{"id":241,"date":"2018-03-02T21:21:21","date_gmt":"2018-03-02T21:21:21","guid":{"rendered":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/?page_id=241"},"modified":"2024-08-15T21:04:20","modified_gmt":"2024-08-15T21:04:20","slug":"past-members","status":"publish","type":"page","link":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/past-members\/","title":{"rendered":"Past Members"},"content":{"rendered":"

Albert M\u00fcller\"\"
\nDept\/Org: Civil & Environmental Engineering
\n<\/em>Staff Scientist, 2015-2024<\/em><\/p>\n

I\u2019ve always been fascinated by the concept of microbial ecology \u2013 the idea that nature is, to a large degree, based on the actions and interactions of microorganisms that seem to be completely hidden to our senses, but nevertheless can be figured out in extreme detail using the clever tricks of molecular microbiology.\u00a0<\/em>During my PhD at DOME in Vienna, I did research on symbiosis (between amoebae and their endosymbionts), biogeography (of thermophilic spore-formers in the world\u2019s oceans), carbon degradation (in Arctic marine sediments), and diversity and phylogeny of sulfate reducing microorganisms. <\/em>Here at Stanford, I\u2019m trying to figure out the spatial constraints on microbial syntrophy when bacteria are faced with insoluble substrates and how methanogens allocate their proteome under different growth conditions.\u00a0<\/em>Outside the lab, I like warm weather, being in nature, observing animals, video games, music, and science fiction.<\/em><\/p>\n

Ali McCully\"\"
\nDept\/Org: Civil & Environmental Engineering<\/em>
\nPost-Doc, 2018-2022<\/em><\/p>\n

I am interested in how diverse microbial metabolisms interact and shape global processes, especially in anaerobic communities. During my PhD at Indiana University, I studied metabolic interactions within a model bacterial coculture to uncover principles that govern microbial mutualisms. After graduating in 2018, I joined the Spormann lab to study the physiology and metabolism of\u00a0microbes living within the deep-sea biosphere. Outside of lab I enjoy playing the bass clarinet, exploring new restaurants, and interacting with animals.<\/em><\/p>\n

Wenyu Gu\"\"
\nDept\/Org: Civil & Environmental Engineering
\n<\/em>Post-Doc, 2017-2022<\/em><\/p>\n

My research goal is to understand and develop novel microbial mechanisms to address environmental and industrial problems, with current research focusing on enzymology of reductive dehalogenase. I\u2019m an animal lover, enjoy reading and traveling.<\/em><\/p>\n

\"\"<\/p>\n

Frauke Kracke
\nDept\/Org: Civil & Environmental Engineering
\n<\/em>Post-Doc, 2016-2022<\/em><\/p>\n

I\u2019m a biochemical engineer by training and I find my motivation in engineering microbial solutions for a more sustainable human future. During my PhD at the University of Queensland, Australia, I started working on bio-electrochemical systems for production of chemicals and fuels from renewables. By using an integrated approach of in silico modelling and in vivo pure culture studies, I developed a strong background in bioelectrochemistry and cellular electron transfer mechanisms. After graduating from UQ in April 2016, I joined the Spormann lab where I continue to look at exciting microbe-electrode interactions with a focus on production applications.<\/em><\/p>\n

John “Jack” Ruth
\nDept\/Org: Chemical Engineering
\n<\/em>Ph.D. Student, 2017-2021\"\"<\/em><\/p>\n

I\u2019m interested in the interface of biology and energy. I\u2019m currently researching the use of anaerobic enzyme complexes from <\/em>Methanococcus maripaludis for cathodic electrosynthesis, focusing on direct and mediated electron transfer from cathodes to oxidoreductase enzymes. When not in lab, I like to ski, play guitar, read novels and go hiking.<\/em><\/p>\n

Jessica Grembi\"\"
\nDept\/Org: Civil & Environmental Engineering
\n<\/em>Ph.D. Student, 2014-2019<\/em><\/p>\n

My interests lay at the intersection of microbial ecology and international public health.\u00a0 My research focuses on the effects of water, sanitation, handwashing (WSH) and nutritional interventions on the\u00a0carriage of enteropathogens for children in low- and middle-income countries.\u00a0 I am particularly interested in how enteropathogen\u00a0exposure early in life can influence the\u00a0development of a gut ecosystem\u00a0that allows optimal absorption of nutrients by the host. I’m particularly interested in the potential for a microbial biomarker for a difficult to diagnose\u00a0subclinical\u00a0condition that reduces the absorptive capacity and increases permeability of the small intestine (environmental enteropathy), understanding the root causes of the pathology, and how these effects might be mitigated through the gut microbial ecosystem.\u00a0<\/em><\/p>\n

