Preparing our first oral presentation

Last day (4th of April) was a strange day… Only talking, only thinking, only deciding what order of the three important tasks we are conducting: manuscript, poster and finally the oral presentation… . However, after the whole session we found out we did not miss our time.

Thus,

-The structure of the Poster has been decided; photographs.

-Also the main scaffold of the oral presentation.

-And all the figure legends and how the reader must reach to our conclussions of the work in the manuscript.

Yes!!!,  we have a plan; and only the final steps remain to be completed. 

On a Next and decissive appoinment we must conclude we are perfectly prepared to astonish to a general audience about our fantastic project which has transformed us.

Students at the begining; just arrive to the lab (November 2015).

Students current state: experts in a microbiology lab.

On the other hand,  it would be highly recommended that you visit the following video: https://www.youtube.com/watch?v=DE5fid23nlM&feature=youtu.be (min 16:25-22:50)

It is a good example how we can do it!!!. Come on it will be a fantastic ending of our project.

Hip, hip Hurra!!.

Do not forget:

Important dates:

Next session: Thurday 21th April at 16:30. Salon de Actos EEZ.

22th April. Dead line for my own ideas…

Thursday 5th of May. First congress; it will be held on IPBlN-CSIC (http://www.ipb.csic.es/)

Dr Francisco Marti­nez-Abarca
Department of Microbiology
EEZ.CSIC.

Last Results, First Conclusions

Hi Team!!!

Again, last session dealt with our favourite activity: “Counting colonies”, isn’t it??

Of course, we did more things!!!. We get it our last (final) result (sumarizes on  table 1).

Table 1: bacterial colony counting of the last two experiments. Dilutions (-4)-(-6) correspond total colonies on TY Km plates; Dilutions (1) to (-1) correspond total colonies on TY Km, Sac plates.

When we use those data to get the graphic of uv effect on bacterial growth; we decide to not consider the data on 3G bacteria plates. It is probably some error  in the dilution protocol performed with this particular isolate. However, a nice and reproducible uv effect on bacterial culture can be observed in the experiments I and II (3I bacterium isolate). From those data we can obtain our results and conclusions of our project (see Figure 1).

Figure 1: Effect of uv treatment on (A) bacterial growth and (B) mutation frequency of S. meliloti bacteria.

All of us must be able to obtain the numbers of this figures based on table 1; understand their meaning and of course understand which are our conclusions:

1. We demonstrate S meliloti growth is sensitive to uv treatments
2. Uv treatments does not increase the mutation frequency in S. meliloti.
3. We cannot discard a putative effect on the type of mutation generated.

Now we have to:

1. Put the figure legend on all figures of the work: (see in resouces Figures) see examples on previous PIIISA manuscripts.
2. Think in the my own ideas section.

Based on our work: manuscript (proceedings), Poster and Oral presentation must be designed.

Come on!!! we almost touching the end of this great adventure!!!!

Francisco Martínez-Abarca

Departamento de Microbiología y Sistemas Simbióticos.

Estación Experimental del Zaidín. CSIC.

Granada.

An experiment that summarizes all our work!!!

Hi All:

As experts in Microbiology we must understand the whole meaning of our last experimental result (Figures 1 and 2).

Figure 1: Aspect of bacterial plates incubated in the Lab after 5 days at 30ºC.

Figure 2: Aspect of bacterial plates incubated in Paula’s drawer after 7 days at Room Temperature.

Analyzing the images we rapidly can undertand what we can interpret from the data and what we can conclude of our research. This is basic to perform our: Poster, Proceedings/Manuscript and Exposition.

Come on!!!  we are in the way to convince to the audience what we have inferred of our research. But, … First of all: we need to have Numbers for every bacteria (3G and 3I):

-Uv effect on bacterial growth (mean and margins!!!)

-Uv effect on mutation frequency (mean and margins).

Come on who is the first!!! I would like We’ll infer the numbers from the plates photographs. Use the blog!!!

I propose to discuss all this result in an extra session next week (14-18 March 2016).

See your email and wassap!!!

Francisco Martínez-Abarca

Departamento de Microbiología y Sistemas simbióticos.

Estación Experimental del Zaidín. CSIC.

Granada

 

We have a title for our work!!

Hi All:

The end of our research is really close. Last session we decided which is the title that explain the work performed. It was at the end of the morning. But it was a very important moment:

“Effect of ultra-violet light on the mutation frequency of a soil bacteria”.

All of us understood, what we already made. Try to determine if our “favourite” bacteria – Sinorhizobium meliloti- can serve as a test for evaluate the DNA damage caused by ultraviolet light exposure.

