@article{rawson_hooper_hansen_gazdik stofer_2023, title={Celiac Disease and a Gluten-Free Diet Lead to Loss of Methanobrevibacter from the Gut Microbiome}, volume={7}, url={http://dx.doi.org/10.26685/urncst.393}, DOI={10.26685/urncst.393}, abstractNote={Introduction: The importance of the human microbiome has become well known in recent years. The microbiome contains a diverse number of organisms including bacteria, archaea, fungi, and protozoa, which when imbalanced, can lead to a variety of dysbioses. Celiac disease (CD) is a condition where the immune system responds to gluten, a protein found in wheat, leading to chronic inflammation in the small intestine. Studies have found that microbial dysbiosis is often associated with patients who have CD, but few have looked at how gluten affects the microbiome in comparison to CD. This research sought to identify microbiome changes between people with CD (on a gluten-free diet), those on a gluten-free diet (without CD), and a control group (without CD and a gluten-free diet). Methods: Twenty-nine eligible participants (screened via a survey) provided a single stool sample (12 CD, 8 gluten-free, and 9 control). The microbial DNA was extracted from the stool samples using the QIAamp PowerFecal DNA Kit (Qiagen) and the V3/V4 region of 16s RNA using the 600-cycleMiSeq kit (Illumina). Sequenced DNA was sent to the University of Utah for analysis. Changes in microbiome diversity were statistically analyzed using a Kruskal-Wallis analysis. Results: No change in alpha or beta diversity was seen between any study groups. In addition, significance was not observed in common phyla normally affected by CD (Firmicutes, Bacteroides, and Actinobacteria). However, a statistically significant difference was seen in the archaeal genera Methanobrevibacter, which was found only in the control group (p = 0.0212). Discussion: Previously reported changes in the microbiome of CD patients were not observed in this study. However, changes could be seen in the archaeal genius, Methanobrevibacter, which was found only control group at an abundance of 3.3%. Thus, when CD individuals were compared to healthy individuals with similar gluten-free diets there was little difference in gut microbial species suggesting that gluten-free diet may normalize CD-related microbiome changes. Conclusion: The absence of Methanobrevibacter from CD and gluten-free groups requires additional analysis to understand what role Methanobrevibacter plays in the microbiome and how a gluten-free diet may affect that role.}, number={2}, journal={Undergraduate Research in Natural and Clinical Science and Technology (URNCST) Journal}, publisher={Undergraduate Research in Natural and Clinical Science and Technology (URNCST) Journal}, author={Rawson, Clayton and Hooper, Victoria and Hansen, Riley and Gazdik Stofer, Michaela A.}, year={2023}, month={Feb}, pages={1–9} }
 @article{washburn_sandberg_gazdik stofer_2022, title={Supplementation of a single species probiotic does not affect diversity and composition of the healthy adult gastrointestinal microbiome}, volume={28}, ISSN={2666-1497}, url={http://dx.doi.org/10.1016/j.hnm.2022.200148}, DOI={10.1016/j.hnm.2022.200148}, abstractNote={Over several years, consumer probiotic consumption has increased substantially. Consequently, the number of over-the-counter probiotic products available to consumers has also increased. Many consumers use probiotics for preventative purposes rather than to treat specific illnesses. The influence of probiotics on the healthy human gut microbiome has not been extensively studied and many questions remain regarding the influence of probiotic supplementation on existing gut flora. In this study, the effect of a commercial probiotic containing Bifidobacterium infantis on the composition and diversity of gut flora in healthy adults was examined. Thirty participants were