Miriam Windler\"\"
\nDept\/Org: Civil & Environmental Engineering
\nPost-Doc, 2015-2019<\/em><\/p>\n

I\u2019m a biologist with a background in plant physiology and phycology. My research interest is mainly the influence of bacterial communities on algal productivity. During my PhD at the University of Konstanz, I studied the effect of bacteria on formation of biofilm and extracellular polymeric substances of algae. Here at the Stanford University, I am focused on how bacteria can increase algal production of biofuel precursors.<\/em><\/p>\n

Ross Milton\"\"
\nDept\/Org: University of Geneva
\n<\/em><\/p>\n

After pursuing a BSc and PhD (Chemistry and Electrochemistry) in the United Kingdom of everlasting sunshine (\u2026<\/a>), Ross made the decision to move to the States to develop his scientific career and experience blue skies for the first time. He is interested in internal electron transfer mechanisms\/pathways of oxidoreductases and developing electron transfer strategies with electrodes, with current research focusing on nitrogenase (the role of ATP hydrolysis) and heterodisulfide reductase (flavin-based electron b<\/em>ifurcation). In his free time he enjoys outdoor activities (hiking\/camping) and has recently taken up squash. He believes that he has all of the funniest jokes and wishes that others would appreciate his jokes more.<\/em><\/p>\n

\"\"<\/p>\n

Srijay Rajan
\nDept\/Org: Civil & Environmental Engineering
\n<\/em>Research Assistant,\u00a0 July, 2015 – March, 2018<\/em><\/p>\n

I\u2019m using an in vitro pharmacokinetic\/pharmacodynamic (PK\/PD) model to research biofilm physiology and antibiotic killing of biofilms. I enjoy hiking, golfing, cooking, reading, and listening to podcasts.<\/em><\/p>\n

Ian Avery Bick\"\"
\nDept\/Org: Civil & Environmental Engineering
\n<\/em>M.S. Student, 2016-2018<\/em><\/p>\n

Avery is a M.S. student in Environmental Engineering & Science with research interests in water quality,\u00a0biological treatment processes, and environmental justice. In the Spormann lab he studies reductive dehalogenation as well as\u00a0the effect of starvation on dechlorination rates in reducing and oxidizing conditions through live\/dead staining and flow cytometry. Outside of the lab, he enjoys biking, producing music, and reading Isaac Asimov and Philip K. Dick novels.<\/em><\/p>\n

Ann Karim\"\"
\nDept\/Org: Zymergen
\n<\/em>Ph.D. Student, April, 2011-December, 2017<\/em><\/p>\n

I am interested in strain engineering of non-traditional microbes.\u00a0 During my time in the Spormann Lab I worked on developing tools for controlling of protein levels in\u00a0<\/em>Methanosarcina acetivorans\u00a0C2A.\u00a0 These tools included a promoter library, a ribosome binding site library, identifying new regulatory sequences for enhancing protein production, and CRISPR interference.<\/em><\/p>\n

Koshlan Mayer-Blackwell
\nPh.D. Student, October, 2010-May, 2016<\/em>
\nDept\/Org: Civil And Environmental Engineering<\/em><\/p>\n

Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. Here we report the development of a nanoliter qPCR platform to identify organohalogen-respiring bacteria and populations by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assays can be operated in parallel within a 5184-well nanoliter qPCR (nL-qPCR) chip at a single annealing temperature and buffer condition. We developed a robust bioinformatics approach to select from thousands of computationally proposed primer pairs those that are specific to individual rdh gene groups and compatible with a single amplification condition. We validated hundreds of the most selective qPCR assays and examined their performance in a trichloroethene-degrading bioreactor, revealing population structures as well as their unexpected shifts in abundance and community dynamics.<\/em><\/p>\n

Holly Sewell
\nPhD student, September, 2010-September, 2015<\/em>
\nDept\/Org: Civil & Environmental Engineering<\/em><\/p>\n

External electron transfer mechanisms for cathodic electron uptake.<\/em><\/p>\n

Anutthaman Parthasarathy
\nPost-Doc, October, 2012 – April, 2015<\/em>
\nDept\/Org: Civil & Environmental Engineering<\/em><\/p>\n

I am a biochemist by training. My specialization is in anaerobic enzymology and metabolism. i have worked on amino acid catabolism in mesophiles and extremophiles, protein purification, protein spectroscopy, CoA biochemistry and hexane degradation from 2005-12. At the Spormann lab, i am working on the heterologous overproduction of the vcrA (reductive dehalogenase) in E. coli with the aim of obtaining pure protein for crystallisation trials. Interest in Biochemical characterisation of vcrA (reductive dehalogenase).<\/em><\/p>\n

