contamination or some physical factor that is playing a major role.
I want to recreate and extend an experiment from a paper and am not sure if my math is corrected. None of the authors is registered here.
The authors did the following (text of the paper in quotation marks):
1.BSA solution:
"The BSA concentration was constant, 100 μM in the reaction mixture. BSA solution was prepared in pH 5 buffer (0.05 M acetate containing 50 μM ascorbic acid).
I found BSA having 66.430Da - so for e.g. 1L of 100µM my math is:
66.430 g/mol x 0,000100mol/L x 1L = 6,643g
So i would solve 6,643g BSA in the acetate-Buffer.
2.Samples:
"Sample solutions of 1.0 mM, 0.8 mM, 0.6 mM, 0.4 mM, 0.2 mM, and 0.1 mM
were prepared in MeOH/H2O (1/9, v-v)"
The Math should be the same as for BSA but with the molecular weight of e sample.
I am quite unsure with the ratios that are mentioned:
3."1/9, v-v "
I am unsure if this is the same as 1:9 and (v/v) - which I would read as 1 part A + 9 parts B. So e.g. 100ml MeOH + 900 ml Water
Finally a ratio of BSA + sample is mentioned:
4. "measured at sample/BSA ratios of 2:1, 3:1, 4:1, and 5:1."
Which would be the same for me as above (that is why i am confused) - e.g 3ml sample + 1ml BSA solution would be 3:1 for me.
How would you interpret/calculate those 4 points? Same as me - or do you see any error or something i interpret wrong?
In data clustering, what is the best normalization method? And, what is the influence of each method on the results?
I read an article and was intrigued by their use of discourse analysis + computational methods to track word use associations. Does anyone know suitable primers for computational content analysis? Also, they use QDA Miner-WordStat, but it's only available on PC are there MAC versions available?
I'm hoping to supplement qualitative discourse analysis with content analysis.
Could anybody recommend a good method to isolate total RNA from human blood plasma?
We need to analyze some important patient samples. But we do not have whole blood - the technician only froze blood plasma! So I'm asking out of desperation.
We need to extract total RNA (we are particularly interested in mRNA). We have between 1 ml and 1.5 ml of plasma, according to the sample.
I am presuming that some cells might remain in the plasma after centrifugation (3500 rpm, 10 minutes) and its separation from the whole blood sample. Does anybody know approx. how many cells might be contaminating the plasma and what yield could be expected? Has anybody successfully extracted RNA this way before?
Psychology People :
I have a hard time believing that , in effect, few (if anyone) believes there might be a bit of "conditioning" to see a new perspective and approach. (Reflect on the fact that Buddha needed to use much repetition (and that in several different contexts) for people to "see" what he was talking about -- that is a fact.) See my next post (Discussion) for more.
I am trying to isolate a nuclear protein NF-kB from raw cells in order to do a western blot.
I have searched some protocol for nuclear isolation and finally came up with one. But in that protocol, apart from adding 420mM Nacl for NE buffer , they have added an extra 400mM using 5M NaCl directly onto nuclear pellet and again 1 pellet volume of NE buffer. Can anyone tell why extra NaCl should be added, and if we add double the volume of NE buffer, won't the protein get diluted? I'm attaching that protocol along with this.
I am currently utilizing the seCLIP sequencing methodology (https://www.nature.com/articles/s41596-022-00680-z) to extract RNA from my RNA-binding proteins. After performing Western blot analysis on IP samples utilizing a target antibody, I obtained positive results. However, when attempting to isolate RNA from the RNA preparatory gel using the IP samples, I observed a very low RNA yield of 1.25 ng/µL.
Here are the few details I think where the problem can happen:
1. Cell density was ∼15 million cells in a 150mm dish and UV crosslinking was done at 1575 and 4000mJ/cm2 with wavelengths of 265nm.
2. I used 10% BIS-TRIS gel for RNA preparation and transferred it overnight at 30V using a nitrocellulose membrane.
3. I have cut the membrane by using a developed western blot as a guide and cut out the membrane region starting from the observed size of my target protein and extending to ∼75kDa larger than my target protein size. After that, I digested the cut membrane pieces with Proteinase K as per the steps mentioned in the above publication and elute the RNA from the membrane. I observed a very low yield of 1.25 ng/µL. How much is the RNA yield we can get? Am I missing anything here to improve the RNA yield?
I would appreciate your assistance in troubleshooting this issue in order to obtain a higher RNA yield.
Hi,
We have few AI (Artificial Intelligence) solutions for different problems in public health. Few of the problems are binary in nature, while the rest is continuous. We need help in calculating sample size for measuring the accuracy of the AI (to reliably predict the problem).
For example, we developed an AI solution to estimate weight of a baby. We expect the AI to predict the weight reliably in 90% of babies - error to be less than 10% of actual weight by gold standard equipment. I can calculate sample size in two ways, I think:
- Assuming that variable of interest is binary - reliability of the AI prediction (yes/no)
- Assuming that variable of interest is continuous - actual error of AI prediction (grams - or %)
What should we choose? In the second option, which SD should we choose for ss calculation?
