Journal of Microbial Pathogenesis

Pseudomonas aeruginosa lung infection is among the most severe complication in patients with chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). CF related pulmonary infection is characterized by antibiotic-tolerant biofilms in the endobronchial mucus with zones of oxygen (O2) depletion mainly due to polymorphonuclear leukocyte (PMN) activity. Despite anoxic conditions, the flexible metabolism of P. aeruginosa growing in biofilms allows this pathogen to obtain energy for growth by denitrification as demonstrated by production of nitrous oxide in CF sputum samples. While the exact mechanisms affecting antibiotic effectiveness on biofilms remain unclear, accumulating evidence suggests that the efficiency of several bactericidal antibiotics such as ciprofloxacin is enhanced by stimulation of the aerobic respiration of pathogens and that lack of O2 increases their tolerance. Understanding the clinical effects of antimicrobials on biofilm development is important to avoid the use of inappropriate drugs in the event of biofilm infection. This article reviews current information about the growth of bacteria within the biofilm and the inhibitory or inducing effect of antimicrobials common in their formation by P. aeruginosa.

The effect of antibiotics used to treat biofilms of other bacteria, such as Staphylococcus aureus or Escherichia coli, has also been briefly discussed. Reoxygenation of O2- depleted biofilms may thus improve susceptibility to ciprofloxacin possibly by restoring aerobic respiration. Such strategy was then tested using re-oxygenation of O2- depleted P. aeruginosa strain PAO1 agarose embedded biofilms by hyperbaric O2 treatment (HBOT) enhancing the diffusive supply for aerobic respiration during ciprofloxacin treatment. The demonstration of enhanced bactericidal activity of ciprofloxacin in P. aeruginosa biofilm during re-oxygenation by hyperbaric O2 treatment (HBOT) is indeed a proof-of-principle study that may translate into improved treatment of both CF and COPD patients.

Waterborne parasitic protozoa outbreaks are on an increase, although there are better surveillance and reporting systems in several countries. The most prevalent water borne parasitic infections producing diarrhea are cryptosporidiosis and giardiasis; the common waterborne parasitic protozoa that cause human infections are Toxoplasma gondii, Cyclospora, Microspora, Naegleria spp., etc. Pathogenic protozoa have a biologically different shape during their life cycle in the host. Although there are various methods available, detection of pathogenic protozoa is more difficult as compared to other methods. For monitoring of the protozoa in the water source system, we mainly conducted direct microscopic observations. In this study, 6 kinds of the waterborne parasitic protozoa were detected by the PCR method in samples collected from Nakdong River. The results of water quality in this investigation showed an average of total coliforms (TC) 40~4,900 MPN/100 mL and fecal coliforms 0~1,100 MPN/100 mL. We applied this method in 38 samples of 10 l of water taken from each of the water treatment steps and in 8 samples taken at home (only for Toxoplasma PCR) in Quindio region in Colombia.

There were 8 positive samples for Cryptosporidium parvum (21 %), 4 for Cryptosporidium hominis (10.5 %), 27 for Toxoplasma gondii (58.6 %), 2 for Giardia duodenalis assemblage A (5.2 %), and 5 for G. duodenalis assemblage B (13.1 %). By IFAT, 23 % were positive for Giardia and 21 % for Cryptosporidium. The water quality during this survey showed an improvement when compared to results of the previous year (conducted during the same period), but the number of bacteria were temporarily increased due to turbidity caused by rainfall. Parasitic protozoa were not detected in any of the source water samples of the Busan metropolitan city. We confirmed the microbiological safety of drinking water produced by the treatment system. Thus, it is necessary to monitor the bacteriological load in water, so as to ensure the safety of water supplies. Further studies are required to compare the specificities and sensitivities of several methods to accurately detect parasitic protozoa.

The limited number of studies on relationship between environmental parameters and bacterial community composition in sediments of Eastern Mediterranean Sea include bacterial biomass, nucleic acid concentration and cultivation independent studies. Cultivation based methods, on the other hand, are important for further studies such as production of secondary metabolites and identification of new species. In the present study, totally nineteen stations with 0-1235 m depths were sampled from sediments of Eastern Mediterranean Sea. The grain size and carbon, nitrogen, phosphorus contents of sediment samples were analyzed. Bacterial isolation was achieved using seven different sediment processing methods and seven isolation media prepared with sterile seawater and then incubation at 20-28 °C up to two months. 16S rRNA gene sequences of 185 strains were deposited into NCBI GenBank database and phylogenetic analysis was performed with 1000 bootstrap neighbor-joining method. Hierarchical cluster analysis was used to compare bacterial community composition. 

