NCBI PubMed Filter

Researchers often search research papers based on their interest and currently they study. Among many research databases PubMed of NCBI is one of the important priority. PubMed stores access of many journal abstracts and direct links to the journal. I recently uploaded a small video under We The Microbiologist, India ‘s Bio-Blog about how to use filters to search your relevant papers.

It is important for researchers to search for particular author, particular organism, some specific title, year, journal and more based on their choices. I hope the above video will help many researchers as well as students.

Happy Learning.

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“I will forever persist” – the unsaid words of Persister cells

Persister cells are antibiotic tolerant cells which can be identified in almost all phases of bacterial cellular growth with antibiotic tolerance. It holds many unfold mysteries of in biofilm resistance. They are not mutants, rather phenotypic wild type variants and the reduced metabolic rate makes them distinguishable. The extensive research behind the mechanism has identified many persister genes and the reason behind the non-dividing state of these cells. The article here discuss over why persister cells persist any invasion on them.

Before we look into some researches it is better to provide a brief introduction about how persister cells develop. There are two types of persister cells based on the intracellular and environmental stress.


Type1 and Type2 persister cells (Credit:Microbe Wiki)

Type 1: These cells develop persistence in stationary phase when nutrients are low enough for numerous cell growths. Bacteria are known to sense these stressful conditions and allow them to push some of their population to be dormant, while rest thrive and risk death. These dormant cells are antibiotic tolerant and starve to live without enough nutrition.

Type 2: These cells believed to be evolved from prolonged antibiotic stress and often some stress imposed by prophages. These cells are not triggered by environment and are slow growing.

Why can’t we stop persister cells?

Dr. Kim Lewis from North-Eastern University unleashes a gene which fakes the action of antibiotics to prevent the growth of biofilm. In year 2004, the research published in Journal of Bacteriology explained about HipA gene which generates a toxin named RelE that allows the persister cells to hibernate. As antibiotics must work on metabolically active growing cells hence outlasting the antibiotic activity then repopulates the infection.

A question does arise about how these persister cells maintain their persistence. The answer was revealed in late 2015, a research published in PNAS about a toxin called HigB that able to recognize and rips up RNA to allow growth inhibition function. Although it does not degrade all RNAs equally under stress, it is exquisitely selective. X-ray crystallography studies reveal the exact mechanism how HigB recognizes mRNA and then interacts with ribosomes. The protein was investigated in the bacterium Proteus vulgaris a potent contender of urinary tract infection.

Efforts were done to further understand and visualize the persister mechanism of cells. A year before, i.e. in 2014 researchers from Imperial College of London publishes a research in journal Science , where they describe the mechanism of forming persisters inside macrophages. They fluorescently labelled protein which is produced inside bacterium Salmonella and found that some group of bacteria form persister cells by rendering their growth while remaining follows normal growth. The phenomenon was observed after macrophages engulfed the bacterium. Thus helping bacterium to survive the antibiotics treated.

Door for success behind impossibility

Researchers were almost confused and tried to open doors of possibility to defeat the hidden troops of bacteria called persisters. It was not impossible but to find out a way was difficult. Yet there are some researches which unwrapped the possibilities.

Researchers from Scripps Research Institute, Howard Huges Medical Institute and Albert Einstein College of Medicine of Yeshiva University came up with promising anti-tuberculosis compound which is able to attack both active and dormant Tuberculosis bacterium. After screening diverse library of compounds they found TCA1 capable to kill 99.9% of the activated replicating TB bacterium. But with combination with Isoniazid or Rifampin is 100% effective in any TB bacterium. Positive shade of the experiment was received after thorough experiment over mice and no adverse side effects were found. The research was published in 2013 in PNAS.

