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After a decade of progress, an expanded role for metabolic engineering.

Over the past decade, metabolic engineering has emerged as an active and distinct discipline characterized by its over-arching emphasis on integration. In practice, metabolic engineering is the directed improvement of cellular properties through the application of modern genetic methods. Although it was applied on an ad hoc basis for several years following the introduction of recombinant techniques [1,2], metabolic engineering was formally defined as a new field approximately a decade ago [3]. Since that time, many creative applications, directed primarily to metabolite overproduction, have been reported [4]. In parallel, recent advances in the resolution and acquisition time of biological data, especially structural and functional genomics, has amplified interest in the systemic view of biology that metabolic engineering provides. To facilitate the burgeoning scientific exchange in this area on a more regular and convenient basis, a new conference series was launched in 1996 followed by a new journal in 1999.

Base Sequence↗

Electron microscopic structural analysis of Photosystem I, Photosystem II, and the cytochrome b6/f complex from green plants and cyanobacteria.

Electron microscopy (EM) in combination with image analysis is a powerful technique to study protein structure at low- and high resolution. Since electron micrographs of biological objects are very noisy, substantial improvement of image quality can be obtained by averaging individual projections. Crystallographic and noncrystallographic averaging methods are available and have been applied to study projections of the large protein complexes embedded in photosynthetic membranes from cyanobacteria and higher plants. Results of EM on monomeric and trimeric Photosystem I complexes, on monomeric and dimeric Photosystem II complexes, and on the monomeric cytochrome b6/f complex are discussed.

Cyanobacteria↗

Measurement of prostaglandin E3 and other eicosanoids in biologic samples using high pressure liquid chromatography and radioimmunoassay.

A method to measure PGE3 in biologic samples is described. Complete resolution of PGE3 from PGE1 and PGE2 is achieved by reversephase high pressure liquid chromatography. Quantification is carried out by radioimmunoassay using an antibody directed against PGE2 that has high cross-reactivity with PGE3. Using this method, a marked increase in PGE3 production by mouse kidney tissue and in rat urine was demonstrated after supplemental feeding of omega-3 fatty acids. This method can also be applied to measurement of 6-keto-PGF1 alpha and TXB2 in the same samples.

Alprostadil↗

Single-chip microelectronic system to interface with living cells.

A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2 ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments.

Action Potentials↗

Electrochemical sensor toolkit for simultaneous glutamate detection at edge of cleft and peri-soma.

Simultaneously monitoring glutamate (Glu) dynamic at edge of synaptic cleft and peri-soma is crucial for understanding Glu-related pathology. Here, we created an electrochemical Glu sensors toolkit with spatial resolution of ∼60 nm, combining biologically engineered Glu binding protein for specifically capturing Glu together with chemically designed ferrocene groups for signal labeling. Modulation conjugation approach between GluR and ferrocene significantly improved sensitivity up to 32-folds. More importantly, protein engineering of residue mutation and linker peptides flexibility expanded linear range from 10 μM to 6 mM, accelerated on/off times down to 35/40 ms. This toolkit realized real-time quantifying of Glu both at edge of cleft and peri-soma, we discovered that Glu was almost released through SLC7A11 channels in calyx of held synapse upon oxygen-glucose-deprivation, while Glu was mainly released through hemichannels upon β-amyloid42 stimulation. Our work provided a methodology for investigating Glu release and reuptake and offered insights for Glu related pathology.

Glutamic Acid↗

Dynamic electric field assisted multi-dimensional liquid chromatography of biological samples.

Complex biological samples require very high resolution separation strategies. The platform introduced here capitalises on the hyphenation of liquid chromatographic (LC) and electric potential gradient electrochromatographic multi-dimensional separation genres. First-dimension selectivity is provided by simultaneous size exclusion (SEC) and strong cation exchange (SCX) chromatography modes, while the second dimension comprises reversed phase (RP) characteristics in a dynamic (time-variant) electric field. The time-variant potential gradient with reversal of polarity is applied across the second dimension monolithic capillary throughout the duration of the solvent strength gradient elution. Hence, the platform offers comprehensive on-line sample clean-up (matrix depletion, analyte enrichment), fractionation (first dimention LC), and separation (second dimension LC) with the prospect of altering selectivity via polarity reversal dynamic electric field tuning.

