Double Domain Research Articles

Sidereal filtering based on single differences for mitigating GPS multipath effects on short baselines

Carrier-phase multipath effects are one of the most significant error sources in precise Global Positioning System (GPS) positioning applications. A new sidereal filtering algorithm based on single differences is developed to mitigate multipath effects for short-baseline high-rate GPS applications such as structural deformation monitoring. This method differs from traditional sidereal filtering in that our method operates on the single differences rather than the coordinates or double differences. A multipath model for the single differences on the reference day is established for each satellite and is used to remove multipath errors from observations of subsequent days by taking advantage of the sidereal repeatability of multipath signals. Using both simulated and real GPS observations, we demonstrate that this method is insensitive to different weighting strategies used in computing single differences from double differences. Applying the proposed method can reduce the root mean square (RMS) of positioning noises by 82% on average. Compared to sidereal filtering (in either coordinate or double differences domain) and aspect repeat time adjustment, this method can further reduce the RMS values by 13 and 7%, respectively. Wavelet spectra have shown that the proposed method is more effective in mitigating multipath errors of both long and short periods. This method is also more advantageous in that it is applicable when different GPS satellites are observed on different days.

Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events

The MutT/Nudix superfamily proteins repair DNA damage and play a role in human health and disease. In this study, we examined two different cases of double MutT/Nudix domain-containing proteins from eukaryotes and prokaryotes. Firstly, these double domain proteins were discovered in Drosophila, but only single Nudix domain proteins were found in other animals. The phylogenetic tree was constructed based on the protein sequence of Nudix_N and Nudix_C from Drosophila, and Nudix from other animals. The phylogenetic analysis suggested that the double Nudix domain proteins might have undergone a gene duplication-speciation-fusion process. Secondly, two genes of the MutT family, DR0004 and DR0329, were fused by two mutT gene segments and formed double MutT domain protein genes in Deinococcus radiodurans. The evolutionary tree of bacterial MutT proteins suggested that the double MutT domain proteins in D. radiodurans probably resulted from a gene duplication-fusion event after speciation. Gene duplication-fusion is a basic and important gene innovation mechanism for the evolution of double MutT/Nudix domain proteins. Independent gene duplication-fusion events resulted in similar domain architectures of different double MutT/Nudix domain proteins.

Histone methyltransferase PRDM8 regulates mouse testis steroidogenesis

A family of PRDM proteins are similar to histone methyltransferases (HMTases) with SET domain in that they modulate different cellular processes, including transcriptional regulation, through chromatin modifying activities. By applying a bioinformatic approach, we searched for proteins containing the SET domain and identified a double zinc-finger domain containing PRDM8 with HMTase activity. In vitro HMTase assay and immunoblot analysis revealed that PRDM8 specifically methylates H3K9 of histones which indicates transcriptional repression activity of PRDM8. Direct recruitment of PRDM8 to the promoter mediated transcriptional repression and indicated no involvement of HDAC. Tissue blot analyses identified PRDM8 transcripts from brain and testis in adult mouse. Consistent with these observations, we demonstrate that PRDM8 repressed the expression of steroidogenic markers, p450c17c and LHR, which indicates its regulatory role in mouse testis development.

Epitaxial growth of C60 thin films on the Bi(0001)/Si(111) surface

The morphology and atomic structure of C60 fullerene films on the Bi(0001)/Si(111)−7 × 7 surface with different coverages have been studied by scanning tunneling microscopy and spectroscopy and low-energy electron microscopy in high vacuum. It is shown that the most favorable sites for nucleation of C60 islands are double steps and domain boundaries on the surface of epitaxial Bi film.

A double WAP domain (DWD)-containing protein with proteinase inhibitory activity in Chinese white shrimp, Fenneropenaeus chinensis

The whey major component, whey acidic protein (WAP), has one or more WAP domains characterized by a four-disulfide core (4-DSC) structure. These kinds of proteins are involved in multiple functions, including proteinase inhibitor activity, antimicrobial activity, ATPase inhibitor activity, and regulatory function in cell proliferation. Recent research indicates that WAP domain-containing proteins play an important role in the innate immunity of crustaceans. In this study, a novel double WAP domain (DWD)-containing protein named Fc-DWD was found for the first time in Chinese white shrimp, Fenneropenaeus chinensis. The open reading frame of Fc-DWD encodes a protein of 117 amino acids, including a signal peptide of 16 amino acids and two WAP domains. The predicted molecular mass of the mature protein is 12.78kDa with an estimated pI of 8.49. The first WAP domain, named WAP 1, composed of 49 amino acids locates in the amino-terminal of Fc-DWD, and the second WAP domain, named WAP 2, composed of 45 amino acids locates in the carboxy-terminal. Fc-DWD mRNA was upregulated in hemocytes, hepatopancreas, gills, and stomach of bacteria- and virus-challenged shrimp. Results of the binding assay showed that rFc-DWD could bind to both Gram-negative bacteria and Gram-positive bacteria. rWAP 1 could only bind to Gram-positive bacteria, but rWAP 2 could bind to both Gram-negative and positive bacteria. Moreover, rFc-DWD exhibited proteinase inhibitory activity against the secretory proteinase(s) from Bacillussubtilis and Pseudomonas aeruginosa. All of these findings suggest that Fc-DWD may play an important role in enabling the host defense to execute its proteinase inhibitory activity against pathogens.

