The control of death and lysis in staphylococcal biofilms: a coordination of physiological signals by Sadykov and Bayles 2012

This paper reviews the involvement of  bacterial cell death and lysis in staphylococcus biofilm development.

Previously it was found that  mutations on either cidABC or lrgAB  operons, known to be involved in cells death and lysis, results in impaired biofilm formation.

It is thought that these 2 operons encode proteins analogous to the bacteriophage-encoded holins and antiholins.

Holins (encoded by cidABC) would be responsible for bacteria cell lysis, and anti-holins (encoded by lrgAB), as the name indicates, for the inhibition of the produced holins creating, therefore, a balance between life and death.

Given the nature of the signals known to induce expression of the Cid/Lrg system, they propose that the expression of these operons are dependent on a variety of environmental conditions that exist within a biofilm, and that the metabolic variability observed within biofilms may determines the differential expression these operons through, for example, membrane potential and oxygen levels, which in turn, dictates which cells die and lyse.

This is an interesting review that explores a yet poorly understood issue of biofilm maturation and te mechanisms underlying such complex regulation.

Reference of the article summarized above:

Sadykov MR, Bayles KW (2012) “The control of death and lysis in staphylococcal biofilms: a coordination of physiological signals”. Curr Opin Microbiol.15(2): 211-215.

RM:  AF 1313


Review of the use of statistics in Infection and Immunity by Cara H. Olsen 2003

I know that you may think that this paper is a bit off from the primary aim of this blog. However, statistics is everywhere and it is very important since our interpretation and conclusions of our data is dependent on the statistic applied.

Therefore, I have decided to share this very easy to follow paper that reviews the major errors in statistic observed in the papers published in the high standard quality Infection and Immunity journal. Since we can learn from errors, here is a brief summary of the most common errors:

1) Fail in the adjustments of the P values when doing multiple analysis.  Since the majority of the analysis performed among different groups are done independently and then taken together there is an increased probability of false significance. Therefore, an appropriated statistical test has to applied in order to compare all the groups and additionally the statistic test applied should  correct for p-values errors.

2) Several conclusions are based only in the interpretation of the dispersion of the data (such as SD or SEM). Standard deviation bars contain no information regarding the precision of the mean. In a matter of fact, it can occur considerable overlap of confidence intervals even when exist statistically significant differences between groups.

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Wake up! Peptidoglican lysis and bacterial non-growth states by Keep et al., 2006

This is an interesting review paper that discuss the mechanisms behind the activation of bacteria from protective states such as dormancy and the more controversial viable- but-not-nonculturable (VNC) state.

This protective or non-dividing states adopted by bacteria under stress are very important in clinical setting since they seem to be responsible for the development of recalcitrant infections that leads to an increased patient’s morbidity and  mortality.

Briefly, in 1998 Mukamolova et al. have introduced the concept of bacterial cytokine, characterizing the 17-kDa protein termed resuscitation-promoting factor (RPF) produced by Micrococcus luteus . Latter, it was found that this protein presented a sequence homology, despite weak, to lysosymes and lytic transglycosylase and, additionally, it was shown that  peptidoglycan is used by this protein as a substract activating, this way, cells division and the inactivation of the non-growth state.

However, much more studies have to be done to understand all the mechanisms that lead to the emergence from protective to active states of growth.

Reference of the paper summarized above:

Keep NH, Ward JM, Cohen-Gonsaud M and Henderson B. (2006)” Wake up! Peptidoglican lysis and bacterial non-growth states”. TRENDS in Microbiology 14(6): 271-276.

The biological role of death and lysis in biofilm development by Bayles 2007

This review present an interesting correlation between the programmed bacterial cell death (PCD) and the programmed eukaryotic cell death, called apoptosis. Despite the reference to several microorganisms, this paper is focused on PCD of Staphylococcus aureus and its consequence in biofilm development.

In S. aureus, the mechanisms that controls the cell death and lysis has been linked to the Cid and Lrg operons, which have an important role in the control of the murein hydrolase activity. Interestingly, the products of these genes are analogous to the bacteriophages-encoded holins and antiholins that are involved in the control of bacteriophage-mediated cell death and lysis. The role of  bacterial cell lysis in antibiotic resistance is also discussed.

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Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal by Mcdougald et al., 2011

The biofilm life cycle comprises three main phases: 1) initial adhesion, 2) maturation/accumulation and 3) dispersal. The last phase, biofilm dispersal, is believed to be of crucial importance for biofilm maintenance and also for infection dissemination. Indeed, S. epidermidis catheter biofilm-related infections have been frequently associated with infection dissemination such as severe cases of sepsis.

Unfortunately, the mechanisms that are involved in the biofilm dispersal are far to be completely understood. In this review, several concepts and proposed mechanisms for biofilm dispersal are summarized.

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Current concepts in biofilm formation of Staphylococcus epidermidis by Fey and Olson, 2010

As any other review, this paper present a compilation of the most important and recent discoveries regarding Staphylococcus epidermidis biofilm formation and dispersal.

The molecules known so far to be involved in the mechanisms used by S. epidermidis to form biofilms are herein reviewed, giving more focus to PNAG and PGA and proteins such as Aap, Bhp and Embp. It also correlates some of the mechanisms that are involved in both commensal and pathogenic lifestyle of the bacterium summarizing some of the newest hypothesis that explain this switching from commensal to pathogenic mode of life.

There’s also an executive summary at the end that is very useful, stressing out the utmost information to retain. Also, authors have highlighted the papers with more impact in this issue.

Is very good for starters and also for updates!! Very easy to follow.

Read it!

Complete reference of the summarized article above:

Fey PD and Olson ME. (2010) “Current concepts in biofilm formation of Staphylococcus epidermidis.” Future Microbiol, 5(6): 917-933.

Internal code: RM AF 1108

RNA-Sequencing: advances, challenges and opportunities by Ozsolak and Milos 2011

The molecular biology field has a wide range of tools available, and now, in the perspective of transcriptomics analysis, there’s a new exciting method called  RNA sequencing (RNA-seq).

In this paper the authors review, as the title indicates, the advances, challenges and opportunities of this new technique. Also, they explore the different RNA-seq approaches such as next generation sequencing methods that can be applied, the advantages or limitations of direct or indirect RNA sequencing and finally, important concepts and diagrams that help us to understand the principle behind the method.

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