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News from the Chair, Max Häggblom Greetings from Lipman Hall!
We have many changes, new faces and much to report on. We have completed a successful cluster search in the areas of microbial biochemistry, physiology and bioinformatics and are delighted with the hire of three new Assistant Professors in 2009 and 2010. William Belden joined the department in 2009. His interests are in understanding the molecular aspects of chromatin‐
remodeling and circadian rhythms using the highly‐tractable model eukaryote Neurospora crassa in combina‐tion with biochemical, genetic and genome‐wide studies. read more about his work on page 2 of this issue. In 2010 we had two new faculty members join the department, Jeffrey Boyd (microbial biochemistry and physiology) and Yana Bromberg (bioinformatics). Jeff and Yana will be fea‐tured in the next issue of the Lipman Log. Prof. G. Charles Dismukes joined Rutgers in 2009 with joint appointments in the Department of Chemistry & Chemical Biology, the Waksman Institute and the Department of Biochemistry and Microbiology. You can read more about his research on biological and chemical methods for re‐newable solar‐based fuel production, photosynthesis, met‐als in biological systems and tools for investigating these systems on page 2. Building on our existing strengths in understanding and exploiting the genetic, metabolic and systematic diversity of microbial life on Earth the depart‐ment is thus on course for a multi‐year, strategic, and transformative initiative with an enhanced focus on micro‐bial physiology, biochemistry, metabolic networks, genet‐ics and genome‐enabled bioinformatics. We are thrilled to have a new graduate program in Micro‐bial Biology rooted in the rich traditions of microbiology at Rutgers. The graduate program launched this fall with an entering class of 13 students, six in the Ph.D. program and seven in the M.S. track. As the name indicates, the pro‐gram is focused on microbial life processes. The graduate program offers advanced study on the biology of microor‐ganisms with a strong focus in microbial physiology and
ecology, evolution, environmental microbiology, and the applications of microbiology. The students have the oppor‐tunity to study the genetic, metabolic, physiologic and evo‐lutionary diversity of microbial life, explore the complex roles that microorganisms play in life on Earth, and de‐velop the multitude of applications of microbes in biotech‐nology, the food industry, agriculture, and medicine. The program will provide a broad range of courses and re‐search opportunities with over 40 faculty members from several departments and institutes across the New Bruns‐wick Campus. “Boisterous Biochemistry and Marvelous Microbes” contin‐ues as our theme for the annual AgField Day/Rutgers Day each April. The G.H. Cook Biochemistry and Microbiology club organized the opportunity for young enthusiasts and budding microbiologists to build their own bug (see page 10). In Dec. 2009 our Student Chapter of the American Society of Microbiology hosted Dr. Diane Newman from MIT for a seminar on “The cell biology of hopanoids: What do their ancient molecular fossils really tell us”. The stu‐dent chapter is also taking an active role in organization of the annual Theobald Smith Society Meeting in Miniature. Overall, our undergraduate and graduate students thus continue to provide a positive force to the department. Our Annual Microbiology Symposium continues to bring together all microbiologists on campus with speakers from SEBS, the Waksman Institute, Camden and several depart‐ments of SEBS. In February 2010 we had the pleasure of welcoming back Prof. Ronald Atlas (Ph.D. in 1972) who then worked under the direction of Prof. Richard Bartha to pioneer the applications of bioremediation of marine oil spills. The next annual Microbiology Symposium is sched‐uled for February 2011. As always, I wish to thank all our donors for your support. Microbiology is featured in the new Rutgers capital campaign, with one of the key goals to obtain core endowment to support sustained research and educa‐tional programs in microbiology, specifically in the form of graduate and undergraduate fellowships. We hope that you will continue to show your support for the department in the future.
The Lipman Log
October 2010
http://aesop.rutgers.edu/~dbm/
INSIDE THIS ISSUE: Chair news 1 New Faculty 2 Microbiology 4 Symposium Our Faculty 5 In Print 6 Theses 7 Our Department 9 Peter Kahn’s Party 13 What’s Shaking 14 Alumni 15
Deep Submergence Vehicle Nautile during launch on the stern of the N/O L’Atalante (pg. 5)
M. Häggblom, R. Atlas, D. Pramer, R. Goodman Fourth Annual Microbial Symposium (pg. 4)
International Workshop on Bioremediation Lahti, Finland (pg. 9)
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This year has brought us a host of new hires. William Belden, Ph. D, joined the Department of Biochemistry and Microbiology as an assistant professor on September 1, 2009. Dr. Belden earned his Ph.D. from Dartmouth College in 2002 and then did is post‐doctoral fel‐lowship at Dartmouth Medical School from 2003‐2009. Dr. Belden’s research is involved in understanding how chromatin‐remodeling and epigenetics affect circadian regulated gene expression. Circadian regulated gene expression, more commonly referred to as the “biological clock,” is what controls daily sleep‐wake cycles in humans. Medical problems as‐sociated with the defects in the biological clock include depression, bipolar disorder, and cancer. The Belden Lab uses the model organism Neurospora crassa to study this process. Neurospora is a filamentous fungus that has been used for more than 40 years to study the biological clock. It has risen to be one of the premier model eukaryotes to study this process. Rhythms are easily monitored using a race tube assay where daily banding in asexual spore production can be easily visualized (Fig. 1.). Combined with numerous molecular biology techniques, this system has lead to numerous discoveries that are conserved in mammals. The Belden lab is current examining a number of chromatin‐remodeling mutants that have implications in cancer. One gene of high interest is the Neurospora homologue of the human mll (mixed lineage leukemia) gene, which is a known causative agent in certain forms of leukemia. Loss of this gene causes the clock to stop running resulting in constant conidiation on the race tube assay (Fig. 1). Neuro‐spora represents a perfect model organism to study the role of this enzyme in clock function because mll is essen‐tial for viability in mammals.
Currently, the Belden lab consists of one technician and three undergraduate students all studying differ‐ent aspects of the biological clock and light regulation. We are all excited to have the Belden lab as part of our de‐partment and we wish him, and his lab, the best of luck.
