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PubMed1997

Structural and functional roles of modules in hemoglobin. Substitution of module M4 in hemoglobin subunits.

The alpha- and beta-subunits of human hemoglobin consist of the modules M1, M2 + M3, and M4, which correspond to the exons 1, 2, and 3, respectively (Go, M. (1981) Nature 291, 90-92). To gain further insight into functional and structural significance of the modules, we designed two kinds of chimeric hemoglobin subunits (chimeric alphaalphabeta- and betabetaalpha-subunits), in which the module M4 was replaced by the partner subunits. CD spectra in the far-UV region showed that the secondary structure of the chimeric alphaalphabeta-subunit drastically collapsed, while the chimeric betabetaalpha-subunit conserved the native globin structure (Wakasugi, K., Ishimori, K., Imai, K., Wada, Y., and Morishima, I. (1994) J. Biol. Chem. 269, 18750-18756). SAXS data also suggested a partially disordered structure of the chimeric alphaalphabeta-subunit. Based on tryptophan fluorescence spectra and computer modeling from x-ray structures of native globins, steric constraint between Trp14 and Tyr125 would be induced in the chimeric alphaalphabeta-subunit, which would perturb the packing of the A- and H-helices and destabilize the globule structure. On the other hand, such a steric constraint was not found for the counterpart chimeric subunit, the betabetaalpha-subunit. The different stabilities of these module-substituted globins imply that modules would not always be stable "structural" units, and interactions between modules are crucial to construct stable globin subunits.

Circular Dichroism↗

PubMed2006

A missense mutation in the seven-transmembrane domain of the human Ca2+ receptor converts a negative allosteric modulator into a positive allosteric modulator.

G protein-coupled receptors (GPCRs) are the most common targets of drug action. Allosteric modulators bind to the seven-transmembrane domain of family 3 GPCRs and offer enhanced selectivity over orthosteric ligands that bind to the large extracellular N terminus. We characterize a novel negative allosteric modulator of the human Ca(2+) receptor, Compound 1, that retains activity against the E837A mutant that lacks a response to previously described positive and negative modulators. A related compound, JKJ05, acts as a negative allosteric modulator on the wild type receptor but as a positive modulator on the E837A mutant receptor. This positive modulation critically depends on the primary amine in JKJ05, which appears to interact with acidic residue Glu(767) in our model of the seven-transmembrane domain of the receptor. Our results suggest the need for identification of possible genetic variation in the allosteric site of therapeutically targeted GPCRs.

Allosteric Site↗

PubMed2000

Membrane permeation by multidrug-resistance-modulators and non-modulators: effects of hydrophobicity and electric charge.

This study was designed to test the hypothesis that lipophilic cationic drugs with only roughly similar structures mediate the reversal of multidrug-resistance (MDR) by interacting with membrane phospholipids. The permeation properties of MDR-modulators and non-modulators were studied by quantifying their ability to induce the leakage of Sulphan blue through the membrane of negatively charged unilamellar liposomes. Of the 22 compounds under investigation, only those bearing a net positive electric charge per molecule (z) > or = 0.2 induced dye leakage. All these efficient drugs are well-known MDR-modulators: calcium-channel blockers (propranolol, verapamil, diltiazem and dipyridamole), calmodulin antagonists (clomipramine and thioridazine) and antiparasitic agents (mepacrine, thioacridine derivatives and quinine). The non-modulators tested, including antineoplastic agents and steroids, did not induce any membrane permeation. The permeation process was a co-operative one (1.1 < Hill coefficient < 4.1) and the permeation doses inducing 50% dye leakage (PD50) were 1.9-11.2 mM. The permeation ability of the MDR-modulators (log(1/PD50)) increased significantly with octanol-buffer distributions per unit net electric charge ((logD)/z). The results provide evidence that a complex interplay occurs between the electric charge and the lipophilicity of the MDR-modulators when a dye leakage is induced through model membranes, and probably also when the MDR is reversed in leukaemic cells.

Anti-Inflammatory Agents↗

PubMed2004

Experimental method based on wavelength-modulation spectroscopy for the characterization of semiconductor lasers under direct modulation.

