Experienced Biomedical Research Scientist
- Houston, Texas (Houston, Texas Area)
Karina Pokusaeva's Overview
- Article Reviewer at Veterinaria Italiana
Karina Pokusaeva's Summary
Scientist with Biomedical Research experience in the field of microbiology and the focus on beneficial microbe-host interaction combined with professional experience in the Pharmaceutical Industry. My main interest is to explore how complex gastrointestinal community of microorganisms interacts with the human host. My current research investigates how particular gut commensals affect host neuronal response by secreted microbial bioactive molecules.
Specialties: Microbiology, probiotics, prebiotics, synbiotics, microbial genetics, microbial system biology, biochemistry, translational biology, gastrointestinal tract, enteric nervous system, microbial-host response
Karina Pokusaeva's Experience
Postdoctoral Research Associate
Educational Institution; 5001-10,000 employees; Research industry
August 2010 – June 2014 (3 years 11 months) Houston, Texas, USA
I joined the Versalovic lab (Therapeutic Microbiology Team) to work on the interaction mechanisms between the host and human gut microbiota. Currently I am investigating suppression of inflammation in cell culture model by beneficial intestinal microorganisms identified in Human Microbiome Project. Specifically, I am investigating the GABA receptor responses to commensal microorganism stimuli via secreted compounds by interdisciplinary studies using translational biology approach.
Collaborating with other scientists and MD fellows at Texas Children’s Hospital, Proteomics Core at Methodist Hospital, University of Texas, Emory University and n3D Biosciences Inc. in the design of novel research methodologies and interpretation of research findings.
Consulting Functional Genomics and Proteomics Core at Digestive Disease Center (Texas Medical Center) with establishing real time quantitative PCR technique using universal probe library (Roche) for validation of microarray data.
Mentoring Ph.D. candidates.
Training students and research assistants.
Reviewing and writing grants and publications.
Published 1 first author review publication.
2011 – 2012 (1 year)
Planning and overseeing the SFA contribution to the annual international ISAPP Conference in terms of programming and grant competitions in conjunction with the Programming and Finance Executives;
Planning membership recruitment activities in conjunction with the President;
Representing the SFA at the annual ISAPP conference
Postdoctoral Research Associate
Educational Institution; 10,001+ employees; Higher Education industry
May 2009 – July 2010 (1 year 3 months) College Station, Texas, USA
Worked on phenotype microarray analysis of E. coli and Streptococcus pyogenes and evaluated technologies for efficient removal of Clostridium difficile Toxins.
Reviewing and writing publications / mentoring undergraduate and graduate students.
Published 2 co-author publications.
Educational Institution; 10,001+ employees; Higher Education industry
2005 – 2010 (5 years) Cork, Ireland
Obtained Ph.D. in Dr. Douwe van Sinderen’s lab, in Bacterial Genomics and Metagenomics research group, at University College Cork and Alimetary Pharmabiotic Centre. PhD dissertation project on the "Molecular Analysis of Carbohydrate Metabolism in Bifidobacterium breve UCC2003".
Implemented novel to the lab HPAEC system and developed enzymatic methods
Supervised undergraduate students and taught/demonstrated Practical Microbiology to 1st-4th year undergraduate students throughout 4 years of PhD. Visited primary and post primary schools in Cork with purpose to promote an understanding and appreciation of science in youngchildren through presenting basics of microbiology, immunology and human health.
Completed the course on Research Commercialization offered by the top three leading schools in Ireland - TCD, UCC & NIUG, which gave me an understanding of relationship between research and commercial opportunity as well as business perspective on the development of university start-up’s and the commercial use made of research in established businesses, both nationally and internationally.
Published 4 first author publications, including 3 research publications and 1 review.
Privately Held; 1001-5000 employees; Medical Devices industry
2004 – 2004 (less than a year) Pabrade, Lithuania
• As a head of a new microbiology laboratory I was responsible for establishing of fully operated laboratory by setting up the right equipment;
• Planned sterile production and its monitoring using ISO and GMP standards.
• Collaborated with peers and with the management team within the company
Analyst at Quality Control sector
Sicor Biotech UAB / TEVA
2003 – 2004 (1 year) Vilnius, Lithuania
• As a member of the Quality Control sector I was responsible for environmental monitoring, microbial identification, sterility tests of API; purified proteins analysis using SDS-PAGE according to ISO and GMP standards.