66.4: Surface Polarity Controlled Horizontal Chevron Defect Free Surface Stabilized Ferroelectric Liquid Crystal Devices

AbstractThe asymmetrical surface polarity controlled hybrid alignment technique was proposed to suppress the alignment defects of half V‐shaped switching FLC materials. When the material was cooled from N* to SmC*, two kinds of layer arrangements were formed with opposite spontaneous polarization directions (Ps). Alignment layers with opposite surface polarity direction were utilized in asymmetrical hybrid cells and produced uni‐surface‐polarity direction. FLC Ps was only controlled by this surface polarity; therefore, double domains were suppressed into mono‐domain. A 2.4” prototype TFT‐LCD was presented with defect‐free alignment texture. This alignment technique provided promising FLC material with well alignment and fast switching for TFT‐LCD application.

DOC2b is a SNARE regulator of glucose-stimulated delayed insulin secretion

Insulin secretion is precisely regulated by blood glucose with unique biphasic pattern. The regulatory mechanism of the second-phase insulin release is unclear. In this study, we report that DOC2b (double C2 domain protein isoform b), a SNARE related protein, was associated with insulin vesicles and translocated to plasma membrane within several minutes upon high-glucose stimulation followed by an interaction with syntaxin4, but not syntaxin1. This binding specificity and the time course of DOC2b translocation were suitable for the regulation of second-phase insulin release. Increased DOC2b expression enhanced glucose-stimulated insulin secretion. In contrast, silencing DOC2b inhibited delayed release of insulin, without affecting rapid (∼7 min) phase secretion. Interestingly, DOC2b had no effects on KCl-triggered insulin release. These data suggest that DOC2b may be a regulator for delayed (second-phase) insulin secretion in MIN6 cells.

ULTRATHIN Al FILM ON THE W(100) SURFACE

We have investigated Al adsorption on the W (100) surface using LEED and low energy Ion Scattering Spectroscopy (ISS). We observe a p(2 × 1) double domain LEED image for the 1.0 ML Al/W (100) surface at annealing temperature 850°C. We also measured the Al adsorption site at the Al/W (100) — p(2 × 1) surface using ISS. It is found that Al atoms adsorbed at 0.7±0.1 Å aside from the center of the bridge sites with a zigzag structure — one atom adsorbs at the right-hand side and next atom at the left-hand side along the [100] direction. The height of the adsorbed Al atoms is determined to be 1.75±0.15 Å above the W surface layer.

Optical image watermarking using fractional Fourier transform

An optical image watermarking scheme using fractional Fourier transform is proposed. The watermark is encrypted using double random fractional order Fourier domain encoding scheme. Encrypted image is water marked into a host image. Embedding watermark sequences into fractional Fourier domain has an important advantage over embedding in spatial domain or in frequency domain. The watermark is recovered by applying corresponding correct fractional orders and random phase masks. The use of fractional Fourier transform offers additional degrees of freedom to enlarge the key size, thus enhancing the level of security. The effect of occlusion of watermarked image on the recovered watermark is also studied. The proposed idea is supported with simulation results.

Low-dimensional nanostructures and fullerene films on semiconductor surface

The morphology and atomic structures of C60 fullerene films on a Bi(0001)/Si(111)-7 × 7 surface and adsorption of fluorofullerene C60Fx molecules on a Si(111)-7 × 7 surface have been studied by scanning tunneling microscopy/spectroscopy and low-energy electron microscopy under ultra high-vacuum conditions. It has been shown that initial nucleation of C60 islands on the surface of an epitaxial Bi film occurs on double steps and domain boundaries, while tunnel spectra do not exhibit any significant charge transfer to the lowest unoccupied molecular orbital states. Fluorofullerene molecules allow local (at the nanoscale level) modification of Si surface through local etching.

Identification of Linkage Disequilibrium SNPs from a Kidney-Yang Deficiency Syndrome Pedigree

In order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required.

Detailed characterisation of an indoor MIMO channel in the double directional spatial domain

The spatial domain characteristics of an indoor multiple-input multiple-output (MIMO) communication system are examined in detail. Using a high-resolution algorithm, the authors were able to effectively estimate multipath parameters on the joint azimuth of arrival/azimuth of departure (AoA/AoD) domain. The analysis showed dense clustering phenomena at the vast majority of considered locations and a strong correlation between the azimuth spreads of the two angular domains with the presence of line-of-sight (Los) specular components or when the distance between the transmitter (Tx) and the receiver (Rx) is low. The authors also noticed higher azimuth dispersions, compared with those reported in the literature, which can be attributed to low antenna heights and local scattering interactions in the vicinity of both the transmit and receive arrays. Finally, the impact of the spatial global parameters on the ergodic MIMO capacity was tested revealing a direct relation between them.