In 2015, Northeastern University researchers described a method called pulse dosing. Their findings were published in the journal Nature where they identify toxin-antitoxin gene pairs which maintain the persister cells. These gene pairs encode proteins called HipA (for toxin) and HipB (for antitoxin) where they can regulate each other to module the functioning of the persister mechanism. It is also found that mutation in gene of HipA allow more persisters to form. Researchers came forward with a mechanism called pulse dosing, where antibiotics are provided at intervals. Post antibiotic treatment initially makes the cells to form persister but as they rise up again another antibiotic treatment is followed.


There are lot of strategies which have followed by researchers but still there are certain gaps behind understanding the mechanism of persister cells that remain vague. Bacteria always follow a cell to cell communication which allows them to collect nutrients and also response to danger. The collective evolution of genetic makeup that bacteria posses with environmental stress made them to modify. We can say the result of one such type of modification is persister cells. They do not posses antibiotic resistance gene yet they are resistant to antibiotic treatment. They do not grow yet they are alive. Persister cells research is now a rising calamity among microbiologists to identify cure against this evil. Yet it is magical to understand that these tiny creatures developed themselves strategies to escape their eradication.

Further Reading

  1. Northeastern University. “New Study Discovers Why ‘Persister’ Cells Never Say Die.” ScienceDaily. ScienceDaily, 15 December 2004.
  2. Marc A. Schureck, Jack A. Dunkle, Tatsuya Maehigashi, Stacey J. Miles, Christine M. Dunham.Defining the mRNA recognition signature of a bacterial toxin protein. PNAS, 2015.
  3. Helaine, A. M. Cheverton, K. G. Watson, L. M. Faure, S. A. Matthews, D. W. Holden.Internalization of Salmonella by Macrophages Induces Formation of Nonreplicating PersistersScience, 2014; 343 (6167): 204
  4. Feng Wang, Dhinakaran Sambandan, Rajkumar Halder, Jianing Wang, Sarah M. Batt, Brian Weinrick, Insha Ahmad, Pengyu Yang, Yong Zhang, John Kim, Morad Hassani, Stanislav Huszar, Claudia Trefzer, Zhenkun Ma, Takushi Kaneko, Khisi E. Mdluli, Scott Franzblau, Arnab K. Chatterjee, Kai Johnson, Katarina Mikusova, Gurdyal S. Besra, Klaus Fütterer, William R. Jacobs, Jr., and Peter G. Schultz.Identification of a small molecule with activity against drug-resistant and persistent tuberculosisPNAS, 2013
  5. Maria A. Schumacher, Pooja Balani, Jungki Min, Naga Babu Chinnam, Sonja Hansen, Marin Vulić, Kim Lewis, Richard G. Brennan.HipBA–promoter structures reveal the basis of heritable multidrug tolerance. Nature, 2015.


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Resistance of bacteria from stomach acid with the power of Intimin

Most of the bacteria usually communicate our body’s inner mechanism by mouth and nose, which are regarded as the most common entry. Many people get diarrhoea when some of these bacteria which have entered become opportunistic. One of the most common is E. coli. These bacteria can able to attach themselves on the walls of the intestines and inject toxins which allow us to fall sick. But one thing which might be missing in between is that, these bacteria which follow their entry into digestive system should get killed by strong acid present in stomach, which we know as a strong barrier of infection.

A research group from “The Bacterial Cell Envelope” research centre at University of Tübingen with Tübingen University Hospitals, investigated the phenomenon how gut bacteria survives the strong acid of stomach to enter into intestines. The results were published in the journal Molecular Microbiology.

Commonly, E. coli and Yersinia are found in small intestines and absorb nutrients. A protein named as intimin (named after intimate adherence) which allows the bacterium to adhere to the intestinal walls. It also form tiny channels between the bacterial wall and the intestinal cells to allow the toxins (causing diarrhoea) to move into intestines.

Intimins are autotransporters and are important virulence factors of both E. coli and Yersinia spp. These proteins have lysin motif which allows the binding with the peptidoglycan. This binding is possible only in acidic conditions, which clearly displays the reason how these bacteria uses the stomach acid for getting resistance. The intimin gets inserted then into the bacterial envelope thus stabilizing the structure of peptidoglycan.

