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  • Researcher Profiles

    New England Biolabs has an extensive research program that is at the forefront of the life science industry. This program includes gene expression, chemical biology, parasitology, RNA biology, DNA enzymes and restriction enzymes.

    Learn more about the research being conducted by our Senior Scientists in the researcher profiles.

    • Bill Jack

      Executive Director, Research
      Ph.D., Duke University, 1983

      Area of focus:

      DNA polymerase function.

      Current Research:

      I currently focus on coordinating and supporting the research activities at NEB. My previous research centered on the biochemical characteristics of hyperthermophilic archaeal DNA polymerases. These studies explored kinetic properties of these enzymes in comparison with both thermophilic and mesophlic counterparts. Of particular concern was the ability of these enzymes, and variants, to incorporate modified nucleotides, including chain terminators. These studies have helped identify polymerases and polymerase variants useful in a variety of molecular biology protocols, as well as rationalizing the inherent fidelity of polymerases.

    • Tom Evans

      Scientific Director
      Ph.D., University of Minnesota, 1996

      Area of focus:

      Nucleic acid amplification, ligation, and repair.

      Current Research:

      My laboratory focuses on enzymes involved in DNA ligation, amplification, and repair.  The ability to ligate DNA in vitro, particularly by T4 DNA ligase, facilitated the growth of the molecular biology field.  Much is known about the mechanism that DNA ligases use to join DNA.  Even so, there are many interesting structure/function and mechanistic questions that are still unresolved.  We use T4 DNA ligase as a model ligase and apply techniques such as stopped flow, rapid chemical quench, and capillary electrophoresis to gain further insights into the mechanism of DNA ligation.  We have determined the ligation fidelity of Taq DNA ligase and shown that T4 DNA ligase is affected by the amount of total DNA present in the reaction (Lohman, G. J., et al., Nucleic Acids Res. (2016) 44(2)e14; Bauer, R. J., et al., PLoS One (2016) 11(3):e0150802).  A serendipitous finding during our work on ligases was that PBCV-1 DNA ligase quite efficiently ligates ssDNA oligos when bridged by RNA (Lohman, G. J., et al., Nucleic Acids Res. (2014) 42(3):1831-1844).  Such an enzyme could be used in RNA-based nucleic acid tests.

      Another interest is in developing improved reagents and methods for DNA amplification.  We perform PCR as part of our work, but we also routinely use sequence-specific isothermal amplification protocols such as Loop-mediated Isothermal Amplifcation (LAMP) or Strand Displacement Amplification (SDA).  These procedures can be extremely fast and because they don’t need to thermocycle they can be useful in areas of the world without reliable power sources.  Currently, we have been taking interesting DNA polymerases from other groups within NEB and evaluating their performance in these techniques.  This work led to the commercialization of three in silico-designed enzymes.  Bst 2.0 and Bst 3.0 are faster and more inhibitor resistant than the commonly used Bst DNA polymerase, LF.  The third enzyme, RTx, is a reverse transcriptase designed specifically for isothermal amplification reactions.  Furthermore, specific SOMAmers were used to create so-called “WarmStart” forms of Bst 2.0 and RTx.  This gives isothermal technologies the advantage of room-temperature set-up and improved reproducibility.  Our work on isothermal techniques led to the development of two new methods to detect DNA amplification, one permits easy multiplexing and the second allows visual confirmation of amplification; no fluorometer needed (Tanner, N. A., et al., Biotechniques (2012) 53(2):81-89; Tanner, N. A., et al., Biotechniques (2015) 58(2):59-68).

      In the past we developed an in vitro DNA repair mix termed “PreCR”.  This repair mix contains 7 enzymes and was designed to be as general as possible in its repair capabilities.  With the advent of new DNA sequencing methods, this repair mix is finding utility in some systems for repairing DNA as part of DNA sample preparation for sequencing because it has been found that PreCR increases library preparation yields.  The affect of DNA damage on sequencing data is something that most researchers do not consider.  Therefore, we are investigating the benefit of sequencing repaired DNA in terms of data quality.  It is anticipated that miscalls due to DNA damage are going to have the most impact in studies on rare somatic variants.

      In summary, my laboratory focuses on the properties and uses of nucleic acid modifying enzymes.  Enzymes are amazing molecules and we hope to learn how better to harness their useful properties to the benefit of other researchers.

    • Jurate Bitinaite

      Senior Scientist
      Ph.D., Vilnius University, 1986

      Area of focus:

      DNA modification and DNA Repair.

      Current Research:

      The current directions of my laboratory include both basic and applied research on enzymes involved in DNA Restriction/Modification, DNA Repair and Epigenetic Modifications. Our continuing research in the field of enzymes that act on DNA is aimed at studies of sequence-specific protein/DNA interactions with the long-term goal to enhance our understanding of the molecular mechanisms responsible for enzyme specificity. We are also developing novel molecular tools and methods for DNA manipulations and for analysis of modified bases in DNA. Over the last years we have created a number of DNA manipulation tools for seamless assembly of recombinant DNA molecules and for analysis and repair of modified bases in prokaryotic and eukaryotic genomes. Building upon our success in DNA engineering, efforts are currently underway to evolve DNA modification enzymes with desired specifications and to develop new approaches and techniques for detection of post-replicative DNA modifications in eukaryotic genomes.

    • Andrew Gardner

      Staff Scientist
      Ph.D., Boston University, 2010

      Area of focus:

      DNA amplification; Genomics.

      Current Research:

      Each time a cell divides, its replication machinery efficiently and accurately copies the entire chromosome. We aim to understand the biochemistry of individual replication enzymes and how they work together as a replisome to accomplish fast and high fidelity synthesis. Recently, we advanced understanding of an essential replicative DNA polymerase, Family D DNA polymerase, by completing the first kinetic characterization of nucleotide incorporation. To broaden understanding of replication pathways and intermediates, we are also focused on developing novel genetic, biochemical, single-molecule and next generation sequencing assays. For example, a single molecule technique enables study of processive (>10 kb) helicase unwinding and multicolor capillary electrophoresis facilitates study of Okazaki fragment maturation. We continue to innovate on assay design to dissect enzyme pathways and discover novel activities.
          
