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PubMed1997

A molecular switch for biochemical logic gates: conformational studies.

This report presents the computer-assisted design of a molecular switching element, in which a molecular switch regulates the enzymatic activity of Ribonuclease A (RNase A). The molecular switch, an appropriately modified amino acid residue, is constructed with an electron donor group and an electron acceptor group, connected to one another with a conjugated double bond bridge. The switching mechanism is based on the azonium-hydrazo tautomerization, by which a charge separation induced in the excited state causes a rearrangement of the molecular electronic structure, resulting in the exchange of locations of single and double bonds. This rearrangement of bonds leads to different three-dimensional conformations of the switch. Using the electrostatically driven Monte Carlo (EDMC) method and the empirical conformational energy program for peptides (ECEPP/3) potential energy function, we carried out an exhaustive search of the conformational space of the switching element. The results of these calculations reveal two sets of conformations: in one set the access to the active site of the enzyme is preferentially blocked, while in the other set the active site is preferentially accessible. Integration of the designed element into biochemical logic gates operating under the rules of threshold value, and experimental implementation of this system, are considered.

Protein Conformation↗
PubMed2003

Signaling from synapse to nucleus: the logic behind the mechanisms.

Signaling from synapse to nucleus is vital for activity-dependent control of neuronal gene expression and represents a sophisticated form of neural computation. The nature of specific signal initiators, nuclear translocators and effectors has become increasingly clear, and supports the idea that the nucleus is able to make sense of a surprising amount of fast synaptic information through intricate biochemical mechanisms. Information transfer to the nucleus can be conveyed by physical translocation of messengers at various stages within the multiple signal transduction cascades that are set in motion by a Ca(2+) rise near the surface membrane. The key role of synapse-to-nucleus signaling in circadian rhythms, long-term memory, and neuronal survival sheds light on the logical underpinning of these signaling mechanisms.

Animals↗
PubMedDate not supplied

A simple logical approach to questioned envelopes examination.

This case report outlines research undertaken as the result of a document examination case in which two envelopes were involved. The combination of the circumstances of the case and the results of the examination allows a simple application of a logical approach to pre-assess the probability that an envelope (or a package) potentially recovered at a suspect's home comes from the same batch (same source) as questioned envelopes. This highlights that it is useful to examine envelopes.

Journal Article↗
PubMed1998

Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC).

A standard set of names and codes for laboratory test results is critical for any endeavor requiring automated data pooling, including multi-institutional research and cross-facility patient care. This need has led to the development of the logical observation identifier names and codes (LOINC) database and its test-naming convention. This study is an expansion of a pilot study using LOINC to exchange laboratory data between Columbia University Medical Center in New York and Barnes Hospital at Washington University in St. Louis, where we described complexities and ambiguities that arose in the LOINC coding process (D.M. Baorto, J.J. Cimino, C.A. Parvin, M.G. Kahn, Proc. Am. Med. Inf. Assoc. 1997). For the present study, we required the same two medical centers to again extract raw laboratory data from their local information system for a defined patient population, translate tests into LOINC and provide aggregate data which could then be used to compare laboratory utilization. Here we examine a larger number of tests from each site which have been recoded using an updated version of the LOINC database. We conclude that the coding of local tests into LOINC can often be complex, especially the 'Kind of Property' field and apparently trivial differences in choices made by individual institutions can result in nonmatches in electronically pooled data. In the present study, 75% of failures to match the same tests between different institutions using LOINC codes were due to differences in local coding choices. LOINC has the potential to eliminate the need for detailed human inspection during the pooling of laboratory data from diverse sites and perhaps even a built-in capability to adjust matching stringency by selecting subsets of LOINC fields required to match. However, a quality standard coding procedure is required and examples highlighted in this paper may require special attention while mapping to LOINC.

Clinical Laboratory Techniques↗
PubMed2000

The logic of causation and the risk of paralytic poliomyelitis for an American child.