Scientists conclude that intimin supports infection process in intestine, using the stomach acid boosting the bacterial virulence.

Research Source:

Jack C. Leo, Philipp Oberhettinger, Manish Chaubey, Monika Schütz, Daniel Kühner, Ute Bertsche, Heinz Schwarz, Friedrich Götz, Ingo B. Autenrieth, Murray Coles, Dirk Linke: “The Intimin periplasmic domain mediates dimerisation and binding to peptidoglycan.” Molecular Microbiology, DOI:10.1111/mmi.12840

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16S rRNA and the Strategy Used in Bacterial Identification

The topic I made here is not as new and is well known among Microbiologists, although specifically including the conserved sequence present in 16S rRNA as the major part of this topic. 16S rRNA the component of smaller subunit of prokaryotic ribosome, used highly in phylogenies after the major introduction made by Dr. Carl Woese and George E. Fox. Ribosome, a major protein complex which helps in the protein synthesis (translation) consists of two units, larger (50S) and the smaller subunit (30S), together making complete 70S [S stands for the Svedberg Unit, a non-SI unit for sedimentation rate]. In this smaller subunit, there is the presence of 16S rRNA which has the signature sequence for the bacterial identification.

Multiple sequences are present in 16S rRNA of a single bacterium. Signature sequences are specific conserved sequences that are always found in all groups of organisms. The sequences which we name it as unique are present in specifically 16S rRNA region, of 5-10bases long. This helps in the major identification of prokaryotic organisms, archea and eukarya. The average length of the 16S rRNA gene is 1522bp. Previously culturing and the biochemical tests used to be used in the bacterial property identification has been set back after the use of the recent diagnostic techniques. Nucleic acid detection method has overcome the limitations in conventional microbiological methods. [1] Recently NGS-based 16S rRNA sequencing has been cost effective technique for the bacterial identification.

Strategies used using 16S rRNA for Bacterial Identification:

  1. Ribosomes containing 16S rRNA are present in all cells.
  2. RNA genes are highly conserved.
  3. Nucleic Acid detection method is the first and efficient technique.

Universal Primers used for 16S rRNA sequencing[2]:

Primer Name 5’ to 3’ Sequence


[2]Based on the availability of large number of 16S rRNA sequences, along with NCBI’s databases there are multiple other databases which are widely used. They are:

  1. EzTaxon-e contains complete hierarchical taxonomic structure (from phylum rank to species rank) for the domain of bacteria and archaea.

  1. Ribosomal Database Project.
  2. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
  3. The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.


  1. 16S Ribosomal RNA Sequencing. Microbiology Virtual Lab, Amrita University Data.
  2. 16S Ribosomal RNA – Wikipedia.
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NCBI GLIMMER Microbial Genome Annotation Tool

GLIMMER is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. GLIMMER (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models to identify coding regions.



It is an online tool although it can be easily be downloadable as a software to analyze transcription units and open reading frames in both the strands of the DNA.

The online link for GLIMMER:


GLIMMER allows to find identification ~97-98% of the subject genes compared with the published annotation. GLIMMER is known to have <1% less accuracy.

The computational methods behind the GLIMMER Technique can be found at


To Start with GLIMMER:

After you go the NCBI’s GLIMMER you can able to download the GLIMMER software or you can choose the online program to feed your FASTA sequence of the gene from the unknown bacteria. (You can try with the FASTA sequence of any known bacteria).


Some additional parameters you need to maintain like the genetic code and the topology of the gene and then you can Run GLIMMER v3.02



After you Run GLIMMER you will get the following result as for example.



The result you get shows the number of ORFs or the open reading frames in the gene followed by the nucleotide starting number from where the ORF starts and then the nucleotide end number where the ORF ends. Minus (-) and plus (+) signifies the Lagging and the Leading strands respectively.