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The Department of Biochemistry and Microbiology Welcomes Drs. William Belden and G. Charles Dismukes
Charles Dismukes joined Rutgers University in the fall semester 2009 as a faculty member with joint appointment in SAS and SEBS. He conducts experimental research programs located in the Depart‐ment of Chemistry & Chemical Biology and the Waksman Institute of Microbiology. His Waksman research program addresses two main topics: photosynthetic water oxidation and synthetic biol‐ogy/metabolomics applied to microbial energy conversion. Dismukes has worked on the fundamental science of photosyn‐thetic water oxidation for 30 years, beginning, along with post‐doctoral associate Yona Siderer, with the identification of the tetramanganese cluster comprising the catalytic center of the
photosystem II complex in spinach. This inorganic core has since been found in all oxygenic phototrophs to date. Current work revolves around searching for novel oxy‐genic phototrophs that split water using unconventional mechanisms distinct from that typified by terrestrial plants. We call these “weirdophiles” to distinguish them from most extremophiles which merely use tuned versions of conventional enzymes and standard mechanisms. This work extends to the evolution of oxygenic photosynthesizing reaction centers and the elucidation of the molecular factors that determine the efficiency of water oxidation. A second area of research aims to discover native or engineer transgenic photosynthetic microorganisms that function as biological factories to manufac‐ture biodegradable polymers and sustainable fuels. His group examines carbohydrates, lipids and biogas production, and microbial metabolism via metabolomics (using NMR and tandem mass spectrometry). All oxygenic phototrophs extract electrons and protons from water and use them to reduce NADP+ and plastoquinone which are subsequently used as energy sources for metabolisms, such as CO2 fixation via the Calvin cycle. Some microbial oxygenic phototrophs (cyanobacteria and microalgae) (Fig. 1) can use reductant, in competition with other intracellular processes, to reduce protons at the hydrogenase and transiently produce H2 gas under anaerobic conditions. They do so by redirecting the electrons (as ferredoxin or NAD[P]H) and protons obtained from catabolism of carbohydrate storage compounds into hydrogenase.
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Figure 1. Race tubes showing a WT Neurospora clock and the mll homologue deletion strain, Dset‐1. The black marks on the tubes indicate one‐days growth. The entire tube consisted of 8 days growth
Figure 1. oxygenic phototrophs
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(Dismukes continued) These carbohydrate storage compounds have ultimately been produced from CO2, water, and sunlight during photosynthesis. Other phototrophs such as green algae and diatoms store a greater fraction of their carbon fixation intermediates as neutral lipids and thus are better candidates for hydrocarbon or bio‐diesel production.
Biohydrogen: Our efforts within the BioSolarH2 team seek to develop the full potential of photosynthetic mi‐crobes for maximum H2 production. Our approach is to probe cellular metabolism using physical, chemical, nutri‐tional and genetic perturbations informed by systems‐level interrogation of metabolite fluxes and real‐time detection of H2, intracellular reductants, NAD(P)H, and protons. This has led to a detailed understanding of the competing pathways that intersect with H2 production (Fig. 2). Our research has identified the metabolic path‐ways for intracellular reductants and protons to produce H2 within cyanobacteria. Cyanobacteria use a pathway that is distinct from that used by the microalgae, thus affording new opportunities for enhanced solar H2 pro‐duction from water. Much or our biohydrogen work is done in collaboration with members of the BioSolarH2 team.
Metabolic Engineering. Our experimental observations of intracellular reductant accu‐mulation (fluorescence of NADH) have shown that the availability of reducing equivalents (NADH) produced during fermentation of carbohydrate storage molecules (glycogen and osmolytes) limits H2 production capacity in some cyanobacteria. To test our hypothe‐ses we have created genetic knock‐outs of pyruvate metabolism by insertional inactiva‐tion mutagenesis; specifically the genes for lactate dehydrogenase and pyruvate‐ferredoxin oxidoreductase in Synechococcus 7002 (jointly with the Bryant lab at Penn State U.) This genetic approach enables the design of tailored made microbes suitable for improved H2 production and has been the basis of improving the yield of biohydrogen
production (Fig. 3). Lipids/Biodiesel. We are working on a project to examine green microalgae and diatoms as efficient sources for accumulating neutral lipids as primary energy storage molecules. As part of our bioprospecting efforts, we have discovered several strong lipid‐producing strains of diatoms from acidic thermal sources which are promising as biodiesel precursors (Fig. 4). Our goal is to elucidate the pathways for lipid production using the special tools that we have developed coupled with knock‐out mutagenesis to test hypotheses for metabolic pathways involved. We are collaborating with Rutgers faculty members on lipid metabo‐lism (Falkowski and Dixon labs). All of these studies have been strengthened by our development of specialized instruments including electrochemical cells for detection of dissolved O2 and H2 gases, intracellular fluorescence detection of pigments and pyridine nucleotides, and electron spin magnetic resonance.
Figure 3. Steps in the process of improving strain development for H2 production
Figure 4. False‐colored image of diatom cell isolated from Norris Hot Spring (Yellowstone National Park): left: bright field microscopy, length 35 �m; right: (red) Chlorophyll fluorescence in the range 670‐690 nm, and (green) Nile Red fluores‐cence in the range 570‐620 nm Green light (520‐550 nm) used for fluorescence.
Figure. 2. Composite map of electron and proton fluxes leading to H2 production in
photosynthetic microbes.
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Keynote Address: Ronald Atlas, Professor of Biology and Public Health University of Louisville Bioremediation to Bioterrorism
Dr. Atlas described his work on bioremediation that began with the discov‐ery that microbial hydrocarbon degradation could be used to treat marine oil spills while he was a graduate student at Rutgers University. Dr. Atlas discussed the Exxon Valdez oil spill, from early studies in 1989 that set the stage for the largest application of bioremediation through the current situation where bioremediation no longer appears to be an appropriate treatment for subsurface oil residues that are sequestered at a few loca‐tions in Prince William Sound. He also discussed his policy work on bio‐safety and biosecurity and the responsibilities of life scientists to protect against the misuse of the life sciences.