Beginning in January 1997, American immunization policy allowed parents and physicians to elect one of three approved infant vaccination strategies for preventing poliomyelitis. Although the three strategies likely have different outcomes with respect to prevention of paralytic poliomyelitis, the extreme rarity of the disease in the USA prevents any controlled comparison. In this paper, a formal inferential logic, originally described by Donald Rubin, is applied to the vaccination problem. Assumptions and indirect evidence are used to overcome the inability to observe the same subjects under varying conditions to allow the inference of causality from non-randomized observations. Using available epidemiologic information and explicit assumptions, it is possible to project the risk of paralytic polio for infants immunized with oral polio vaccine (1.3 cases per million vaccinees), inactivated polio vaccine (0.54 cases per million vaccinees), or a sequential schedule (0.54-0.92 cases per million vaccinees).

Adult↗
PubMedDate not supplied

Database mining using soft computing techniques. An integrated neural network-fuzzy logic-genetic algorithm approach.

Two different soft computing (SC) techniques (a competitive learning neural network and an integrated neural network-fuzzy logic-genetic algorithm approach) are employed in the analysis of a database subset obtained from the Cambridge Structural Database. The chemical problem chosen for study is relevant to the relationship between various metric parameters in transition metal imido (LnMdNZ, Z = carbon-based substituent) complexes and the chemical consequences of such relationships. The SC techniques confirmed and quantified the suspected relationship between the metal-nitrogen bond length and the metal-nitrogen-substituent bond angle for transition metal imidos: increased metal-nitrogen-carbon angles correlate with shortened metal-nitrogen distances. The mining effort also yielded an unexpected correlation between the NC distance and the MNC angle-shorter NC correlate with larger MNC. A fuzzy inference system is used to construct an MNred-NC-MNC hypersurface. This hypersurface suggests a complicated interdependence among NC, MNred, and the angle subtended by these two bonds. Also, major portions of the hypersurface are very flat, in regions where MNC is approaching linearity. The relationships are also seen to be influenced by whether the imido substituent is an alkyl or aryl group. Computationally, the present results are of particular interest in two respects. First, SC classification was able to isolate an "outlier" cluster. Identification of outliers is important as they may correspond to unreported experimental errors in the database or novel chemical entities, both of which warrant further investigation. Second, the SC database mining not only confirmed and quantified a suspected relationship (MNred versus MNC) within the data but also yielded a trend that was not suspected (NC versus MNC).

Journal Article↗
PubMed2003

Molecular logic: a half-subtractor based on tetraphenylporphyrin.

Spectroscopic changes from a solution of the amphophile 5,10,15,20-tetraphenylporphyrin in N,N-dimethylformamide using inputs of acid (HClaq) and base (KOBut) are interpreted as XOR and INHIBIT logic operations. The combination of these two operations gives rise to a device that acts as a molecular half-subtractor.

Journal Article↗
PubMed2005

Endonuclease-based logic gates and sensors using magnetic force-amplified readout of DNA scission on cantilevers.

The endonuclease scission of magnetic particles functionalized with sequence-specific DNAs, which are associated on cantilevers, is followed by the magnetic force-amplified readout of the reactions by the nano-mechanical deflection/retraction of the cantilevers. The systems are employed to develop AND or OR logic gates and to detect single base mismatch specificity of the endonucleases. The two endonucleases EcoRI (E(A)) and AscI (E(B)) are used as inputs. The removal of magnetic particles linked to the cantilever by the duplexes 1/1a and 2/2a via the simultaneous cleavage of the DNAs by E(A) and E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "AND" gate. The removal of the magnetic particles linked to the cantilevers by the duplex 3/3a by either E(A) or E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "OR" gate. The magnetic force-amplified readout of endonuclease activities is also employed to reveal single base mismatch specificity of the biocatalysts.

Biosensing Techniques↗
PubMed2005

Organic nanodielectrics for low voltage carbon nanotube thin film transistors and complementary logic gates.