GLIMMER is quite efficient and can be useful for the microbial genetics studies. Read more about GLIMMER at

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Fat Gene found to be associated with Obesity

Scientist finally identified the culprit behind the original gene responsible for obesity. This recent news published in the journal Nature. Earlier in 2007 several genomic studies highlights that FTO is strongly associated with the risk of obesity and type 2 diabetes. Then subsequent studies in mice revealed that there is a valid relation between the gene and the body mass. So several geneticist including the project head Dr. Marcelo Nóbrega, geneticist at University of Chicago clarified the doubts finally with the new identification of the gene which is actually responsible for obesity.

The finding:

The absolute finding began when there is significant mutation revealed in non-coding portions of FTO. Dr. Nóbrega found something amiss. The moment which made the researchers a pause was the regulatory regions contained some of the elements which are specific for lungs. The obvious question that comes up “Why are there regulatory elements that presumably regulate FTO in the tissue where it isn’t expressed?”

Long-range interactions in the IRX3-FTO locus. (Source: Nature)

Long-range interactions in the IRX3-FTO locus. (Source: Nature)

This was isn’t a red flag but provided the zeal in Dr. Nóbrega to find out what is the actual cause behind this. Instead some other regulatory gene might have been associated with FTO. Nóbrega presents his results in several meetings and conferences, and there people who had or have been working came up and suggested that there is obvious something wrong out there where the mystery yet to be resolved.

So Nóbrega and his team starts working to make their understanding into much wider platform to resolve the associated or nearby genes of FTO which is actually responsible in regulating it. IRX3 is the gene which is half a million base away from FTO whose expression of mutation actually get matched. IRX3 is a transcription factor – whose protein is involved in regulating the expression of other genes and known for its high expression in brain providing a consistent role in regulating energy metabolism and eating behavior.





Genemania online tool shows the co-expression map between FTO and IRX3

Genemania online tool shows the co-expression map between FTO and IRX3

They subsequently examined in mice, zebrafish and even on human cell lines where the identical results reveal that FTO is physically in contact with the promoter of IRX3.

The ultimate belief about GWAS

There is obvious a misconception about genome wide association studies (GWAS) that it just highlights about the association, and is the marker of the genome but actually don’t reveal which gene is actually affecting. Now the medication which was actually thought should be behind FTO has turned towards IRX3.


  • New contender of ‘fat gene’ found. Nature News. By Brian Owens. 12th March 2014.
  • Obesity-associated variants within FTO form long-range functional connections with IRX3. Smemo et al. 2014.

Further Reading:

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Genetic Background of Alzheimer’s Disease

Alzheimer’s disease, the well known progressive neurologic disease of the brain, leading to irreversible loss of neurons and the loss of intellectual abilities, including memory and reasoning, which become severe enough to impede social or occupational functioning. There are multiple researchers and also it has carried an importance of current research which carried an important understanding about the genetical background of Alzherimer’s. [Know more about Alzheimer’s here:]

Here in this article I would like to highlight some major understanding about Alzheimer’s disease, especially the genetical research and understanding.

A research published in Journal of Neuroscience where the UK researchers, University of Kentucky identified several variations in DNA sequence, where each can modify Alzheimer’s risk. They identified a potential genetic variation near the gene CD33, which is thought to inhibit clearance of amyloid beta (a hallmark of Alzheimer’s disease, know more here The results obtained, indicating the inhibition of CD33 may reduce Alzheimer’s disease. A drug was tested for acute myeloid leukemia targets CD33, suggesting the potential for treatments based on CD33 to mitigate the risk for Alzheimer’s disease. Although they suggested that further studies must be conducted before this treatment approach could be tested in humans.

Another research where four new genes have been identified where researchers from a consortium of 44 universities and research institutions in the United States, including Rush University Medical Center, identified four new genes linked to Alzheimer’s disease. The research was published in the journal Nature Genetics. The genetic analysis was performed with more than 11,000 people with Alzheimer’s disease, along with the same number of elderly people with no symptoms of dementia. Earlier a gene of apolipoprotein E-e4, APOE-e4, identified over 15 years ago, has the largest effect on risk. Then more additional genes was identified, CR1, CLU, and BIN1. But in through this research adds more four genes MS4A, CD2AP, CD33, and EPHA1 — and contributes to identifying and confirming two other genes, BIN1 and ABCA7, thereby doubling the number of genes known to play a role in Alzheimer’s disease.