• Was responsible for writing relevant SOPs.
• Collaborated with peers within and outside our sector
Laboratory Assistant at the Department of Microbiology
Educational Institution; 1001-5000 employees; Higher Education industry
2003 – 2003 (less than a year) Vilnius, Lithuania
• Analyzed soils samples using classical microbiology methods to predict oil enrichment in the samples.
• Performed protein activity assays;
• Studied thermophilic endospore-forming bacteria isolated from oil wells in Lithuania (Geobacillus sp.), screening for strains with the ability to tolerate n-butanol and to use it as a sole carbon source.
• Collaborated with other scientists at Vilnius University.
Karina Pokusaeva's Projects
Team Members: Karina Pokusaeva, Coreen Johnson, James Versalovic, Chunxu Gao, Vanessa Jackson, Takeshi Yamada, Gabriela Uribe, Tor Savidge, Emily Hollister, David Engler
- January 2011 to Present
Intestinal bacteria produce neurotransmitter, could play role in inflammation
We identified, to our knowledge, the first bifidobacterial strain, Bifidobacterium dentium, that is capable of secreting large amounts of gamma-aminobutyric acid (GABA). This molecule is a major inhibitory neurotransmitter in the central and enteric nervous systems.
GABA is one of the chief inhibitory neurotransmitters in the human central nervous system. It plays a role in regulating pain and some pain relieving drugs currently on the market act by targeting GABA receptors on neural cells.
I am interested in understanding the role the human microbiome might play in pain and scanned the genomes of potentially beneficial intestinal microorganisms, identified by the Human Microbiome Project, for evidence of a gene that would allow them to create GABA.
Lab analysis of metagenomic DNA sequencing data allowed us to demonstrate that microbial glutamate decarboxylase encoding gene is very abundant in intestinal microbiota as compared to other body sites. One of the most prolific producers of GABA was B. dentium, which appears to secrete the compound to help it survive the acid environment.
I was interested to explore if GABA produced by intestinal human isolate B. dentium could have an effect on GABA receptors present in immune cells. Together with our collaborators Dr. Yamada we found that when the cells were exposed to secretions from the bacteria, they exhibited increased expression of the GABAA receptor in the immune cells.
While the findings are preliminary, they suggest the possibility that B. dentium and the compounds it secretes could play a role in reducing inflammation associated with inflammatory bowel diseases.
Karina Pokusaeva's Skills & Expertise
- Cell Culture
- Molecular Biology
- Molecular Cloning
- DNA extraction
- Life Sciences
- Protein Expression
- Gel Electrophoresis
- Protein Purification
- Microbial Genetics
- RNA isolation
- Site-directed Mutagenesis
- DNA microarray
- Gene Expression
- Gene Regulation
- Enzyme Assays
- Enzyme Kinetics
- Vector NTI
- Clone Manager
- GraphPad Prism
- Bacterial Genetics
- Bacterial Culture
- Microarray Analysis
- Assay Development
Karina Pokusaeva's Courses
University College Cork
- Research Commercialization Course
- Scientific Writing Workshop
- Summer Course Glycosciences
Postdoctoral Research Associate
Baylor College of Medicine
- Training on Writing Winning Grants presented by Stephen W. Russell, PhD, of Grant Writers’ Seminars and Workshops
- Life Science Entrepreneurship (MGMT/BIOE 633)
Karina Pokusaeva's Volunteer Experience & Causes
ISAPP Student and Fellow Association
2011 – present (3 years)
- Science and Technology
Affiliated with the International Association for Probiotics and Prebiotics
ESCAPE Family Resource Center
2011 – present (3 years)
ESCAPE’s mission is to prevent child abuse and neglect before a child is hurt by providing intervention, education, and support programs to families in crisis.