      Another aim of the Gardner laboratory is to match nature's sophistication in a test tube. A reconstituted replisome, naturally evolved for the task of copying entire genomes, has the potential to enable routine in vitro genome synthesis and manipulation. In single cell genomics, long, linear DNA amplification (>100,000 bp) is required to accurately reproduce the sequence and copy number variation of a single cell genome. In synthetic biology, methods for DNA assembly are limited to about 20 kb and larger fragments must be assembled in vivo at a very low frequency thereby limiting utility. A reconstituted replisome may fulfill this need for ultra long DNA synthesis.

    • Greg Lohman

      Staff Scientist
      Ph.D., Massachusetts Institute of Technology, 2007

      Area of focus:

      Nucleic acid enzyme mechanism and kinetics; DNA Ligases

      Current Research:

      DNA Ligases are critical players in the maintenance of genome integrity, replication and repair.  These enzymes further play key roles in methodologies including traditional cloning methods, modern synthetic biology gene assembly methods, e.g. Golden Gate and Gibson Assembly, the preparation of libraries for next generation sequencing, and molecular diagnostics methods such as the ligase detection reaction and the ligase chain reaction.

      Despite this central importance in both biology and biotechnology there is, surprisingly, a great deal to still to learn about the kinetic mechanism of DNA ligases.  Many questions remain, including the kinetics of enzyme dynamics, the details of DNA binding, inhibition by non-substrate DNA, and the determinants of substrate specificity and base-pair mismatch discrimination.   My Research group is studying these reaction details, with the ultimate goal of describing the global kinetic mechanism of DNA ligation.  We utilize a variety of fast timescale kinetics methodologies including rapid chemical quench and stopped flow, high throughput capillary electrophoresis assays, and next generation sequencing methods to study ligase reactivity and develop new and improved ligation-based methodologies.  We aim to develop high throughput, information dense assays that can be used both for the investigation of the ligation reaction mechanism and the development of improved ligase and methods.

    • Nathan Tanner

      Staff Scientist
      Ph.D., Harvard University, 2010

      Area of focus:

      Isothermal amplification, Point-of-need molecular diagnostics, Single-molecule analysis of replication enzymes

      Current Research:

      Amplification of nucleic acids is a fundamental process in biotechnology, used in applications from molecular cloning to sequencing and molecular diagnostics. This wide variety of amplification techniques and applications requires a flexible toolbox of enzymes and methods to enable such a diverse user base. We are focused on stocking and improving this collection of reagents and techniques, with efforts to develop improved amplification polymerases and enzymes as well as new amplification methods for applications in both laboratory and point-of-need settings. Using a variety of methods, including isothermal amplification (LAMP, SDA, etc.), qPCR, and digital methods we work to ensure NEB offers unique and optimized reagents with a broad expertise in nucleic acid amplification.

    • Jennifer Ong

      Senior Scientist
      Ph.D., University of Cambridge, 2004

      Area of focus:

      Protein Engineering, DNA Polymerases.

      Current Research:

      Our group develops and implements strategies to create better enzymes, focusing on DNA polymerases and amplification technologies.  In particular, we aim to study DNA polymerase fidelity using both experimental and computational methods.  We utilize high-resolution fidelity assays based on next generation sequencing technology to better understand the source, frequency and type of errors generated during amplification.  In parallel, our group aims to discover novel reagents that minimize errors during replication – either through engineering novel DNA polymerase variants with ultra low error rates or utilizing enzymatic repair systems to reverse mutation-inducing DNA damage.  Our protein engineering efforts synergistically combine various methods and sources of information to inform our mutagenesis predictions: we use natural genetic diversity, evolutionary relationships and structural information together with computational methods, directed evolution and high-throughput assays to improve enzyme function.  Expanding the capabilities of polymerases fits with the core mission of New England Biolabs:  by broadening the capabilities of our enzymes, we enable the development of new technologies.

    • Shuang-yong Xu

      Senior Scientist
      Ph.D., University of Iowa, 1989

      Area of focus:

      Structure and function study of restriction enzymes (BpuSI, EcoP15I, NotI, PacI, and SauUSI).
      Study of HNH-family restriction enzymes and nicking enzymes; engineering rare nicking enzymes using a HNH-nicking domain.
      Cloning and expression of BisI-like methylation-dependent restriction enzymes.

      Current Research:

      My research interests include structure and function studies of restriction enzymes and catalytic mechanism. I’m also interested in engineering strand-specific nicking enzymes and artificial endonucleases for genome editing. 

    • Zhenyu Zhu

      Senior Scientist
      Ph.D., University of Mississippi, 1999

      Area of focus:

      High fidelity restriction enzymes and 5-hydroxymethyl cytosine related enzymes.

      Current Research:

      The primary interest of my lab is protein engineering. We have focused this interest mostly on the engineering of high fidelity restriction enzymes. Many restriction enzymes tolerate a degree of ‘wobble’ in their recognition sequences and as a result they cut DNA at additional, off-target, sites. This unwanted cleavage activity, first observed with EcoRI more than 30 years ago, is termed ‘star-activity’. The molecular basis for star-activity varies from enzyme to enzyme, and becomes more apparent during digestions at high enzyme or glycerol concentrations, or for extended incubation times. Star activity is minor for many restriction enzymes, but for some it can be very problematic, radically altering digestion patterns. Using a systematic engineering and screening method, my lab has succeeded in isolating improved forms of many problem enzymes, forms that display much-reduced or no detectable star-activity. We call these ‘high-fidelity’ (HF) restriction enzymes. Currently, 31 such HF enzymes are available from NEB: BamHI-HF, NotI-HF, KpnI-HF, SacI-HF, SalI-HF, PstI-HF, PvuI-HF, ScaI-HF, SspI-HF, HindIII-HF, NcoI-HF, NheI-HF, SpeI-HF, EcoRV-HF, BstEII-HF, NcoI-HF, BsrGI-HF, EcoRI-HF, EagI-HF, SphI-HF, StyI-HF, StyI-HF, SbfI-HF, BmtI-HF, PvuII-HF, BsaI-HF, DraIII-HF, AgeI-HF, MfeI-HF, MluI-HF, and NruI-HF. More will be available soon.