enrolled in the study and randomly assigned to probiotic (n = 15) or placebo (n = 15) groups. Over the course of the study, three stool samples were collected to facilitate baseline, probiotic/placebo effect, and return to baseline measurements. The probiotic/placebo effect samples were collected after taking a probiotic/placebo tablet daily for 30 days, and the return to baseline sample was collected 30 days after completing the treatment course. V3/V4 16S rRNA sequencing was performed on all samples and data was analyzed using QIIME. No significant difference in gut community diversity or composition between probiotic and placebo groups was observed. This finding suggests that use of a single species probiotic in healthy individuals does not significantly influence microbial gastrointestinal diversity.}, journal={Human Nutrition & Metabolism}, publisher={Elsevier BV}, author={Washburn, Rachel L. and Sandberg, Daniel and Gazdik Stofer, Michaela A.}, year={2022}, month={Jun}, pages={200148} }
 @article{gazdik stofer_2020, title={Maggie’s Illness: Protein Structure and Function in Cystic Fibrosis}, url={https://static-nsta-org.webpkgcache.com/doc/-/s/static.nsta.org/case_study_docs/case_studies/cf_protein_structure.pdf}, journal={National Center for Case Study Teaching in Science}, publisher={SUNY Buffalo / NSTA}, author={Gazdik Stofer, Ma}, year={2020} }
 @article{gazdik stofer_2020, title={The Unluckiest Man in the World? An Examination of Immune System Function}, url={https://static-nsta-org.webpkgcache.com/doc/-/s/static.nsta.org/case_study_docs/case_studies/hiv_cured.pdf}, journal={National Center for Case Study Teaching in Science}, publisher={SUNY Buffalo / NSTA}, author={Gazdik Stofer, Ma}, year={2020} }
 @article{ford_coombs_stofer_lopansri_webb_ostronoff_asch_hoda_2019, title={Decrease in vancomycin-resistant<i>Enterococcus</i>colonization associated with a reduction in carbapenem use as empiric therapy for febrile neutropenia in patients with acute leukemia}, volume={40}, ISSN={0899-823X 1559-6834}, url={http://dx.doi.org/10.1017/ice.2019.93}, DOI={10.1017/ice.2019.93}, abstractNote={Abstract}, number={7}, journal={Infection Control & Hospital Epidemiology}, publisher={Cambridge University Press (CUP)}, author={Ford, Clyde D. and Coombs, Jana and Stofer, Michaela Gazdik and Lopansri, Bert K. and Webb, Brandon J. and Ostronoff, Fabiana and Asch, Julie and Hoda, Daanish}, year={2019}, month={May}, pages={774–779} }
 @article{ford_stofer_coombs_lopansri_webb_motyckova_petersen_2017, title={Decrease in Vancomycin-Resistant Enterococcus Colonization After Extensive Renovation of a Unit Dedicated to the Treatment of Hematologic Malignancies and Hematopoietic Stem-Cell Transplantation}, volume={38}, url={http://dx.doi.org/10.1017/ice.2017.138}, DOI={10.1017/ice.2017.138}, abstractNote={OBJECTIVEWhile a direct relation between hospital construction and concomitant infection rates has been clearly established, few data are available regarding the environmental decontamination effects of renovation in which surfaces are replaced and regarding subsequent infection incidence.}, number={9}, journal={Infection Control & Hospital Epidemiology}, publisher={Cambridge University Press (CUP)}, author={Ford, Clyde D. and Stofer, Michaela A. Gazdik and Coombs, Jana and Lopansri, Bert K. and Webb, Brandon J. and Motyckova, Gabriela and Petersen, Finn Bo}, year={2017}, month={Sep}, pages={1055–1061} }
