Universal Building Block Research Articles

The inverting second generation current conveyors as universal building blocks

The inverting second generation current conveyor ICCII includes two types. This paper concentrates on the two new types of the inverting current conveyor namely ICCII + and ICCII - . Although it may seem that there is only minor difference between the two types, there is a significant difference as will be evident from some applications considered in this paper. Both the ICCII + and the ICCII - are universal building blocks as will be demonstrated in this paper.

Metamagnetics with rainbow colors

A family of coupled nanostrips with varying dimensions is demonstrated exhibiting optical magnetic responses across the whole visible spectrum, from red to blue. We refer to such a phenomenon as rainbow magnetism. The experimental and analytical studies of such structures provide us with a universal building block and a general recipe for producing controllable optical magnetism for various practical implementations.

Engineered Biosynthesis of a Novel Amidated Polyketide, Using the Malonamyl-Specific Initiation Module from the Oxytetracycline Polyketide Synthase

Tetracyclines are aromatic polyketides biosynthesized by bacterial type II polyketide synthases (PKSs). Understanding the biochemistry of tetracycline PKSs is an important step toward the rational and combinatorial manipulation of tetracycline biosynthesis. To this end, we have sequenced the gene cluster of oxytetracycline (oxy and otc genes) PKS genes from Streptomyces rimosus. Sequence analysis revealed a total of 21 genes between the otrA and otrB resistance genes. We hypothesized that an amidotransferase, OxyD, synthesizes the malonamate starter unit that is a universal building block for tetracycline compounds. In vivo reconstitution using strain CH999 revealed that the minimal PKS and OxyD are necessary and sufficient for the biosynthesis of amidated polyketides. A novel alkaloid (WJ35, or compound 2) was synthesized as the major product when the oxy-encoded minimal PKS, the C-9 ketoreductase (OxyJ), and OxyD were coexpressed in CH999. WJ35 is an isoquinolone compound derived from an amidated decaketide backbone and cyclized with novel regioselectivity. The expression of OxyD with a heterologous minimal PKS did not afford similarly amidated polyketides, suggesting that the oxy-encoded minimal PKS possesses novel starter unit specificity.

Experimental demonstration of 10-gb/s data format conversions between NRZ and RZ using SOA-loop-mirror

This paper describes the demonstration of a simple all-optical data format conversion scheme between return-to-zero (RZ) and nonreturn-to-zero (NRZ) that employs a semiconductor optical amplifier (SOA) in a nonlinear optical loop mirror. The format conversion has been performed between the most widely used data formats-NRZ and RZ formats. The format conversion scheme is based on gain variation by an intensity-dependent phase change in an SOA-loop mirror. The input data stream acts as a control signal that induces the phase differences between clockwise- and counterclockwise-propagating data inside an SOA-loop mirror. It is possible to change the data format of the output data stream by controlling the phase differences of the clockwise and counterclockwise pulse in an SOA-loop mirror appropriately. For the converted NRZ data from RZ data, 10-Gb/s error-free transmission up to 78 km over standard single-mode fiber has been obtained. By comparing the conventional NRZ transmission with the Mach-Zehnder modulation scheme, the proposed RZ-to-NRZ conversion shows an improved transmission performance. The NRZ-to-RZ conversion has clear eye openings up to 78 km. On the contrary, the conventional RZ binary data from a mode-locked laser has a nearly closed eye even at 52 km. The converted RZ data has a 2-dB conversion power margin to the injected NRZ data, which indicates an increase in the receiver sensitivity due to the signal format conversion. The improved transmission distance of the converted RZ signal is due to the duobinary coding effect of the SOA-loop mirror. The SOA has the possibility of high-speed operation over 40 Gb/s, and the SOA-loop mirror has the capabilities of format and wavelength conversions. Therefore, the SOA-loop mirror can be a universal building block in future all-optical networks. In addition, the proposed format conversion scheme can serve as an important format converter between the ultrafast optical-time-division-multiplexed networks and the lower line-rate wavelength-division-multiplexed networks.

Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase fromShewanella oneidensisat 1.6 Å: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity

Isopentenyl pyrophosphate (IPP) is a universal building block for the ubiquitous isoprenoids that are essential to all organisms. The enzymes of the non-mevalonate pathway for IPP synthesis, which is unique to many pathogenic bacteria, have recently been explored as targets for antibiotic development. Several crystal structures of 2C-methyl-D-erythritol-2,4-cyclophosphate (MECDP) synthase, the fifth of seven enzymes involved in the non-mevalonate pathway for synthesis of IPP, have been reported; however, the composition of metal ions in the active site and the presence of a hydrophobic cavity along the non-crystallographic threefold symmetry axis has varied between the reported structures. Here, the structure of MEDCP from Shewanella oneidensis MR1 (SO3437) was determined to 1.6 A resolution in the absence of substrate. The presence of a zinc ion in the active-site cleft, tetrahedrally coordinated by two histidine side chains, an aspartic acid side chain and an ambiguous fourth ligand, was confirmed by zinc anomalous diffraction. Based on analysis of anomalous diffraction data and typical metal-to-ligand bond lengths, it was concluded that an octahedral sodium ion was 3.94 A from the zinc ion. A hydrophobic cavity was observed along the threefold non-crystallographic symmetry axis, filled by a well defined non-protein electron density that could be modeled as farnesyl pyrophosphate (FPP), a downstream product of IPP, suggesting a possible feedback mechanism for enzyme regulation. The high-resolution data clarified the FPP-binding mode compared with previously reported structures. Multiple sequence alignment indicated that the residues critical to the formation of the hydrophobic cavity and for coordinating the pyrophosphate group of FPP are present in the majority of MEDCP synthase enzymes, supporting the idea of a specialized biological function related to FPP binding in a subfamily of MEDCP synthase homologs.

A universal building block for advanced modular design of microwave filters

A universal building block for modular design of microwave filters is introduced. The second order block contains two resonators which are not coupled to each other. By adjusting the strengths and signs of its coupling coefficients, the block can be used to design bandpass, bandstop and linear-phase filters. For bandpass filters, Chebychev as well as symmetric and asymmetric pseudo-elliptic responses with one or two finite transmission zeros can be designed. For linear-phase filters, two finite transmission zeros can placed practically anywhere in the complex plane as long as the realizability condition is met. Bandstop filters with no finite reflection zeros as well as symmetric and asymmetric pseudo-elliptic responses with one or two finite reflection zeros can be achieved by the same building block. The block is so flexible it can even generate bandstop responses with complex finite reflection zeros for group delay control. Higher order filters are designed modularly by cascading the appropriate number of building blocks. Coupling matrices of a number of cases are presented to demonstrate the flexibility and the universality of the building block.

Universal building blocks

Universal building blocks

A Bicyclic Autotrophic CO2 Fixation Pathway in Chloroflexus aurantiacus

Phototrophic CO(2) assimilation by the primitive, green eubacterium Chloroflexus aurantiacus has been shown earlier to proceed in a cyclic mode via 3-hydroxypropionate, propionyl-CoA, succinyl-CoA, and malyl-CoA. The metabolic cycle could be closed by cleavage of malyl-CoA affording glyoxylate (the primary CO(2) fixation product) with regeneration of acetyl-CoA serving as the starter unit of the cycle. The pathway of glyoxylate assimilation to form gluconeogenic precursors has not been elucidated to date. We could now show that the incubation of cell extract with a mixture of glyoxylate and [1,2,3-(13)C(3)]propionyl-CoA afforded erythro-beta-[1,2,2'-(13)C(3)]methylmalate and [1,2,2'-(13)C(3)]citramalate. Similar experiments using a partially purified protein fraction afforded erythro-beta-[1,2,2'-(13)C(3)]methylmalyl-CoA and [1,2,2'-(13)C(3)]mesaconyl-CoA. Cell extracts of C. aurantiacus were also shown to catalyze the conversion of citramalate into pyruvate and acetyl-CoA in a succinyl-CoA-dependent reaction. The data suggest that glyoxylate obtained by the cleavage of malyl-CoA can be utilized by condensation with propionyl-CoA affording erythro-beta-methylmalyl-CoA, which is converted to acetyl-CoA and pyruvate. This reaction sequence regenerates acetyl-CoA, which serves as the precursor of propionyl-CoA in the 3-hydroxypropionate cycle. Autotrophic CO(2) fixation proceeds by combination of the 3-hydroxypropionate cycle with the methylmalyl-CoA cycle. The net product of that bicyclic autotrophic CO(2) fixation pathway is pyruvate serving as an universal building block for anabolic reactions.

Classification of Terpenoids according to the Methylerythritolphosphate or the Mevalonate Pathway with Natural 12C/13C Isotope Ratios: Dynamic Allocation of Resources in Induced Plants

Plants utilize two different pathways for the biosynthesis of isopentenyl diphosphate, the universal building block of all terpenes (see scheme). Application of compound-specific isotope-ratio mass spectrometry (GC-C-IRMS) to volatile terpenoids allows distinction between the pathways on the basis of natural 12C/13C ratios.

