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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:

      The major interest of my laboratory is the analysis of DNA polymerase function, with a particular focus on those isolated from hyperthermophilic archaea. Our past studies have explored the basic kinetics of these polymerases in comparison with both thermophilic and mesophilic polymerases. One aspect of our study has been the utilization of modified nucleotides by archaeal DNA polymerases and selected archaeal DNA polymerase variants. We have noted an increased propensity of the archaeal DNA polymerases to incorporate acyclonucleotide terminators (lacking both 2’ and 3’ carbons of the sugar residue), in comparison with thermophilic and mesophilic DNA polymerase counterparts. Our continuing research is directed toward expanding this understanding with the goal of creating and discovering DNA polymerases that have an even greater ability to incorporate modified nucleotides.

      We have also analyzed how the polymerases act in concert with other proteins during replication in vivo. One model system we have used is replication of the chromosome of Sulfolobus islandicus Rod-shaped Virus 2, focusing particularly on the initiation of replication. Through these studies we hope to more completely understand and harness the power of in vivo replication for in vitro applications.

    • Tom Evans

      Division Head
      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 still unresolved.  We use T4 DNA ligase as a model ligase and apply techniques such as stopped flow, rapid quench, and capillary electrophoresis to gain further insights into the mechanism of DNA ligation.  Our work has elucidated the rate constants for the various steps in the T4 DNA ligase reaction pathway.  Furthermore, we demonstrated that product release is the rate-limiting step for T4 DNA ligase nick sealing reactions under turn-over conditions (Lohman, G. J., et al., J. Biol. Chem. (2011) 286:44187).

      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 Strand-displacement Amplification.  These procedures have the sensitivity of PCR, but 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 has led to the development of a DNA polymerase with properties superior to Bst DNA polymerase, LF.  Furthermore, a so-called “WarmStart” form of the enzyme is inactive at room temperature, but becomes active at temperatures above about 48oC.  This gives isothermal technologies the advantage of room-temperature set-up and improved reproducibility.

      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.  It is unlikely that all the repair capability of PreCR is needed for this specific application.  Therefore, we are developing a PreCR mix focused on the needs of NextGen sequencing sample preparation.

      As part of our interest in DNA repair we investigated mismatch repair in the thermophilic bacterium Aquifex aeolicus.  This deeply branched bacterium was found to have a mismatch repair pathway that had properties of both Escherichia coli and human mismatch repair (Mauris, J., & Evans, T. C., Jr., J. Biol. Chem. (2010) 285:11087; Mauris, J., & Evans, T. C., Jr., PLoS One (2009) 4:e7175).  Perhaps this pathway orchestration is ancestral to both the E. coli and human pathways.

      I hope that it is apparent from these project descriptions that my laboratory is interested in research that is both basic and applied.  Inevitably a mixture of long, medium and short-term research goals are synergistic and intellectually stimulating.

    • Andrew Gardner

      Staff Scientist
      Ph.D., Boston University, 2010

      Area of focus:

      DNA amplification; Genomics.

      Current Research:

      All organisms replicate their genomes during cell division to pass along genetic information to the next generation. To understand genome replication, my lab studies the DNA replication enzymes and mechanisms from the hyperthermophilic archeaon, Thermococcus.

      DNA polymerases are core replication enzymes that synthesize DNA and are important reagents for PCR amplification, DNA sequencing and genotyping. Our lab studies the kinetic basis for DNA polymerase function and fidelity. In particular, we engineer DNA polymerase mutants that incorporate modified nucleotides and are therefore useful as molecular tools in DNA sequencing and genotyping applications.

      In addition to studying the biochemistry of DNA polymerases, we are focused on understanding how the Thermococcus replication machinery called the 'replisome' functions to efficiently copy the cell's genome. Specifically, we are interested in defining key enzyme components and mechanisms that initiate replication, carry out rapid and accurate genome synthesis, and terminate synthesis. Our ultimate goal is to reconstitute the Thermococcus replisome in vitro and enable amplification of very long DNA fragments. We are also developing methods to use Thermococcus replisome as a molecular tool in synthetic biology and single cell genome amplification.

    • Jennifer Ong

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

      Area of focus:

      Protein Engineering, DNA Polymerases.

      Current Research:

      The goal of our lab is to develop and implement strategies to create better enzymes, focusing on DNA polymerases and amplification technologies. In particular, we aim to develop directed evolution and rational design strategies to improve enzyme function, using natural genetic diversity and evolutionary relationships to inform our mutagenesis efforts. Looking forward, I anticipate a need for engineered polymerases to meet the stringent demands required by developingtechnologies: high sensitivity to amplify DNA from single cells, extreme processivity to build synthetic genomes, high fidelity for cloning and sequencing, and extreme stability. Currently, we are interested in improving the speed, fidelity and thermostability of our DNA polymerases. 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.