      The second interest of our lab is on reverse transcriptase and its application in low-input RNA sequencing. Low-input RNA sequencing has been widely used in single cell analysis, which is revolutionizing our understanding of the enormous diversity of the transcriptome in both normal and pathological states. To optimize low-input RNA sequencing technology, we carry out different approaches including protein engineering with the aim to increase reverse transcription efficiency, attenuate amplification distortion, reduce false positive errors and increase coverage uniformity.

    • Christopher Taron

      Scientific Director
      Ph.D., University of Illinois, 1999

      Area of focus:

      Protein expression and glycobiology.

      Current Research:

      We are currently involved in developing technologies for heterologous protein production in various yeast hosts. In one research program, we work with Kluyveromyces lactis, an efficient yeast expression platform that has been used to produce proteins at industrial scale in the food industry for two decades. Our research involves engineering genetically enhanced host strains, developing novel strategies for yeast bioreactor growth and devising improved methods for harvesting expressed proteins. Our goal is to devise solutions to various bottlenecks associated with protein expression in yeast that can be implemented at both lab and industrial scales.

      Additionally, we conduct basic research on carbohydrate modifications of secretory proteins in yeast and mammalian cells. Specifically, we study the biosynthesis, regulation and function of glycosylphosphatidylinositol anchors (GPIs), covalent glycolipid protein modifications that tether proteins to the surface of eukaryotic cells. One aim is to examine the roles that variations in GPI glycan structure and/or N-glycan structure may play in targeting GPI-anchored proteins to specific membrane domains in polarized mammalian cells. We are currently developing novel enrichment techniques to improve the sensitivity of proteomics and glycomics methods used to analyze GPI anchored proteins non-destructively released from the surface of living cells.

    • Mehmet Berkmen

      Staff Scientist
      Ph.D., University of Vienna, University of Houston, 2000

      Area of focus:

      Strain engineering and disulfide bonded protein folding.

      Current Research:

      We are interested in understanding the molecular mechanisms that govern oxidative folding of proteins. Many important proteins require disulfide bonds for their folding and stability, including antibodies, interferons, proteases and signaling proteins. The formation of the correct disulfide bonds in a protein requires the coordinated activity of enzymes belonging to the thioredoxin family. In eukaryotes, disulfide bond formation is compartmentalized to the endoplasmic reticulum where 30% of all proteins fold; of those, half are predicted to form disulfide bonds. In Gram negative prokaryotes, disulfide bond formation occurs in the periplasm. A deep understanding of the processes involved in disulfide bond formation is critical to the production of complex disulfide-bonded proteins.

      Our research focuses on how disulfide bond formation is catalyzed. In addition, we are interested in how mis-oxidized proteins are isomerized back to their native correctly folded state. We investigate these principles in vivo using the model organism E. coli. Specifically, our research is focused on understanding the mechanisms of forming disulfide bonds within the two distinct compartments of E. coli, the reducing cytoplasm and the oxidizing periplasm. We hope to, (i) improve our understanding of the mechanism of oxidative-folding, (ii) identify novel enzymes which can assist in the oxidative-folding of proteins and (iii) engineer mutant E. coli strains which can express at high yields multi-disulfide bonded proteins.

    • Shaorong Chong

      Senior Scientist
      Ph.D., University of Michigan, 1994

      Area of focus:

      Reconstituted cell-free systems, synthetic biology, protein evolution, protein interactions.

      Current Research:

      My lab intends to (1) understand biology by recreating biological processes through in vitro reconstitution, and (2) serve biology by

      in vitro engineering proteins or enzymes with desired properties. Our approach is to use a bacterium/phage-based protein synthesis system, reconstituted from minimal, defined and purified components, to decode the information stored in a genome, which can be of the bacterial or human origin, and to explore the sequence space of a protein that is not yet explored by evolution.

      We have reconstituted the minimal protein translation machineries of Escherichia coli and Thermus thermophilus in vitro from defined and purified components. Like PCR, which synthesizes DNA in a few hours under defined and controlled conditions, a reconstituted protein synthesis reaction produces proteins also in a few hours under defined and controlled conditions. Both in vitro systems are amenable to high throughput and nanotechnology platforms. As a technological tour de force, the reconstituted protein synthesis system may turn out to have the same impact on phenotypic information (proteins) as the next-generation sequencing technologies on genetic information (DNA).

      Using such reconstituted systems as a “cleaner” cell-free protein synthesis reagent, we are synthesizing a variety of biologically important proteins for in vitro characterization, and exploring a variety of in vitro protein evolution techniques to engineer proteins or enzymes with enhanced catalytic activity, binding affinity or thermostability. Using such reconstituted systems as a starting point, we are reconstructing, from genetic materials (DNA and RNA), important biological processes such as transcription, replication, protein post-translational modification and protein interaction, for in vitro characterization and screening of synthetic or natural macro- and small-molecule modulators.

      Protein synthesis is the most conserved and fundamental process in all organisms, and is probably the first deciding step after the “RNA World” that catapulted the evolution towards the emergence of a proteinaceous primitive cell. It may even be possible to recreate such critical period of evolutionary history by providing a primitive genome with a minimal protein synthesis machinery and “rebooting the operating system” written inside the genomic codes.