Blood Chemical Analysis↗

Conformational differences among solution structures of the type Ialpha, IIalpha and IIbeta protein kinase A regulatory subunit homodimers: role of the linker regions.

The regulatory (R) subunits of the cAMP-dependent protein kinase (protein kinase A or PKA) are multi-domain proteins responsible for conferring cAMP-dependence and localizing PKA to specific subcellular locations. There are four isoforms of the R subunit in mammals that are similar in molecular mass and domain organization, but clearly serve different biological functions. Although high-resolution structures are available for the cAMP-binding domains and dimerization/docking domains of two isoforms, there are no high-resolution structures of any of the intact R subunit homodimer isoforms. The results of small-angle X-ray scattering studies presented here indicate that the RIalpha, RIIalpha, and RIIbeta homodimers differ markedly in overall shape, despite extensive sequence homology and similar molecular masses. The RIIalpha and RIIbeta homodimers have very extended, rod-like shapes, whereas the RIalpha homodimer likely has a compact Y-shape. Based on a comparison of the R subunit sequences, we predict that the linker regions are the likely cause of these large differences in shape among the isoforms. In addition, we show that cAMP binding does not cause large conformational changes in type Ialpha or IIalpha R subunit homodimers, suggesting that the activation of PKA by cAMP involves only local conformational changes in the R subunits.

Animals↗

Structural and dynamic studies of proteins by solid-state NMR spectroscopy: rapid movement forward.

Starting only a few years ago, many solid-state NMR spectroscopy laboratories have become engaged in solving the complete structures of biological macromolecules using high-resolution methods based on magic angle spinning. These efforts typically involve structurally homogeneous samples, and utilize recently developed pulse sequences for the sequential correlation of resonances, the detection of tertiary contacts and the characterization of torsion angles. Thereby, systems have been studied that evaded other, more established, structure determination methods.

Nuclear Magnetic Resonance, Biomolecular↗

Structure of Escherichia coli AMP nucleosidase reveals similarity to nucleoside phosphorylases.

AMP nucleosidase (AMN) catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate. The enzyme is found only in prokaryotes, where it plays a role in purine nucleoside salvage and intracellular AMP level regulation. Enzyme activity is stimulated by ATP and suppressed by phosphate. The structure of unliganded AMN was determined at 2.7 A resolution, and structures of the complexes with either formycin 5'-monophosphate or inorganic phosphate were determined at 2.6 A and 3.0 A resolution, respectively. AMN is a biological homohexamer, and each monomer is composed of two domains: a catalytic domain and a putative regulatory domain. The overall topology of the catalytic domain and some features of the substrate binding site resemble those of the nucleoside phosphorylases, demonstrating that AMN is a new member of the family. The structure of the regulatory domain consists of a long helix and a four-stranded sheet and has a novel topology.

Amino Acid Sequence↗

Quantitative analysis of nucleic acids, proteins, and viruses by Raman band deconvolution.

A constrained, iterative Fourier deconvolution method is employed to enhance the resolution of Raman spectra of biological molecules for quantitative assessment of macromolecular secondary structures and hydrogen isotope exchange kinetics. In an application to the Pf1 filamentous bacterial virus, it is shown that the Raman amide I band contains no component other than that due to alpha-helix, indicating the virtual 100% helicity of coat proteins in the native virion. Comparative analysis of the amide I band of six filamentous phages (fd, If1, IKe, Pf1, Xf, and Pf3), all at the same experimental conditions, indicates that the subunit helix-percentage ranges from a high of 100% in Pf1 to a low of 71% in Xf. Deconvolution of amide I of Pf3 at elevated temperatures, for which an alpha-to-beta transition was previously reported (Thomas, G. J., Jr., and L. A. Day, 1981, Proc. Natl. Acad. Sci. USA., 78:2962-2966), allows quantitative evaluation of the contributions of both alpha-helix and beta-strand conformations to the structure of the thermally perturbed viral coat protein. Weak Raman lines of viral DNA bases and coat protein side chains, which are poorly resolved instrumentally, are also distinguished for all viruses by the deconvolution procedure. Application to the carbon-8 hydrogen isotope exchange reaction of a purine constituent of transfer RNA permits accurate determination of the exchange rate constant, which is in agreement with calculations based upon curve-fitting methods.