Classification of Terpenoids according to the Methylerythritolphosphate or the Mevalonate Pathway with Natural 12 C/13 C Isotope Ratios: Dynamic Allocation of Resources in Induced Plants.

Plants utilize two different pathways for the biosynthesis of isopentenyl diphosphate, the universal building block of all terpenes. Application of compound-specific isotope-ratio mass spectrometry (GC-C-IRMS) to volatile terpenoids allows distinction between the pathways on the basis of natural 12 C/13 C ratios.

Biosynthesis of anthraquinones in cell cultures of the Rubiaceae

Plants and their derived cell and tissue cultures in the family Rubiaceae accumulate a number of anthraquinones. There are two main biosynthetic pathways leading to anthraquinones in higher plants: the polyketide pathway and the chorismate/o-succinylbenzoic acid pathway. The latter occurs in the Rubiaceae for the biosynthesis of Rubia type anthraquinones. In this pathway, ring A and B of the Rubia type anthraquinones are derived from shikimic acid, α-ketoglutarate via o-succinylbenzoate, whereas ring C is derived from isopentenyl diphosphate, a universal building block for all isoprenoids. At present, it is known that isopentenyl diphosphate is formed via the mevalonic acid pathway or the 2-C-methyl-D-erythritol 4-phosphate pathway. Recent findings demonstrate that the 2-C-methyl-D-erythritol 4-phosphate pathway, not the mevalonic acid pathway, is involved in the formation of isopentenyl diphosphate, which constitutes ring C of anthraquinones in the Rubiaceae. This review summarizes the latest results of studies on the biosynthetic pathways, the enzymology and regulation of anthraquinone biosynthesis, as well as aspects of the metabolic engineering. Furthermore, biochemical and molecular approaches in functional genomics, which facilitate elucidation of anthraquinone biosynthetic pathways, are briefly described.

NEURAL NETWORK INTEGRATED CIRCUITS WITH SINGLE-BLOCK MIXED SIGNAL ARRAYS

This paper discusses the design and implementation of a family of mixed-signal neural network integrated circuits for general and application-specific purposes. Regular Arrays of a nonlinearly-loaded multiplier block form the core of multi-layer neural networks. Input-output circuitry and network size, however, vary depending on design applications. Salient features of the present architecture, such as modularity and reduced interconnection problems and areas are highlighted and circuit design and improvements are presented for its universal building block. Other design issues such as supply voltage and power reduction and pin limitations are discussed together with experimental results.

Spoken Word Recognition: A Stage-processing Approach to Language Differences

In recognising spoken words, the retrieval of a unique mental representation from the speech input involves the exceedingly difficult task of locating word boundaries in a quasi-continuous stimulus and of finding the single representation that corresponds to highly variable acoustical forms. Many cognitive psycholinguists have proposed that these segmentation and categorisation problems are easier to solve at the sublexical than at the word level: Some sublexical representation would mediate the mapping between the acoustic signal and the mental lexicon. Accordingly, much effort has gone into disclosing a hypothesised universal perceptual building block, for example the syllable. More recent advances in speech processing research indicate, however, that speakers of different languages process speech by relying on units or segmentation strategies that are appropriate to the phonological properties of their maternal tongue. Recent data on this topic will be reviewed, with special emphasis on the stage-processing approach of the experimental situations and phenomena reported. For example, the syllabic effects observed in fragment detection and the phenomenon of blending dichotically presented words are discussed. It will be argued that although there is a strong case for language specificity in listeners' intuitions about the phonological structure of their language as well as in word recognition, less evidence is available regarding the early perceptual stages.

Use of a CCII — as a universal building block

This paper purports to show a second generation negative current conveyor (CCII-), which can be used as a basic building block for the design of typical RC-active applications and also to build-up more complex active devices. A practical bipolar circuit has been fabricated to implement the CCII — functionality. Simulation results are provided for such a circuit and a couple of applications are proposed to demonstrate its practical use.

Gamma-band responses in the brain: a short review of psychophysiological correlates and functional significance

The present study shows that gamma-band (40 Hz) activities exist in a number of brain structures of different species, with seemingly different functional/behavioral correlates. This rhythm has also different dynamics in various structures and under different experimental conditions: it exists spontaneously and/or can be evoked, induced or emitted with different latencies and relations to sensory-cognitive events. Recent measurements of gamma-band activity at the cellular level stress high level functional correlates such as binding of features. In contrast, field potential measurements in both humans and animals demonstrate that gamma-band responses may have multifold functions both in ‘obligatory’ sensory and in cognitive processing. With respect to the generators of gamma activity, experimental data hint at the existence of a distributed gamma system in the brain. Furthermore, an interpretation of gamma rhythms as universal functional building blocks is suggested.