    • Ellen Guthrie

      Senior Scientist
      Ph.D., University of Illinois, 1986

      Area of focus:

      Glycobiology

      Current Research:

      The major area of interest in my laboratory is the study of enzymes used for glycan characterization and modification.  We are involved in the screening, cloning, overexpression, purification and characterization of novel glycosidases. The substrate specificity of these novel enzymes is determined using labeled complex carbohydrate substrates as well as using LC/MS analysis. In addition, we are working on developing tools and methods to make the study of glycans and glycobiology simpler and faster for other researchers.

    • Elisabeth Raleigh

      Emeritus Scientist
      Ph.D., Massachusetts Institute of Technology, 1981

      Area of focus:

      Adding new genes to bacterial chromosomes and controlling their spread.

      Current Research:

      My continuing scientific interest is to understand the limits of horizontal exchange in bacteria. This interest grew from the use and study of transposons during my Ph.D. work at MIT and as a postdoctoral fellow at Harvard. At New England Biolabs the topic fit well with the company’s cloning effort with restriction enzyme genes. My research at NEB identified enzymes that exclude entering restriction systems by attacking the very modified bases that are needed protect the host DNA from cleavage by the invading system. The theme of the lab has been use of genetic approaches to assist understanding the in vitro and in vivo behavior of these and other enzymes. Many RM genes are clustered in genomes, found in variable loci called genome islands. At present, the dynamics and mechanism of acquisition and replacement of genome islands are our focus. The results should contribute to understanding the dynamics of biotic response to changing environments.

    • Paul Riggs

      Senior Scientist
      Ph.D., Massachusetts Institute of Technology, 1984

      Area of focus:

      Protein expression and regulation of translation.

      Current Research:

      We are engaged in studying protein expression in E. coli, with a particular interest in the control of ribosome biogenesis and translation. One focus of our research is understanding how phage modify the host transcriptional and translational apparatus to subvert it for making progeny phage particles, reasoning that this process mimics recombinant protein expression in some important ways. To this end, we are examining the effect of two T4 ADP-ribosyltransferases that modify a number of E. coliproteins early in T4 infection. Another focus of our lab is to understand the regulation of RNA polymerase by factors that bind to the polymerase rather than promoter DNA. One of these factors, DksA, is central in regulating ribosome biogenesis, but its exact mode of action is poorly understood. The ultimate goal of these studies is to understand global translational regulation and use this knowledge to optimize translation for expressing recombinant proteins.

    • James Samuelson

      Senior Scientist
      Ph.D., Ohio State University, 2000

      Area of focus:

      Protein expression and strain engineering.

      Current Research:

      Our efforts are primarily focused on enzyme engineering with the objective of producing high-value functional proteins for applications in biochemical research. The wealth of genome sequence data allows for rapid sampling of native enzymes for desired biochemical activities. Yet, we seek to generate improved biocatalysts through mutagenesis and application of well-designed selection schemes or screening strategies. When possible, cell-based selections are applied upon focused libraries in order to directly isolate expression clones with an activity of interest. A second motivation in the lab is to engineer or select improved protein production hosts. For example, NiCo21(DE3) is a strain designed for the production of His-tagged target proteins with minimal contamination by host metal-binding proteins. Other current projects involve strain engineering to eliminate undesirable host proteins that may be difficult to remove from target recombinant protein via conventional chromatography. Finally, we continue to investigate novel means to produce difficult proteins including membrane proteins and other toxic proteins.

    • Christopher Noren

      Scientific Director
      Ph.D., University of California, Berkeley, 1990

      Area of focus:

      Phage display, protein modification, metalloenzymology.

      Current Research:

      Our lab is interested in extending the limits of encoded biopolymer libraries to include semisynthetic functionality. This is based on the observation that a unique nucleophile can be specifically placed within a random phage-displayed peptide library in the form of a co-translationally incorporated selenocysteine residue (K.E. Sandman et al., (2000) J. Am. Chem. Soc. 122: 960-961). The incorporated selenocysteine can be uniquely chemically modified, prior to each round of phage panning, with pharmacophores, translation-state analogs, or other small molecules under conditions where the rest of the phage coat is unreactive, resulting in selection of semisynthetic peptide ligands that bind to a target of interest. Other applications of the technology include labeling tumor-targeting phage for medical imaging applications (K.A. Kelly et al., (2008) PLOS Medicine 5: 657-667), tethering phage to a solid support for direct mechanical manipulation (A.S. Khalil et al., (2007) Proc. Nat. Acad. Sci. USA 104: 4892-4897), and covalently attaching enzyme substrates to phage for catalysis-based screening of novel enzyme activities (J.G. Swoboda et al., (2006) Chembiochem 7: 753-756).

    • Ivan Correa

      Senior Scientist
      Ph.D., State University of Campinas, 2003

      Area of focus:

      Synthetic chemistry, bioorthogonal probes, protein labeling, epigenetics.

      Current Research:

      A major focus of my laboratory is the design and synthesis of chemical probes for studying biomolecules in vitro and in living cells. We strive to bring concepts from synthetic chemistry into biological systems to track, manipulate, separate, and interrogate proteins, nucleic acids, glycans, and other cellular species. We are particularly interested in the development of chemical and bioanalytical tools for the investigation of structurally modified DNA and RNA nucleotides with biological significance. Projects involve the application of multi-stage mass spectrometry and chemical synthesis for the identification, screening and quantification of epigenetic and epitranscriptomic modifications. Efforts from our lab have led to the development of probes for the chemoenzymatic labeling and detection of 5-hydroxymethyl-cytosine and to the characterization of the activity and specificity of novel 5-methylcytosine oxygenases. We are engaged in multiple research collaboration projects aiming at the study of DNA and RNA modifications in various organisms as well as at the replication and transcription of synthetic unnatural bases.