Thanks for reading and suggesting in advance.
PS - both the methods are applied on same study participant.
Although the preprints submissions can be interesting to check the repercussions, criticisms and suggestions pointed out, I think that a not very good choice of platform can have limited results. Among the platforms researched, I observed that OSF, Scielo and Elsevier preprints offer a reasonable structure for preprints submissions and analysis. In this sense, I kindly ask for suggestions on which platform may be the most indicated for a preprint submission in the field of social sciences.
Hi all!
Does anyone use endophenotypes for research purposes? I found very interesting papers explaining the value of endophenotypes (mostly in psychiatry), but I think the concept is perfectly applicable to any medical condition. Unfortunately, I can't find a methodological paper explaining the process of constructing an endophenotype.
Is there a formal statistical/methodological approach to do this? or more than the process of making them, is there an evidence-based process to probe their suitability?
Specifically, I'll be interviewing people in a community where the idea of fluid gender is likely scoffed at by most people. However, I still need to know their self-identified genders, so I have to find a way to ask without also distancing myself from them through the very act of asking. For instance, a participant might not only not believe in gender fluidity but also be insulted that I would even ask because that would imply that I can't tell if they consider themselves to be a woman or a man or something else. For those with experience in this sort of environment, how do you ask the question?
Hello,
In my research, I have a questionnaire that has 5 scales (20 items), I adopted it from previous studies. The five scales are mixed not listed in order. Now, after my qualitative investigation, I would like to add more scales to figure out relationships. My question is, how can I add those scales to the already existing survey I have?
Is there a particular way of distributing the scales? for example, I have a scale about grit 6 items/ 6 items, shall I just add it to the bottom of the previous questionnaire? Shall I distribute the 12 items among the questionnaire items? How can I do this? is there any guide or resource that helps me to know how to incorporate scales into a survey? on what basis?
Thank you
Hello dear colleagues, I would like to open discussion about the bioinformatic methods that can be used in the field of natural products, which methods do you know ? where can they be used ? under which conditions ? and what are their benefits ?
I think this topic will be a good opportunity to share our knowledge and help each other discover new methods. Thank you very much.
I am looking for taxon-specific DNA markers (barcodes?) that would indicate the presence of certain taxa within feces from a non-specific predator. The markers should not be able to amplify the predators DNA.
Hello,
I dissolved glibenclamide both in Ethanol and DMSO but whenever I use this solution in culture medium it seems precipitate. Can you please suggest me the dissoving tricks of glybenclamide and probucol ?
Thanking you,
Jayonta
I would be interested in what you see as the advantages and disadvantages of mixed-methods research in the social sciences. Do you do research with a mixture or combination of e.g. qualitative and quantitative research? Do you combine different quantitative or qualitative methods?
What challenges do you face (e.g., sampling, implementation, scope) and where do you see the limitations of the combination?
Hi everyone. I'm having problems to operate the Burkard Computer Sprayer Apparatus. Does anyone have some experience with this equipament? We are trying to change the operation paterns but the manual does not explain minutely the procedures. Thank you very much.
Although ethnomethodology presents some characteristics close to symbolic interactionism, it would be a misunderstanding to ignore the distinctions that separate both approaches. In this sense, what aspects of ethnomethodology and symbolic interactionism can be compared and what differences can be drawn between them?
Hi
I'm looking for a tool Tool for operationalizing variables into indicators into questions to be used in a questionnaire? This tool could be a directory, search engine etc...
---
Here's the background story
I need a questionnaire for an impact evaluation of a school (the variables include creativity, loyalty, job prospects). The test sample are about 150-300 alumni of the school. The school sample are alumni of other schools .
This is a new task for me so would appreciate some tips/ideas/resources on how to address it. The budget for this task is not high so we're not expecting super accuracy.
In order to create this questionnaire, I can :
1- Find a previous questionnaire for a similar study (impact of a school on values, attitudes, etc.. )
2- Choosing a couple of item questions from a group of questionnaires from already established scales/measures or previous studies (mix and match exercise).
3- Converting each variable into an indicator and each indicator into a question or two, but there has to be a precedent in the literature for this. For example, if I want to operationalize creativity by the strangeness of thoughts I have per day and the question as
: How often do you have strange thoughts per day?, then I need to point to a study that has done the same. (perhaps there's a tool or resources for this)
I appreciate your thoughts.
[ These criticisms may apply more to studies in the behavioral sciences, those being the ones I know about. ]
There is a big tendency for researchers to do research that [supposedly] TRIES to "build on" previous research. AND, there is a belief that such studies will lead to better understanding of (/definition-of) core concepts in a "field". AND, ALSO, other even less related (less concretely or physically interrelated) studies, such as interdisciplinary studies, are believed to lead to better understanding as well.