The Program: Microbes, models, and experimental tests of ecological theory Peter Morin, Ecology, Evolution, and Natural Resources Antimicrobial peptides as an alternative to traditional methods to control foodborne pathogens Karl Matthews, Food Science What makes you tick? Lessons from a mold Kwangwon Lee, Biology (Camden) Unusual genetic and physiological aspects of microbial phthalate degradation Gerben Zylstra, Biochemistry and Microbiology and Biotech Center Viruses and transposons of filamentous fungi and Oomycetes Brad Hillman, Plant Biology and Pathology Cool bugs in the Arctic Max Häggblom, Biochemistry & Microbiology Fast evolution in single‐stranded DNA viruses Siobain Duffy, Ecology, Evolution and Natural Resources Looking inside the black‐box of microbial solar‐to‐biomass energy conversion Charles Dismukes, The Waksman Institute; Department of Chemistry and Chemical Biology The Biological Clock, it’s time to remodel William Belden, Biochemistry and Microbiology Poster session: over 50 students and postdocs presented posters
The Fourth Annual Mini‐Symposium on Microbiology at Rutgers University: Cultivating Traditions, Current Strength,
and Future Frontiers
Doug Eveleigh, David Pramer, Ron Atlas
M. Häggblom, R. Atlas, D. Pramer, R. Goodman
N. Tumer, D. Pramer, R. Atlas
Students with Charles Dismukes
Please mark your calendars for our 2011 mini symposium on February 3 ‐ 4th, 2011
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OUR FACULTY
Costantino Vetriani is an associate professor in the Department of Biochem‐istry and Microbiology and IMCS, and the Direc‐tor of the Microbiology Undergraduate Program at Rutgers University. He studies microorganisms
that live in the deep ocean. He began his research activ‐ity in a clinical microbiology lab and, as a Ph.D student, he was trained as a prokaryotic molecular geneticist. In 1995 he moved from Rome, Italy, to the United States, where he joined the Center of Marine Biotechnology in Baltimore, MD and, later on, Rutgers University. In 1995 Costa Vetriani participated in the Microbial Diversity summer course at the Marine Biological Laboratory in Woods Hole, MA. For him, that was a career changing experience, and one that he would recommend to any mi‐crob io logy s t u d e n t . Since 1996 C o s t a Vetriani par‐t i c i p a t e d either as research or chief scientist in 16 deep‐sea expeditions in the Pacific and Atlantic Oceans, and dove in the Deep‐Submergence Vehicle Alvin many times. Costa Vetriani is a passionate SCUBA diver and underwater photogra‐pher. For more information about Costa Vetriani's re‐search, visit the Deep‐Sea Microbiology Lab website. Costantino Vetriani partici‐pated in an oceanographic expedition aboard the French Navire Ocean‐ographique L’Atalante in April/May 2010. He dove in the Deep‐Submergence Vehicle Nautile to explore and sample the deep‐sea vents located on the East Pacific Rise at 9° and 13°N.
High tempera‐ture deep‐sea hydrothermal vent on the East Pacific Rise at 13°N, depth 2,600 meters.
Costantino Vetriani and Richard Lutz were awarded a one‐year $136,295 grant from NSF Bio Oce entitled: Integrating geological, chemical, and biological proc‐esses: Implications for ecological succession on the East Pacific Rise. Ileana Perez, (graduate student in Costantino Vetriani’s lab) received the Philanthropic Educational Organiza‐tion (PEO) Scholar Award ($ 15,000) for the coming aca‐demic year (www.peointernational.org/). P.E.O. Scholar Awards were established in 1991 to provide substantial merit‐based awards for women of the United States and Canada who are either pursuing a doctoral level degree or are engaged in postdoctoral research at an accredited college, university or institution. For more information about the award: www.peointernatioanl.org./about/psa‐fact‐sheet. Max Häggblom received the 2010 Selman A. Waksman Hon‐orary Lecture‐ship Award from the Theo‐bald Smith Society. Pic‐tured here receiving the reward plaque from TSS President Randolph Greasham. The Waksman Award is awarded to a scientist who has a distinguished career in science and who has made a significant contri‐bution to the field of microbiology. Recent recipients of the award from our department include Gerben Zylstra, Tamar Barkay and Douglas E. Eveleigh.
Ning Zhang assistant professor in the De‐partments of Plant Biology and Pathology and Biochemistry and Microbiology received a Travel Award from FES IN/NORDFORSK Research Network to attend Fungal Metage‐nomics Workshop and International Mycologi‐cal Congress held at the University of Edin‐burgh, Scotland in July‐August 2010.
Ning Zhang received the Rutgers SEBS Pre‐tenure Fac‐ulty Career Award, "Is Dogwood Anthracnose Exotic? New Approaches to Explore the Biogeography and Evo‐lution of Plant‐Associated Fungi". November 2009‐June 2010 ($ 12,783).
Navire Oceanographique L’Atalante before leaving for sea at the dock in Manzanillo, Mexico.