Janus Haagensen
\nFebruary, 2008 – April, 2015<\/em>
\nDept\/Org: DTU Centre for bio sustainability, H\u00f8rsholm, Denmark<\/em><\/p>\n

Phenotypic diversity and bistability in<\/em> Vibrio cholerae.<\/p>\n

Anne-Kristin Kaster
\nMarch, 2011 – June, 2014<\/em>
\nDept\/Org: Leibniz-Institut DSMZ<\/em>
\nJunior research Group Leader<\/em><\/p>\n

Reductive dehalogenation; single cell genomics<\/em><\/p>\n

Simone Haag
\nSeptember, 2013-February, 2014<\/em><\/p>\n

Svenja Lohner
\nPh.D. Student, November, 2008-September, 2013<\/em>
\nDept\/Org: Science Buddies<\/em>
\nStaff scientist<\/em><\/p>\n

Heterologous expression and in vitro maturation of VcrA and other reductive dehalogenases. Microbial electrosynthesis of hydrocarbons via autotrophic CO2 fixation.<\/em><\/p>\n

Ian Marshall
\nJune, 2007 – September, 2012<\/em>
\nDept\/Org: Center for Geomicrobiology, Aarhus University, DK<\/em><\/p>\n

Characterization of interspecies interactions in complex microbial ecosystems.<\/em><\/p>\n

Dagmar Woebken
\nPost-Doc, August, 2008 – December, 2011<\/em>
\nDept\/Org: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna<\/em>
\nGroup Leader<\/em><\/p>\n

During my time as a postdoctoral fellow in the Spormann Lab I investigated the function of microorganisms in coastal microbial mats. My goal was to link the identity and function of microorganisms in these laminated cyanobacteria-dominated mats using molecular techniques such as nanoSIMS and metatranscriptomic studies.<\/em><\/p>\n

Tyrrell A. Nelson
\nJuly, 2008 – July, 2011<\/em>
\nDept\/Org: University of California San Francisco, dept. of Pathology<\/em>
\nSenior Research Associate<\/em><\/p>\n

Microbial metabolic processes and interactions within human\/animal hosts. High throughput NGS multiplexed metatranscriptomic and metagenomic assay development.<\/em><\/p>\n

Paul J. McMurdie II
\nJune, 2005 – December, 2010<\/em>
\nDept\/Org: Second Genome, Inc.<\/em>
\nBiostatistician<\/em><\/p>\n

http:\/\/www.stanford.edu\/~mcmurdie\/<\/em><\/p>\n

Genomic Adaptation for Organohalide Respiration of Vinyl Chloride and Other Priority Pollutants by the Anaerobic Bacterium<\/em> Dehalococcoides.<\/p>\n

Jana M\u00fcller
\nJanuary, 2004 – December, 2010<\/em>
\nDept\/Org: Calysta Biosystems<\/em><\/p>\n

Regulation of biofilm formation in two \u03b3-proteobacteria:<\/em> Shewanella oneidensis and<\/em> Vibrio cholerae A1552.<\/p>\n

Carmen D. Cordova
\nJune, 2004 – July, 2010
\nDept\/Org: Natural Resources Defense Council<\/em>
\nSustainable Livestock Science Fellow<\/em><\/p>\n

Molecular basis of respiratory plasticity in <\/em>Shewanella oneidensis MR-1.<\/em><\/p>\n

Laura Hug
\nMay, 2009 – August, 2009<\/em>
\nDept\/Org: University of California Berkeley,\u00a0Banfield Lab<\/em><\/p>\n

In collaboration with Joey McMurdie, creation of an unsupervised binning pipeline and visualization tool for metagenome sequence datasets.<\/em><\/p>\n

Frank L\u00f6ffler
\nMarch, 2009-September, 2009<\/em>
\n

Discovering ways to clean the environment, counter the damage humans do to ecosystems, and improve environmental health. How naturally occurring bacteria break down pollutants like chlorinated solvents, radioactive wastes, and greenhouse gases.<\/em><\/p>\n

Sebastian F. Behrens
\nJanuary, 2004-October, 2008<\/em>
\nDept\/Org: University of T\u00fcbingen<\/em>
\nAssistant Professor (akad. Rat)<\/em><\/p>\n

Environmental microbiology\/molecular microbial ecology. Linking environmental processes to the spatial-temporal distribution and metabolic activity of key functional groups of microorganisms. I follow an interdisciplinary approach that combines the disciplines biogeochemistry with microbiology and molecular biology to understand the basic microbial ecology principles driving the biogeochemical cycling of metals, metalloids, the biodegradation of organic contaminants, and greenhouse gas emissions from the molecular to the ecosystem scale.<\/em><\/p>\n