I believe neither of these is necessarily the case or even likely true (and, to a notable extent, never true, with some research as it is). I believe it is more often NOT true that progress is being made these ways, since the unit of analysis and its aspects are not clear, OR that real (proven) developed relations have not been found. Given the present research ways (many having long, numerous historical/philosophical roots), I believe that more often than good, real desired results (from findings), the results will NOT be interpretable in any reliable or valid way. This an area where some good scientific analytic philosophers could be of good help (thus, the reason for the existence of this discussion question).
My view is that if you do not have well-guided/well-justified and WELL-related studies, specifically, with all phenomenon involved or of present interest RELATING AS MUCH AS POSSIBLE TO DIRECT OBSERVATIONS OF essentially FOR-SURE FOUNDATIONAL OVERT PHENOMENON __AND___/__OR___ a clear case or clear reflection of such actual phenomenon (and, here too, CONCRETE LINKS at some time were shown and INVOLVED), then you are "off-track". Such is needed for science advancement ITSELF (<-- this being key to science and a MAJOR indication OF REAL SCIENCE itself). [ (In Psychology, the subject and aims of studies and findings should be to illuminate KEY Behavior PATTERNS, by clearly relating all of them to directly observable overt behavior patterns that ARE reliably and validly seen (with clear concrete foundations) OR to such "things" THAT WERE (and, ideally: have been) once so clearly and reliably seen during development (i.e. ontogeny)) (yet notice: STILL there is plenty of latitude left for many types of concepts to be involved in proposed explanations, given development and the demonstrated possibilities of the huge capacities of the Memories).) ]
Need a quick organic method to extract testosterone from testes for ELISa.?
ETOH OR MEOH extraction o/n? Evaporate alcohol. Ethy
l ether extraction. Resuspend in buffer???? NO COLUMN Protocols please or LC/MS
I'm doing a protocol that requires acetone precipitation of proteins. The protocol says to leave it in -20 for 'at least an hour'. I tried leaving it for an hour as well as another sample overnight but there doesn't seem to be much difference with the amount of protein pelleted out between the two. Does anyone have experience with this? As in, do you get a better protein yield after an hour or overnight, or is it all the same? Thank you!
I am interested in relationships between photovoice or auto-photography as research methods and social-spatial difference, either as captured in the photographs, or as embodied or lived by the participants. I would particularly appreciate suggestions of literature from the past 10 years.
Recommendations of reading on participant-photography and social-spatial difference would also be relevant in this case.
Hi everyone,
When looking into thematic analysis, you always find a notion of it as a method rather than methodology. Therefore, I was wondering, if TA can ever be considered as methodology? If so, under what conditions, and what philosophical stances does it represent?
If it's always just a method, is there any particular methodology that links with it?
I hope this makes sense. Thank you for your replies.
I need some transparent medium for mounting small insects. I need a medium that a bit dissolves soft tissues and not needs complicated chemical procedure with mounting.
I want to calculate Potential evapo-transpiration with less data requirement so which method can be used for this which will give accurate and appropriate results.
Dear colleagues,
I am looking for software for Systems mapping and Causal loop diagrams. It would be wonderful if any of you with experience in this could share some information.
Have you used any? Any advice or feedback? Pros and cons?
Thanks in advance,
Fabio
I know that Shi et al 2016 inferred hosts for novel RNA virus genomes by searching their genes across cellular genome databases, so linking them with endogenous virus elements (EVEs).
Are you aware of other methods infer hosts for RNA virus contigs?
Thank you,
Guillermo
To obtain serum from fresh blood, it should be drained to a dry collecting tube. We have access to Buffy coats with CPD as the anticoagulant. How can we obtain serum from this?
I am trying to chose a housekeeping gene for samples infected (and control) with different bacteria
I've been asked to give feedback on a study that used a survey with the option for comments in each question. Some participants decided to share additional observations and thoughts for some questions. I've found that these additional comments carry rich qualitative data so I'm suggesting they analyze them and integrate them into the results (since they're currently not).
However, I'm not sure how to justify this methodologically (or even if it's appropriate). Even though these comments add insightful information about the participant's perceptions, they only account for a portion of them.
Options I'm currently considering:
(1) Use a common theme analysis for the qualitative data and relabel the study from quantitative to mixed-methods.
(2) Still define it as quantitative, but mention that some qualitative data was gathered as optional comments and analysed as well (would this be methodologically correct?).
(3) Do not use the qualitative data for the results, since it doesn't come from all participants.
Any thoughts?
Thank you very much in advance!
Hello everyone
I have leaf samples (+/- 50g) collected from different streams for shotgun metagenomic sequencing and I want to know if there is a way of selectively extract fungal DNA from the leaves without having "host" DNA contamination (leaves DNA).
When leaves fall into the streams they are usually colonized by terrestrial fungi and bacteria but they are promptly replaced by aquatic fungi (constituting more than 90% of the total microbial biomass). These fungi are ubiquitous and have morphological and physiological adaptations that dictate their success as colonizers and decomposers of leaf litter. These features allows them to grow within the leaf structure so washing or sonicating the leaves will not anything.