      We have also worked extensively on the chemistry of NEB’s protein labeling systems, SNAP-tag, CLIP-tag, ACP-tag and MCP-tag, and generated a variety of substrates with unique properties, including fluorescent dyes, blockers, biotin labels, and functionalized building blocks. Our efforts on the synthesis of SNAP-tag fluorescent probes have enabled researchers to image biological structures with greater resolution and less background. Current efforts are aimed at the development of fluorogenic probes for wash-free imaging in living cells, of multifunctional probes for detection of protein-protein interactions, and of fluorescent probes for super-resolution and single molecule imaging.

       

       

    • Cristian Ruse

      Staff Scientist
      Ph.D. , Case Western Reserve University, 2003

      Area of focus:

      mass spectrometry, proteomics

      Current Research:

      Proteins sequence ultimately determines their structure and results in a many diverse functionalities from enzymatic catalysis to molecular signaling and physical interactions.  These cellular blocks are the direct manifest of genes potential functions and their detailed description necessitates studies of the protein complement of cells, including identification, modification, quantification, and localization.  Mass spectrometry (MS) uses mass analysis to characterize proteins in vastly different complexities and environments. The fundamental measurement of protein and peptide masses is brought to fruition by a combination of biochemical steps (commonly referred as sample preparation), analytical techniques (nano liquid chromatography) and physical phenomena (ionization).  Following successful introduction and detection of proteinaceous ions within mass spectrometers, different fragmentation strategies further characterize their intrinsic properties and sequences.  We develop new mass spectrometry approaches for protein characterization using multiple fragmentation stages while maintaining the analytical dimension of the separation.

    • Lana Saleh

      Staff Scientist

      Area of focus:

      Current Research:

      In eukaryotes, methylation on both DNA and RNA is reversible and exists in the form 5-methylcytosine (5mC) on DNA and N6-methyladenosine (m6A) on RNA. The primary interest of my group is the biochemical characterization of oxygenases involved in the demethylation processes of these bases, such as the ten eleven translocation (TET) enzymes in the case of 5mC and FTO and AlkBH5 in the case of m6A. These oxygenases are members of the Fe(II)/alpha-ketoglutarate-dependent dioxygenases, which employ a radical-based mechanism for the oxidation of the methyl moiety on their corresponding substrates. My group is interested in understanding the chemical mechanism that these enzymes employ to generate these oxidized bases, as well as deciphering their modes of substrate recognition and product release. We are also interested in how the various members of the nucleic acid oxygenase sub-family evolved to perform various oxidative functionalities and understand the factors that ultimately dictate their specificity.

      1. Oxidative demethylation of 5mC on DNA and RNA

      The TET enzymes have been implicated in the oxidation of 5mC into three oxidized forms, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC). These bases have been thought to be intermediate products on the pathway to active demethylation in mammals but recent literature have presented evidence to the possibility of these modified bases functioning as epigenetic

      markers involved in cellular regulation and developmental processes. We are in the process of performing in vitro biochemical characterization of the mammalian TETs (mTETs) and their evolutionary distant relative, NgTET1, from the unicellular protist Naegleria gruberi, and relating the in vitro modus operandi to the in vivo biological reports. We are also interested in studying various other members of the TET/JBP family of which mTETs and NgTET1 are members. Specifically, we are keen to identify novel oxygenases that exhibit oxidative functionality to 5mC on mRNA and long non-coding RNA. Last but not least, we are utilizing structural and bioinformatics tools to identify TET homologs with altered oxidized-product distribution and substrate specificity.

      2. Oxidative demethylation of m6A on RNA and DNA

      m6A on RNA is known to play a role in various RNA metabolism processes such as splicing, nuclear export, translation ability, and stability. My group focuses on the functional and biochemical characterization of various m6A demethylases, which catalyze the conversion of m6A to adenosine (A) on RNA, such as FTO and AlkBH5, and DNA, such as a predicted AlkB homolog from Caenorhabditis elegans. In its demethylation reaction, FTO has been shown to catalyze the formation of two oxidized intermediates, hydroxy-6-methyladenosine (hm6A) and formyl-6-adenosine (f6A) on the pathway to formation of A. On the other hand, neither intermediate has been detected in the reaction of mammalian AlkBH5. Therefore, one of the aspects we are interested in studying in the lab is the possible divergences in the chemical demethylation mechanisms of these two enzymes or whether the lack of detection of the same intermediates in the reaction of AlkBH5 is merely related to low in vitro activity of this enzyme. We are also focused on identifying the nature of optimum substrates of the afromentioned enzymes using an array of biochemical tools such as liquid chromatography (LC)-triple quad mass (QQQ) spectrometry-based kinetic assays, UV-visible spectroscopy, stopped-flow spectroscopy, and next generation sequencing methods.

      3. Biotechnological tools for methylome sequencing on DNA and RNA.

      My group is exploring the biotechnological application of the TET enzymes and the m6A demethylases in single-base resolution methylome sequencing of DNA and RNA, respectively, with the ultimate goal of developing commercial sequencing kits, which will serve as a molecular diagnostic tool for the epigenome and transcriptome-wide mapping of 5mC and m6A to understand the role of these bases and their modifications in various biological processes and disease states.
    • Peter Weigele

      Staff Scientist
      Ph.D., University of Utah, 2003

      Area of focus:

      Microbial electrochemical systems & synthetic biology methods.

      Current Research:

      Our lab is focused on the application of biotechnology to sustainable energy. Our goals are two-fold. One is to develop the Personal Bioreactor– a compost-powered microbial fuel cell (MFC) for off-grid lighting and low-power applications. The other is to engineer an “Electric coli”, an E. coli strain capable of producing electricity from glucose and similar electron donors.