    • 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 basic 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 the identification of protein domains involved in sequence-specific protein/DNA interactions with the long-term goal to enhance our understanding of the molecular mechanisms responsible for substrate specificity. We are also developing novel molecular tools and methods for DNA manipulation and for analysis of modified bases. Over the last years we have created a number of DNA manipulation tools for seamless assembly of recombinant DNA molecules. We have utilized these tools to develop a technique referred to as USER-friendly DNA engineering and cloning method that allows performing numerous site-specific DNA manipulations and directional cloning in a simultaneous experimental arrangement. Building upon our success in DNA engineering, efforts are currently underway to evolve a number of DNA modification enzymes with altered substrate specificities and to develop new approaches and techniques to study post-replicative DNA modifications in eukaryotic genomes.

    • 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 the over-production and improvement of restriction endonucleases. These enzymes are essential laboratory tools for the manipulation and analysis of DNA, and New England Biolabs is the oldest and most prominent supplier of them in the world. To assist in their analysis and manipulation, most restriction enzymes are now cloned and overexpressed in E.coli. My lab has been instrumental in cloning and expressing a large number of them. 

      My lab has focused on engineering restriction enzymes with reduced ‘star activity’. Many restriction enzymes display a degree of ‘wobble’ in their recognition sequence specificities 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, we have succeeded in isolating star-less forms of many problem enzymes, forms that display much-reduced, or undetectable, star-activity. We call these ‘high fidelity’ (HF) restriction enzymes.

    • Christopher Taron

      Division Head
      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.

    • 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. At present, the dynamics and mechanism of acquisition and replacement of RM gene loci are the focus. The results should contribute to understanding the dynamics of biotic response to changing environments.

    • 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 glycobiology. 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. Ultimately we plan to crystallize some of these proteins to gain an understanding of what structural motifs are common to these enzymes. We are also working on tools for MS glycan analysis.

    • James Samuelson

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

      Area of focus:

      Protein expression and strain engineering.

      Current Research:

      E.coli strains are preferred hosts for the production of recombinant proteins. However, many eukaryotic proteins do not fold efficiently in E. coli. The causes for misfolding are complex but may be related to the rapid rate of translation in E. coli, overly robust production of target protein in excess of cellular chaperone capacity or the problem may be partly due to the fact that many eukaryotic proteins are thought to fold in a co-translational manner in the native cell. Therefore, we are testing new fusion partners and expression strategies that facilitate co-translational protein folding. 

      Furthermore, our mission is to engineer expression hosts that facilitate downstream protein purification processes. For example, the NiCo21(DE3) strain was designed and engineered specifically to aid researchers in expressing and purifying His-tagged recombinant proteins.

    • 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.

    • 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.

    • 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.

    • Christopher Noren

      Division Head
      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

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

      Area of focus:

      Synthetic chemistry, bioorthogonal probes, protein labeling, epigenetics.

      Current Research:

      The ability to characterize functioning biomolecules in living cells is paramount to improve our knowledge of complex biological networks. The major focus of my laboratory lies in the design and generation of chemical probes for modification of proteins, nucleic acids, and glycans. Specifically attaching chemical probes to individual proteins represents a powerful approach to the study and manipulation of protein function in living cells. Current projects in my research group include the synthesis of fluorogenic probes for direct monitoring of fluorescence signals in living cells with high sensitivity and low background, crosslinking probes for the investigation and detection of protein-protein and protein-nucleic acid interactions, and fluorescent probes for super-resolution and single molecule imaging. We are also engaged in designing chemical reporter strategies to track, manipulate, and interrogate other cellular species such as oligonucleotides, glycans, and lipids. In this context, we are particularly interested in the development of bioorthogonal probes for visualization and enrichment of glycoproteins and for epigenetics research.

    • 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:

      The current focus of my laboratory is to investigate protein dynamics in living cells utilizing various site-specific protein labeling techniques, such as SNAP/CLIP-tag, enzymatic labeling, and intein-mediated protein ligation. In particular, I am interested in the study of receptors related to tumor progression and early diagnosis, and producing fluorescent imaging probes for live cell and animal imaging of tumor models. The research efforts also aim at the development of versatile tools and reagents for optical analysis of protein dynamics in living cells. The ultimate goal is to establish a platform for monitoring proteins inside cells, analysis of cellular communications and study of animal models of disease and embryology.

      In addition, my research in protein splicing has provided insight into the chemical mechanism and structural basis of protein self-splicing as well as strategies to utilize self-splicing inteins for protein engineering. A number of novel methods have been developed for protein/antibody affinity purification, protein labeling and tagging, ligation and cyclization of expressed proteins.