The above two research investigates that CD33 plays major role in Alzheimer’s disease. Hence it allows easy focus that some cell signaling ability takes up a major role behind the unrevealed story behind this disease.

In the next recent research in 2013, researchers from Washington University School of Medicine in St. Louis identified several genes linked to the tau protein, which is found in the tangles that develop in the brain as Alzheimer’s progresses and patients develop dementia. APOE, had been identified as a risk factor for Alzheimer’s appears to be connected to elevated levels of tau. Researchers in an article said “Some of the effects are mediated through amyloid-beta and others by tau. That suggests there are at least two ways in which the gene can influence our risk for Alzheimer’s disease.” [Read More here:]. Finally in addition to their research along with APOE, the researchers found that a gene called GLIS3, and the genes TREM2 and TREML2 also affect both tau levels and Alzheimer’s risk.

Regarding tau protein early research was carried out in 2009, published in The American Journal of Pathology based on the hypothesis that an unfolded protein response contributed to neurodegeneration in Alzheimer’s disease partially though its effects on the accumulation of hyperphosphorylated tau, a major component of tangles in Alzheimer’s disease patients. They identified that markers of the unfolded protein response were expressed in areas of tau accumulation in patients with Alzheimer’s disease.

So in conclusion of this report, it is obvious to understand that for any genetic analysis signaling pathway and protein modification towards a disease is important. Alzheimer’s disease which allows researchers to reach a proper research finding that Alzheimer’s disease are caused due to multiple gene involvement. Initially CD33 was identified which holds a major role on amyloid beta, followed by other genes too. “tau” protein also been identified to have some major impact on Alzheimers, hence amyloid beta along does not always play the role alone. Even in this story I pushed back a little from the solutions identified from the genetic analysis but the better understanding of correlation highlights major importance toward the disease.


M. Malik, J. F. Simpson, I. Parikh, B. R. Wilfred, D. W. Fardo, P. T. Nelson, S. Estus. CD33 Alzheimer’s Risk-Altering Polymorphism, CD33 Expression, and Exon 2 Splicing. Journal of Neuroscience, 2013; 33 (33): 13320

Naj et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer’s disease. Nature Genetics, 2011

Carlos Cruchaga, John S.K. Kauwe, Oscar Harari, Sheng Chih Jin, Yefei Cai, Celeste M. Karch, Bruno A. Benitez, Amanda T. Jeng, Tara Skorupa, David Carrell, Sarah Bertelsen, Matthew Bailey, David McKean, Joshua M. Shulman, Philip L. De Jager, Lori Chibnik, David A. Bennett, Steve E. Arnold, Denise Harold, Rebecca Sims, Amy Gerrish, Julie Williams, Vivianna M. Van Deerlin, Virginia M.-Y. Lee, Leslie M. Shaw, John Q. Trojanowski, Jonathan L. Haines, Richard Mayeux, Margaret A. Pericak-Vance, Lindsay A. Farrer, Gerard D. Schellenberg, Elaine R. Peskind, Douglas Galasko, Anne M. Fagan, David M. Holtzman, John C. Morris, Alison M. Goate. GWAS of Cerebrospinal Fluid Tau Levels Identifies Risk Variants for Alzheimer’s Disease. Neuron, 2013

Hoozemans JJM, van Haastert ES, Nijholt DAT, Rozemuller AJM, Eikelenboom P, Scheper W. The Unfolded Protein Response Is Activated in Pretangle Neurons in Alzheimer’s Disease Hippocampus. American Journal Of Pathology, 2009


Updated Story:

This is a little update of what I have mentioned earlier in this article. A new research analyzed and published in the journal Nature Genetics revealing eleven new genetic susceptibility factors for Alzheimer’s Disease. An article published on 27th October 2013 at Science Daily news blog here:

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Bacteria of Intestinal Tract, view in year 1915

I came across a post in twitter shared by @thisischristina and a big thanks to her since while I read this, I found it very interesting to share it. So you can relate it with your current view now in 2013. Hope this interests you, if so then please do comment and find the full article as “main article” posted below this.