 @article{webb_healy_majers_burr_gazdik_lopansri_hoda_petersen_ford_2017, title={Prediction of Bloodstream Infection Due to Vancomycin-Resistant Enterococcus in Patients Undergoing Leukemia Induction or Hematopoietic Stem-Cell Transplantation}, volume={64}, url={http://dx.doi.org/10.1093/cid/cix232}, DOI={10.1093/cid/cix232}, abstractNote={Bloodstream infection (BSI) to due vancomycin-resistant Enterococcus (VRE) is an important complication of hematologic malignancy. Determining when to use empiric anti-VRE antibiotic therapy in this population remains a clinical challenge. A single-center cohort representing 664 admissions for induction or hematopoietic stem-cell transplant (HSCT) from 2006 to 2014 was selected. We derived a prediction score using risk factors for VRE BSI and evaluated the model’s predictive performance by calculating it for each of 16232 BSI at-risk inpatient days. VRE BSI incidence was 6.5% of admissions (2.7 VRE BSI per 1000 BSI at-risk days). Adjusted 1-year mortality and length of stay were significantly higher in patients with VRE BSI. VRE colonization (adjusted odds ratio [aOR] = 8.4; 95% confidence interval [CI] = 3.4–20.6; P < .0001), renal insufficiency (aOR = 2.4; 95% CI = 1.0–5.8; P = .046), aminoglycoside use (aOR = 4.7; 95% CI = 2.2–9.8; P < .0001), and antianaerobic antibiotic use (aOR = 2.8; 95% CI = 1.3–5.8; P = .007) correlated most closely with VRE BSI. A prediction model with optimal performance included these factors plus gastrointestinal disturbance, severe neutropenia, and prior beta-lactam antibiotic use. The score effectively risk-stratified patients (area under the receiver operating curve = 0.84; 95% CI = 0.79–0.89). At a threshold of ≥5 points, per day probability of VRE BSI was increased nearly 4-fold. This novel predictive score is based on risk factors reflecting a plausible pathophysiological model for VRE BSI in patients with hematological malignancy. Integrating VRE colonization status with risk factors for developing BSI is a promising method of guiding rational use of empiric anti-VRE antimicrobial therapy in patients with hematological malignancy. Validation of this novel predictive score is needed to confirm clinical utility.}, number={12}, journal={Clinical Infectious Diseases}, publisher={Oxford University Press (OUP)}, author={Webb, Brandon J. and Healy, Regan and Majers, Jacob and Burr, Zachary and Gazdik, Michaela and Lopansri, Bert and Hoda, Daanish and Petersen, Finn Bo and Ford, Clyde}, year={2017}, month={Jun}, pages={1753–1759} }
 @article{ford_gazdik_lopansri_webb_mitchell_coombs_hoda_petersen_2017, title={Vancomycin-Resistant Enterococcus Colonization and Bacteremia and Hematopoietic Stem Cell Transplantation Outcomes}, volume={23}, url={http://dx.doi.org/10.1016/j.bbmt.2016.11.017}, DOI={10.1016/j.bbmt.2016.11.017}, abstractNote={The association between pre-hematopoietic stem cell transplantation (HSCT) vancomycin-resistant Enterococcus (VRE) colonization, HSCT-associated VRE bacteremia, and HSCT mortality is disputed. We studied 161 consecutive patients with acute leukemia who underwent HSCT at our hospital between 2006 and 2014, of whom 109 also received leukemia induction/consolidation on our unit. All inpatients had weekly VRE stool surveillance. Pre-HSCT colonization was not associated with increases in HSCT mortality but did identify a subgroup of HSCT recipients with a higher risk for VRE bacteremia and possibly bacteremia from other organisms. The major risk factor for pre-HSCT colonization was the number of hospital inpatient days between initial admission for leukemia and HSCT. One-third of evaluable patients colonized before HSCT were VRE-culture negative on admission for HSCT; these patients had an increased risk for subsequent VRE stool surveillance positivity but not VRE bacteremia. Molecular typing of VRE isolates obtained before and after HSCT showed that VRE strains frequently change. Postengraftment VRE bacteremia was associated with a much higher mortality than pre-engraftment VRE bacteremia. Pre-engraftment bacteremia from any organism was associated with an alternative donor and resulted in an increase in hospital length of stay and cost. Mortality was similar for pre-engraftment VRE bacteremia and pre-engraftment bacteremia due to other organisms, but mortality associated with post-engraftment VRE bacteremia was higher and largely explained by associated severe graft-versus-host disease and relapsed leukemia. These data emphasize the importance of distinguishing between VRE colonization before HSCT and at HSCT, between pre-engraftment and postengraftment VRE bacteremia, and between VRE bacteremia and bacteremia from other organisms.