    • 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.

    • Yu Zheng

      Senior Scientist
      Ph.D., Boston University, 2004

      Area of focus:

      DNA modification-dependent enzymes and engineering.

      Current Research:

      My research interest in the long term is on the evolutionary potential of natural enzymes, specifically DNA enzymes, and directed evolution strategies to improve them. Current research interests of my lab focus on three broad directions: (1) Directed evolution of restriction endonucleases toward altered specificity using the in vitro compartmentalization (IVC) method. Due to their cytotoxicity, restriction endonucleases are difficult targets for genetic selections using living hosts. We have established an in vitro system for their selection (Zheng and Roberts, 2007). (2) Computational and experimental studies of active DNA enzymes in sequence databases. This involves biological sequence analysis and comparative genomics approach to identify meaningful target genes followed by biochemical characterization. We are interested in mining genes that are likely to act on nucleic acids from the growing sequence data collection. Our recent focus is on a family of methylation-specific nuclease enzymes. (3) Protein-priming DNA replication systems. We are interested in studying terminal protein priming DNA replication of bacteriophage F29 and its application potential.

    • Clotilde Carlow

      Division Head
      Ph.D., University of London, 1984

      Area of focus:

      Drug discovery and diagnostics for filariasis.

      Current Research:

      Parasitic nematodes infect over one half of the world’s population, causing significant mortality and morbidity. They also cause significant problems in plants and animals. River blindness (onchocerciasis) and lymphatic filariasis, two diseases caused by filarial nematodes, are among the most important tropical diseases. Research in my laboratory is centered on the biology of filarial nematodes and their Wolbachia endosymbionts. We use the free-living nematode Caenorhabditis elegans as, a model for parasitic nematodes, since it shares many essential developmental processes and structural features. In addition, it offers a wealth of information since its genome has been completely sequenced, and there is a substantial collection of genetic information on many genes and genome-wide studies on gene function using RNAi. Since the sequence of the genome of the human filarial nematode Brugia malayi is also available, we use comparative and functional genomics to identify conserved nematode genes with an essential function that likely play an important role in nematode biology. These studies also allow us to identify those proteins that are absent from mammals that can be pursued further as potential drug targets.

      Filarial parasites are unique among nematodes in harboring obligate intracellular Wolbachia bacterial endosymbionts. These rickettsia-like bacteria are related to the Wolbachia endosymbionts of arthropods that are known to regulate a number of essential processes in their insect host including reproduction, gender and survival. We are pursuing molecular approaches to learn more about filarial Wolbachia which are essential for parasite development and survival. Our recent studies have revealed that Wolbachia may have a nutritional role and supply vitamin B2 to the worm host. We have also identified a number of Wolbachia enzymes that show promise as drug targets.

      Currently, point-of-care diagnosis of filarial infection is largely based on microscopic examination of blood or tissue, and morphological assessment of stained microfilariae. We are working towards developing inexpensive, field-appropriate, molecular-based diagnostic tools to detect infection. We have recently developed a simple test that amplifies Brugia DNA with high specificity, sensitivity and rapidity under isothermal conditions. The test has the potential to be developed further as a field tool for use in the management of mass drug administration programs for brugian filariasis.

    • 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 nematode 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, reproduction and survival. We have recently completed the genome sequence and annotation of the endosymbiont genome from B. malayi and we are now investigating the biochemical basis for the mutually dependent relationship with its nematode host. To achieve this aim, we are using genomic, molecular, biochemical, immunofluorescent and interactome proteomics approaches. The goal is to understand the nature of the symbiotic relationship and ultimately eliminate filariasis disease, 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 a global research network and to this end, we are members of The Wolbachia Consortium, the Filarial Genome Network and have been involved with the sequencing and annotation of the B. malayi genome. We are also part of a worldwide consortium funded by the Bill and Melinda Gates Foundation, through the Liverpool School of Tropical Medicine, to identify and pursue drug targets identified from Wolbachia genomics. 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, with both “First-Gen” and “Next-Gen” capabilities.

    • Fran Perler

      Senior Scientist

      Area of focus:

      Molecular Biology and Genetics, Archaea, DNA Enzymes.

      Current Research:

      I began research at NEB working on Malaria and then Onchocerciasis (River Blindness). This was followed by cloning thermostable DNA polymerases, including Vent, Deep Vent and 9N. The inteins in Vent polymerase made its cloning extremely difficult, which stimulated me to study inteins. Inteins are intervening protein sequences that splice themselves out of precursor proteins. During the last 20 years, I focused on the mechanism of protein splicing. My group has defined three classes of intein splicing mechanisms and worked on other aspects of intein-mediated protein splicing, including trans-splicing, determining intein motifs, intein evolution and intein applications. I now work in the DNA Enzymes Division on enzymes involved in archaeal replication including DNA polymerases and primases.