Bacteriophages↗

Scanning Near-field Optical/Atomic Force Microscopy detection of fluorescence in situ hybridization signals beyond the optical limit.

Fluorescence in situ hybridization (FISH) is widely used in molecular biological study. However, high-resolution analysis of fluorescent signals is theoretically limited by the 300-nm resolution optical limit of light microscopy. As an alternative to detection by light microscopy, we used Scanning Near-field Optical/Atomic Force Microscopy (SNOM/AFM), which can simultaneously obtain topographic and fluorescent images with nanometer-scale resolution. In this study, we demonstrated high-resolution SNOM/AFM imaging of barley chromosome (Hordeum vulgare, cv. Minorimugi) FISH signals using telomeric DNA probes. Besides detecting the granular structures on chromosomes in a topographic image, we clearly detected fluorescent signals in telomeric regions with low-magnification imaging. The high-resolution analysis suggested that one of the telomeric signals could be observed by expanded imaging as two fluorescent regions separated by approximately 250 nm. This result indicated that the fluorescent signals beyond the optical limit were detected with higher resolution scanning by SNOM/AFM.

Chromosomes↗

Fluorescent methods for studying subnuclear particles.

Fluorescence assays can be used to reveal molecular interactions through rapidly demonstrable particle-associated events. The additional fact that in many cases fluorescent particles may be analyzed on a per-event basis lends credence to such techniques as probes for biologically significant perturbations and their resolution. Perhaps more importantly, the sorting capability of the flow cytometer enables detailed study of these events in cells in relation to their positions in the cell cycle. Further studies on the effect of drugs and other modalities on the organization of the genome and the nuclear matrix should prove of interest because the interactions of chromatin and this subnuclear particle could be predictive of the state of DNA metabolism under such conditions. With the additional ability of following such organizational changes through the cell cycle, the mechanisms of reversal of perturbing events might be elucidated.

Cell Cycle↗

S-Nitrosoglutathione-induced mouse thymocyte apoptosis studied by fluorescence near-field scanning optical microscopy.

This study is an attempt to deeply understand the mechanisms ensuring self-tolerance of T cells via clonal deletion of thymocytes and exploring T lymophocyte homeostasis by observing the apoptosis of single mouse thymocyte induced by S-nitrosoglutathione (GSNO, a nitric oxide donor) using fluorescence near-field scanning optical microscopy (NSOM) in illumination mode. The GSNO-induced thymocytes were stained with propidium iodide containing 0.01% Triton X-100 and excited with light of 488 nm and the emitting fluorescence at 525 nm. According to the NSOM fluorescence image and the simultaneously obtained topography image, the feature of mouse thymocyte apoptosis was characterized by scattering pattern of the fluorescence spots with the size 0.2-2.1 micro m at the full width at half-maximum of fluorescence intensity 78-80 kHz in the GSNO-treated thymocyte nucleus. Whereas there is no fluorescence from the untreated thymocyte. The intensity of the fluorescence from the dexamethasone-treated thymocyte was much stronger than that from GSNO-induced thymocytes. Furthermore, the fluorescence distribution in the latter were concentrated in the nucleus. Those results also demonstrate the advantages of NSOM such as high spatial resolution and the topography of biology samples.

Animals↗

Mucosal melanotic macule, reactive type: a simulation of melanoma.

Two patients with spontaneously resolving hyperpigmented patches of the oral mucosa are reported. Histologically, lesions in both cases showed large pigment-laden dendritic cells singly dispersed at all levels of the epidermis, which simulated in situ melanoma. The absence of such cells in the basal layer of the epidermis served to histologically distinguish these lesions from a biologically malignant melanocytic tumor. Spontaneous resolution in both patients suggests that the condition is reactive. We propose the term mucosal melanotic macule, reactive type, for this lesion, which has been described previously under the misnomer oral melanoacanthoma.