An experimental method is presented for characterization of the combined intensity and frequency modulation produced when the injection current of a laser diode is modulated. The reported technique is based on the analysis of the harmonic signals produced when a modulated laser is used to probe a gas absorption line by the so-called wavelength-modulation spectroscopy method. Based on a theoretical model of this technique, we present two methods that facilitate the determination of (i) the deviation in laser frequency and (ii) the phase shift between intensity and frequency modulation. These methods are illustrated experimentally by measurement of the modulation parameters of a 2-microm distributed-feedback laser by use of a CO2 absorption line. The experimental results have been compared with those obtained with another traditional method and have shown full agreement in the frequency range (400 Hz-30 kHz) considered.

Journal Article↗

PubMed2005

Phase-modulation fluorometer using a dynode-voltage burst-modulated photomultiplier tube.

We propose a new scheme for a phase-modulation fluorometer (PMF) in which a photomultiplier tube (PMT) is used as a photo detector whose gain is modulated sinusoidally with a burst signal of period T and duty ratio 0.5. The carrier wave of the burst modulation signal is synchronized with an incident fluorescence signal. In order to modulate the gain of the PMT, one of the dynodes in the PMT was deeply biased and the burst signal was superimposed. Because the fluorescence signal is converted to a direct current (dc) signal by the PMT internal modulation, we can make the value of the load resistance of the PMT relatively large under the condition tau < or = T/2, where tau is a time constant of a low-pass filter attached to the output of the PMT. The proposed scheme brings about advantages in sensitivity and noise immunity in detecting weak fluorescence in comparison with those of the conventional PMF. The combined technique of the burst modulation of the gain of the PMT and the alternating current (ac) signal detection alleviates the influence of the background light.

Journal Article↗

PubMed2001

Integrin modulating factor: a 30-kD protein that modulates the expression and function of alpha5beta1 integrin receptor.

The integrin family of cell surface receptors consists of transmembrane glycoproteins involved in cellular morphology, cytoarchitecture, cell-cell, and cell-extracellular matrix interaction. Changes in integrin receptor expression are associated with malignant transformation. The adhesion promoting activity of several members of the integrin receptors may be modulated. Integrin Associated Proteins and integrin modulating factor that may modulate integrin receptors expression and function have been reported. In this article, we report the identification of a 30-kD protein produced in SiHa cell culture medium that can modulate the expression and function of alpha5beta1 integrin receptor in HeLaS3 cells. The cell adhesion assay clearly demonstrated that HeLaS3 cells grown in a serum-free culture medium of SiHa cells (fresh medium: culture medium = 3:1) stimulated the ligand binding activity of alpha5beta1 receptor to fibronectin in a time-dependent manner, having a peak activity at 72 hours of culture. Immunocytochemical localization showed a very high expression of alpha5beta1 receptor in HeLaS3 cells grown in a SiHa culture medium for 72 hours. The (NH4)2SO4 fractionation demonstrated that proteins present in 80-100% (NH4)2SO4 saturated fraction of serum-free SiHa culture medium have a significant stimulatory effect on the binding of HeLaS3 cells to fibronectin ligand via the alpha5beta1 integrin receptor. High pressure liquid chromatography (HPLC) separation of 80-100% (NH4)2SO4 saturated fraction showed a 30- kD protein in polyacrylamide gel electrophoresis (PAGE) analysis that has a maximum stimulatory effect on the binding of HeLaS3 cells to fibronectin ligand via the alpha5beta1 integrin receptor. In conclusion, our observations indicated that human cervical tumor cells SiHa produce a 30-kD protein that can modulate the expression and function of alpha5beta1 fibronectin integrin receptor of HeLaS3 cells. These findings strengthen the concept that some cellular proteins, also called Integrin Associated Protein, may regulate the integrin receptor expression and function. Studies are in progress to characterize this 30-kD integrin modulating factor and its role in the regulation of integrin receptor function.

Binding Sites↗

PubMed1994

Corneal endothelial modulation: bFGF as direct mediator and corneal endothelium modulation factor as inducer.