Causes I care about:
- Animal Welfare
- Human Rights
- Science and Technology
Organizations I support:
- ISAPP Student and Fellow Association
- ESCAPE Family Resource Center
- Texas Children's Hospital
Karina Pokusaeva's Publications
Authors: Karina Pokusaeva, Wang, X. (First Author), Kim, Y (Second Author), Sturino, J.M. (Fourth Author), Wood T. K. (Last Author)
- Nature Communications
Phages are the most abundant entity in the biosphere and outnumber bacteria by a factor of 10. Phage DNA may also constitute 20% of bacterial genomes; however, its role is ill defined. Here, we explore the impact of cryptic prophages on cell physiology by precisely deleting all nine prophage elements (166 kbp) using Escherichia coli. We find that cryptic prophages contribute significantly to resistance to sub-lethal concentrations of quinolone and β-lactam antibiotics primarily through proteins that inhibit cell division (for example, KilR of rac and DicB of Qin). Moreover, the prophages are beneficial for withstanding osmotic, oxidative and acid stresses, for increasing growth, and for influencing biofilm formation. Prophage CPS-53 proteins YfdK, YfdO and YfdS enhanced resistance to oxidative stress, prophages e14, CPS-53 and CP4-57 increased resistance to acid, and e14 and rac proteins increased early biofilm formation. Therefore, cryptic prophages provide multiple benefits to the host for surviving adverse environmental conditions.
Authors: Karina Pokusaeva, Joseph S. (First Author), Zorych, I (Second Author), Mallick, B. (Third Author), Chang, Y.Y. (Fifth Author), Carroll, R.J. (Sixth Author), Bliznuyk, N. (Last Author)
- Int J Biostat
We propose statistical methods for comparing phenomics data generated by the Biolog Phenotype Microarray (PM) platform for high-throughput phenotyping. Instead of the routinely used visual inspection of data with no sound inferential basis, we develop two approaches. The first approach is based on quantifying the distance between mean or median curves from two treatments and then applying a permutation test; we also consider a permutation test applied to areas under mean curves. The second approach employs functional principal component analysis. Properties of the proposed methods are investigated on both simulated data and data sets from the PM platform.
Authors: Karina Pokusaeva, Neves, A.R, Zomer, A., O'Connell Motherway, M., MacSharry, J., Curley, P., Fitzgerald, G.F., Van Sinderen, D
- Microbial Biotechnology
Growth of Bifidobacterium breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI-type regulator encoded by rbsR, located immediately upstream of rbsA. Gel mobility shift assays using purified RbsRHis indicate that the promoter upstream of rbsABCDK is negatively controlled by RbsRHis binding to an 18 bp inverted repeat and that RbsRHis binding activity is modulated by d-ribose. The rbsK gene of the rbs operon of B. breve UCC2003 was shown to specify a ribokinase (EC 220.127.116.11), which specifically directs its phosphorylating activity towards d-ribose, converting this pentose sugar to ribose-5-phosphate.
Authors: Karina Pokusaeva, Kuisiene, N., Jasinskyte, D., Rutiene, K., Saleikiene, J., Chitavichius, D.
- CENTRAL EUROPEAN JOURNAL OF BIOLOGY
Four novel heat-stable bacteriocin-like substances were found to be produced by Geobacillus stearothermophilus strains isolated from oil-wells in Lithuania. Geobacillus stearothermophilus 32A, 17, 30 and 31 strains were identified as producers of bacteriocins with bactericidal activity against closely related Geobacillus species and several pathogenic strains: Bacillus cereus DSM 12001 and Staphylococcus haemolyticus P903. The secretion of the analysed bacteriocins started during early logarithmic growth and dropped sharply after the culture entered the stationary phase of growth. The antimicrobial activity of the bacteriocins against sensitive indicator cells disappeared after treatment with proteolytic enzymes, indicating their proteinaceous nature. Bacteriocins were stable throughout the pH range between 4 and 10, and no loss in activity was noted following temperature exposures up to 100°C. Direct detection of antibacterial activity on SDS-PAGE suggests that the inhibitory peptides have a molecular weight of 6–7.5 kDa. Such bacteriocins with broad activity spectra, including antipathogenic action, are attractive to the biotechnology industry as they could be used as antimicrobial agents in medicine, agriculture and food products
Authors: Karina Pokusaeva, O'Connell-Motherway, M., Zomer, A., Fitzgerald, G.F., Van Sinderen, D.
- Appl Environ Microbiol.