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Ahn J, Park J‐W, McConnell JA, Ahn Y‐B, Häggblom MM. 2010. Kangiella spongicola sp. nov., a halophilic marine bac‐terium isolated from the marine sponge Chondrilla nu‐cula. Int. J. System. Evol Microbiol in press. Ahn Y‐B, Chae J‐C, Zylstra GJ, Häggblom MM. 2009. Phenol degradation via phenylphosphate and carboxylation to 4‐hydroxybenzoate by a new by strain of the sulfate‐reducing bacterium Desulfobacterium aniline. Appl Environ Microbiol 75:4248‐4253. Ahn Y‐B, Kerkhof LJ, Häggblom MM. 2009. Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba. Int J System Evol Microbiol 59:2133‐2139. Andrianasolo E, Haramaty L, Rosario‐Passapera R, Bidle K, White E, Vetriani C, Falkowski P, Lutz R. 2009. Ammonificin A and B, hydroxyethylamine chroman derivatives with antim‐icrobial and apoptosis‐induction activities from a cultured marine hydrothermal vent bacterium Thermovibrio ammoni‐ficans. J Nat Prod. 72:1216‐1219. Barkay T, Kritee K, Boyd E, and Geesey G. 2010. A thermo‐philic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase. Environ Microbiol in press. Bini E. 2010. Archaeal transformation of metals in the envi‐ronment. FEMS Microbiology Ecology. 73:1‐16. Bugel SM, White LA, Cooper KR. 2010. Impaired reproduc‐tive health of killifish (Fundulus heteroclitus) inhabiting New‐ark Bay, NJ, a chronically contaminated estuary. Aquat Toxi‐col 96 (3): 182‐193. Chang H‐K and Zylstra GJ. 2010. Xanthomonads, p 1805‐1811. In K N Timmis (ed), Handbook of Hydrocarbon and Lipid Microbiology Springer Verlag GmbH, Heidelberg. Chang H‐K, Dennis JJ, and Zylstra GJ. 2009. Involvement of two transport systems and a specific porin in the uptake of phthalate by Burkholderia spp. J Bacteriol 191:4671‐4673. Kim D, Choi K Y, Yoo M, Choi JN, Lee CH, Zylstra GJ, Kang BS, and Kim E. 2010. Benzylic and aryl hydroxylations of m‐xylene by o‐xylene dioxygenase from Rhodococcus sp. strain DK17. Appl Microbiol Biotech in press. Kim D, Lee CH, Choi JN, Choi KY, Zylstra GJ, and Kim E. 2010. Aromatic hydroxylation of indan by the o‐xylene‐degrading Rhodococcus sp. strain DK17. Appl Environ Microbiol 76:375‐277. Krumins V, Park J‐W, Son E‐K, Rodenburg LA, Kerkhof LJ, Häggblom MM, Fennell DE. 2009. Sustained PCB dechlorina‐tion enhancement in Anacostia River sediment. Water Re‐search 43:4549‐4558.
McCormick JM, Paiva MS, Häggblom MM, Cooper KR, White LA. 2010. Embryonic exposure to tetrabromobisphenol A and its metabolites, bisphenol A and tetrabromobisphenol A dimethyl ether disrupts normal zebrafish (Danio rerio) devel‐opment and matrix metalloproteinase expression. Aquatic Toxicology, in press. Männistö MK, Tiirola M, Häggblom MM. 2009. Effect of freeze‐thaw cycles on bacterial communities of Arctic tundra soil. Microbial Ecology 58:621–631. Männistö MK, Tiirola M, McConnell J, Häggblom MM. 2010. Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov. isolated from soil and lichen samples of Finnish Lapland. Int. J. System. Evol. Microbiol. In press. Ni Chadhain S and Zylstra GJ. 2010. Functional Gene Diver‐sity, Biogeography, and Dynamics, p 2413‐2422 In K N Tim‐mis (ed), Handbook of Hydrocarbon and Lipid Microbiology Springer Verlag GmbH, Heidelberg. Rauschenbach I, Narasingarao P, Häggblom MM. 2010. Desulfurispirillum indicum sp. nov. a selenate and selenite respiring bacterium isolated from an estuarine canal in Southern India. Int J System Evol Microbiol in press. Schuler L, Jouanneau Y, Ní Chadhain SM, Meyer C, Pouli M, Zylstra GJ, Hols P, Agathos SN. 2009. Characterization of a ring‐hydroxylating dioxygenase from phenanthrene‐degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene. Appl Microbiol Biotechnol 83:465‐475. Sul WJ, Park J, Quensen III JF, Rodrigues JLM, Seliger L, Tsoi TV, Zylstra GJ, and Tiedje JM. 2009. DNA‐stable isotope probing integrated with metagenomics: retrieval of biphenyl dioxygenase genes from PCB‐contaminated river sediment. Appl Environ Microbiol 75:5501‐5506. Turgeon BG, Condon B, Liu J, and Zhang N. 2010. Protoplast Transformation of Filamentous Fungi. In Molecular and Cell Biology Methods for Fungi, Methods in Molecular Biology series Humana Press pp 3‐20. Villafane A, Voskoboynik Y, Cuebas M, Ruhl I and Bini E. 2009. Response to excess copper in the hyperthermophile Sulfolobus solfataricus strain 98/2. Biochemical and Bio‐physical Research Communications 385:67‐71. Youngster LKG, Kerkhof LJ, Häggblom MM. 2010. Commu‐nity characterization of anaerobic methyl tert‐butyl ether (MTBE) degrading enrichment cultures. FEMS Microbiol Ecol 72:279‐288. Youngster LKG, Rosell M, Richnow HH, Häggblom MM. 2010. Assessment of MTBE biodegradation pathways by two‐dimensional isotope analysis in mixed bacterial consortia under different redox conditions. Appl. Microbiol. Biotech‐nol. 88:309‐318.