PURPOSE: Previously reported from this laboratory are two distinct factors responsible for corneal endothelium modulation: basic fibroblast growth factor (bFGF) and the corneal endothelium modulation factor (CEMF) that is released by inflammatory cells. The altered phenotypes mediated by these two distinct factors--marked increase in cell proliferation, cell shape changes, and synthesis of fibrillar collagens--are identical. The current study sought to determine if bFGF is the direct mediator for corneal endothelium modulation and if CEMF plays a role in inducing bFGF production. METHODS: bFGF synthesis mediated by CEMF was analyzed by immunoblot assay; cycloheximide was used to block protein synthesis. bFGF-Specific antisense oligonucleotide primer was used to inhibit CEMF-mediated bFGF synthesis and to block further the autocrine activity of bFGF. Cell proliferation was measured by cell counting. The steady-state levels of RNA were determined by Northern blot analysis. CEMF was further purified to homogeneity by sequential electrophoresis, elution, and renaturation of protein. RESULTS: The synergistic effect of CEMF and bFGF on corneal endothelial cells was measured by their growth-promoting activity on quiescent corneal endothelial cells. There was a dose-dependent cell proliferation mediated by bFGF at any given CEMF concentration. Thus, bFGF at 10 ng/ml with CEMF at 2.5 micrograms/ml demonstrated saturable synergistic activity on endothelial cell proliferation. When the steady-state levels of collagen RNA were measured under these conditions, the untreated cells showed the doublets of 5.6 and 5.0 kb of alpha 2(I) collagen RNA. The cells treated simultaneously with bFGF and CEMF contained mostly lower transcript, compared to the significant level of upper transcript in control cells. However, there was no significant change in the level of 6.9-kb type IV collagen RNA qualitatively or quantitatively; nonetheless, the level of alpha 2(IV) collagen RNA was lowest in cells treated with bFGF plus CEMF. Neither exogenous bFGF nor CEMF caused induction of bFGF messenger RNA in corneal endothelial cells, whereas simultaneous treatment with bFGF and CEMF selectively enhanced the 4.9-kb transcript. When protein synthesis was inhibited by cycloheximide, bFGF synthesis was blocked in the presence of CEMF, leading to inhibition of corneal endothelium modulation. The effect on endothelial cell growth of bFGF antisense primer was analyzed. Antisense primer blocked by 50% the enhanced growth potential mediated by bFGF induced with CEMF. Finally, CEMF was purified to homogeneity: the purified protein is approximately 17 kD and assumes the modulating activities. CONCLUSIONS: These findings suggest that de novo synthesis of bFGF induced by CEMF is required for corneal endothelium modulation.

Animals↗

PubMedDate not supplied

[Modulated extremely high frequency electromagnetic radiation of low intensity activates or inhibits respiratory burst in neutrophils depending on modulation frequency].

The influence of low-intensity modulated electromagnetic radiation of extremely high frequencies (EHF EMR) on synergistic reaction of calcium ionophore A23187 and phorbol ester PMA in activation of the respiratory burst of the peritoneal neutrophils of mice line NMRI was investigated. The production of reactive oxygen species by the neutrophils was estimated by luminol-dependent chemiluminescence technique. The cells were irradiated in the far field zone of the channel radiator for 20 min in the presence of A23187 and then were activated by PMA after switching off the irradiation. It was shown, that continuous EHF EMR (50 microW/cm2) inhibited quasi-resonantly the synergistic reaction. The maximum effect was about 25% at carrier frequency of 41.95 GHz. Modulated radiation with carrier frequency of 41.95 GHz and modulation frequency of 1 Hz activated the synergistic reaction, but at modulation frequencies of 0.1, 16 and 50 Hz inhibited one. At fixed modulation frequency of 1 Hz the nonlinear dependence of the effect on the carrier frequency was found. The synergistic reaction was activated in the frequency range of 41.95-42.05 GHz and was inhibited at the frequencies of 41.8-41.9 GHz. The effect was observed only at raised intracellular free calcium concentration and at calcium fluxes through plasma membrane. The obtained results prove the possibility of control over cell functioning by low-intensity modulated EHF EMR, presumably, manipulating by connected systems of enzyme reactions.

Animals↗

PubMed2005

Benzodiazepine modulation of partial agonist efficacy and spontaneously active GABA(A) receptors supports an allosteric model of modulation.

Benzodiazepines (BZDs) have been used extensively for more than 40 years because of their high therapeutic index and low toxicity. Although BZDs are understood to act primarily as allosteric modulators of GABA(A) receptors, the mechanism of modulation is not well understood. The applicability of an allosteric model with two binding sites for gamma-aminobutyric acid (GABA) and one for a BZD-like modulator was investigated. This model predicts that BZDs should enhance the efficacy of partial agonists. Consistent with this prediction, diazepam increased the efficacy of the GABA(A) receptor partial agonist kojic amine in chick spinal cord neurons. To further test the validity of the model, the effects of diazepam, flurazepam, and zolpidem were examined using wild-type and spontaneously active mutant alpha1(L263S)beta3gamma2 GABA(A) receptors expressed in HEK-293 cells. In agreement with the predictions of the allosteric model, all three modulators acted as direct agonists for the spontaneously active receptors. The results indicate that BZD-like modulators enhance the amplitude of the GABA response by stabilizing the open channel active state relative to the inactive state by less than 1 kcal, which is similar to the energy of stabilization conferred by a single hydrogen bond.