}, number={2}, journal={Biology of Blood and Marrow Transplantation}, publisher={Elsevier BV}, author={Ford, Clyde D. and Gazdik, Michaela A. and Lopansri, Bert K. and Webb, Brandon and Mitchell, Birgitta and Coombs, Jana and Hoda, Daanish and Petersen, Finn Bo}, year={2017}, month={Feb}, pages={340–346} }
 @article{ranganathan_bai_lyubetskaya_knapp_peterson_gazdik_c. gomes_galagan_mcdonough_2016, title={Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon}, volume={44}, url={http://dx.doi.org/10.1093/nar/gkv889}, DOI={10.1093/nar/gkv889}, abstractNote={Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we used experimental and computational approaches to characterize Cmr's DNA binding properties and identify a putative regulon. Cmr binds a 16-bp palindromic site that includes four highly conserved nucleotides that are required for DNA binding. A total of 368 binding sites, distributed in clusters among ∼200 binding regions throughout the Mycobacterium bovis BCG genome, were identified using ChIP-seq. One of the most enriched Cmr binding sites was located upstream of the cmr promoter, and we demonstrated that expression of cmr is autoregulated. cAMP affected Cmr binding at a subset of DNA loci in vivo and in vitro, including multiple sites adjacent to members of the DosR (DevR) dormancy regulon. Our findings of cooperative binding of Cmr to these DNA regions and the regulation by Cmr of the DosR-regulated virulence gene Rv2623 demonstrate the complexity of Cmr-mediated gene regulation and suggest a role for Cmr in the biology of persistent TB infection.}, number={1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Ranganathan, Sridevi and Bai, Guangchun and Lyubetskaya, Anna and Knapp, Gwendowlyn S. and Peterson, Matthew W. and Gazdik, Michaela and C. Gomes, Antonio L. and Galagan, James E. and McDonough, Kathleen A.}, year={2016}, month={Jan}, pages={134–151} }
 @article{gazdik_coombs_burke_lopansri_2016, title={Comparison of Two Culture Methods for Use in Assessing Microbial Contamination of Duodenoscopes}, volume={54}, url={http://dx.doi.org/10.1128/jcm.02754-15}, DOI={10.1128/jcm.02754-15}, abstractNote={ABSTRACT}, number={2}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Gazdik, Michaela A. and Coombs, Jana and Burke, John P. and Lopansri, Bert K.}, editor={Diekema, D. J.Editor}, year={2016}, month={Feb}, pages={312–316} }
 @article{webb_brunner_ford_gazdik_petersen_hoda_2016, title={Fecal microbiota transplantation for recurrentClostridium difficileinfection in hematopoietic stem cell transplant recipients}, volume={18}, url={http://dx.doi.org/10.1111/tid.12550}, DOI={10.1111/tid.12550}, abstractNote={Abstract}, number={4}, journal={Transplant Infectious Disease}, publisher={Wiley}, author={Webb, B.J. and Brunner, A. and Ford, C.D. and Gazdik, M.A. and Petersen, F.B. and Hoda, D.}, year={2016}, month={Aug}, pages={628–633} }
 @article{ford_lopansri_gazdik_webb_snow_hoda_adams_petersen_2016, title={Room contamination, patient colonization pressure, and the risk of vancomycin-resistant Enterococcus colonization on a unit dedicated to the treatment of hematologic malignancies and hematopoietic stem cell transplantation}, volume={44}, ISSN={0196-6553}, url={http://dx.doi.org/10.1016/j.ajic.2016.03.044}, DOI={10.1016/j.ajic.2016.03.044}, abstractNote={Contaminated surfaces and colonization pressure are risk factors for vancomycin-resistant Enterococcus (VRE) colonization in intensive care units (ICUs). Whether these apply to modern units dedicated to the care of