Crystallization and preliminary X-ray diffraction analysis of recombinant pentalenene synthase.

Recombinant pentalenene synthase, a 42.5-kDa sesquiterpene cyclase originally isolated from Streptomyces UC5319 and cloned in Escherichia coli, has been crystallized in space group P6(3) with unit cell dimensions a = b = 183.5 A and c = 56.5 A. Hexagonal prismatic crystals, approximately 0.2 x 0.2 x 0.3 mm, diffract to approximately 2.9 A resolution using monochromatic synchrotron radiation. From the universal (and achiral) building block, farnesyl pyrophosphate, pentalenene synthase catalyzes the formation of four stereocenters in the construction of the three fused five-membered rings of pentalenene; this novel sesquiterpene is a precursor to the pentalenolactone family of antibiotics.

A universal building block for the approximate analysis of a shared buffer ATM switch architecture

A universal analytic approximation is proposed for the performance analysis of a general queueing model of a shared buffer ATM switch architecture with bursty arrivals. The forms of the joint, aggregate and marginal state probabilities are characterised via entropy maximisation. As an application, a continuous-time maximum entropy (ME) solution is implemented at equilibrium by assuming that the arrival process to each port of the ATM switch is modelled by a Compound Poisson Process (CPP) with geometrically distributed batches. Consequently, efficientz-transform-type recursive expressions of low computational cost are derived. Validation tests against simulation show that the ME approximation is credible with a very good error-level. Moreover, performance bounds for the mean queue length and cell-loss probability at each output port are experimentally defined over those generated by Interrupted Poisson Processes (IPPs) having the same first two interarrival-time moments.

Implementation of an active-R filter building block in semi-custom VLSI

A universal active-R building block was successfully designed and implemented using semi-custom VLSI (analogue gate-array) technology. The circuit makes use of the inherent charge storage in the low-frequency PNP transistors buffered by high-frequency NPN transistors which eliminates the need for capacitors and results in active-R filters that approximate the desired frequency response at high frequencies better than active-RC filters. A two-chip chip set is proposed for use as a practical building block for the p-plane design approach to active-R filters. The first chip contains two p-plane integrators which can be used to design any active-R filter. The second chip contains the parameter-compensation circuit which monitors the circuit on the first chip and uses this information to adjust the bias point on the integrator transistors in order to maintain constant integrator characteristics over a wide range of conditions including process variations, bias conditions, and temperature changes. As a result, ...

Hexamers of subunit II from Limulus hemocyanin (a 48‐mer) have the same quaternary structure as whole Panulirus hemocyanin molecules

Hemocyanins are copper-containing proteins that transport oxygen in a variety of invertebrates. Considerable evidence has accumulated that arthropodan hemocyanins are multimers of a fundamental hexameric unit. X-Ray crystallographic structure determination has revealed that the hemocyanin molecule from the spiny lobster Panulirus interruptus is a single hexamer having 32 point group symmetry. Using crystals of subunit II, one of 8 polypeptide types comprising the octahexameric hemocyanin of the horseshoe crab Limulus polyphemus, and the molecular replacement method for crystallographic phase determination we show that subunit II forms assemblies with the same hexameric quaternary structure as the whole Panulirus hemocyanin molecule. Observation of the same hexameric motif in two widely separated species provides strong additional evidence that this quaternary structural unit is a universal building block of arthropodan hemocyanins.

A Compound P300-40Hz Response of the Cat Hippocampus

In companion reports (Başar-Eroglu et al., in press a,b) it was shown that the hippocampal P300 response had a frequency content with prominent theta enhancement, especially near CA3 region. Moreover, frequency analysis revealed a marked component in the 40 Hz frequency range. In the present study, a detailed account about "40 Hz response accompanied by the N200-P300 compound response" is given. These results were obtained by use of digital adaptive filtering method described in previous studies (Başar et al., 1987, Başar, 1980). The physiological interpretation of the visual 40 Hz component gained tremendous importance since the discovery of Gray and Singer (1987, 1989) of 40 Hz oscillations in the visual cortex. Our analysis shows clearly that the 40 Hz response component is not only a cortical response pattern. Moreover, the 40 Hz response is accompanied by a P300 response and we discuss that it is also a universal building block of brain responsiveness. The 40 Hz response should be correlated with multimodal sensory and cognitive function.