Jonathan G\u00f6ke\u00a0
\nM.S. Student, May, 2007-July, 2007
\n

Masters Thesis on assembly of Dehalococcoides strain VS genome in collaboration with Joey McMurdie.
\n<\/em><\/p>\n

Galit Meshulam-Simon
\nNovember, 2001 – September, 2006<\/em>
\nDept\/Org: Aurora Algae<\/em>
\nResearch Scientist<\/em><\/p>\n

Jochen M\u00fcller
\nMay, 2000-March, 2003<\/em>
\nDept\/Org: Helmholtz Centre for Environmental Research – UFZ<\/em>
\nSenior Scientist<\/em><\/p>\n

Microbes of environmental importance. The role of microbes involved in degradation of organic pollutants and in the global sulfur cycle through genomic, functional genomic, genetic, and biochemical approaches.<\/em><\/p>\n

http:\/\/www.ufz.de\/index.php?en=19709<\/p>\n

Alison Cupples
\nJanuary, 1999-December, 2003<\/em>
\nDept\/Org: Michigan State University<\/em>
\nAssociate Professor<\/em><\/p>\n

http:\/\/www.egr.msu.edu\/~cupplesa\/<\/em><\/p>\n

Harry Beller
\nJanuary, 1995-December, 1998<\/em>
\nDept\/Org: Lawrence Berkeley National Laboratory and Joint BioEnergy Institute<\/em>
\nDirector of Biofuels Pathways (JBEI)<\/em><\/p>\n

Johannes Gescher
\nDept\/Org: Karlsruhe Institute of Technology<\/em>
\nProfessor<\/em><\/p>\n

Dissimilatory iron reduction.<\/em><\/p>\n

Josie Yu
\nDept\/Org: San Mateo County Workforce Development<\/em>
\nEducation Liaison<\/em><\/p>\n

Kai Thormann
\nDept\/Org: Max Planck Insitute for Terrestrial Microbiology, Marburg<\/em>
\nAssistant Professor<\/em><\/p>\n

Lily Chao
\nDept\/Org: Amyris<\/em>
\nEnzymologist<\/em><\/p>\n

Cyclic di-GMP Signaling in<\/em> Shewanella oneidensis.<\/p>\n

Luke Burow
\nDept\/Org: IP Australia<\/em><\/p>\n

Ecophysiology and metatranscriptomics of hydrogen producing microbial mats.<\/em><\/p>\n

Plamena Entcheva-Dimitrov
\nDept\/Org: Abbott Vascular, Santa Clara, CA<\/em>
\nResearch Scientist<\/em><\/p>\n

Ren\u00e9e Saville
\nDept\/Org: Calysta Biosystems<\/em><\/p>\n

Dynamics and control of<\/em> Shewanella oneidensis biofilms.<\/em><\/p>\n

Shauna Rakshe\u00a0
\nDept\/Org: Chemical Engineering<\/em><\/p>\n

Cyclic di-GMP Signaling in<\/em> Shewanella oneidensis.<\/p>\n

Soni Shukla
\nDept\/Org: Geneweave Bioscience<\/em>
\nResearch Scientist<\/em><\/p>\n

Wing-On (Jacky) Ng\u00a0<\/p>\n

Dale A. Pelletier
\nDept\/Org: Oakridge National Laboratory<\/em>
\nSenior Research Scientist<\/em><\/p>\n

Edward Driggers
\nDept\/Org: Microbia<\/em><\/p>\n

Heenam Kim
\nDept\/Org: The Institute for Genome Research (TIGR)<\/em><\/p>\n

Hope A. Johnson
\nDept\/Org: Department of Biology, Cal State Fullerton<\/em>
\nAssistant Professor<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"

Albert M\u00fcller Dept\/Org: Civil & Environmental Engineering Staff Scientist, 2015-2024 I\u2019ve always been fascinated by the concept of microbial ecology \u2013 the idea that nature is, to a large degree, based on the actions and interactions of microorganisms that seem to be completely hidden to our senses, but nevertheless can be figured out in extreme … Continue reading “Past Members”<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_mi_skip_tracking":false,"_exactmetrics_sitenote_active":false,"_exactmetrics_sitenote_note":"","_exactmetrics_sitenote_category":0},"_links":{"self":[{"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/pages\/241"}],"collection":[{"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/comments?post=241"}],"version-history":[{"count":20,"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/pages\/241\/revisions"}],"predecessor-version":[{"id":553,"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/pages\/241\/revisions\/553"}],"wp:attachment":[{"href":"https:\/\/web.stanford.edu\/group\/spormanngroup\/cgi-bin\/wordpress\/wp-json\/wp\/v2\/media?parent=241"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}