Taking this into account, my goal is to extract fungal DNA from the leaves but with minor contribution of leaves DNA to assure maximum microbial annotation/detection.
Thanks!!!
I just looked up one of my publications on RG and noticed a new section ("Methods"), just after the abstract – and I'm really curious as to why the method suggested is "diagnosis", rather than "qualitive methods", "interviews" or "depth-hermeneutics", which are more relevant to my paper:
It seems there is an automated process behind it from RG perhaps drawing on certain concepts from the abstract ("top methods in this publication") – "diagnosis" in my case. I think we should be able to override/edit this automation, as the current function is misleading, in my view. It would be really usfeul if this new methods function WORKED and we could use it to profile our methods and link to other research based on similar methodologies!
Can anyone share a protocol for a ferrozine assay for tissue samples that is reproducible, including the lysis protocol? Also, what is the minimal amount of iron detectable using this protocol and which method was used to quantify the tissue amount (by protein?)?
I am trying to grow Kasumi-1 cell line. I use RPMI 1640 and 20 % FBS but cells never seem to be growing. They keep on shrinking in size and eventually die off.
I am writing a qualitative project using autoethnography. As all journals have word count constraints, I struggle to fit my methods section (beyond mere descriptiveness) in my manuscript. As it stands, my methods section loses the minutiae of the meaning making process. I've recently learned that Elsevier offers an option to submit a MethodsX file, offering a space for authors to further detail their methods/methodology. I understand that MethodsX is also an open access journal in Elsevier's database, and would like ask the community for some advice about this option.
-KS
I isolated phage against MRSA, and took a micrograph by TEM. My phage is a member of Siphoviridae. I tried centrifuging PEG 6000 (8%) at 10,000rpm for 15min but there wasn't an appropriate pellet for SDS-PAGE. Another time I used PEG 8000 (20%) centrifuged at 12000rpm for 20min. Unfortunately, there was again not enough pellet. How can I enhance my pellet?
I am specifically interested in works of art for which ratings on multiple dimensions are readily available--for instance, ratings of beauty or of liking that were acquired from a sample of volunteers. Features of interest also include the actual features of the artworks themselves, like brightness, complexity, etc. I have been pointed towards several options:
- Prediction of beauty and liking ratings for abstract and representational paintings using subjective and objective measures (https://osf.io/2sy4f/)
- JenAesthetics (https://www.inf-cv.uni-jena.de/jenaesthetics.html)
- The Strohminger Grotesque Art Database (https://ninastrohminger.com/grotesque)
I wondered whether there might be others I am missing? Thanks, in advance, for any help anyone is able to provide!
Being an academic of finance and accounting subjects, I always look for new and contemporary ideas, thoughts, research, methods, models, processes involved with the research in the broad area of finance and accounting. once I found a website containing researches in the last 10 years, but unfortunately I lost it in the bookmarks.
Can we share the sources for getting such resources for learning and enrichment of knowledge in Finance and Accounting?
I am planning a citizen science project where participants will be asked to log the occurrence and magnitude of gastrointestinal events throughout the day. Is there an app that would be well suited for this (for both iOS and Android)? Ideally one that requires only the press of a button to log an event to keep it as simple as possible.
Thank you for any answers
Jonas
Hello!
I'm gonna start to work with HepG2 cells and I would to know what are best culture conditions for these cells. I have been reviewed some articles and people use many types of medium and additives.
Hi everyone,
has anyone used Zeba spin desalting columns?
Can they be reused?
They are quite expensive and it would be great if they can be reused...
Also, manufacturer (Thermo Scientific) hasn't provided information whether they are polypropylene/polyethilene/dextran/sephadex or whatsoever-based columns...
Cheers,
Zeljko
Results from qualitative studies cannot be generalized. Therefore, is it possible to propose a social practice model based on the findings that cannot be generalized? I see some published articles and thesis that present models as a result of qualitative research. I will be glad if you help, thanks in advance :))
hi guyz!
i need your help..
im working now with my thesis..
i need some supplementary articles...unfortunately, i cant access here in our country articles from science direct....if you dont mind, kindly download this article for me...
doi:10.1016/j.phytochem.2004.04.013
thank you!
In your opinion, what is the difference between a good teacher and a great teacher?
and what are the main teaching styles and how they Impact Students?
I have been getting a precipitate the last few times I have tried to use my CHAPS lysis buffer for IP of Hela cells. We have made fresh CHAPS buffer but are still seeing a white precipitate form.
The recipe we are using is:
150mM NaCl
50mM Tris-HCl
1mM EDTA
1% CHAPS
pH to 8.0
Any suggestions on what might be causing this, and how to fix it?
I am looking for help on how to formulate a phrase.
I have excluded patients with entirely missing data, but have included cases with only incomplete documentation. How do I include this in my paper and express that therefore statistics and reported results do not align with the total number of included cases?