The limited number of studies on relationship between environmental parameters and bacterial community composition in sediments of Eastern Mediterranean Sea include bacterial biomass, nucleic acid concentration and cultivation independent studies. Cultivation based methods, on the other hand, are important for further studies such as production of secondary metabolites and identification of new species. In the present study, totally nineteen stations with 0-1235 m depths were sampled from sediments of Eastern Mediterranean Sea. The grain size and carbon, nitrogen, phosphorus contents of sediment samples were analyzed. Bacterial isolation was achieved using seven different sediment processing methods and seven isolation media prepared with sterile seawater and then incubation at 20-28 °C up to two months. 16S rRNA gene sequences of 185 strains were deposited into NCBI GenBank database and phylogenetic analysis was performed with 1000 bootstrap neighbor-joining method. Hierarchical cluster analysis was used to compare bacterial community composition. 

The majority of mitochondrial pre-mRNAs in trypanosomes undergo massive uridine insertion/deletion editing to create open reading frames. Although required, editing is not sufficient to produce most of the translationally-competent mitochondrial mRNAs. Pre and post-editing adenylation and uridylation reactions are essential for mRNA stabilization and ribosome recruitment. Adenylation prior to editing by KPAP1 poly(A) polymerase stabilizes transcripts that are edited beyond few initial sites, while A/Utailing by KPAP1 and RET1 TUTase commits the fully-edited mRNA for translation. The temporal separation of these events suggests that a mechanism must exist to prevent premature A/U-tailing and to couple the completion of editing with A/U-tailing. To identify protein factors responsible for mRNA 3' modification and coordination with editing, we built a comprehensive protein interactions network of mRNA polyadenylation, editing, and translation complexes.

RNAi knockdowns, in vivo RNA binding sites mapping and in vitro reconstitution indicate that pre-mRNA is initially stabilized by binding of a specific pentatricopeptide repeat-containing protein (PPR). This factor, termed Kinetoplast Polyadenylation Factor 3 (KPAF3), defines the 3' end of pre-edited mRNA by impeding mRNA degradation by the 3' processome. KPAF3 also stimulates KPAP1’s poly(A) polymerase activity to ensure that only A-tailed mRNAs proceed through the editing pathway. We also identified a distinct PPR factor, KPAF4, that binds to a junction between the mRNA and poly(A) tail and blocks premature A/U-tailing. These findings will be presented in a context of integrating editing, polyadenylation and uridylation processes with mRNA selection by the ribosome.

Stress conditions cause microorganisms to adjust their normal functions to counter the deleterious effects of the stress. This includes modulating relevant proteins in response to the stress. In our studies, we seek to decipher the message inherent in the picture painted by the network of the modulated proteins, with the aim of understanding the physiology of the bacteria and viruses. For example, under exposure to sub-lethal concentrations of the herbicide, glyphosate, and its breakdown product, amino methyl phosphonic acid (AMPA), E .coli upregulated 18 and downregulated 14 proteins under glyphosate stress. Under AMPA stress, the bacterium upregulated 32 and downregulated 8 proteins. E. faecalis upregulated 67 and downregulated 16 proteins under glyphosate stress, but upregulated 172 and down-regulated 104 proteins under AMPA stress. For E. coli, majority of the regulated proteins under glyphosate and AMPA stress where transport, stress response and nitrate metabolic proteins. Exposure of Helicobacter hepaticus under the stress of bile –an antimicrobial agent which is produced in the liver, concentrated in the gallbladder and released into the gut during digestion of fatty foods, resulted in the modulation of different proteins. In bovine, porcine or human bile, the bacterium modulated differently the expression of several virulence determinants including the cytolethal distending toxin (CDT), urease, superoxide dismutase, flagellin and ferritin. 

For example, superoxide dismutase was downregulated in the three types of bile; CDT was downregulated in bovine and human bile, but was unaffected by porcine bile; urease was downregulated in bovine bile, upregulated in porcine bile and unaffected in human bile. The data suggested that bile serves as an environmental cue for protein expression by H. hepaticus, and may modulate its virulence factors. Genetic modification of organisms, e.g. insertion of unrelated foreign gene into the genome of an organism (transgenesis) also can be considered a type of stress given that the organisms are forced to adapt to the effects of the genetic manipulation. The introduction of the haemagglutinin and nucleoprotein genes of the H1N1 influenza virus into the genome of Modified Vaccinia virus Ankara resulted in the modulation of 32 virus encoded proteins that are involved in various pathways of the virus replication. Overall, application of proteomics in conjunction with other complimentary molecular biology tools, has enabled us to contribute towards understanding the physiology of these organism.