There has been an enormous numbers of bacteria making a favorable community from millions to trillions, and approximately 5.5 grams when dried. The question was obvious that time that how such large amount of bacteria prevailing there even though such large numbers are not taken in food. The conclusion was also much simple and that was the daily proliferation of the bacteria in the intestine. Although there are more facts to share like lots of early bacteria enters into the body from the first food after birth. So some early residents are still being present in the intestinal tract maintaining the versatile community.

Some of the bacteria which is identified as residents are B. bifidus, E. coli, B. lactis and Micrococcus ovalis. Among these, B. bifidus dominates among the intestinal flora and was found to be protective against growth of some other bacteria which might produce putrifaction or disease. There are lots of reasons for which B. bifidus sound to be prevalent in 1915 times research and it is well mentioned in the article.

Moving towards the distribution of bacteria, where stomach is practically sterile under normal conditions. The obvious explanation of this is the acidic gastric contents. Although sometimes when the acidic conditions becomes diminished due to some disease then the bacterial content increases. This is how those bacteria reach to the duodenum, and then to the lower levels. Large amount of bacteria are found in the ascending branch of the colon. Then from the ascending colon it moves and prevalent to the descending part.

Along with the disease causing ability of the bacteria, there are some of their community which helps the human being to assist the digestion of food through the elaboration of certain fragments and also these organisms are under normal conditions in the sense of the protection of host.

In conclusion intestinal bacteria may become menace to the host causing typhoid, dysentery, cholera, etc., although some organisms are found to be symbiotically faithful for the host. Hence we don’t be in contact with such diseases all the time. The article represents several theoretical experiments and observations of early research to understand the interactions.


Main Article:

A.I. Kendall. The Bacteria of the Intestinal Tract of Man. Science. Pg: 209-212 [Link:]

Read More:

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Biofilm Strategy in Staphylococcus spp.

I felt of discussing something entirely new and challenging and came out with the biofilms. This is very extraordinary understanding and currently many researchers are working on understanding biofilm production by certain species and particularly in Staphylococcus spp, which is known to cause nosocomial infections (hospital acquired). Although the topic may be not new to you but better understanding of how they form and why they form may lead to some new knowledge uptake. You can also add comments below this article to make it more understanding to the readers.

Biofilm formation by Staphylococcus aureus (Wikipedia)

So what are biofilms? – Biofilms are adherent communities of bacteria containing within a complex matrix.         The adherents are known to be embedded inside the extracellular polymeric substances (EPS) which is commonly known as EPS matrix. Biofilms are found on both living as well as non-living surfaces. Biofilm EPS or slime generally composed of extracellular DNA, polysaccharides and proteins. There are varied reasons why biofilms are produced by certain bacteria. It is known that Staphylococcal biofilms can escape immune recognition, because of their chronic and indolent nature. Biofilms serve to be very useful for Staphylococcus in many ways including development of antibiotic resistance, and as mentioned to escape immune reponse.

Development of biofilms starts with the initial weak reversible adhesion on to a surface with van der Waals forces. Some motile bacteria anchor themselves more permanently using cell adhesion structures, pili. Secondly, hydrophobicity plays role to determine the bacteria able to form biofilms, since increased hydrophobicity have reduced repulsion between extracellular matrix and the bacteria. Recently, quorum sensing also sound to play major role, where cells communicate among themselves, transmitting signals (using products like AHL) during colonization. Once the colonization has started, biofim grows with the cell division. Dispersion is the final stage of the development of biofilm where the biofilm changes only its shape and size.

