37 Questions 46 Answers 0 Followers
Questions related from Muhammad Arslan
Hey All, I am trying to find the NCBI nonredundant database for the autotrophic bacteria for microbial autotrophy study. I found this paper, in which the database is mentioned but there is no...
06 March 2023 7,185 0 View
Just wondering if someone has done it? We usually use environmental DNA (eDNA) for library preparation and I am wondering if eDNA concentration is very low, can we initially amplify the 16S region...
19 April 2021 2,869 1 View
We have columns containing lake water and oilsands tailings (2:1). We periodically use nitrogen gas (once a week) to make the water environment anoxic (DO
25 March 2021 7,396 3 View
Hi all, Can anyone please comment if there are some labs which provides DNA-SIP services commercially? I am super interested in this study but we don't have access to specific rotor type (vTI...
11 September 2020 493 0 View
Hi all, This question is more about the basic theory of doing BOD and then applying the concept to a type of waswater that contains extremely reclacitrant compounds which cannot be degraded in 100...
12 July 2020 4,572 3 View
I want to check the chemical oxygen demand of a sample in which inoculum was added previously. I am wondering if the presence of bacteria would cause any issue with COD? I assume that bacterial...
16 January 2020 4,272 3 View
I am trying to search some literature on genes involved in degradation of classical naphthenic acids (NA). I have previously worked with CYP and ALK gene family but they are mostly studied for...
06 September 2019 6,944 2 View
Hi all, I preserved my water samples (obtained from plant rhizosphere) at 4 °C two years ago that were contaminated with sulfamethoxazole and trimethoprim. I am wondering if I can still use them...
17 May 2019 8,611 1 View
Hi all, I am a little bit confused with the statement that fisher alpha should not be mixed with alpha diversity, i.e. Fisher alpha is index. Does it mean that we cannot used Fisher alpha to...
30 January 2019 6,123 0 View
Hi all, I am checking plant endophytic bacteria and i have came accross this finding that there are only sulfur oxidizers and not reducers inside plant. We assume that there is no flux of sulfur...
14 October 2018 9,330 3 View
Hi all, I am wondering if you can comment on statistical interpretation of dysbiotic microbiome. For example, we treated a system with antimicrobials and now community is changed. Initial...
09 October 2018 2,693 2 View
Hi all, I am wondering if there is any tool available to do this job? Or similar plotting. What i want to do actually is to show that the community has been changed. Before exposure and after...
02 August 2018 509 4 View
Hi all, As we all know that 16S amplicon seq data by Illumina sequencing is semi-quantitative and therefore I want to normalize my data output with the qPCR 16S data. Can you please recommend me...
27 July 2018 1,996 3 View
Hi all, I am wondering if anyeone of you can help me to quantify/assess the dysbiosis using some kind of ranking or by a scale! or quantitative interpretation. Yes, we can argue that change in...
02 July 2018 2,611 1 View
Hi all, I am trying to calculate organic loading rate for the vertical flow constructed wetland. I have COD of 493 mg/L with the flow rate 0.5 m3/d. Multiplication gives me 246.5 kg COD/m3/d. But...
27 June 2018 5,835 3 View
Hi all, Consider a reaction that proceeds autocatalytically with the kinetics v=k*a*b. At which concentrations of A reaction will be fastest? Also what will be the concentration of B? Assumption...
22 April 2018 10,007 8 View
Dear all,I am writing this message to ask if you can comment on layering multiple images in 3d-space (cf attachment). I have confocal images and wants to do better presentation. Your comment would...
06 June 2017 4,488 3 View
Hi all, I want to do rarefaction analysis for the plant "Juncus effusus" transcriptome assembly. At the moment I have Fasta file with final assembly. I wonder how can I use this dataset? Is there...
30 May 2017 1,510 2 View
Hi all, I am wondering if there is any smart way of doing function prediction for specific bacteria genera (say curvibacter) by using JGI/IMG database (or WGS)? Looking forward for suggestions!
08 April 2017 1,496 2 View
Hi all, I am looking for strain who is closest strictly aerobic to my anaerobic strain (Anoxybacillus flavithermus)? Can you suggest me most precise method using database search etc. and not...
23 March 2017 6,673 1 View
Hi all, I am trying to plot rank abundance curve for my 16S rDNA data in which I have different treatments. When I do so, I get one curve only describing about the presence of each species....
16 March 2017 4,992 5 View
Dear all, I am writing this message to seek your help regarding the conversion of excel file to .biom file. I must tell you that I am not a bioinformatic person and so an absolute beginner. I just...
26 February 2017 6,187 0 View
Hi all, Can you suggest me a method to create a heat map based on actual data and not the relative percentages? I need it because I have different treatments with increasing the overall...
17 February 2017 1,104 3 View
Hi all, I need expert opinions on this matter as my plant samples are detached during washing step of FISH. I used agarose as well as transparent nail polish for this purpose and to me agarose...
11 August 2016 6,073 19 View
Hi All, I want to ask if we are trying to amplify plant endophytes (specifically firmicutes) from the bulk DNA (extracted by MPbio kit), how can we check the binding of primers with chloroplast...
01 July 2016 861 3 View
Dear all, I am wondering if there is anyway to develop a positive control for ROS generation study in plants. In principle, I have higher signal in stressed plants compared to non-stressed but...
01 June 2016 3,672 4 View
If we want to determine the copy number (by qPCR) of all microorganisms within plant tissues, how can we avoid the chloroplast and mitochondrial DNA! Thanks
13 May 2016 2,772 2 View
Hi All, I would like to hear your comments on colonization of plant endophytes and plant pathogens within plant tissue (Juncus effuses). Where we can expect they have higher chances to be found? I...
27 April 2016 8,509 3 View
Briefly, I am looking to test if there is some pathogenicity caused by (endophytic) bacteria residing within plant tissues. What methods one can adopt to test it in situ? Moreover, please comment...
12 April 2016 9,467 1 View
Hi All, I want to perform meta-analysis for comparison between control and experiment group but most of the times i find only percentages data and not actual data-set! Do you think that it would...
19 March 2016 2,720 6 View
Hi everyone, I would be glad to hear your comments on labeling of certain antibiotics (ampicillin, amoxicillin, erythromycin etc) with 13C so that I can determine their fate in soil to plants and...
20 October 2015 2,354 3 View
Hello everyone! I want to generate a phylogenetic tree of my 16S rRNA sequence but NCBI shows similarity with compelete genome. When click on accession number it goes to complete genome page. Can...
12 October 2015 1,250 6 View
Hello everyone, We have a novel strain whose 16S rRNA has been already submitted to NCBI. Now, we want to publish this information in some journal. Can anyone help me in this regard. I have...
13 September 2015 3,523 4 View
We have sequenced a strain of Anoxybacillys flavithermus AK1. Now, i want to prepare circular map of whole genome using DNA Plotter. The software can load only one fasta file which is why I need...
15 May 2015 3,420 14 View
We have sequenced a strain of Anoxybacillys flavithermus AK1. Now, i want to prepare circular map for our paper. While searching, i found software DNA plotter which is really good. However, it has...
14 May 2015 8,256 21 View
Actually, I want to find the the16S rRNA for "Anoxybacillus flavithermus strain TNO-09.006". Its whole genome sequence is present in the database but i want 16S rRNA sequence to do phylogeny along...
11 March 2015 3,672 9 View
I would appreciate a detailed answer as I really need it urgently. Actually, I want to quantify Total Petroleum Hydrocarbon (TPH) from the foreshore sand (different stations with different source...
21 December 2014 1,369 5 View