We report the implementation of three dimensionally cross-linked, organic nanodielectric multilayers as ultrathin gate dielectrics for a type of thin film transistor device that uses networks of single-walled carbon nanotubes as effective semiconductor thin films. Unipolar n- and p-channel devices are demonstrated by use of polymer coatings to control the behavior of the networks. Monolithically integrating these devices yields complementary logic gates. The organic multilayers provide exceptionally good gate dielectrics for these systems and allow for low voltage, low hysteresis operation. The excellent performance characteristics suggest that organic dielectrics of this general type could provide a promising path to SWNT-based thin film electronics.

Crystallography, X-Ray↗
PubMed2006

Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a "lab-on-a-molecule" prototype.

We demonstrate the first three-input molecular AND logic gate based on three chemical inputs as a direct way of detecting congregations of chemical species. The AND gate operates in water and responds to Na+, H+, and Zn2+ inputs with an enhanced fluorescence signal when pre-set concentration thresholds are exceeded. Future "lab-on-a-molecule" devices could have application in medicine for rapid disease screening.

Journal Article↗
PubMed2006

Light-driven OR and XOR programmable chemical logic gates.

Photoelectrodes made of nanocrystalline titanium dioxide modified with various pentacyanoferrates exhibit unique photoelectrochemical properties; photocurrent direction can be switched from anodic to cathodic and vice versa upon changes in photoelectrode potential and incident light wavelength (PhotoElectrochemical Photocurrent Switching, PEPS effect). At certain potentials, anodic photocurrent generated upon UV irradiation has the same intensity as the cathodic photocurrent generated upon visible irradiation. Under these conditions, simultaneous irradiation with UV and visible light results in compensation of anodic and cathodic photocurrents, and zero net photocurrent is observed. This process can be used for construction of unique light-driven chemical logic gates.

Journal Article↗
PubMed2025

Logical Exploration of Cinnamoyl-Containing Nonribosomal Peptides via Metabologenomic Targeting and Regulator Overexpression.

A targeted method for discovering cinnamoyl-containing nonribosomal peptides (CCNPs), a unique class of bioactive compounds, was devised by using cinnamoyl isomerase, a key enzyme in the biosynthesis of the cinnamoyl moiety, as a genome mining probe. A total of 39 hit strains were obtained, including 35 from polymerase chain reaction-based screening of the in-house bacterial library (2.5% of 1400 strains) targeting the cinnamoyl isomerase-encoding gene and 4 from the genome mining of online databases. Sequence similarity networking and phylogenetic analyses of the isomerase amplicons (∼530 bp) classified the CCNPs into three major substructure-based groups (Z-, E-, and M-type CCNPs) and revealed distinct clade-structure relationships (13 clades). To overcome the challenge of silent biosynthetic gene clusters, we activated these clusters by overexpressing conserved cluster-situated LuxR regulators combined with extensive culture optimization. CCNP production was metabolomically detected in the bacterial extracts by using the characteristic UV absorption and MS/MS fragments of cinnamoyl moieties. CCNP production was observed in 20 of the 39 hit strains, resulting in the isolation of 6 new CCNPs, including oxy-skyllamycin B (2), gwanacinnamycin (3), and luxocinnamycins A-D (4-7), with high structural novelty. Their structures were elucidated using comprehensive spectroscopic analyses and multiple-step chemical derivatizations, and the putative biosynthetic pathways were bioinformatically proposed. Gwanacinnamycin (3) exhibited significant antimycobacterial activity, whereas luxocinnamycin A (4) displayed moderate antiproliferative activity against stomach cancer cells. Our findings highlight a targeted metabologenomic approach combined with transcriptional regulator overexpression as a logical and efficient platform for the discovery of bioactive compounds from nature.

Peptides↗
PubMed2002

New approach to pharmacophore mapping and QSAR analysis using inductive logic programming. Application to thermolysin inhibitors and glycogen phosphorylase B inhibitors.