      Efforts in the lab span both engineering and biology. Together with Folusho Ajayi, Post-doctoral Scholar in the lab, we have developed small, inexpensive, easy-to-build MFC-type “bio-batteries” fueled by bacteria and dried pasture grasses. These bio-batteries couple biologically catalyzed oxidation of organic substrates to the production of electricity. We have characterized these bio-batteries by electrochemical techniques, and determined which processes limit overall power density. Current efforts are aimed at increasing the efficiency of the biobattery’s cathode.

      We are also examining the cellular machinery responsible for electron transfer between the bacterial cell surface and a fuel cell electrode at the molecular level. Using methods developed by Yuri Londer, Research Scientist in the lab, we are expressing and characterizing components of an “electrosome”, an outer-membrane multiheme-cytochrome complex essential to electricity production. A complete extracellular electron export pathway functioning in E. coli will allow us to better study this phenomenon and develop industrial applications based on cell-electrode interactions.

    • Ming-Qun Xu

      Senior Scientist
      Ph.D., State University of New York at Albany, 1989

      Area of focus:

      Protein engineering, protein labeling and imaging.

      Current Research:

      My research efforts are focused on enzyme engineering and development of versatile tools for research and diagnosis applications. My lab is currently working on improving catalytic activities, stability and utility of enzymes using various protein engineering approaches. These research activities aim at development of applications in next-generation sequencing and deglycosylation. In addition, I am also interested in spatial and temporal analysis of protein dynamics in living cells using fluorescent labeling and single molecule fluorescence techniques.

    • Sir Richard Roberts

      Chief Scientific Officer
      Ph.D., University of Sheffield, 1968

      Area of focus:

      Bioinformatics of restriction and modification.

      Current Research:

      My laboratory has a long history of research on restriction enzymes and their associated DNA methyltransferases. We are developing methods to find new enzymes with novel properties using a combination of bioinformatics and biochemical experimentation to analyze the DNA sequence information from the many microbial genome sequences that are now available. Most recently, this takes advantage of SMRT sequencing to determine methyltransferase specificities thereby giving recognition sequences for Type I and Type III restriction systems and allowing a match between recognition sequences for Type II methyltransferases and their associated restriction enzymes. We are also broadening our use of bioinformatics to explore microbial genome sequences in a project called COMBREX that aims to provide functional predictions for open reading frames in complete DNA microbial sequences and to test those predictions experimentally. This is essential if we are to improve the quality of bioinformatics predictions. We also run REBASE (www.neb.com/rebase), a database of information about restriction enzymes and their associated methyltransferases.

    • Clotilde Carlow

      Scientific Director
      Ph.D., University of London, 1984

      Area of focus:

      Drug discovery and diagnostics for filariasis.

      Current Research:

      My laboratory conducts research on filarial nematode parasites that cause important neglected tropical diseases in humans such as elephantiasis (lymphatic filariasis) and river blindness (onchocerciasis).  Our work includes basic research on parasite biology and their Wolbachia endosymbionts, as well as applied research projects focusing on the development of new diagnostic tests and therapies.  A great deal of this work involves collaborations with scientists from academia and industry.

      Accurate parasite detection is essential for the success of filariasis control programs.  We are interested in developing new and improved methods for diagnosis of infection in humans and surveillance of insect vectors. Our current major areas of focus are on the identification of new biomarkers using comparative genomics, and the development of sensitive and specific nucleic acid-based diagnostic assays that are simple to perform and ideally suited to low resource settings.  We are also using similar approaches to develop a number of new diagnostic tests for a variety of tick borne infections that occur in the United States and many countries worldwide.

      Current control of filariasis is largely based on the use of a limited number of drugs which have limited efficacy.  Our basic research on parasite biology and the symbiotic relationship between filarial parasites and their bacterial symbionts has led to the discovery of a number of new drug targets present in parasites or Wolbachia, but lacking in humans.  In addition, we have demonstrated the existence of established therapeutic targets that may be repurposed for filarial disease.  We are working with partners to identify inhibitors of these targets that may represent new drug leads.  

    • Laurence Ettwiller

      Staff Scientist

      Area of focus:

      Current Research:

      The major topic of the Ettwiller group is to bridge the large enzyme discovery and optimization efforts  conducted at NEB with the latest massive parallel sequencing technologies.

      With the central aim to develop innovative large scale applications, our research involves the elaboration of both experimental methodologies and data analysis strategies inherent to such applications. The outcomes of these efforts are twofold: first, unique new abilities to address biological questions; and second, the perspective of improving existing or novel technologies.

    • Jeremy M. Foster

      Staff Scientist
      Ph. D., University of Liverpool, 1989

      Area of focus:

      Genomics and glycobiology of filarial nematodes

      Current Research:

      Parasitic filarial nematodes threaten the wellbeing of 1 in 5 people on the planet and represent a major cause or morbidity and economic loss that trap heavily infected communities in poverty.  The few available therapies do not kill adult worms but instead aim to prevent transmission through annual treatments targeting the larval forms transmitted by insect vectors. Recent evidence indicates that these drugs are losing their effectiveness and furthermore there is no vaccine available. Wolbachia endosymbionts of filarial nematodes are essential for parasite development and adult worm survival providing a new avenue towards filarial disease control. Research in the laboratory aims to uncover aspects of filarial and Wolbachia biology that might highlight molecules or processes for further development as drug targets, vaccine candidates or diagnostic reagents.

      We use NextGen sequencing technologies to examine diversity within and between different geographic isolates of filarial nematodes and their Wolbachia endosymbionts, and make comparisons to strains that have been artificially maintained in the laboratory for many years. This reveals genes under varying selection pressures and required for life cycle progression between the human and insect hosts. Selected genes are then subjected to detailed functional characterization.