hematologic malignancies and hematopoietic stem cell transplant (HSCT) procedures is unknown.We reviewed the records of 780 consecutive admissions for acute leukemia, autologous HSCT, or allogeneic HSCT in which the patient was at risk for hospital-acquired VRE and underwent weekly surveillance. We also obtained staff and room cultures, observed staff behavior, and performed VRE molecular strain typing on selected isolates.The overall rate of VRE colonization was 11.4 cases/1,000 patient days. Cultures of room surfaces revealed VRE isolates in 10% of terminally cleaned rooms. A prior VRE-colonized room occupant did not increase risk, and paired isolates from 20 patients and prior occupants were indistinguishable on molecular typing in only 1 pair. VRE colonization pressure was significantly associated with acquisition. Cultures of unit personnel and shared equipment were negative except for weighing scales. Observation of unit clinical personnel showed high compliance for hand sanitation and but less so for gowns. Conversely, ancillary staff showed poor compliance.Transmission of VRE from room surfaces seems to be an infrequent event. Encouraging adherence to surveillance, disinfection, and contact isolation protocols may decrease VRE colonization rates.}, number={10}, journal={American Journal of Infection Control}, publisher={Elsevier BV}, author={Ford, Clyde D. and Lopansri, Bert K. and Gazdik, Michaela A. and Webb, Brandon and Snow, Gregory L. and Hoda, Daanish and Adams, Barbara and Petersen, Finn Bo}, year={2016}, month={Oct}, pages={1110–1115} }
 @article{ford_lopansri_gazdik_snow_webb_konopa_petersen_2015, title={The clinical impact of vancomycin‐resistant <i><scp>E</scp>nterococcus</i> colonization and bloodstream infection in patients undergoing autologous transplantation}, volume={17}, ISSN={1398-2273 1399-3062}, url={http://dx.doi.org/10.1111/tid.12433}, DOI={10.1111/tid.12433}, abstractNote={Abstract}, number={5}, journal={Transplant Infectious Disease}, publisher={Wiley}, author={Ford, C.D. and Lopansri, B.K. and Gazdik, M.A. and Snow, G.L. and Webb, B.J. and Konopa, K.L. and Petersen, F.B.}, year={2015}, month={Oct}, pages={688–694} }
 @article{gazdik_2014, title={Mystery of the Seven Deaths: A Case Study on Cellular Respiration}, volume={43}, url={http://www.jstor.org/stable/43633230}, note={Retrieved August 29, 2021}, number={5}, journal={Journal of College Science Teaching}, author={Gazdik, M.}, year={2014}, pages={71–73} }
 @inbook{mystery of the seven deaths: a case study on cellular respiration_2014, url={https://my.nsta.org/resource/94400}, booktitle={Science Stories You Can Count On: 51 Case Studies with Quantitative Reasoning in Biology}, year={2014} }
 @article{casey_ford_gazdik_2014, title={The role of transcriptional regulation in maintaining the availability of mycobacterial adenylate cyclases}, volume={2}, ISSN={2167-8359}, url={http://dx.doi.org/10.7717/peerj.298}, DOI={10.7717/peerj.298}, abstractNote={Mycobacterium species have a complex cAMP regulatory network indicated by the high number of adenylate cyclases annotated in their genomes. However the need for a high level of redundancy in adenylate cyclase genes remains unknown. We have used semiquantitiative RT-PCR to examine the expression of eight Mycobacterium smegmatis cyclases with orthologs in the human pathogen Mycobacterium tuberculosis, where cAMP has recently been shown to be important for virulence. All eight cyclases were transcribed in all environments tested, and only four demonstrated environmental-mediated changes in transcription. M. smegmatis genes MSMEG_0545 and MSMEG_4279 were upregulated during starvation conditions while MSMEG_0545 and MSMEG_4924 were downregulated in H2O2 and MSMEG_3780 was downregulated in low pH and starvation. Promoter fusion constructs containing M. tuberculosis H37Rv promoters showed consistent regulation compared to their M. smegmatis orthologs. Overall our findings indicate that while low levels of transcriptional regulation occur, regulation at the mRNA level does not play a major role in controlling cellular cyclase availability in a given environment.}, journal={PeerJ}, publisher={PeerJ}, author={Casey, Sarah J. and Ford, Mica J. and Gazdik, Michaela A.}, year={2014}, month={Mar}, pages={e298} }