And where would you advise I put this information? Under the Methods section? Discuss it under limitations?
Thank you, I appreciate your help!
Best methods suitable for isolation and purification of plant pathogenic fungi and bacteria from plant and soil samples....Latest methods....Any special advantages....Procedure to be followed...etc.
I am organizing some materials for the MSc and PhD students and want to categorize the references in some dimensions so the students can choose by their own.
Please enlighten and attach the reference of past studies.
thanks
I plan on doing cell culture on Thermanox cover slips so that I can take TEM images of my monolayer cultures. I've seen that I can place the cover slips into well plates for culturing purposes, but I don't know how to go from "I have my cells in suspension, ready to be seeded" to "the cells are now seeded on the cover slip".
Do I have to be very precise with where I pipet the cell suspension? Do I just fill up the entire well with the cell suspension? Any insight would be very helpful!
As all of us are familiar with the different journal ranking systems and requirement conditions, in many cases we meet different kind of fees, charges for publishing our researches. Usually only the submitting and the previewing cost US$ 50-250, which is non-refundable and the paper may be rejected by the editors without being sent for review. Others introduce fees for the publishing US$ 500 -1000 (extra fees for colour graphs, maps etc. or for appeals against a Chief Editor's decision). For good English, they offer some links for the grammar review: US$ 100-200. Besides all of this, they employ embargo for 12-36 months, and ask US$ 600-2500 for open access. I think these fees sometimes unreasonable, so it is hard not to find the business factor behind them.
Hi All,
As it says in the title really. From what I can find online, a lot of literature focus on just OM proteins/vesicles rather than whole out membrane preps. So if anyone has some papers they wouldn't mind sharing, or know if there's a specific search phrase I should be using, I'd really appreciate a comment :D
Many Thanks in advance,
Peter
I am conducting a Large N fsQCA, and I need a basic bibliography on this topic. Especially on scope conditions, necessary tests, and its relation to the deterministic ontology of the method. Would someone indicates it for me, please? Thanks!
I have been trying to estimate some biochemical parameters in urinary bladder but homogenization is problem with me as indicated by very low amount of protein in homogenate.
Dear colleagues,
I am working on an intervention study with 3 different groups of students. One group represents the intervention group and consists of a seminar with a practical phase and computer science content. Another group has only a theory seminar with computer science content and the last group has a seminar with other content. The last group is used to check how stable the constructs are. The 3 measurement points are equally spaced as pre-inter-post-tests in a quasi-experimental setting. Latent growth curve modelling doesn´t fit! Is there a method that uses the strength of the 3 measurement time points with a small sample size?
Thank you
Martin
I am going to use this method to load protein hydrolysates into milk phospholipid nanoliposomes. However, I couldn't find a lot of information about this method. I'd appreciate it if someone can provide me some more information on this specific topic.
A few days ago a colleague of mine made me think about the impact the COVID19 crisis will have on cohort studies. Especially those focused on causes of mortality and the elderly will be deeply impacted by the number of deaths due to the pandemic.
Is this something manageable?
How big is this matter in your mind?
How can this be handled?
I need di- and tri-peptides for my intended work. I was going through internet and came across three different methods..1) by Solid state peptide synthesis (SSPS) 2) Liquid Phase Peptide Synthesis and 3) by Bacterial expression....However for first two..we dont have lab facility...so I wanted to know whether Bacterial expression could be carried out for synthesizing small peptides? Which one would be better?
I have a data which consists of an excess of zero counts. The independent variables are number of tree, diameter at breast height and basal area, and the dependent variable (predictors) is number of recruits (with many zero counts).
So, I want to use Zero-inflated negative binomial model and Hurdle negative binomial model to analyze. My problem is I do not know the code of these models in R package.
Do kits such as the NEBNext microbiome DNA enrichment kits really work for the enrichment of (all) viral DNA and how species specific is the host DNA removal (I'm working with bovine blood samples)? Any practical experience?
Hi everyone,
I'm trying to find a home for an instructional manuscript on how to use NVivo to perform qualitative methods (abstract below). I've tried three different journals (Current Psychology, Psychological Methods, Qualitative Health Research) with no luck (they say its good content, but not a good fit). Any suggestions?
-David
Abstract:
From 1995-2016, there has been a 15-fold increase in qualitative scholarship in the social sciences but the rigor and quality of published work has ranged widely. Little scholarship provides concrete, pragmatic explanation of (and direction regarding) execution of systematic, high-rigor qualitative analysis. The present article guides the developing qualitative researcher through technical and procedural aspects of analyzing qualitative data with specific attention to reliability and rigor. Guidance addressing transcription, importing data, forming coding pairs, performing initial/open coding (examples of three types), determining core themes, systematic team-based coding, maintaining a data audit trail, creating a Numeric Content Analysis (NCA) table, and preparing work for publication is provided. Material includes several tables and figures that offer practical demonstrations of how to use Nvivo in data analysis. Transcription tips and outsourcing benefits and cautions are also offered. Altogether, the present article provides qualitative researchers practical guidance for executing multiple stages of qualitative analysis.