Two -glucosidase-encoding genes (agl1 and agl2) from Bifidobacterium breve UCC2003 were identified and characterized. Based on their similarity to characterized carbohydrate hydrolases, the Agl1 and Agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the -1,6-glucosidases (EC 18.104.22.168). Recombinant Agl1 and Agl2 into which a His12 sequence was incorporated (Agl1His and Agl2His, respectively) exhibited hydrolytic activity towards panose, isomaltose, isomaltotriose, and four sucrose isomers—palatinose, trehalulose, turanose, and maltulose—while also degrading trehalose and, to a lesser extent, nigerose. The preferred substrates for both enzymes were panose, isomaltose, and trehalulose. Furthermore, the pH and temperature optima for both enzymes were determined, showing that Agl1His exhibits higher thermo and pH optima than Agl2His. The two purified -1,6-glucosidases were also shown to have transglycosylation activity, synthesizing oligosaccharides from palatinose, trehalulose, trehalose, panose, and isomaltotriose.
Authors: Karina Pokusaeva, Mary O'Connell-Motherway, Aldert Zomer, , Gerald F. Fitzgerald, Douwe van Sinderen
- Appl Environ Microbiol
- March 2011
Cellodextrins, the incomplete hydrolysis products from insoluble cellulose, are accessible as a carbon source to certain members of the human gut microbiota, such as Bifidobacterium breve UCC2003. Transcription of the cldEFGC gene cluster of B. breve UCC2003 was shown to be induced upon growth on cellodextrins, implicating this cluster in the metabolism of these sugars. Phenotypic analysis of a B. breve UCC2003::cldE insertion mutant confirmed that the cld gene cluster is exclusively required for cellodextrin utilization by this commensal. Moreover, our results suggest that transcription of the cld cluster is controlled by a LacI-type regulator encoded by cldR, located immediately upstream of cldE. Gel mobility shift assays using purified CldR(His) (produced by the incorporation of a His(12)-encoding sequence into the 3' end of the cldC gene) indicate that the cldEFGC promoter is subject to negative control by CldR(His), which binds to two inverted repeats. Analysis by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) of medium samples obtained during growth of B. breve UCC2003 on a mixture of cellodextrins revealed its ability to utilize cellobiose, cellotriose, cellotetraose, and cellopentaose, with cellotriose apparently representing the preferred substrate. The cldC gene of the cld operon of B. breve UCC2003 is, to the best of our knowledge, the first described bifidobacterial β-glucosidase exhibiting hydrolytic activity toward various cellodextrins.
Authors: Karina Pokusaeva, Gerald F. Fitzgerald, Douwe van Sinderen
- Genes and Nutrition
- August 2011
Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plant-derived oligo- and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.
Immunomodulatory Effects of the Intestinal Microbiota and Compounds Derived from Beneficial Microbes
- Functional Food Reviews
Among the numerous health benefits attributed to beneficial bacteria, the abilities of microbes to interact with the epithelial barrier and immune system of the host are being explored by an increasing number of experimental studies. A greater understanding of how these bacteria interact with the host immune system will lead to creation of new functional foods targeted to improve human health. This article summarizes some mechanisms by which probiotics benefit human gut health and focuses on the immunomodulatory effects of probiotic bacteria, including lactobacilli and bifidobacteria. It also provides an overview of the current knowledge of host–microbe interactions in the human gastrointestinal tract and discusses the health-promoting benefits of probiotics with respect to immunomodulation.
Karina Pokusaeva's Languages
English(Full professional proficiency)
Lithuanian(Native or bilingual proficiency)
Russian(Native or bilingual proficiency)
Karina Pokusaeva's Education
Karina Pokusaeva's Additional Information
Cooking, traveling, latin dancing
- Groups and Associations:
Member of ISAPP - http://www.isapp.net/ Member of ESNM - http://www.esnm.eu/index.php
- Honors and Awards:
2005-2009 A full-time scholarship to do PhD studies at University College Cork, Ireland
2008 - SGM Scientific Meeting Grant 2008 (to attend SGM meeting)
2008 - SGM Scientific Meeting Grant 2008 (to attend Ninth Symposium on Lactic Acid Bacteria)
2009 - Postdoctoral Scholar Registration Grant 2009 (to Attend Sackler Colloquia, Microbes and Health)
2011 - Travel scholarship (to attend ISAPP-SFA meeting in Berkeley, CA)
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