5^th International Conference on Microbial Physiology and Genomics September 29-30, 2016 London, UK

Chair

Mohannad Al Saghir

Ohio University ,USA

Co-Chair

Ruslan Afasizhev

Boston University School of Dental Medicine,USA

Chair

Mohannad Al Saghir

Ohio University ,USA

Co-Chair

Ruslan Afasizhev

Boston University School of Dental Medicine,USA

Session Introduction

Mette Kolpen

University of Copenhagen, Denmark

Title: Enhancement of the bactericidal activity of antibiotics in hypoxic biofilms as seen in patients with chronic pulmonary disease

Biography:

Mette Kolpen has completed her PhD from University of Copenhagen and is currently a Postdoctoral Fellow at University of Copenhagen, Germany. She has published 13

scientific articles in peer-reviewed international journals and books. She has during the previous 6 years demonstrated O2 depletion in the endobronchial mucus of cystic

fibrosis (CF) patients.

Abstract:

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. 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.

Ella Cullen

University of Stirling, United Kingdom

Title: Ultra-fast drug resistance predictions from NGS sequence data using Cloud Computing

Biography:

Ella Cullen is a graduate Trinity College Dublin’s School of Genetics. She has worked on several projects relating to human disease, including psoriasis and

neurodevelopmental disorders. She now works with NSilico Life Science. NSilico’s focus is on the development of easy-to-use Ella Cullen clinical and bioinformatics

software which can significantly accelerate the research process. Ella works with the company’s research teams, which have a particular focus on infectious disease and

cancer. She also works on forming collaborative projects with labs and companies around the world.

Abstract:

Rapid and accurate prediction of drug resistance in pathogens is a growing need, affecting patient care and emerging personal

medicine. Bacterial genome sequencing has been introduced in many hospitals as a cheaper alternative to gene targeted

sequencing and PCR, but many handling issue remain to be overcome. Here, we address some of the challenges, by offering a cloudbased

solution that while keeping security and privacy at the heart of the development allows remote management of large datasets,

and ultra-fast drug resistance predictions without the need for local installation, maintenance or bioinformatics knowledge. Validated

using literature references, we have implemented a profiler that reconstitutes (from raw sequences) the genes associated with resistance

and produces an ultra-fast and accurate prediction of drug resistance. If raw sequences are available, regardless of the platform

used, the profiler will generate a prediction within minutes, in contrast to other solutions which typically require hours of analysis

time and interpretation. The profiler currently focuses on Mycobacterium tuberculosis and 9 key drugs, including Aminoglycosides

(Kanamycin, Capreomycin, Amikacin, Viomycin), Ethambutol, Ethionamide, Fluoroquinolones, Isoniazid, Para-Aminosalisylic

Acid, Pyrazinamide, Rifampicin, and Streptomycin.

Arinze Okoli

Genok - Centre for Biosafety, Norway

Title: Application of Proteomics in the study of Microbial Physiology: taking advantage of changes in the microbe’s normal functions under stress conditions

Biography:

Arinze Okoli is associated with GenØk –Centre for Biosafety, Tromsø, Norway. He has published several papers in reputed journals. He is committed to highest standards

of excellence and it proves through her authorship of many books. His research interests include Microbiology.

Abstract:

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.

Khalid Habib

Baghdad-University, Iraq

Title: Influence of Temperature and pH on the Growth of Lactobacillus reuteri ATCC 23272 using Optical Density assay

Biography:

KhalidA. Habeb currently working as Professor in microbiology Department of Biology / College of Science for Women / University of Baghdad, Iraq.

Abstract:

Background & Aim: Lactobacillus reuteri, which is a normal flora in intestine and the female genital tract, can be used as probiotic

bacteria to give health benefits. The aim of this study is to evaluate the effect of two physiological factors (temperature and pH) on the

growth of Lactobacillus reuteri ATCC 23272.

Method: In this study, Lactobacillus reuteri ATCC 23272 was cultivated in MRS broth and adjusted to four different initial pH

values and incubated at four different temperatures degrees. For all of the resulted 16 subgroups (each subgroup consists of 10 broth

samples), initial optical density was adjusted to (1.4) at 540 nm. After incubation, the final optical density and pH were measured and

the data were collected and analyzed statistically.