Adolescent↗

Mixing crowded biological solutions in milliseconds.

In vitro studies of biological reactions are rarely performed in conditions that reflect their native intracellular environments where macromolecular crowding can drastically change reaction rates. Kinetics experiments require reactants to be mixed on a time scale faster than that of the reaction. Unfortunately, highly concentrated solutions of crowding agents such as bovine serum albumin and hemoglobin that are viscous and sticky are extremely difficult to mix rapidly. We demonstrate a new droplet-based microfluidic mixer that induces chaotic mixing of crowded solutions in milliseconds due to protrusions of the microchannel walls that generate oscillating interfacial shear within the droplets. Mixing in the microfluidic mixer is characterized, mechanisms underlying mixing are discussed, and evidence of biocompatibility is presented. This microfluidic platform will allow for the first kinetic studies of biological reactions with millisecond time resolution under conditions of macromolecular crowding similar to those within cells.

Biocompatible Materials↗

Structural differences in solution and crystalline forms of met-myoglobin.

For several decades X-ray diffraction studies have been the paragon of biological structure studies at atomic resolution. Diffraction provides three-dimensional structure information, which is essential to our fundamental understanding of protein function. However, since X-ray diffraction cannot be done to atomic resolution on proteins in their native solution or membrane-bound state, the possibility exists that the conformations of the protein in crystals are slightly different from the conformations in solution, and attempts to interpret details of the structure may be misleading and without physiological relevance. In this paper, we show that this concern is justified for a familiar protein, myoglobin. Performing X-ray absorption fine structure experiments on both solution and crystalline met-myoglobin (met-Mb), we find significant differences in the local environment of the iron between the two states. Specifically, the average iron-nearest neighbor atom distance in the crystalline form is 0.05 A shorter than that in the solution form, and the iron-nearest neighbor bond is more rigid in the crystalline met-Mb. Possible artifactual explanations for the differences have been ruled out.

Animals↗

Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase.

Endogenous protein kinase inhibitors are essential for a wide range of physiological functions. These endogenous inhibitors may mimic peptide substrates as in the case of the heat-stable protein kinase inhibitor (PKI), or they may mimic nucleotide triphosphates. Natural product inhibitors, endogenous to the unique organisms producing them, can be potent exogenous inhibitors against foreign protein kinases. Balanol is a natural product inhibitor exhibiting low nanomolar Ki values against serine and threonine specific kinases, while being ineffective against protein tyrosine kinases. To elucidate balanol's specific inhibitory effects and provide a basis for understanding inhibition-regulated biological processes, a 2.1 A resolution crystal structure of balanol in complex with cAMP-dependent protein kinase (cAPK) was determined. The structure reveals conserved binding regions and displays extensive complementary interactions between balanol and conserved cAPK residues. This report describes the structure of a protein kinase crystallized with a natural ATP mimetic in the absence of metal ions and peptide inhibitor.

Animals↗

Visualization of signaling pathways and cortical cytoskeleton in cytolytic and noncytolytic natural killer cell immune synapses.

Recent applications of imaging approaches and other methods of cell biology have provided high-resolution visualization of the location of fluorescent proteins in living and fixed cells during cell-cell interactions between lymphocytes, antigen presenting cells and target cells. We review the composition and dynamics of molecular and cytoskeletal events occurring during natural killer cell interactions with susceptible and nonsusceptible target cells. The natural killer cell immune synapse and the concomitant changes in cytoskeletal components and cytoplasmic organelles are described. The findings are compared with the observations made in T helper cells and cytotoxic T cells. It is concluded that the cytolytic immune synapses display spatial-temporal dynamics that are accelerated as compared with T helper cells. In addition, the cytolytic conjugates have unique characteristics relating to their effector function. Furthermore, the natural killer cell immune synapses in cytolytic and noncytolytic interactions are distinctly different and display patterns consistent with characteristic signaling pathways identified in biochemical studies of disrupted cells. The precise relationship between different stages of the natural killer cell immune synapse formation and progression in signal transduction pathways is yet to be established.

Actins↗