Allosteric Regulation↗

PubMed1998

Chemical synthesis of human protein S thrombin-sensitive module and first epidermal growth factor module.

Human plasma protein S is a nonenzymatic cofactor for activated protein C (APC) in the inactivation of coagulation factors Va and VIIIa, and helps to provide an essential negative feedback on blood coagulation. Previous indirect evidence suggested that the thrombin-sensitive region (TSR: residues 47-75, 1 disulfide) and the first epidermal growth factorlike region (EGF1: residues 76-116, 3 disulfides) of protein S may be functionally important for expression of its APC cofactor activity. To study the functional importance of these modules directly, access to the isolated TSR and EGF1 modules would be preferred. Recombinant expression of protein S intact TSR and correctly folded EGF1 has not been possible. Here we describe the synthesis of both TSR and EGF1 modules by stepwise solid phase peptide synthesis using the in situ neutralization/2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluron ium hexafluorophosphate activation procedure for tert-butoxycarbonyl chemistry. For the TSR, correct intramodular disulfide bonding was confirmed. To overcome folding difficulties with the EGF1, a two-step oxidation procedure was used in which the cysteines involved in the middle, crossing, disulfide bond (Cys85-Cys102) remained protected with acetamidomethyl (Acm) groups after hydrogen fluoride treatment of the peptide resin. Selective formation of the first two disulfide bonds (Cys80-Cys93 and Cys104-Cys113) was followed by release of the Acm groups and subsequent formation of the third disulfide bond (Cys85-Cys102). CD studies revealed 54% of beta-sheet/turn in the EGF1 that is characteristic for EGF modules. Deuterium exchange studies suggested a very tightly packed core in EGF1 that is not accessible to the bulk solvent, likely a result from the compact structure caused by its three disulfide bonds. The 30% beta-sheet structure observed in the TSR involved amide protons that could be readily exchanged by deuterons, likely reflecting a more flexible structure of the TSR loop in contrast to the rigid structure of EGF1. The establishment of synthetic access to the TSR and EGF1 of protein S provides a versatile tool to study interactions of these modules with the blood coagulation components of the anticoagulant plasma protein C pathway.

Amino Acid Sequence↗

PubMed1997

Calcium binding to tandem repeats of EGF-like modules. Expression and characterization of the EGF-like modules of human Notch-1 implicated in receptor-ligand interactions.

The Ca(2+)-binding epidermal growth factor (cbEGF)-like module is a structural component of numerous diverse proteins and occurs almost exclusively within repeated motifs. Notch-1, a fundamental receptor for cell fate decisions, contains 36 extracellular EGF modules in tandem, of which 21 are potentially Ca(2+)-binding. We report the Ca(2+)-binding properties of EGF11-12 and EGF10-13 from human Notch-1 (hNEGF11-12 and hNEGF10-13), modules previously shown to support Ca(2+)-dependent interactions with the ligands Delta and Serrate. Ca2+ titrations in the presence of chromophoric chelators, 5,5'-Br2BAPTA and 5-NBAPTA, gave two binding constants for hNEGF11-12, Kd1 = 3.4 x 10(-5) M and Kd2 > 2.5 x 10(-4) M. The high-affinity site was found to be localized to hNEGF12. Titration of hNEGF10-13 gave three binding constants, Kd1 = 3.1 x 10(-6) M, Kd2 = 1.6 x 10(-4) M, and Kd3 > 2.5 x 10(-4) M, demonstrating that assembly of EGF modules in tandem can increase Ca2+ affinity. The highest affinity sites in hNEGF11-12 and hNEGF10-13 had 10 to 100-fold higher affinity than reported for EGF32-33 and EGF25-31, respectively, from fibrillin-1, a connective tissue protein with 43 cbEGF modules. A model of hNEGF11-12 based on fibrillin-1 EGF32-33 demonstrates electronegative potential that could contribute to the higher affinity of the Ca(2+)-binding site in hNEGF12. These data demonstrate that the Ca2+ affinity of cbEGF repeats can be highly variable among different classes of cbEGF containing proteins.