Biofilm formation steps

Quorum sensing – An accessory gene regulator(agr) is thought to play an important role in quorum sensing system in causing serious biofilm associated diseases by Staphylococcus aureus. In an experiment by Yarwood (2004) and his colleagues, from University of Lowa examined the agr dependent transcription in biofilms. The observation of their research draws much significant conclusion. While disruption of agr expression, there is no significant influence in biofilm formation, but where this the presence of agr , there is an enhanced biofilm formation. Under those conditions where agr expression enhanced biofilm formation, biofilms of an agr signaling mutant were particularly sensitive to rifampin but not to oxacillin. Time lapse confocal scanning laser microscopy showed that, similar to the expression of an agr-independent fluorescent reporter, biofilm expression of an agr-dependent reporter was in patches within cell clusters and oscillated with time. In some cases, loss of fluorescence appeared to coincide with detachment of cells from the biofilm. Their studies indicates that biofilm development and behavior depends on environmental conditions. It also gives suggestion that detachment of cells expressing agr from biofilms may have important clinical implications. In 2006, Kong et al., highlights that along with agr, the post translationally modified peptide has an autoinducing signal towards quorum sensing. This second quorum sensing system, called luxS is found in variety of gram positive and gram negative bacteria. Both agr and luxS has different role, agr enhances biofilm detachment by up-regulation of the expression of detergent-like peptides, whereas luxS reduces cell-to-cell adhesion by down-regulating expression of biofilm exopolysaccharide.

Targeting quorum sensing has been now a potential target. While promising reports exist about quorum-sensing blockers in gram-negative bacteria, the use of the Staphylococcal quorum-sensing system as a drug target is now seen in an increasingly critical way. Inhibition of quorum-sensing in Staphylococcus has been shown to enhance biofilm formation. Furthermore, down-regulation or mutation of the Staphylococcus quorum-sensing system increases bacterial persistence in device-related infection, suggesting that interference with quorum-sensing would enhance rather than suppress this important type of Staphylococcal disease. The chemical nature and biological function of another proposed Staphylococcal quorum-sensing inhibitor, named “RIP”, are insufficiently characterized. Targeting quorum-sensing systems might in principle constitute a reasonable way to find novel antibacterial drugs.

ica Operon – The ability to form a biofilm affords at least two properties: the adherence of cells to a surface and accumulation to form multilayered cell clusters. A trademark is the production of the slime substance Polysaccharide Intercellular Adhesin (PIA), a polysaccharide composed of beta-1,6-linked N-acetylglucosamines with partly deacetylated residues, in which the cells are embedded and protected against the host’s immune defence and antibiotic treatment. Mutations in the corresponding biosynthesis genes (ica operon) lead to a pleiotropic phenotype; the cells are biofilm and haemagglutination negative, less virulent and less adhesive on hydrophilic surfaces. ica expression is modulated by various environmental conditions, appears to be controlled by SigB and can be turned on and off by insertion sequence (IS) elements. A number of biofilm-negative mutants have been isolated in which polysaccharide intercellular adhesin (PIA) production appears to be unaffected.

Other factors- Along with quorum sensing and ica operon, there are other proteins have been identified that are also involved in biofilm formation, such as the accumulation-associated protein (AAP), the clumping factor A (ClfA), the staphylococcal surface protein (SSP1) and the biofilm-associated protein (Bap).

Multidrug tolerance or antibiotic tolerance is the ability of the disease causing microbe to resist killing by antibiotics. This multidrug tolerance in biofilms is caused by a small subpopulation of microbial cells called persister cells. Persisters are not mutants but rather dormant cells that can survive the antimicrobial treatments that kill majority of their genetically identical siblings. Persisters enter into a slow growing physiological state which makes them insensitive to the action of antimicrobial drungs.


While concluding this article, I must say that this article is based on totally on Staphylococcus sp. and not highlighting any cure mechanisms against biofilms. I just have highlighted the major artifacts about biofim formation by Staphs. Please do comment and add some of your ideas over biofilms.