Results: The incubation temperature and the initial pH of the culture medium had a significant effect on the growth rate of Lactobacillus

reuteri ATCC 23272. The optimal conditions for the growth were (Temp. 30oC, pH 6.5) with an optical density around (1.9297) at 540

nm, while the lowest growth rate was at (Temp. 25oC, pH 3.5) with an optical density around (0.0002) at 540 nm.

Conclusion: The physiological environment has a great influence on the growth rate of Lactobacillus reuteri ATCC 23272.

Miklos Fuzi

Semmelweis University, Hungary

Title: Diverse fitness associated with resistance to fluoroquinolones influenced the clonal dynamics of various multiresistant pathogens

Biography:

Miklos Fuzi has completed his PhD in 2001 and has been engaged in the investigation of clonality and antibiotic resistance during the last 15 years. He has published 38

papers in reputed journals. He is an Associate Professor at Semmelweis University, Budapest, Hungary.

Abstract:

Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant

Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae. The resulting

dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a

similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major

international clone (ribotype 027) of Clostridium difficile. The overwhelming part of the available epidemiological data supports

the connection. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for

pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Moreover, the mechanism was observed to select

for the CTX-M-15 type ESBL in K. pneumoniae that may account for the widespread dissemination of this enzyme. The findings

suggest that the use of fluoroquinolones as a function of clonal distribution could ameliorate the state of antibiotic resistance. When

the proportions of multiresistant clones influenced by fluoroquinolones are low the use of these antibiotics remains highly beneficial.

However when their proportion increases the consumption of fluoroquinolones should transiently be reduced.

Marie Joelle Virolle

University Paris Sud, France

Title: Strong antibiotic production is correlated with an oxidative metabolism in Streptomyces

Biography:

Marie Joelle Virolle is associated with University of Paris-Sud, France. Marie Joelle has published several papers in reputed journals. Marie Joelle is committed to highest

standards of excellence and it proves through the authorship of many books. Marie Joelle research interests include Systems Biology, Molecular Biology and Microbiology.

Abstract:

The Streptomyces genus is well known for its outstanding ability to produce secondary metabolites of great interest for human kind

such as antibiotics. Antibiotic biosynthesis occurs in the periods of slow or no growth and is triggered by phosphate limitation, a

condition known to be correlated with energetic stress. However, the metabolic changes underlying the transition between primary

and secondary metabolism remains largely elusive. Comparative physiological and proteomic studies of two closely related model

strains, S. lividans and S. coelicolor, weak and strong producers of the same antibiotics, respectively, were carried out. These studies

clarified for the first time the nature of the metabolic transition between primary and secondary metabolism. This switch triggered

by energetic stress results from a transition from a glycolytic to an oxidative metabolism in order to restore the energetic balance of

the cell. Our results indicate that in condition of energetic stress, the acetyl-CoA generated by glycolysis, rather than being stored as

lipids of the triacylglycerol family, is used to fuel the Krebs cycle, more favorable than glycolysis for energy generation. Krebs cycle

yields molecules that are direct precursors of amino acids used for peptidyl antibiotic biosynthesis as long as sufficient nitrogen is

available. When nitrogen becomes limiting, acetyl-CoA would then be used for direct biosynthesis of polyketide antibiotics. A tool

based on these novel principles was conceived and implemented to enhance the expression of the numerous biosynthetic pathways

present in the Streptomyces genomes.

Inna Afasizheva

Boston University School of Dental Medicine, USA

Title: Pentatricopeptide repeat (PPR) RNA binding proteins regulate mRNA processing in mitochondria of Trypanosoma brucei

Biography:

Inna Afasizheva has received her PhD from Institute of Molecular Biology, Russian Academy of Sciences. She is a Professor of Molecular and Cell Biology at Boston

University Medical Campus, USA. She has published more than 30 papers in high ranking journals.

Abstract:

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 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. 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.