IN PRINT
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Ph.D. THESES: 2009/2010
Jessica M. McCormick: “Microbial Transformations of Brominated Flame Retardants and the Impact on Envi‐ronmental Fate and Toxicity to the Developing Zebraf‐ish (Danio rerio) Embryo.” Graduate Program in Micro‐biology and Molecular Genetics. Advisors: Max Häggblom and Lori White. Abstract: Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant worldwide. TBBPA contamination has been detected in dust, sedi‐ments, and aquatic environments and in human serum, breast milk and other tissues of aquatic and terrestrial animals. Microorganisms in the environment can trans‐form TBBPA either by anaerobic dehalogenation to bisphenol A (BPA) or aerobic O‐methylation to TBBPA dimethyl ether (TBBPA DME). Our data demonstrate that TBBPA O‐methylation is a ubiquitous reaction in the environment. However, O‐methylating organisms comprise only a minor portion of the total heterotro‐phic population. Mycobacterium spp. were able to O‐methylate TBBPA at a faster rate than BPA. To deter‐mine whether microbial metabolism alters the toxicity of TBBPA, zebrafish embryos were exposed to TBBPA and its metabolites. My data show that BPA and TBBPA DME exhibit lower potency that TBBPA, demonstrating that microbial metabolism results in products with re‐duced toxicity. In addition, while all three caused edema and hemorrhage, only TBBPA caused decreased heart rate, edema of the trunk, and tail malformations. Matrix metalloproteinase (MMP) expression was meas‐ured due to the role of these enzymes in the remodel‐ing of the extracellular matrix during tissue morpho‐genesis, wound healing and cell migration. Our data suggest that the trunk and tail phenotypes seen after TBBPA exposure could be due to alteration of proper MMP expression/ activity. Unlike TBBPA, microbial me‐tabolism of BPA to BPA monomethyl and dimethyl ether appears to result in increased toxicity to the de‐veloping zebrafish embryo causing increased mortality at 5 and 28 days post fertilization and lower LC50 values. Taken together, the data presented in this thesis indi‐cate that microbial metabolism of BFR results in changes in the compounds toxicity. Further, these data illustrate a new mechanism for microbial transforma‐tion of BPA, producing metabolites warranting further study to understand their prevalence in the environ‐ment. Melitza Crespo‐Medina: “Diversity of Chemosynthetic Thiosulfate Oxidizing Bacteria from Diffuse Flow Hydrothermal Vents and Their Role in Mercury Detoxi‐fication.” Graduate Program in Microbiology and Mo‐lecular Genetics. Advisor: Dr. Costantino Vetriani
Abstract: The mixing of hydrothermal fluids with sea‐water creates chemical, temperature, and pH gradients that support chemosynthetic primary production at deep‐sea vents. These fluids are enriched with reduced sulfur compounds and its oxidation under aerobic con‐ditions is considered the main chemosynthetic proc‐esses at the vents. The main objective of my research was to gain a better understanding of the aerobic chemosynthetic thiosulfate oxidation processes at deep‐sea hydrothermal vents, by studying the abun‐dance and diversity of chemosynthetic thiosulfate oxi‐dizing bacteria, and their role on the detoxification of
heavy metals, with an emphasis on mercury detoxifica‐tion. Fluids, sediments, and biomass from microbial colonization experiments were collected during several expeditions to the East Pacific Rise (EPR) at “9º50’N, 104º17’W” and to the Guaymas Basin, Gulf of Califor‐nia. Microbial isolations were carried out from diluted and undiluted samples. Isolates were identified by DNA extraction, 16S rRNA amplification, and sequencing. The isolates obtained in pure cultures were related to the genera Thiomicrospira, Halothiobacillus, Hydro‐genovibrio, Thioclava, Thalassospira, and Pelagibaca, as well as a new isolate EPR 70, which was described as a new species, Salinisphaera hydrothermalis. The isolates were further characterized, and their functional genes encoding enzymes for carbon fixation (RubisCO) and thiosulfate oxidation (SoxB) were analyzed. The Most Probable Number (MPN) technique was carried out in order to determine the abundance of chemosynthetic thiosulfate oxidizing bacteria, and the values obtained were compared with the total number of microorgan‐isms per sample, estimated from microscopic direct counts. Our data show that this group of microorgan‐isms represented from 103 to 107 cells per ml of sample, which accounts for about 0.002% to 14.1% of the total cell counts per sample. The chemical composition of the fluids was analyzed, and results indicated that hydrothermal fluids were enriched in mercury with con‐centrations comparable to the concentrations found in contaminated surface waters. MPN counts were done with the addition of mercury in order to determine the percentage of chemosynthetic thiosulfate oxidizing bacteria that were mercury resistant. Results indicated that from 0.2 to 24.6% of the chemosynthetic bacteria were resistant, suggesting an adaptation to life in the presence of this toxic metal.
Aramis Alexis Villafane Martinez: “Regulation of ex‐pression of copper responsive genes in Sulfolobus sol‐fataricus.” Graduate Program in Microbiology and Mo‐lecular Genetics. Advisor: Elisabetta Bini. Abstract: Copper is an essential micronutrient, but toxic in excess. Cells must maintain their internal level of copper within a narrow range of concentrations. This is accomplished mainly by copper efflux mediated by ATP‐driven copper transporters that are induced at the level of transcription. Sulfolobus solfataricus can adapt to fluctuations of copper levels in its environment. To bet‐ter understand the molecular mechanism behind its response to copper, the expression of the cluster of genes copRTA, which encodes the copper‐responsive transcriptional regulator CopR, the copper‐binding pro‐tein CopT, and CopA, has been investigated. Expression data obatined by quantitative real‐time RT‐PCR showed that only copA was induced by copper. By comparing the patterns of copA expression and cellular copper accumulation, as determined by Inductively Coupled Plasma Optical Emission spectrometry, it was con‐cluded that the level of copA depends on the internal fluctuations of copper. To investigate the role of CopR,