 @book{reynolds_hall_hylton_rutherford_tarver_thompson_waldrop_wilson_gazdik_2012, title={Solenostemon scutellarioides cytosolic glyceraldehyde-3-phosphate dehydrogenase (gapC) gene, partial cds}, number={JX419387}, institution={National Center for Biotechnology Information}, author={Reynolds, K.D. and Hall, T.M and Hylton, K.E and Rutherford, M.R. and Tarver, D.T. and Thompson, E.L. and Waldrop, S.G. and Wilson, W.A. and Gazdik, M.A.}, year={2012} }
 @article{gazdik stofer_powell_2012, title={The Impact of Student-Directed Research at an Undergraduate  Liberal Arts Institution}, volume={33}, journal={Council on Undergraduate Research Quarterly}, author={Gazdik Stofer, Michaela and Powell, Jason}, year={2012}, pages={22–27} }
 @book{atkins-ball_colon-berlingeri_fladd_gazdik_gomell_ovalle_romano_tempest_2011, title={To Test or Not to Test: The Role of Genetic Counseling}, institution={NHGRI}, author={Atkins-Ball, D. and Colon-Berlingeri, L. and Fladd, L. and Gazdik, M.A. and Gomell, L. and Ovalle, R. and Romano, S. and Tempest, T.}, year={2011} }
 @article{gazdik_bai_wu_mcdonough_2009, title={Rv1675c (cmr) regulates intramacrophage and cyclic AMP-induced gene expression inMycobacterium tuberculosis-complex mycobacteria}, volume={71}, url={http://dx.doi.org/10.1111/j.1365-2958.2008.06541.x}, DOI={10.1111/j.1365-2958.2008.06541.x}, abstractNote={Summary}, number={2}, journal={Molecular Microbiology}, publisher={Wiley}, author={Gazdik, Michaela A. and Bai, Guangchun and Wu, Yan and McDonough, Kathleen A.}, year={2009}, month={Jan}, pages={434–448} }
 @article{gazdik_2009, title={Use of rubrics as an assessment tool}, volume={15}, number={2}, journal={Focus on Microbiology Education}, author={Gazdik, M.A.}, year={2009}, pages={9–11} }
 @article{bai_gazdik_schaak_mcdonough_2007, title={The
            Mycobacterium bovis
            BCG Cyclic AMP Receptor-Like Protein Is a Functional DNA Binding Protein In Vitro and In Vivo, but Its Activity Differs from That of Its
            M. tuberculosis
            Ortholog, Rv3676}, volume={75}, url={http://dx.doi.org/10.1128/iai.00658-07}, DOI={10.1128/iai.00658-07}, abstractNote={ABSTRACT}, number={11}, journal={Infection and Immunity}, publisher={American Society for Microbiology}, author={Bai, Guangchun and Gazdik, Michaela A. and Schaak, Damen D. and McDonough, Kathleen A.}, year={2007}, month={Nov}, pages={5509–5517} }
 @phdthesis{gazdik_2007, title={Unraveling the cAMP-regulatory networks of Mycobacterium bovis BCG and Mycobacterium tuberculosis}, school={School of Public Health, SUNY Albany}, author={Gazdik, M.A.}, year={2007} }
 @article{gazdik_mcdonough_2005, title={Identification of Cyclic AMP-Regulated Genes in
            Mycobacterium tuberculosis
            Complex Bacteria under Low-Oxygen Conditions}, volume={187}, url={http://dx.doi.org/10.1128/jb.187.8.2681-2692.2005}, DOI={10.1128/jb.187.8.2681-2692.2005}, abstractNote={ABSTRACT}, number={8}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Gazdik, Michaela A. and McDonough, Kathleen A.}, year={2005}, month={Apr}, pages={2681–2692} }
 @phdthesis{gazdik_2004, title={Evidence for an unexplored regulatory system in mycobacteria: The role of cAMP in Mycobacterium bovis BCG}, school={School of Public Health, SUNY Albany}, author={Gazdik, M.A.}, year={2004} }
 @phdthesis{gazdik_2001, title={Production and analysis of transgenic tobacco containing altered vitamin C content}, school={Rutgers University}, author={Gazdik, M.A.}, year={2001} }