      Lateral gene transfer (LGT) is a mechanism of genome evolution that can enable acquisition of new biological properties. We have identified extensive LGT from Wolbachia to the genomes of their filarial hosts. Many of the transferred genes are full length and transcribed. We are performing RNA interference studies to examine the roles of RNA transcripts and protein products resulting from gene transfer.

      Filarial nematodes survive in immunocompetent mammalian hosts for more than 10 years. The nematode surface is rich in glycoconjugates that are implicated in mechanisms of immunomodulation and immune evasion. We are applying new reagents and technologies to characterize specific classes of surface glycoconjugate and identify unusual sugar modifications that might serve as vaccine components or diagnostic tools.

    • Richard Morgan

      Senior Scientist
      Ph.D., Boston University, 2009

      Area of focus:

      Engineering DNA recognition specificity of restriction enzymes, and identification of new restriction modification systems.

      Current Research:

      Discovery is central to my research, which focuses on enzymes that interact with and act upon DNA. The bacterial restriction-modification (R-M) systems serve as models for many protein - DNA interactions, including how proteins recognize specific sequence motifs within the DNA and how they catalyze either cleavage or modification of the DNA. I seek to discover and characterize new R-M systems, particularly new forms or subgroups of R-M systems, as well as to develop new methodologies for R-M system discovery, such as Single Molecule, Real Time (SMRT) sequencing technologies that enable direct characterization of DNA modifications. I seek to apply bioinformatic tools and experimentation to investigate how these enzymes function and evolve, with emphasis on how they achieve their exquisite specificity and how they evolve to change their specificity. I am also interested in how these systems evolve and help shape microbial communities where these systems likely function as regulators of genetic exchange.

    • Janos Posfai

      Senior Scientist
      Ph.D., University of Szeged, 1991

      Area of focus:

      Bioinformatics of restriction enzymes.

      Current Research:

      Fundamental problems of Nature can be framed in mathematical terms, and scientific insight can be gained by rigorous analysis of symbolic models. In my research, I construct such abstract models of biological systems (DNA molecules, genes, genomes, proteomes, and their relationships), and run algorithmic analysis of the models to reveal their hidden features. Bacterial restriction-modification system genes are in my focus, identifying and classifying RM systems, uncovering their role and describing their evolution has occupied me over the years. Components of RM systems are important tools of molecular biology experiments. To assist experimental applications, I create and maintain resources (e.g. genome digest maps), develop data analysis algorithms, and script computational tools. The general questions of “What is in the data?”, and “How to access it?” continues to intrigue me, and I am determined to find the answers for specific domains.

    • Sriharsa Pradhan

      Senior Scientist
      Ph.D., University of Glasgow, 1995

      Area of focus:

      Epigenetic gene regulation and inheritance.

      Current Research:

      In eukaryotes, the epigenome plays an essential role in regulation of gene expression. DNA hypermethylation in chromatin usually leads to gene silencing and is essential for a variety of epigenetic processes in the majority of eukaryotes, including animals, fungi and plants. Similarly, post-translational modifications (methylation, acetylation, phosphorylation, ubiquitination and ADP ribosylation) of histones determine the interaction of regulatory and structural proteins with the nucleosome thereby, altering chromatin structure. There are numerous examples of aberrant DNA methylation in pathological conditions, including cancer. The acquisition of a cancer specific DNA methylation pattern plays an important role in oncogenic transformation and thus can be used as an early diagnostic marker. Recently, it has been shown that changes in global levels of individual histone modifications are also associated with tumorigenesis and that these changes are predictive of cancer.

      My laboratory is focused on understanding the regulation of DNA and protein modifications, in particular the writer (enzymes that attach a particular modification mark on DNA or amino acids), reader (protein that binds to the modified DNA or amino acids) and eraser (enzymes that remove an established modification mark from DNA or amino acids) machinery, and their interaction with each other. We also investigate the role of various transcription factors and tumor suppressor proteins as epigenetic modulators during cellular growth, development and programmed cell death. Finally, we integrate epigenomic information with biochemistry, structural biology and live cell imaging to decipher the intricate epigenetic mechanisms involved in the functioning of a cell.

    • Barton Slatko

      Senior Scientist
      Ph.D., University of Texas, Austin, 1977

      Area of focus:

      Filariasis genomics and Wolbachia symbiosis.

      Current Research:

      My laboratory is interested in the evolution and biology of the Wolbachia endosymbiont, which is present in the majority of human and animal filarial parasites, including Onchocerca volvulus (the agent of River Blindness), Wuchereria bancrofti and Brugia malayi (agents of lymphatic filariasis) and Dirofilaria immitis (the agent of canine and feline heartworm disease). The symbiont is obligate in that it is required for proper host nematode development and reproduction. Having completed the genome sequence and annotation of the endosymbiont genome from B. malayi and been involved in the sequencing and annotation of the B. malayi host, we are now investigating the biochemical basis for their mutually dependent relationship. To achieve this aim, we are using molecular, biochemical, cytological, NextGen DNA sequencing and interactome proteomics approaches. The goal is to understand the nature of the symbiotic relationship and ultimately eliminate filariasis disease, a Neglected Tropical Disease (NTD) which affects over 120 million people (with 1 billion individuals at risk) and is the second leading cause of disablement worldwide.

      We are part of global research networks and to this end, we are members of The Wolbachia Consortium, the Filarial Genome Network (see: http://xyala.cap.ed.ac.uk/research/nematodes/fgn/filgen1.html  and http://www.nematodes.org/nembase4/).  We have been part of a worldwide consortium funded by the Bill and Melinda Gates Foundation, thru the Liverpool School of Tropical Medicine to identify and pursue drug targets identified from Wolbachia genomics and drug discovery (see:  http://www.a-wol.net/).