A key problem in QSAR is the selection of appropriate descriptors to form accurate regression equations for the compounds under study. Inductive logic programming (ILP) algorithms are a class of machine-learning algorithms that have been successfully applied to a number of SAR problems. Unlike other QSAR methods, which use attributes to describe chemical structure, ILP uses relations. This gives ILP the advantages of not requiring explicit superimposition of individual compounds in a dataset, of dealing naturally with multiple conformations, and of using a language much closer to that used normally by chemists. We unify ILP and standard regression techniques to give a QSAR method that has the strength of ILP at describing steric structure with the familiarity and power of regression methods. Complex pharmacophores, correlating with activity, were identified and used as new indicator variables, along with the comparative molecular field analysis (CoMFA) prediction, to form predictive regression equations. We compared the formation of 3D-QSARs using standard CoMFA with the use of ILP on the well-studied thermolysin zinc protease inhibitor dataset and a glycogen phosphorylase inhibitor dataset. In each case the addition of ILP variables produced statistically better results (P < 0.01 for thermolysin and P < 0.05 for GP datasets) than the CoMFA analysis. Moreover, the new ILP variables were not found to increase the complexity of the final QSAR equations and gave possible insight into the binding mechanism of the ligand-protein complex under study.

Algorithms↗
PubMed2005

Tuning the CD spectrum and optical rotation value of a new binaphthalene molecule with two spiropyran units: mimicking the function of a molecular "AND" logic gate and a new chiral molecular switch.

With the view to developing new chiral molecular switches and logic gates, a new binaphthalene molecule with two spiropyran units (1) was synthesized and characterized. Absorption and 1H NMR spectral studies of 1 after reaction with acid/base indicate acidichromism can occur to compound 1. The synergistic actions of acid and UV light irradiation result in a remarkable change for the CD spectrum of the relatively dilute solution of 1, mimicking the behavior of a chiral "AND" gate, since the "ouput" is the CD signal. Furthermore, the optical rotation value of the relatively concentrated solution of 1 can be reversibly tuned after sequential reactions with acid and base, and thus a chiral molecular switch with nondestructive "output" signal is realized. The present results not only add a new example of chiral molecular switch with nondestructive readout but also provide a chiral "AND" gate based on the axial chiral binaphthalene to which switchable units are linked.

Journal Article↗
PubMed2006

A new tetrathiafulvalene-anthracence dyad fusion with the crown ether group: fluorescence modulation with Na+ and C60, mimicking the performance of an "AND" logic gate.

In this Note, we describe a new TTF-anthracene dyad fusion with the crown ether unit. It is interesting to find that the fluorescence of this new dyad can be modulated with Na+ and C60, and its fluorescence intensity can be largely enhanced only in the presence of both Na+ and C60. Such fluorescence modulation behavior mimics the performance of a two-input "AND" logic gate.

Journal Article↗
PubMed2006

Logic gates and elementary computing by enzymes.

Different selected enzymes, glucose oxidase (GOx), catalase (Cat), glucose dehydrogenase (GDH), horseradish peroxidase (HRP), and formaldehyde dehydrogenase (FDH), are used alone or coupled to construct eight different logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated gluconic acid or NADH are the output signals that follow the operation of the gates. Different enzyme-based gates are XOR, INHIBIT A, INHIBIT B, AND, OR, NOR, Identity and Inverter gates. By combining the AND and XOR or the XOR and INHIBIT A gates, the half-adder and half-subtractor are constructed, respectively, opening the way to elementary computing by the use of enzymes.

Animals↗
PubMed2006

Digital logic circuit based on a single molecular system of salicylidene Schiff base.

The salicylidene Schiff base N-3,5-dichloro-salicylidene-(S)-alpha-phenylethylamine (SPEA) has been synthesized and characterized. Stimulated by one optical input (UV light) and two chemical inputs (OH(-) and Zn(2+)), SPEA undergoes reactions of photochemistry, deprotonation, and complexation. Tailing these reactions by means of the UV-vis absorption spectra and fluorescence spectra, two obvious optical outputs, an absorption band at 323 nm and a fluorescent emission peak at 460 nm, have been obtained. On the basis of encoding binary digits in these inputs and outputs applying positive logic conventions, one monomolecular circuit, which integrates one OR, two NOT, and four AND gates, has been achieved.

Journal Article↗