Now, we are close to the end, but… we need to put an extra effort to get it.

Fig 1.  Carmen and Cristina mixing bacterial culture previously to the uv treatments

In resources (see here), we have the current state of our “manuscript”.  We need to fill all the parts of our comunication (Highlights, Summary, Introduction, mat and methods, Results, Conclussions. It is extremely helpful to visit what students made last year (see here). 

Special focus should be made in the part of MY OWN IDEAS. This is a summary of the meaning of this project for everyone. 

You must think on it.

Come on, we are deal with the finishing of a Fantastic Project

Hip, hip Hurra!!!!

Francisco Martínez-Abarca
Departamento de Microbiología y Sistemas Simbióticos.
Estación Experimental del Zaidín. CSIC.
Granada

Reading into strange results

Last entry finished with:

“…We repeated the experiements over a new culture of 3G S. meliloti strain (I remind you the previous was 3I). In which every treatment (0, 15 and 30 seconds of uv) was made twice. Now, Plates are in Paula’s home (and also in the Lab).

Hopefully, these new results allow to determine uv effect more accurately. …”

The experiment performed was plates 1 and 4 no uv treatment; plates 2 and 5, 15’’ uv treatment; and plates 3 and 6, 30’’ uv treatment.

However,  last results did not show the expected numbers (Fig. 1). 

Fig 1: Aspect of all plates incubated at Paula’s home after 6 days at room temperature.  Numbers and dilutions performed are indicated in the last blog entry. 

Analyzing the plates we found that uv treatment was properly made on both groups of plates (those growing on Paula’s home and also the lab one). However, the plates to count the mutants present in every culture give an unexpected  high numbers,  even in the most diluted plates (see figure).

What is the explanation of this strange result? 

Have we got a different mut frequency in this experiment?

If we analyze the differences in the protocol with the previous experiment performed, we can inffer where it could be the problem. Also we can see in the previous blog (¿Dónde mutan los genes?) some clues about what could occur in this last experiments (particularly in the post Consecuencias del brain storming).

I would like we could discuss here in the blog what is happening; how we can avoid it and try to repeat properly the experiment (Next session 2nd of March).

I encourage you to give an answer. Who is the first?? (specially those who came on last experimental session).

Francisco Martínez-Abarca

Estación Experimental del Zaidín. CSIC.

Departamento de Microbiología y Sistemas Simbióticos.

Granada

When the mess is less mess

Last session confirm we are too much closer to the end of our Project. Again, we find out our Project deals with counting bacteria, don’t we?. But examining your faces yesterday  we also realized the meaning to count bacterial colonies in a plate: 

to know the number of bacteria present in a particular tube or treatment. 

All serial dilutions performed aim to obtain that number as accurate as posible. In this regard and analyzing the data obtained in the last experiment Paula’s home we could observe an interesting “tendency” in the data. Remind last experiment (see Figure 1).

Figure 1: This figure summarizes what we did in the previous sesión (18th Jan) and yesterday (16th Feb). A S. meliloti culture was distribuited to three plates and stress under uv treatments (0, 15’’ and 30’’). All further steps where designed in order to get the number of bacteria and mutants present in the different treatments.

As we could observed; some of the plates were a real mess (Lab plates see previos entry in the blog). However, after a detail analysis of Paula’s home bacteria plates we could obtain some numbers (see table 1):

Table 1: Colony counts of the respective dilutions and treatments performed

These numbers reflect an interesting result. If we interpret properly what they mean we can observe a clear effect on bacterial growth by uv treatment (Table 2)

 Table 2: Effect of uv treatment on bacterial counts

And also an astonishing “tendency” of the putative frequency of mutants on the plate’s uv treatments (Table 3)

Table 3: Effect of uv treatment on mutation frequency

All of us (teachers, coordinators, friends,  … included) must know how these data appear (all calculations performed). And, most important, we must be aware about the meaning and importance of this last result.

As expected in Science. Experiments must be reproducible. 

What we are waiting for next session?

We repeated the experiements over a new culture of 3G S. meliloti strain (I remind you the previous was 3I). In which every treatment 0, 15 and 30 seconds of uv) was made twice. Now, Plates are in Paula’s home (and also in the Lab).

Hopefully, these new results allow to determine uv effect more accurately.

Come on as I mention previosly the end of the Project is much closer.

And finally only mention that the PIIISA commission (in Granada) did not allowed to hold our next session of 2nd March in the PARQUE DE LAS CIENCIAS in Granada.

We’ll see in the EEZ next session.

Francisco Martínez-Abarca
Estación Experimental del Zaidín. CSIC.
Granada