Blotting, Western↗

PubMed1991

Temporal modulation transfer functions in the European starling (Sturnus vulgaris): I. Psychophysical modulation detection thresholds.

Temporal modulation transfer functions (TMTF) were obtained from four European starlings (Sturnus vulgaris) using a psychophysical Go/NoGo procedure combined with the method of constant stimuli. The TMTF for a continuous, broad-band noise of 55 dB SPL had a low-pass characteristic with a cut-off frequency of 123 Hz. For an 800 ms gated stimulus of the same sound-pressure level, the TMTF had the shape of a band-pass filter with the most sensitive modulation frequency at around 20 Hz. At 75 dB the band-pass shape of the TMTF was preserved, whereas at 35 dB SPL the TMTF had a low-pass characteristic. The cut-off frequency of the TMTF for continuous noise depends on which part of the spectrum carries the information on the envelope fluctuations. If only sound energy below 1 or 1.5 kHz is modulated, then the cut-off frequencies are 40 and 38 Hz, respectively. If only sound above 3 kHz carries the information on the modulation, then the cut-off frequency is 125 Hz and the shape of the TMTF is similar to that found for broadband noise. The results are discussed with respect to the coding of sinusoidal amplitude modulations by the auditory system and to different measures of time, frequency and intensity resolution in the starling.

Acoustic Stimulation↗

PubMed2004

A preliminary study of the role of modulated electron beams in intensity modulated radiotherapy, using automated beam orientation and modality selection.

PURPOSE: To develop an algorithm for optimal beam arrangement selection in intensity-modulated radiotherapy (IMRT) of mixed photon and electron beams. To apply this algorithm to study the utility of modulated electron beams in the context of IMRT planning. METHODS AND MATERIALS: The optimization algorithm selects, for a user-specified number of beams, the optimal IMRT arrangement (beam orientations, and photon/electron modality for each orientation) using a novel fast heuristic intensity modulation procedure. The algorithm was employed to select optimal beam arrangements for breast (two, four, and six axial beams) and head-and-neck (three, four, five, and seven nonaxial beams) cases. RESULTS: For the two cases, increasing the number of selected beams: (1) increased the number of electron beams for the breast case, but not more than one electron beam was selected for the head-and-neck case; (2) decreased critical structure doses for both cases; and (3) decreased target homogeneity for the breast case, but improved it for the head-and-neck case. CONCLUSIONS: In the two cases analyzed using the selection algorithm, the primary role of modulated electrons differs based on treatment site-normal tissue dose reduction in breast and target homogeneity improvement in head and neck. Although this preliminary study with two cases appears to suggest that the role of intensity-modulated electrons differs based on treatment site, further investigation of large numbers of cases and varied treatment sites are required to establish a definitive conclusion.

Algorithms↗

PubMed2005

Neutralization of a common cold virus by concatemers of the third ligand binding module of the VLDL-receptor strongly depends on the number of modules.

Concatemers of various numbers of the third ligand binding repeat of human very-low density lipoprotein receptor arranged in tandem were fused to maltose-binding protein and expressed as soluble polypeptides. These artificial receptors protected HeLa cells against infection with human rhinovirus serotype 2 (HRV2) to a degree that strongly increased with the number of repeats present; maximal protection was seen for the pentameric concatemer (MBP-V33333). This V3 pentamer neutralized HRV2 more efficiently than a recombinant protein with the entire ligand binding domain of the native receptor encompassing all 8 non-identical repeats. A concatemer of seven V3 modules (MBP-V3333333) was also less neutralizing. Neutralization was correlated with the degree of inhibition of virus binding to the cell surface. The results were in agreement with kinetic measurements using Biacore instrumentation demonstrating an increase in avidity with the number of modules present. At low concentrations of the receptor fragments, a 1:1 Langmuir kinetics was observed which became of complex type in the higher concentration range. This is most likely a consequence of receptor molecules simultaneously binding via several modules. Since there is no viral aggregation, neutralization of viral infectivity results from blockage of the receptor binding sites and possibly from inhibition of viral uncoating by crosslinking the viral capsid subunits via multi-module binding. Finally, the low affinity of the single V3 module allowed demonstrating the possibility of mapping the binding epitope of the V3 receptor fragment by saturation transfer difference nuclear magnetic resonance methodology.

Animals↗

PubMed2000

Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities.