I want to quantify the amount of D2O and HDO present in water below 1% level.
1) For now, I only need to know the amount of deuterium present in water.
2) But, it would be better if I can analyze the ratio of D2O, HDO and H2O .
Can you recommend an analysis method? Simple method is better.
Thanks
I worked on antibiofilm activity of some enzymes by crystal violet assay on 96- wells , but what's the best way to destaining CV 95% ethanol or 33% glacial acetic acid and why ?
We know that the amplification efficiency significance in optimization and validation of PCR data. Here I am stuck with above formula how it was derived. Of course, the above formula derivation is not important as most of the PCR are fully automated but I am very much curious to know the mathematical background of PCR. So please can anyone show the path to resolve it?
Hi:
we are working on isolating bacterial strains that produce secreted cholesterol oxidase using a minimum medium with cholesterol as the sole carbon source. I noticed that the cholesterol forms an emulsion and obviously doesn't like to dissolve well. So the bugs might see very little cholesterol in solution. This problem is not mentioned in the paper we follow.
The questions are: a) does that matter? and if so b) What do I do to get cholesterol dissolved? What would be a good detergent to use without killing the bugs?
" Pitfall trapping is the standard method for collecting ground-dwelling arthropods and soil fauna in studies of ecological and agricultural entomology " ( Ruiz-Lupión et al. 2019).
In my current research assistant position I am working on analysis of macro-fauna in forests. We use pitfall traps to assess the abundance of macro-fauna in a given area. I'm curious to learn more about other methods used for this sort of analysis.
- What methods for pitfall trapping have you used, if any?
- What were the advantages/disadvantages and what would you have changed about the method you used.
Our methods are as follows:
- Briefly, we plant a plastic cup in the ground with a cover on top (to make sure mammals or larger animals do not enter the trap but only macrofauna can enter)
- we leave the cup for several weeks
- The macrofauna fall into the cup and are preserved by antifreeze, which are then taken into lab for identification and abundance counts
- By measuring the area of the cup's top, and how many bugs have fell into said area, we can then gain a better understanding of the abundance of macrofauna in the area
In a study reviewing pitfall traps, Ruiz-Lupión et al. (2019) states the factors which should be considered by ecologists using pitfall traps. They state, "the capture rate of arthropods in pitfall traps is proportional to their activity, and the number of individuals that each trap catches may or may not reflect their true abundance, and instead just their activity. Thus, the rate of capture is proportional to the joint effects of abundance and activity, something that has very often been overlooked by ecologists for a long time... [Nonetheless,] activity estimates from pitfall trap catches can still be biased because of multiple factors such as the surrounding habitat structure or the environmental conditions such as temperature and water availability. Additional factors could be the vertical distribution of the soil and leaf litter layers, as well as the attraction or repulsion of preservative fluids, detergents, or baits, the effects of which vary according to the taxon, sex, season, and environment. Specifically, if a trap retains excessive amounts of water, it could act as an attractor for the fauna, especially during drought periods, therefore biasing the estimates of activity. "
References:
Dolores Ruiz-Lupión (2019). New Litter Trap Devices Outperform Pitfall Traps for Studying Arthropod Activity. Insects 2019, 10(5), 147; https://doi.org/10.3390/insects10050147
Hello!
Hope everyone is doing alright during these turbulent and uncertain times.
I am working on my masters dissertation (MSc International Management) and would like to answer the research question of "how adaptable are frugal health care systems in developed markets?" (such as U.S.). I am really stuck as I cannot get hold of any experts to interview and data/literature is limited, as I have found so far. Does anyone have an idea of how I could tackle the methodology or has any tips on where to get data from in this area.
P.S. : Would not mind changing the angle on research question in order to make finding data/literature easier.
Many thanks in advance, feel free to contact me, if you have further questions.
- Juliana
How will 4% w/v SSA interfere with the NADP/NADPH ratio? Can this method of deproteinization be used as an alternative to 10 kDa cut-off spin columns in order to measure NADP/NADPH ratio?
Hi everybody. I am facing an issue about reproduction data analysis in chronic toxicity test with C.dubia. US EPA Method 1002.0 ( https://www.epa.gov/sites/production/files/2015-08/documents/short-term-chronic-freshwater-wet-manual_2002.pdf) instructions tell:
" The response used in the statistical analysis is the number of young produced per adult female, which is determined by taking the total number of young produced until either the time of death of the adult or the end of the experiment, whichever comes first. An animal that dies before producing young, if it has not been identified as a male, would be included in the analysis with zero entered as the number of young produced "
Including dead animals in the count gives me back too high standard deviation values which don't fit well in my analysis. I would like to know if alternatives are available: feel free to link me to other papers, works, methods etc.. which could help. Thanks a lot to anyone will spend time to help me.
