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Introduction
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June 1989 - September 2017
Publications
Publications (43)
Significance
Trypanosoma brucei is a highly invasive pathogen capable of penetrating deeply into host tissues. To understand how flagellar motility facilitates cell penetration, we used cryo-electron tomography (cryo-ET) to visualize two genetically anucleate mutants with different flagellar motility behaviors. We found that the T. brucei cell body...
Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of eight functional units (FUs). Each FU contains two Cu ions, which can reversibly bind an oxygen molecule. Here, we report a 4.5 Å cryo-EM structure of...
The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered by ATP hydrolysis. We present five cryo-EM structures of TRiC in apo and nucleotide-induced states without imposing symmetry during the 3D reconstructio...
Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit
portal but lacking DNA, which matures into an infectious virion. This process, conserved among dsDNA viruses such as herpes
viruses and bacteriophages, is key to forming infectious virions. Bacteriophage P22 has served as a mo...
Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and
macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory
for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is...
Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic
photosynthetic microorganism. Single particle cryo-electron microscopy (cryo-EM) yields
icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6 Å and 9 Å resolution,
respectively. The asymmetric reconstruction reveals how symmetry mismatches are
accommodated a...
The Electron Microscopy Data Bank (EMDB) [1] is the global repository for the Internet retrieval of high-resolution three-dimensional images of macromolecular complexes and subcellular structures. Established in 2002 at the European Bioinformatics Institute (EBI), it is now an international effort of EBI, Rutgers University (RCSB) in New Jersey, an...
The advancement of science thrives on futuristic imagery. Such images can be abstractly n-dimensional and physically multimodal. They frequently consist of very large quantities of pixels that must be sub-sampled at multiple resolutions. Because there does not exist even one generic image standard for their long-term preservation and interoperation...
Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a b...
Although the overwhelming development of molecular techniques in recent decades has made ultrastructural studies less popular, to the point that ultrastructural interpretation is becoming a dying art, it still remains an indispensable tool for cell and developmental biologists. The introduction of EM-immunocytochemistry and three-dimensional visual...
The biosciences need an image format capable of high performance and long-term maintenance. Is HDF5 the answer?
Phenoloxidases (POs) occur in all organisms and are involved in skin and hair coloring in mammals, and initiating melanization in wound healing. Mutation or overexpression of PO can cause albinism or melanoma, respectively. SDS can convert inactive PO and the oxygen carrier hemocyanin (Hc) into enzymatically active PO. Here we present single-partic...
The oocytes of many invertebrate and non-mammalian vertebrate species are not only asymmetrical but also polar in the distribution of organelles, localized RNAs and proteins, and the oocyte polarity dictates the patterning of the future embryo. Polarily located within the oocytes of many species is the Balbiani body (Bb), which in Xenopus is known...
Actin carries out many of its cellular functions through its filamentous form; thus, understanding the detailed structure of actin filaments is an essential step in achieving a mechanistic understanding of actin function. The acrosomal bundle in the Limulus sperm has been shown to be a quasi-crystalline array with an asymmetric unit composed of a f...
Recent studies discovered a novel structural role of RNA in maintaining the integrity of the mitotic spindle and cellular cytoskeleton. In Xenopus laevis, non-coding Xlsirts and coding VegT RNAs play a structural role in anchoring localized RNAs, maintaining the organization of the cytokeratin cytoskeleton and germinal granules in the oocyte vegeta...
Advances in electron cryomicroscopy (cryo-EM) have made possible the structural determination of large biological machines in the resolution range of 6-9 angstroms. Rice dwarf virus and the acrosomal bundle represent two distinct types of machines amenable to cryo-EM investigations at subnanometer resolutions. However, calculating the density map i...
During Xenopus oogenesis, the message transport organizer (METRO) pathway delivers germinal granules and localized RNAs to the vegetal cortex of the oocyte via the mitochondrial cloud (Balbiani body). According to the traditional model, the mitochondrial cloud is thought to break up at the onset of vitellogenesis and the germinal granules and METRO...
Little is known about the formation of germline cyst and the differentiation of oocyte within the cyst in vertebrates. In the majority of invertebrates in the initial stages of gametogenesis, male and female germ cells develop in full synchrony as a syncytia of interconnected cells called germline cysts (clusters, nests). Using electron microscopy,...
The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers,...
Examination of the three-dimensional structure of intact herpes simplex virus type 1 (HSV-1) virions had revealed that the
icosahedrally symmetrical interaction between the tegument and capsid involves the pentons but not the hexons (Z. H. Zhou,
D. H. Chen, J. Jakana, F. J. Rixon, and W. Chiu, J. Virol. 73:3210–3218, 1999). To account for this, we...
The three-dimensional structure of rice dwarf virus was determined to 6.8 Å resolution by single particle electron cryomicroscopy. By integrating the structural analysis with bioinformatics, the folds of the proteins in the double-shelled capsid were derived. In the outer shell protein, the uniquely orientated upper and lower domains are composed o...
The tutorial presents 3D visualization as implemented at NCMI: beginning with a brief overview of the history and philosophy of scientific visualization, proceeding to a description of general methodologies used throughout the field of visualization, and concluding with specific applications in electron microscopy, confocal microscopy and x-ray dif...
Sophisticated tools are needed to examine the results of cyro-microscopy. As the size and resolution of three dimensional macromolecular structures steadily improve, and the speed at with which they can be generated increases, researchers are finding they are inundated with larger datasets and at the same time are compelled to expediently evaluate...
Human herpesviruses are large and structurally complex viruses that cause a variety of diseases. The three-dimensional structure
of the herpesvirus capsid has been determined at 8.5 angstrom resolution by electron cryomicroscopy. More than 30 putative
α helices were identified in the four proteins that make up the 0.2 billion–dalton shell. Some of...
Collaboration between local microscopists and image processing specialists, and their remote biological colleagues, has been hampered by the difficulty of i) transferring the three-dimensional reconstructions of macromolecules resulting from the cryomicroscopy and image processing, ii) viewing the results in a meaningful way, and iii) communicating...
The use of animation can significantly enhance the visualization of three-dimensional (3D) structures. It can present a focused train of thought, or it can be used to systematically scan through previously unfathomable quantities of data to examine for unknown features and consistencies. In order to establish a modern animation facility requires a...
The National Center for Macromolecular Imaging (NCMI) is a resource supported by the National Center for Research Resources (NCRR) of NIH. Its mission is to advance electron imaging of macromolecular assemblies to near atomic resolution. We have focused on biological assemblies which are too large or too complex to be studied by conventional x-ray...
400 keV electrons yield a better relative image contrast than 100 keV electrons for a beam-sensitive organic crystal when spot-scan imaging is used [J. Brink and W. Chiu, J. Microscopy 161 (1991) 279]. A FORTRAN 77 program has been written to operate the spot-scan imaging system on a computer workstation under the VMS operating system which is inte...
The evolution of images has led to imagery having a digital manifestation. Unlike previous forms of imagery, digital images are ephemeral and inherently numeric; these images are directly accessible only through computers and as such they are capable of representing abstract and physical modalities beyond two-dimensions. As science embraces such te...