The sixth ligand-binding module of the low-density lipoprotein receptor contributes to the binding of apolipoprotein B100-containing lipoproteins. 1H NMR spectroscopy, DYANA and X-PLOR structure calculations were used to determine that this module has a well defined structure with a backbone conformation similar to other modules. Structures from calculations that simulated the presence of a calcium ion showed increased resolution without large increases in energy, increased deviations from idealised geometry or violations of experimental constraints. Investigation of the surface properties of this module indicates there are significant differences from the fifth module, which binds apolipoprotein E-containing lipoproteins in addition to apolipoprotein B100-containing lipoproteins.

Algorithms↗

PubMed2003

Aquatic modules for bioregenerative life support systems: developmental aspects based on the space flight results of the C.E.B.A.S. MIN-MODULE.

The Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) is an artificial aquatic ecosystem which contains teleost fishes, water snails, ammonia oxidizing bacteria and edible non-gravitropic water plants. It serves as a model for aquatic food production modules which are not seriously affected by microgravity and other space conditions. Its space flight version, the so-called C.E.B.A.S. MINI-MODULE was already successfully tested in the STS-89 and STS-90 (NEUROLAB) missions. It will be flown a third time in space with the STS-107 mission in January 2003. All results obtained so far in space indicate that the basic concept of the system is more than suitable to drive forward its development. The C.E.B.A.S. MINI-MODULE is located within a middeck locker with limited space for additional components. These technical limitations allow only some modifications which lead to a maximum experiment time span of 120 days which is not long enough for scientifically essential multi-generation-experiments. The first necessary step is the development of "harvesting devices" for the different organisms. In the limited space of the plant bioreactor a high biomass production leads to self-shadowing effects which results in an uncontrolled degradation and increased oxygen consumption by microorganisms which will endanger the fishes and snails. It was shown already that the latter reproduce excellently in space and that the reproductive functions of the fish species are not affected. Although the parent-offspring-cannibalism of the ovoviviparous fish species (Xiphophorus helleri) serves as a regulating factor in population dynamics an uncontrolled snail reproduction will also induce an increased oxygen consumption per se and a high ammonia concentration in the water. If harvesting locks can be handled by astronauts in, e. g., 4-week intervals their construction is not very difficult and basic technical solutions are already developed. The second problem is the feeding of the animals. Although C.E.B.A.S.-based aquaculture modules are designed to be closed food loop systems (edible herbivorous fish species and edible water plants) which are already verified on Earth this will not be possible in space without devices in which the animals are fed from a food storage. This has to be done at least once daily which would waste too much crew time when done by astronauts. So, the development of a reliable automated food dispenser has highest priority. Also in this case basic technical solutions are already elaborated. The paper gives a comprehensive overview of the proposed further C.E.B.A.S.-based development of longer-term duration aquatic food production modules.

Animals↗

PubMedDate not supplied

Responsive hybrid hydrogels with volume transitions modulated by a titin immunoglobulin module.

The I28 immunoglobulin (Ig)-like module of human cardiac titin, an elastic muscle protein, was used to cross-link acrylamide (AAm) copolymers into hybrid hydrogels. Cross-linking was accomplished through metal coordination bonding between terminal histidine tags (His tags) of the I28 module and metal-chelating nitrilotriacetic acid (NTA)-containing side chains on the copolymer. In solution, the beta-sheet structure of the I28 module unfolded with a transition midpoint of about 58 degrees C as the temperature was elevated. Hydrogels cross-linked with the I28 module demonstrated positive temperature responsiveness; they swelled to 3 times their initial volume at temperatures above the melting temperature of the cross-links. Positive temperature responsiveness is unusual for synthetic hydrogels. The I28 hybrid hydrogels demonstrate that cross-linking synthetic polymers with natural, well-characterized protein modules is a practical strategy for creating new materials with unique environmental responsiveness predictably determined by the mechanical properties of the protein cross-links. These new materials may be useful for controlled chemical delivery.

Acrylamides↗

PubMed2003

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.

Much of a cell's activity is organized as a network of interacting modules: sets of genes coregulated to respond to different conditions. We present a probabilistic method for identifying regulatory modules from gene expression data. Our procedure identifies modules of coregulated genes, their regulators and the conditions under which regulation occurs, generating testable hypotheses in the form 'regulator X regulates module Y under conditions W'. We applied the method to a Saccharomyces cerevisiae expression data set, showing its ability to identify functionally coherent modules and their correct regulators. We present microarray experiments supporting three novel predictions, suggesting regulatory roles for previously uncharacterized proteins.

Algorithms↗