Hi!
I graduated with a Neuroscience and Psychology BSc in 2016, and my final year project was a bench-lab in vitro study of omega-3 oils applied to fluorescently-stained cortical neurons. I realised that although I had a passion for neuroscience, my first foray into applied research was not promising; I hated the tedium of the process.
I then did an MSc in Mental Health Sciences, with my thesis originally using an EEG/MEG dataset on psychosis patients. Again, I loathed trying to learn (the tedium of) Matlab and learnt instead that I'm fundamentally not a coder.
I changed to studying the mid-term after-effects of a psychedelic drug using a battery of questionnaires. I loved this psychometric approach, and it was easy enough running simple statistical analyses. However this was firmly psychological, not neuroscience.
Now I'm doing a PhD largely employing thematic and other qualitative analyses of altered states, which I thoroughly enjoy. But again, I'm still attempting to retain some know-how in neuroscientific methods. I'm doing some basic secondary EEG analyses on the aperiodic signal - though not loving even the rudimentary coding necessary.
My question is what are some other neuroscience techniques available out there which I may be more suited to? Can one even be a 'neuroscientist' without having to use a wet-lab - or matlab?
Perhaps tDC or tMS? Could someone maybe elaborate on the types of questions that can be answered with these; or the analyses that are run after them?
Other than f/MRI, which I assume always require programming - do other neuroimaging modes e.g. PET/SPECT also require this?
I'd also be very interested to hear people's thoughts on/experience with working to incorporate as much understanding of neuroscientific findings in strictly psychology studies - While writing psychology papers, referring strongly to the neuro literature to inform and discuss the study's aims and findings?
Thank you very much,
I'd be really appreciative of any insight :)
Pascal
I am doing a plaque assay with HeLa cells and infecting them with poliovirus. I dont get plaques?
Method i use:
1. I take a 80-90% confluent plate of HeLa cells. I do the assay in the 6 well plates from Nunc.
2. Dilute the virus in serum free DMEM-10-2 through 10-11.
3. Wash the plates with 1X serum free DMEM.
4. I infect the cells with virus 300 ul for 30-50 minutes at RT/rocking.
5. Overlay with 5ml(2XRPMI without phenol red) + 2.5 ml 1.5% Agarose +2.5 ml 1.5% Agar.
6. keep in the 37 degrees incubator, 5% CO2 for 48 hours
7. Fix with 10%(v/v)formaldehyde in 1XPBS for 30 minutes.
8. Stain-0.5%(w/v) crystal violet in 10% EtOH for 5 minutes. and wash with water.
We want to do a study that test if the placement of your mobile phone effects your memory. If it being next to you, decreases your memory by disturbing your attention. So the phone will either be next to you on the table, in your pocket/bag or in another room.
Is it necessary to have multiple complex tasks, such as the operation span test and another one or is that one enough?
As we are quite short on time, studying long term memory is not possible.
Thank you for your answers.
I am a first-year PhD student who would like to hear about other researchers' experience related to interdisciplinarity within the humanities, especially those combining both text and visual elements:
- Which are some suitable methods that can be applied?
- Should both areas of studies be represented in a balanced way?
- Any tip that you would have loved to hear before developing your own interdisciplinary project
I am currently developing a project where the primary mode of inquiry is rooted in practice based methods and techniques. The project is focused on a social dance form. I have read several books/articles in which practiced based methodologies are used, however, I am wondering if there are methods/techniques out there that they better satisfy my project. What practice-based methods/techniques may be beneficial for examining social dance styles?
is flconazole really soluble in water...? in which tybe of water? should it warm or normal?can we dissolve it any other solvent like DMSO in place of water,to determine it's MIC.
There are several methods for calculating Mixing Height but requires upper air data. Is there any source for finding mixing height using surface met. data. Kindly help me to find them.
Distinguished colleagues,
I am going to update my methods of delivering lectures at university. Any publication link or comments on this regard will be highly appreciated!
Thank you in advance!
Best regards,
Dr. Vardan Atoyan
Distinguished colleagues,
I need your professional opinion for my ongoing research. Any input, support, publication links or comments will be highly appreciated!
Thank you in advance!
Best regards,
Dr. Vardan Atoyan
What are the methods, techniques, lines of thought, university labs considered vanguards in hydrogeology?
Hi -
Has anyone ever had the issue when they are doing Loss on ignition analysis in a muffler oven at 1000C? Previously I worked with a newer muffler oven and had no issues weighing and baking soils at 1000C. I recently started using an different muffler oven which is a little older, but is properly functioning. I baked my soils and crucibles at 550C and it was fine. I then turned it up to 1000C and baked it at 1000C for 6 hours and turned it down to 105C to take the crucibles out after cooling. However, after I took the crucibles out all of them seemed to be changing colors from neutral ceramic white to green from the bottom up. Also it looks like there are small crystals or precipitate forming on the crucibles, more densely from the bottom up. Attached are a couple of pictures. Does anyone have any experience with this or have any suggestions on how to get to the bottom of this or fix it?