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the knockout mutant strain PBL2070, carrying a disrup‐tion of the copR gene, was created. The mutant was incapable of growth in the presence of excess copper, and under the same conditions no transcription of copA was observed. These data suggested that CopR posi‐tively regulates transcription of copA. Strain PBL2070, its parent strain and PBL2070 complemented with a wild type copy of copR, were compared with respect to their physiological and transcriptional response to cop‐per. Results confirmed that, under copper stress, CopR, activates the transcription of copA, and its presence restores the wild type phenotype resistant to copper. Finally, a reporter system based on the thermostable b‐glucuronidase of S. solfataricus was developed. This system was applied to the analysis of the copTA pro‐moter region fused to the S. solfataricus β‐glucuronidase reporter. GUS activity assays showed that after copper addition, the activity of GusB was con‐sistent with the transcriptional changes observed for copA under similar conditions. The results provide the basis for a model of the molecular mechanisms of cop‐per homeostasis in Sulfolobus. Laura Youngster: "Microbial Degradation of the Fuel Oxygenate Methyl Tert‐butyl Ether (MTBE)" Graduate Program in Microbiology and Molecular Ge‐netics, Advisor: Max Häggblom Abstract: Groundwater contamination with the syn‐thetic fuel oxygenate, methyl tert‐butyl ether (MTBE), is an extensive problem. MTBE biotransformation proc‐esses are slow and MTBE degrading organisms are diffi‐cult to isolate, creating challenges relating to site as‐sessment, enhancement of natural attenuation and monitoring bioremediation in situ. In this study we analyzed MTBE degrading cultures using a variety of isolation independent techniques. We demonstrated that low concentrations of some aryl O‐methyl ether compounds enhanced the rate of MTBE degrada‐tion. Propyl iodide caused a light‐reversible inhibition of MTBE depletion, suggesting that the anaerobic MTBE O‐demethylation reaction was corrinoid depend‐ent. Terminal‐restriction fragment length polymor‐phism (T‐RFLP) and sequence analysis of 16S rRNA genes from one anaerobic MTBE degrading enrichment culture showed a phylogenetically diverse population with no exact matches to previously isolated or de‐scribed species. Stable isotope probing experiments verified that microorganisms from an anaerobic MTBE degrading enrichment culture used 13C from 13C‐MTBE for growth and cell division and that a particular sub‐population assimilated this carbon prior to the rest of the population. We also analyzed carbon and hydrogen stable isotope fractionation occurring during MTBE deg‐radation. In anaerobic cultures, substantial fractiona‐tion of hydrogen was found only in cultures supplied with syringic acid during MTBE degradation, providing the first experimental suggestion of multiple anaerobic MTBE O‐demethylation mechanisms. During aerobic MTBE degradation by the psychrophilic bacterium, Variovorax paradoxus, carbon and hydrogen fractiona‐tion were not influenced by incubation temperature during degradation. This work represents a significant contribution to the current body of knowledge about
MTBE degradation and the data presented will be use‐ful in many aspects of studying, enhancing and moni‐toring MTBE degradation under a variety of conditions. Hui Liu: “Microbial Reductive Dechlorination of Weathered Polychlorinated Dibenzo‐p‐dioxins and Dibenzofurans in Contaminated Sediments” Graduate Program in Environmental Science, Advisor: Max Häggblom
Abstract: Sediments contaminated with weathered polychlorinated dibenzo‐p‐dioxins and dibenzofurans (PCDD/Fs) are problematic around the world. River Kymijoki is highly contaminated with PCDFs mainly originating from the production of the wood preserva‐tive Ky‐5 until the 1980s. Limited information is avail‐able on the in situ microbial reductive dechlorination of weathered PCDD/Fs. The overall objectives of my thesis work was to assess the potential for anaerobic micro‐bial dechlorination of weathered PCDFs and to gain information on their application in bioremediation and detoxification of contaminated sediment using Kymijoki River sediments as a case model. Experiments in meso‐cocosms (30 L), microcosms (200 mL) and enrichment cultures (40 mL) demonstrated the potential for dechlo‐rination of weathered PCDFs as well as spiked PCDD/Fs by the indigenous microorganisms of Kymijoki River sediment. The relative decrease of highly chlorinated dibenzofurans (CDFs) was accompanied with an in‐crease of tetra‐ and penta‐CDFs over a 7‐year period in mesocosms. Amendment of tetrachlorobenzene (TeCB) and pentachloronitrobenzene (PCNB), and bioaugmen‐tation of Dehalococcoides ethenogenes strain 195 selec‐tively stimulated dechlorination of weathered PCDFs after 18 months in microcosms. Dechlorinating enrich‐ment cultures were established from the microcosms and spiked with 1,2,3,4‐TCDD/F and OCDF with PCNB as a co‐substrate. 1,2,3,4‐TCDD was dechlorinated mainly via 1,2,3‐TrCDD to 2,3‐DiCDD and 2‐MCDD over 13 months incubation. Dechlorination of 1,2,3,4‐TCDF was slow and less extensive compared to that of 1,2,3,4‐TCDD, with 2,4‐DiCDF as the most abundant dechlorina‐tion product accumulating after 13 months. More ex‐tensive dechlorination of 1,2,3,4‐TCDD was observed in the presence of PCNB, which demonstrated that PCNB was capable of enhancing the dechlorinating potential of the indigenous microorganisms in Kymijoki sedi‐ments. Dechlorination of spiked OCDF was observed with the production of hepta‐, hexa‐, penta‐ and tetra‐CDFs over 3 months incubation. DGGE analysis revealed diverse Chloroflexi community in mesocosms and a highly selected Chloroflexi community in the enrich‐ment culture. One of the stimulated Chloroflexi popula‐tions clustered closely with the Pinellas subgroup of Dehalococcoides, which includes strain CBDB1. Our re‐sults suggest that dechlorination of weathered PCDD/Fs contaminants may be mediated by indigenous micro‐bial populations as a means for in situ bioremediation of PCDD/F contaminated sediments.
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Robison Scholarship Award 2010
Congratulations to Ines Rauschen‐bach and Ramay‐dalis Cruz‐Matos the 2010 Robison S c h o l a r s h i p Awardees for Ex‐cellence in Gradu‐ate Studies pic‐tured here with Max Häggblom.
Josie Bonventre (Cooper Lab) was awarded a graduate student grant of $5000 from the New Jersey Water Re‐sources Research Institute for a project entitled, "Comparative toxicological assessment of gasoline oxy‐genates MTBE, ETBE and TAME, and their metabolites, in the zebrafish cardiovascular system". Sanjana Kirloskar, an undergraduate student in the Bini Lab, received support of ($3,000) from the SUPER Pro‐gram to work in the lab during the summer. Her project involved the preparation of clone libraries from water samples collected from various sites surrounding the effluents of waste water treatment plants to study anti‐biotic resistance genes.
Katherine S. Wydner, visiting professor from Saint Pe‐ter’s College, Jersey City, NJ, will collaborate with the Bini Laboratory during the summer on a project aimed to study the mechanisms of selection of antimicrobial resistance.