  1. Jeremy M. Yarwood, Dauglas J. Bartels, Esther M. Volper, E. Peter Greenberg. 2004.Quorum sensing in Staphylococcus aureus biofilms. Journal of bacteriology. 186(6): 1838-1850.
  2. Kong KF, Vuong C, Otto M. 2006. Staphylococcus quorum sensing in biofilm formation and infection. International Journal of Medical Microbiology. 296: 133-139.
  3. Otto M. 2004. Quorum-sensing control in Staphylococci — a target for antimicrobial drug therapy? – Review Article. FEMS Microbiology letters. 241(2): 135-141.
  4. Götz F. 2002. Staphylococcus and Biofilms. Molecular Mirobiology. 43(6): 1367-1378.
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Understanding in a NEW mode of MDR TB

Multidrug-resistance tuberculosis (MDR TB), a known form of tuberculosis that is resistant to one or multiple primary drugs (isoniazid and rifampin) used normally in the treatment of tuberculosis.

Extensively drug resistant TB (XDR TB) is resistant to at least isoniazid and rifampin among first line of anti-TB drugs and is resistant to any anti-fluroquinolone and at least one of the three second line injectable drugs. When bacteria develops its ability to withstand the antibiotic attack, lead to the development of resistance to one or several forms of treatment and this ability relays it to the offspring. Due to this inheritance of the bacteria, the effect of resistance bacteria spreads from one person to another. However, it is of obvious reasons that inadequate treatment and improper use of the ant-TB drugs remain the main reasons of drug resistance TB.

The improper treatment remains the star mark for MDR TB development. Some physicians does not prescribe proper treatment regimens or also when patient does not properly adhere to the treatment. Improper treatment leads these bacilli to develop natural resistance over the drug and transmit this to inheritance. Eventually majority bacilli become resistant in the body. Once a strain of MDR TB develops it can be transmitted to others.

MDR TB has been a major concern in HIV-infected persons. Some of the major factors include:

  • Delayed diagnosis and delayed determination of drug susceptibility.
  • Susceptibility of immunocompromised individuals for not only acquiring MDR TB but also for the rapid disease progression. In turn leading to transmission to other immunosupressed patients.
  • Inadequate isolation procedure and other environmental safety concerns, like in remote areas or in confined areas (prison).
  • Noncompliance or intermittent compliance with anti-tuberculosis drug therapy.

New quest in TB:

Tuberculosis causing germ likely to have grown in ancient man when he started to live in larger communities. It probably early humans out of Africa at least 70,000 years ago. While communicating this study, it has been identified that 39 new genes drives this dangerous drug resistant TB [Read More:]. A report published in the Asian Scientist, 8th August 2013 based on a new promising drug discovery for MDR TB by South Korian and Singapore Researchers, and the drug was successfully tested on mice. The research was published in the journal Nature Medicine where this drug inhibits the growth of M. tuberculosis through a novel mechanism rather than the known previous drugs [Read More]. Although it is new to understand the multiple ways to inhibit MDR TB, and step wise multiple mutation would be one of the major cause of M. tuberculosis to be drug resistant and is proved in a research published in a journal Nature Genetics [Read More:].

The success of treatment lies in how quickly the case of TB is been identified. Tests to determine resistance to various drugs take several weeks, hence an effective drug regimen must be identified. There are multiple strains of MDR TB which are resistant to seven or more drugs, making the identification of proper drug to be difficult. The better way to deal with this problem is to recommend the newly discovered cases of TB in populations at high risk for MDR TB to be treated with four drugs rather than the standard three as part of the initial treatment.



  1. Centers for Disease Control and Prevention. []
  2. American Thoracic Society, Centers for Disease Control and Prevention and Infectious Disease Society of America.
  3. World Health Organization, Global Tuberculosis Control Report, 2012.
  4. Asian Scientist, Channel New Asia, Science Daily

Suggested Reading:

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