Edit: I just want to note I tried to clean these crucibles with an HCl acid bath, and the greenness did not go away and the precipitate crystals seems to arise once it is fully dry again.
I would appreciate any suggestions for effective methods for teaching geology to a blind student.
What is the suitable method for disposal
Can anyone please help me to find all the biochemical tests for bacteria?
Our lab looks at tumor growth in the bone microenvironment, and in doing so, I section mouse tibia on a fairly regular basis. These tibia have been manually cleaned, fixed in z-fix for a total of 48h (24h at RT, change z-fix, 24h at 4 degrees), then decalcified (10% EDTA, pH 6.5) for a total of 2 weeks at 4 degrees (changed after 1 week). They were then rinsed well with deionized water, put into 70% ethanol, and sent to Histoserv for paraffin embedding and initial sectioning for H&E sections. I then section these blocks for addition staining, and most of the time, everything is okay. However, I come across some blocks where, for some reason, part of the bone will chip out during the sectioning (as the blade goes through the block, you can actually see the chip of bone come out). I have tried to re-paraffin these blocks by softening them, placing the chip back in place, putting a small layer of paraffin on top using a spatula, then re-molding the block. Sometimes this works, sometimes this doesn't. Does anyone have any suggestions for what to do when the bone chips out of the block? Thank you!
I want to use a surface again, that has already been mounted with prolong antifade mountant and am looking for a removal method for this.
Any help is much appreciated
I am currently doing senesecence-related beta-gal staining. The problem is I have to spend a lot of time to count the cells, which was indeed countless.
Does any one have an idea about how many cell counts are considered "enough"? How many different scopes should be taken in consideration of repitition?
Hello,
I have two methods I want to compare, however I have different sample sizes in each method. One has 12 samples and the other 25. The idea is to see if collecting more samples gives better results.
I was thinking a Bland Altman but don't you need the same sample sizes? Do I just do a normal unpaired t-test for this?
Kind regards.
It should be estimating total mineral content as iron. Does anyone have suggestions?
I want to detect 50-bp segment of the recA gene Bordetella avium. Seqence of probe and primers: 5-CATCGCGCTGGGTG-3 NED fluorescent reporter on the 5' end and nonfluorescent black hole quencher at the 3' end. Primer forward CGGTTCGCTGGGCTTGG and rewers CACGCGGCAGCCCGC. Can I change probe dyes to FAM on the 5' end and on BHQ-1 on the 3' end without losing specificity of reaction? I will be thankful for any help
I am having issues transferring my large protein (220kDa) at 30V for 2 hours (RT). It is often patchy with incomplete bands (annoyingly I occasionally I get a clear transfer!). For my other protein at around 40kDa (for b actin) I have no issues.
I have read that for larger proteins people either run overnight at 4 degrees at 20V or for 3 hours at 70V.
Ideally I would like to run in the shortest time possible! One of the reasons why is the power pack i use is pretty old and I don't know how well it would withstand the cold room (rusting)!
But my main worry is losing the smaller proteins if I up the voltage for a prolonged time.
I am using pre-cast tris-glycine 4-20% and the transfer buffer is composed of 10% methanol, and tris-glycine buffer (x2) for a wet transfer.
I was wondering what protocols work for you or if you have any suggestions on what I should try first?
Hi all,
I am currently comparing two groups (control/exp) using SEM. Each latent construct (5 in total) has at least 8 if not 20 individual indicators, as such I am using appropriate parceling techniques in each. The first step requires I conduct a CFA for each construct of interest - to do so, I must have at least four indicators. In the full SEM, as there are 5 latent constructs in total, to improve overall fit, I wanted to reduce the number of parameters to be estimated to be two indicators for reach latent, rather than three. My question is, is it permissible to run a CFA with three indicators for each individual latent, but in the final SEM - only two indicators (using an appropriate parceling technique - rather than just dropping items).
I have the plant extract and want to isolate the flavonoids from that. Which solvent system will be good for that.
I am looking for any insight or proven practice regarding the usage of email for research. Is there a program/website/process to anonymize both a researcher and participants' email addresses but still allow them to communicate?
Craigslist has a feature where the buyer and seller can email each other using auto-generated, anonymous email addresses ([email protected]). These emails go to the buyer/seller's main email accounts, but they strip the messages of any headers/identifying information. In effect, these emails through Craigslist are anonymous.
Is this something we could utilize for research? Could we have participants email a generic email address that would allow both the researcher and participant's real email address to be redacted, yet allow for communication?
Has anyone else tried something similar?
Thank you!
I had a questionnaire with 18 close-ended items about factors of students' failure in English courses.
At the end of the questionnaire I asked respondents an open-ended question:
Why did you fail English in the previous semester(s)?
I made it optional and only 27 out of 56 responded to this question.
Was it correct?
Regards!
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