Drs. Max Häggblom and Anna‐Lea Rantalainen (University of Helsinki) organized a one‐week short course on "Assessment and Remediation of Contami‐nated Sediments" held Oct. 12‐16, 2009 at the Univer‐sity of Helsinki Department of Environmental Sciences in Lahti, Finland. Additional in‐structors in‐cluded Drs. Donna Fennell, Lee Kerkhof and Lily Young from Rutgers, as well as lec‐turers from the University of Helsinki. The course was taken by ten graduate students and advanced M.S. stu‐dents interested in assessment of contaminated sedi‐ments and development of technologies for their reme‐diation. The course covered sampling and analysis of sediments for different chemical contaminants, assess‐ment of chemical fate and ecotoxicology, and a com‐parison of different approaches for remediation with a focus on identification of the microorganisms mediating biodegradation, and the development and applications of bioremediation technologies.
Prof. Max Häggblom was the lead instructor at the In‐ternational Workshop on Bioremediation organized at the Birla Institute of Technology and Science ‐ Pilani, Goa Campus, India, January 4‐16, 2010. Dr. Häggblom’s participation in the course was funded by the Indo‐US Science & Technology Forum and the American Society for Microbiology through Indo‐US Professorship Award. Dr. Srikanth Mutnuri (Assistant Professor, Biological Sciences, Birla Institute of Technology and Science) was the host organizer. The aim of the workshop was to share knowledge in the field of environmental microbi‐ology and bioremediation of hazardous waste sites and to foster new collaborative research and training efforts in this field. Young scientists from India were trained in the fundamental of biodegradation of toxic chemicals and in the application of these metabolic processes for bioremediation of toxic waste sites through the use of microbes. The knowledge gained by the participants in the course will enable them to make a modern ap‐proach to their teaching and research work at their home institutions. The course consisted of lectures, laboratory bench work and demonstrations, as well as student team projects. The 21 participants in the work‐shop came from different institutions in India and in‐cluded graduate students (M.Sc., M.E. and Ph.D.), fac‐ulty, and scientists in industry. While in Goa Dr. Haggblom also visited Goa University and presented a seminar to the faculty and students of
the Division of Microbiology and met with researchers of the National Centre for Antarctic & Ocean Research in Goa to develop research collaborations.
OUR DEPARTMENT
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(Our Dept. Continued) Aspa Chatziefthimiou a graduate student in Tamar Barkay’s lab was featured in a recent banner page “Forest Teller’ on the Rutgers’ website. Article writ‐
ten by: Amy A. Reilly and Paula Walcott‐Quintin “After a child‐hood spent among the dry pine groves of the Mediterra‐nean, Aspa C h a t ‐z i e f t h im i o u was amazed by the leafy green forest of North America when she came here at age 18. Now one of her daily highlights is a walk through the woods near her home with her dog, Starr. “I love it. When you go into the forest, you’re going back to where you belong. I go to meditate,” says Aspa, a doctoral student in the Department of Ecology, Evolu‐tion, and Natural Resources at the Rutgers School of Environmental and Biological Sciences. So when Peter Morin, director of Rutgers’ Hutcheson Memorial Forest, was recruiting students as tour guides to that virgin forest, Aspa was quick to sign up. In Aspa’s case, under Professor Tamar Barkay in the Department of Biochem‐istry and Microbiology, she collects soil samples con‐taminated with mercury and studies the microorgan‐isms that can detoxify the element.” See more about this article at http://www.rutgers.edu/about‐rutgers/smallest‐forest
Jili Feng, a doctoral student from Northwest Agricultural and For‐estry University, located in Yan‐gling District, Xianyang, Shaanxi, China was a visiting scientist in the Häggblom lab from April 2009 to 2010 working on a project on MTBE biodegradation.
Dr. Yuan Ren from South China University of Technol‐ogy in Guangzhou was a visiting scientist in the Haggblom Lab from Sept 2009 to 2010 working on de‐veloping methods to stimulate anaerobic dechlorina‐tion of PCBs in contaminated sediments.
Ines Rauschenbach received the 2010 Theobald Smith Soci‐ety’s Graduate Scholar‐ship for excellence in her field of research.
The Department welcomes our newest staff member, Beth Nugent. Beth will be working with the professors on grant proposals and grant management.
Faculty, staff and students of the Department May, 2009
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In June Prof. Haggblom taught a 2‐week 3 credit course on the Microbiology and Cul‐ture of Cheese and Wine. The course was taught in Cluny, in Bur‐gundy, France, and was offered through Rut‐gers Study Abroad with the participation of Drs. Stephen Reinert (Dean of Rutgers Study Abroad) and Catherine Healey (Resident Direc‐tor for Rutgers Study Abroad Programs in
France). The intensive two‐week course combined ap‐plied microbiology with socioeconomic and cultural history, on site in southern Burgundy, one of the most pastoral and physically beautiful regions in all of France. The course combined lectures, group projects and field trips with wine and cheese tasting melding a compre‐hensive appreciation of the science, history and culture of cheese and wine. Seven enthralled students majoring in microbiology, biochemistry, food science animal sci‐ence and nutritional sciences were enrolled. In addition to lectures on the microbial fermentations of cheese and wine we discussed the importance of terroir and patrimoine and the role of monks, dukes, merchants, wine makers and cheese makers. During the two weeks we had several excursions to dairies and wineries. Highlights included the cheese dairy at Ab‐baye de Cîteaux, the Château du Clos de Vougeot on the Côte d'Or, and the Hospices de Beaune medieval hospital followed by a cheese tasting at Fromagerie Alain Hess in Beaune. After paying homage to Pasteur with a visit to his house in Arbois we concluded the course with a “eat and tell” of our favorite cheeses. The course is scheduled to be offered again in June 2011.
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Ag Field Day is an annual celebration of our college community spirit, and of the close ties enjoyed by students, faculty, staff, alumni, volunteers, and New Jersey residents. This year the Department of Biochemistry and Micro‐biology put on a great show featuring “Build your own Microbe”, an activity for children run by the Undergradu‐ate Biochemistry and Microbiology Club, T‐shirts ‐ the Rutgers’ Student Chapter of ASM sold t‐shirts of original design, and other fun with microorganisms including the microbes of Passion Puddle – a microscopic look at the abundant life in a hay infusion made from local waters, and the joy of home brewing. Many thanks to Ines Rauschenbach, Jessica McCormick, Chuck O’Brien, Kate Parisi, Justyna Marcinow, Aaron Lulla, Nick Sawyer, Alana Murday, Andrew Truong, Francis Wu, Amy Suhotliv, Pat Cantarella, Nathaniel Girer, Ileana Perez, Maryam Honar‐baksh, Drs. Gavin Swiatek, and Diane Davis. Join in the fun next year Rutgers Day/Ag Field Day Saturday, April 30, 2011 ‐ Save the date!
