Can a 16S-23S ML tree discriminate microorganisms at species level?

20 July 2018 0 4K Report

Maybe this is a well known topic, but I'm a new bie.

By far 16S alone is reported as being insufficent for species level discrimination. I was wandering how much 16S-23S tree topology is accurate, related to MLSA made on 6 whole-gene housekeeping sequences concatenated. Can it be reliable to distinguish same genus candidates?

thank you

Badges
Science topic

More Simone Becarelli's questions See All

Isolates of Hymenoscyphus fraxineus?

Dear Dr. Cai, my name is Simone Prospero and I work in the team of Phytopathology at the Swiss Federal Institute for Forest Snow and Landscape Research (WSL;...

01 March 2021 1,133 1 View

How is mathematical giftedness supported in different countries?

I hope for a global overview on mathematical giftedness and its support in school and/or on an extracurricular level. What programmes/opportunities are offered?

08 July 2020 7,124 4 View

GROMACS - how to solve problem coming out during a creation of new Force Field?

Following Gromacs Manual and other suggestions from different topics I create a molecule with Avogadro, I decided to employ oplsaa ff (I copied it in a local directory giving a new name) and I...

25 March 2020 4,438 3 View

How to create a fictitious atom in shelx?

Dear all, I am dealing with some crystal structure in which it is possible to replace Br- anions with Cl- anions. I am trying the refinement by setting the occupancy factor according to the molar...

24 February 2020 4,122 2 View

Trying to run RT-PCR for PDCD4 gene in human serum, can't get any values. Checked primers and they seem okay, any suggestions?

We are having difficulty detecting PDCD4 in serum. We have ordered an ELISA to attempt this, but have not tried it yet. Afraid something is wrong with serum.

08 January 2018 4,637 3 View

How to check for primer dimers?

I am having problems with high efficiency of my primers and one reason could be the formation of primer dimers. I dont see any big peak on the melt curve, but I dont know if this increased peak is...

19 September 2017 7,270 4 View

Checking RNA integrity for qPCR with electrophoresis but it does not show 28S/18S ~ 2. Should I extract again?

I have run RNA samples in 1% agarose gel but I cannot visually see a ratio 28S/18S ~ 2. What I might be doing wrong? Also, the samples marked with numbers, should I still consider them for qPCR?

12 September 2017 6,958 6 View

How can extract eva-copolymer from a wax blend?

Hello everybody,I must extract Ethylene Vinyl Acetate (EVA) copolymer from a mixture consisting of: EVA / Liquid Paraffin / Microcrystalline Wax. Can anybody give me some advice? Thank you

26 April 2017 8,351 3 View

Is there any phenotype database for Streptomyces?

I'm identifying my Streptomyces isolates at the specie level. I already performed all the phenotype / chemotaxonomic tests, and constructed a phylogenetic tree. However, I didn't find the...

16 April 2017 1,713 3 View

Griess Reagent usage in fibroblast cell culture?

Hello, I am trying to measure NO in cell culture (fibroblast cells). Using Griess reagent I try to follow the paper from Wang et al., 1996 which gives a basic protocol that does not differ from...

07 October 2016 8,597 1 View

How does the gut microbiome affect the fibrotic process within the liver?

and Can the gut microbe be used for the treatment or diagnosis of liver fibrosis?

02 March 2021 557 2 View

How do you mesh a thin solid in Fluent?

Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...

24 February 2021 8,856 3 View

How to indicate the degree of litter decomposed by microbes?

Any technique could detect the degree of litter decomposed by microbes? Or any indexes could do this job? I want to split the contribution of microbes during decomposition, so any suggestions...

23 February 2021 1,362 5 View

Can I get information about research laboratories that are currently having in culture, internationally/locally standardised microorganisms?

Microorganisms of interest include; E.coli; Salmonella typhimurium; Pseudomonas aeroginosa; Streptoccocus pneumoniae; Staphyloccocus aureus and Candida albicans. Locations closer to Port...

18 February 2021 6,500 3 View

Can I consider the OOB score of RF model as the same as R^2 score?

In a topology optimization machine learning prediction algorithm, can I consider the OOB score of RF as the same as R^2 score. Could that be a more unbiased way of validating the model

14 February 2021 3,540 1 View

How do you calculate a discrimination index for polytomous data?

Hello, I'm currently running a PCA on a polytomous data set (5 point Likert). I want to create a discrimination index to narrow down my items before running the PCA. After looking around, I'm...

13 February 2021 3,517 2 View

Charmm/GROMACS Residue 'ZN' not found in residue topology database?

I am trying to do some MD simulations of a protein with zinc ions. I am trying to use a charmm forcefield (I have tried 2017 and 2021) and Gromacs. I get an error when doing pdb2gmx Residue 'ZN'...

12 February 2021 9,367 2 View

CDNA synthesis or qPCR did not work?

Hi everyone! I extracted RNA from urine pellet using phenol-chloroform method. The yield of RNA was 160ng/uL. 3uL of RNA was used for cDNA synthesis in 20 uL reaction using Go-Script kit....

05 February 2021 6,587 4 View

Do anyone have a full MATLAB code for structural topology optimization using Genetic Algorithm? Such as a cantilever beam?

Do anyone have a full MATLAB code for structural topology optimization using Genetic Algorithm? Such as a cantilever beam? Could you provide some MATLAB code to me , a beginner for GA. Thank...

03 February 2021 3,789 5 View

How do microbes tell the presence of an inorganic minaral in the soil?

Due to their ubiquitous nature, there is a tendency of the presence of microbes in a given mineral(s). For instance, if microorganisms that love the of pH less than 6 in the pH value, is isolated...

03 February 2021 4,630 10 View