    • 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:

      Our group focuses on understanding the mechanism by which proteins such as restriction and modification enzymes achieve specificity for the particular DNA sequence they recognize and bind to. For many years, the main determinants of recognition have been thought to be unique patterns of hydrogen bonds between the protein and the edges of the base pairs in the major and minor DNA grooves. Analysis of restriction enzyme-DNA crystal structures coupled with experiments we have conducted suggest that hydrogen bonds play only a minor role, however, and that steric and electrostatic conflicts towards non-cognate sequences are the main determinants. The binding-sites of highly specific proteins have built-in obstructions to the 'wrong' base pairs, we find, that through clashes and repulsions prevent binding to any DNA sequence in which non-cognate base pairs are present.

      The goal of our work is to develop a clear and accurate understanding of the recognition mechanism, and then to apply this to the assembly of 'designer' proteins with novel properties that recognize new DNA sequences of choice. We anticipate such proteins, with properties not found in nature, could spur technological advances and lead to new insights into biochemistry, epigenetics, and structural biology, much as the discovery of natural restriction enzymes led to the development of DNA cloning and modern molecular biology.

    • Janos Posfai

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

      Area of focus:

      Bioinformatics of restriction enzymes.

      Current Research:

      Understanding biological systems through the use of mathematical concepts and computer science tools is in the center of my interests. Specifically, my goal is to develop advanced data mining, classification and pattern recognition algorithms that enable the reliable identification and precise functional description of restriction modification systems. My most recent studies investigate what role domain fusions play in the evolution of such systems. I am also engaged in the development of a genome digest web resource, which would support new restriction enzyme applications in the fields of cell differentiation and cancer research.  Developmental self organization, neural networks, and their possible role in the emergence of autism is another field where I am actively involved.

    • 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:

      Restriction enzyme discovery and characterization. Protein engineering in restriction endonucleases to generate enzymes with novel properties, such as new recognition sequence or position of DNA cleavage. Evolution and distribution of restriction-modification systems in bacterial and archaeal populations.

    • 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.

    • Sriharsa Pradhan

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

      Area of focus:

      Epigenetic gene regulation and inheritance.

      Current Research:

      In the eukaryotes, chromatin modification is important in the regulation of gene expression. DNA hypermethylation usually causes gene silencing and is involved in a variety of epigenetic gene regulatory processes in the majority of eukaryotes, including animals, fungi and plants. Similarly, histone modifications (methylation, acetylation, phosphorylation, ubiquitination and ADP ribosylation) determine the interaction of regulatory and structural proteins that may in turn regulate chromatin structure. There are numerous examples of the presence of altered DNA and histone methylation pattern in several pathological conditions, including cancer. The acquisition of cancer specific DNA and histone methylation pattern plays an important role in oncogenic transformation and thus could be used for an early diagnostic marker. My laboratory is focused on understanding the process of histone and DNA methylation in mammals, with greater emphasis on enzymes and their cross-talk with other cis or trans-acting factors during cellular growth, development and apoptosis. Recently, we have initiated studies to understand the role of genomic 5-hydroxymethylcytosine and its enzymatic apparatus in gene regulation. We are also studying the role of protein methylation as a means for signal transduction, which should allow us to study the role of protein methylation in cellular context.

    • Brett Robb

      Division Head
      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.

    • 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.

    • Ira Schildkraut

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

      Area of focus:

      Enzymatic manipulation of RNA.

      Current Research:

      I began working at NEB at the bench in 1977 after a postdoc position in Biology at MIT. I screened for and characterized new restriction endonucleases. Because of NEBs early success in cloning and overexpressing a large number of restriction systems, my lab focused on preliminary crystal characterization of restriction endonucleases so that we could interest protein crystallographers in solving the structure of this intriguing group of enzymes. From there we turned to the problem of engineering these activities. Recently rejoining NEB after being absent for a decade, I have begun looking at enzymes that are involved with or can be provoked into manipulating RNA molecules.

    • 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. 

      We have also developed the p19 protein to detect known small RNAs, either using labeled complementary RNA probes or electronic detection via nanopore. A second research interest is the characterization of RNA ligases. Mutant thermophilic ligases have been created that allow efficient joining of ssRNA or ssDNA to adenylated linkers at elevated temperatures. This enzyme will enhance NextGen sequencing of RNAs for transcriptome analysis. Understanding the biochemistry of RNA ligases should give new insight into their biological function.