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Peter Kahn’s 70th Birthday Party was celebrated on April 9th at the Unitarian Society with over 100 family, friends, colleagues,
students and former students ‐ a night of celebratory “roasting” ensued!
There once was a man named Peter
Whose voice spoke without rhyme nor
meter
Words from his tongue like shots from a
gun
He articulates his mind in form of a pun
Of his tongue tis said ‐ none be fleeter
With Love from Karen Overbye & Tom Fulton
Members of your groaning circle of friends
Young boys who revel in punditry,
Are rarely accomplished in chemistry.
Except for the mensch,
Whose thirst we would quench,
With a toast on this day he turns
seventy.
Richard D. Ludescher
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Twin girls for Laura Youngster (Häggblom Lab) and Frank born on May 12, 2009 weighing in at 3lbs each please welcome Claudette and Eloise! Mom and Dad are very tired!
Congratulations to Eileen and Michael Glick, their new granddaughter Naomi Rachel Glick was born on August 7, 2009, 7lbs 5oz (pictured): Leslie, David and Naomi Glick.
Welcome to Santiago Gray born October 23, 2009 at 6:48 PM. Mom Isabel Gray (Häggblom Lab) is doing well!
Audrey Lu was born on Nov. 2, 2009. She and her older brother Alexander Lu age 2, keep Hui (Häggblom Lab) & Zhidong very busy!
Congrats to Ines Rauschenbach (Häggblom Lab) and Brian Onyrscuk married on July 30, 2010 and honeymooned in Hawaii!
Welcome Aurelia Maria Pangallo born May 18, 2010 weighing in at 7 lbs 7 oz. congrats to her parents Kristin (White Lab) and Dominick Pangallo.
Eloise Claudette
What’s Shaking!
Laura, Frank, Claudette and Eloise pictured at Ag/Field Day, 2010.
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Tom Kelleher (Ph.D. 1975 ‐1980) working at Amgen sent this note as a departmental log contribution. In 1998, I took on the antibiotic project with Cubist Pharmaceuticals, a small startup located in my childhood neighborhood of Cambridge, MA., because it was a chance to develop a classic antibiotic fermentation and recov‐ery program just like the antibiotic programs of Rutgers‐fame in past decades. As classic antibiotics go, that ex‐perience and Daptomycin launch in 2003 went off just as I was taught it should at the Department of Biochemis‐try and Microbiology at Lipman Hall. Daptomycin was the first new class of antibiotic to be commercialized since Vancomycin in 1972. By coincidence, Alexander Fleming was a regular contributor at many of the very large‐scale and mature contract facilities that produced Daptomycin for clinical trials. The current commercial process is available for viewing at Kelleher et al. US Patent 6696412 appl. 09/735,191, February 2004. In 2009, Daptomycin (Cubicin) exceeds $500 million in sales and it is emerging as the antibiotic‐of‐last‐resort for Vancomycin‐resistant Enterococcus (VRE) and Methicillin‐resistant Staphylococcus aureus (MRSA). As noted above, more recently I have been working at Amgen.
H. Boyd Woodruff (Ph. D., 1940) received the 2010 Dennis Fenton Distin‐guished Graduate Alumni Award in recognition of his pioneering studies in antibiotic research (the discovery of the first actinomycete antibiotic, actino‐mycin, 1940 (with Professor Selman Waksman), and his career accomplish‐ments in directing the Microbiology programs at Merck Co ‐ which resulted in such pharmaceuticals as anticancer agents (actinomycin D), the antipernicious anemia factor (vitamin B12), the remarkable anthelmintic Ivermectin (a cure for river blindness), the cholesterol inhibiting statins (Mevacor, the world’s first statin), products that revolutionized world medicine and public health. Con‐gratulations Boyd.
Dr. Dolph Klein, 81, died January 30, 2010 in Durham. A born‐and‐bred New Yorker, Dr. Klein earned a B.Sc. from City College of NY, a Ph.D. in microbiology from Rutgers, in 1961 with the Department of Agricultural Microbiology, Rutgers, The State University, New Brunswick, New Jersey
working with Dr. David Pramer, and did his post‐doctoral work at Purdue, before becoming a researcher at the Univ. of Minnesota. In 1974, Dr. Klein moved to North Carolina to serve as Director of Clinical Microbiol‐ogy at the Duke University Medical Center, turning his laboratory into one with a national reputation for excellence. Dr. Klein retired from Duke as an Associate Professor Emeritus of Molecular Genetics and Microbiology in 2003.
Dolph had a charming personality, and was loved and admired by many as a family man, a professional, and even at the end as a patient. He was an avid bowler and table tennis player who became active in genealogy later in life, ingeniously reconstructing his nearly forgotten family tree, and graciously volunteering to help computerize written records for the benefit of future family researchers. He is survived by his brother, Bernard; his four sons, Michael, Laurence, Robert and Steven; and six grandchildren. Dolph was laid to rest February 1 alongside his be‐loved wife of nearly 50 years, Naomi (nee Keller, d. 2006), in New Montefiore Cemetery in Long Island, New York.
Alumni
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We keep updating our email/address contact list - please email any changes in address or email to:
Kathy Maguire E-mail: [email protected]
Thanks to individuals and organizations who provided financial support to the Department over the year.
Department of Biochemistry and Microbiology School of Environmental and Biological Sciences
Lipman Hall—76 Lipman Drive New Brunswick NJ 08901-8525
Main No. 732.932.9763
Editors: Max M. Häggblom, Douglas E. Eveleigh and Kathy Maguire