      Recently, we have been sequencing and analyzing the microbiomes of individuals with and without intestinal parasitic diseases to ascertain their nutritional status upon infection and have also initiated several metagenomic projects, including one pond diversity with the aim of eventual bioremediation one  investigating Xenorhabdus nematophila developmental profiling.

      Over the years my laboratory has also been involved with the development of new products, many of which have been direct offshoots of ongoing research projects. My laboratory is also the DNA sequencing core facility for NEB scientists.

    • Geoffrey Wilson

      Senior Scientist
      Ph.D., Sussex University, 1976

      Area of focus:

      The molecular mechanism(s) of protein-DNA sequence-specificity; structural analysis of crystallized sequence-specific proteins; engineered restriction-like enzymes with novel properties.

      Current Research:

      Studies restriction and modification enzymes to understand the mechanisms of DNA sequence-recognition and site-specific catalysis, and to learn how they can be engineered by domain-fusions and site-specific mutagenesis to make useful reagents for new molecular biology applications.

    • Brett Robb

      Scientific Director
      Ph.D., University of Toronto, 2004

      Area of focus:

      Small RNA biology, post-transcriptional gene regulation, mRNA modifications, tools and methods development for RNA research.

      Current Research:

      We now appreciate that small RNAs direct a set of conserved gene silencing phenomena in conjunction with a group of related effector protein complexes. Silencing can occur post-transcriptionally via mRNA degradation and/or repression of translation, or at the level of transcription.

      In recent years techniques that exploit small RNA guided silencing pathways have been widely adopted as research tools, however, there remain vast gaps in our understanding of how the processes work, and the nature of their biological roles.

      My lab is interested in both the components and targets of the protein-RNA complexes that mediate the spectrum of small RNA guided gene regulatory responses in mammalian cells. By characterizing these complexes and their targets, we hope to gain insight into the biology of these pathways.

      Along the way, we actively develop reagents and methods to apply to our research questions, and to enable discovery and applied research in the broader scientific community.

    • Larry McReynolds

      Senior Scientist
      Ph.D., Massachusetts Institute of Technology, 1974

      Area of focus:

      The complexity of RNA regulation in the cell requires novel reagents to aid in their isolation, ligation and sequencing. We have developed novel RNA ligases and other proteins for this purpose. One example is the use of the siRNA binding protein, p19, to capture and clone endogenous dsRNAs. This has allowed us to identify novel antisense transcripts in bacteria.

      Current Research:

      The discovery of novel regulatory functions for non-coding RNAs has created a demand for new tools for their isolation, detection and cloning. NextGen sequencing of RNA combined with new isolation methods have allowed us to discover new regulatory pathways in bacteria and parasitic nematodes. We have used the p19 siRNA binding protein from a plant virus to enrich short dsRNAs over 100,000 fold. When cloned and sequenced, these RNAs identify new anti-sense transcripts complementary to both coding and non-RNAs in E. coli and in parasitic nematodes. 
       
      A second research interest is the characterization of RNA ligases. Mutant thermophilic ligases have been created that allow ligation of ssRNA or ssDNA to adenylated linkers at elevated temperatures.  We have made the interesting observation that besides ligation these thermophilic ligases can also modify RNA3’p and DNA3’p.  They generate RNA 2’, 3’ cyclic phosphate or DNAppA.  In addition we have exploited the ability of Chlorella virus DNA ligase (SplintR TM ligase) to efficiently ligate DNA oligos hybridized to a microRNA splint to create a specific and sensitive detection method.  Understanding the biochemistry of RNA ligases should give new insight into their biological function and create novel tools for RNA detection. 

    • Ira Schildkraut

      Emeritus Scientist
      Ph.D., University of Miami, 1974

      Area of focus:

      Enzymatic manipulation of RNA.

      Current Research:

      A few years ago I rejoined NEB after being absent for a decade. My current research interests are concerned with identifying enzymes/activities that can be used to manipulate RNA. We have determined that both the S. cerevisiae 5' deadenylase and the E.coli RppH can remove 7mG caps from eukaryotic RNA. We have also shown that Vaccinia Capping Enzyme (VCE) can add a 3' modified GMP to the 5' triphosphate of RNA. Together these newly described activities have enabled us to develop a method for the enrichment of primary transcripts of prokaryotic RNA. This method overcomes the challenge of the overabundant ribosomal RNA inherent in all microbial RNA preparations regardless of genus. The method is based on the unique ability of the enzymatic capping reaction to add a biotinylated molecule to the 5' triphosphate of prokaryotic transcripts. Biotinylated transcripts are subsequently selected on streptavidin magnetic beads while the unwanted processed, eukaryotic and ribosomal transcripts are eliminated. The methods yield NextGen sequencing libraries for whole transcriptomes / metatranscriptomes or can be adjusted to determine the transcriptional start sites to one base pair resolution. The methods are currently being adapted to reveal the same for eukaryotic organisms.

    • George Tzertzinis

      Senior Scientist
      Ph.D., Boston University, 1989

      Area of focus:

      RNA-mediated mechanisms of gene regulation, sensitive luminescence reporters, cell differentiation.

      Current Research:

      My laboratory's research interests are centered on different aspects of eukaryotic gene regulation especially as it relates to cell differentiation. In the past, we have studied regulatory roles of ligand-activated transcription factors, primarily nuclear receptors in parasites and mammalian cells (1,2). We have also been studying the function of non-coding RNAs such as siRNAs and microRNAs in regulating transcriptional and post-transcriptional events in mammalian cells, and developing methodologies and tools for their use (3,5). We are currently interested in the function of nuclear transcription factors in the maintenance or differentiation of cell fate and studying their mechanism of action via epigenetic regulation. We are employing secreted luciferases as sensitive reporters of dynamic change in order to detect and monitor gene expression in live differentiating cells.

      Additionally, we are developing luminescence-based assays for cell characterization, epigenetic analyses, and imaging techniques that can be applied in our research projects.