Modelling and calculating the harmonic penetration of the high power traction using the double domain simulation method

The paper presents the results of a long term research work. The authors are modelling the penetration and elimination of harmonic disturbance originating from the high power railways. This kind of problem is usually handled using time domain or frequency domain simulation. As it is well known, the modelling of harmonic sources is more accurate in time domain simulation, while the frequency dependence of the passive network is more accurate in frequency domain. That is why a novel method was developed named double domain simulation method, which is a combination of frequency and time dependent models. To calculate the sophisticated model of the electric locomotive as a non-linear load a time dependent model must be used. The traction supply system together with the equivalent supply network impedance could be calculated accurately in frequency domain. An iteration algorithm is developed converting the variables in every iteration step between the time and frequency domain. The application of the double domain simulation method to solve the harmonic filtering of high power railway system is introduced. The results prove that the method is suitable for studying the effect of different filtering methods, like the passive, active and hybrid filtering.

CHOTTO1, a Double AP2 Domain Protein of Arabidopsis thaliana, Regulates Germination and Seedling Growth Under Excess Supply of Glucose and Nitrate

Arabidopsis chotto1 (cho1) mutants show resistance to (-)-R-ABA, an ABA analog, during germination and seedling growth. Here, we report cloning and characterization of the CHO1 gene. cho1 mutants showed only subtle resistance to (+)-S-ABA during germination. The cho1 mutation acts as a strong enhancer of the abi5 mutant, whereas the cho1 abi4 double mutant showed ABA resistance similar to the abi4 single mutant. This suggests that CHO1 and ABI4, but not ABI5, act in the same genetic pathway. Map-based cloning revealed that the CHO1 gene encodes a putative transcription factor containing double AP2 domains. The CHO1 gene was expressed predominantly in seed, with the strongest expression in imbibed seed. Induction of CHO1 expression was observed 4 h after seed imbibition and reached a maximum level at 24 h. Induction of CHO1 expression did not occur in the abi4 mutants, indicating that this is an ABI4-dependent process. Microarray experiments showed that a large number of genes involved in primary metabolism and the stress response were up-regulated in the cho1 mutant. Growth of abi4 and cho1 mutant seedlings was resistant to high concentrations of glucose. In addition, growth of cho1 mutant seedlings was partially resistant to excess nitrate (50 mM), as evident from their expanded green cotyledons. However, their growth was normal under moderate nitrate concentrations (< 10 mM). This nitrate response was specific to the cho1 mutants and was not observed in the abi4 mutants. Taken together, our results indicate that CHO1 regulates nutritional responses downstream of ABI4 during germination and seedling growth.

Caspase 8 Promotes Peripheral Localization and Activation of Rab5

Caspase 8 is a cysteine protease that initiates apoptotic signaling via the extrinsic pathway in a manner dependent upon association with early endosomes. Previously, we identified caspase 8 as an effector of migration, promoting motility in a manner dependent upon phosphorylation on Tyr-380 by Src family kinases and its subsequent association with Src homology 2 domain-containing proteins. Here we demonstrate the regulation of the small GTPase Rab5, which mediates early endosome formation, homotypic fusion, and maturation by caspase 8. Regulation requires the Tyr-380 phosphorylation site but not caspase proteolytic activity. Tyr-380 is essential for interaction with the Src homology 2 domains of p85α, a multifunctional adaptor for phosphatidylinositol 3-kinase, that possesses Rab-GAP activity. Interaction between caspase 8 and p85α promotes Rab5 GTP loading, alters endosomal trafficking, and results in the accumulation of Rab5-positive endosomes at the edge of the cell. Conversely, caspase 8-dependent GTP loading of Rab5 is overcome by increased expression of p85α in a Rab-GAP-dependent manner. Thus, we demonstrate a novel function for caspase 8 as a modulator of p85α Rab-GAP activity and endosomal trafficking.

DOC2B: A Novel Syntaxin-4 Binding Protein Mediating Insulin-Regulated GLUT4 Vesicle Fusion in Adipocytes

OBJECTIVE— Insulin stimulates glucose uptake in skeletal muscle and adipose tissues primarily by stimulating the translocation of vesicles containing a facilitative glucose transporter, GLUT4, from intracellular compartments to the plasma membrane. The formation of stable soluble N-ethyl-maleimide–sensitive fusion protein [NSF] attachment protein receptor (SNARE) complexes between vesicle-associated membrane protein-2 (VAMP-2) and syntaxin-4 initiates GLUT4 vesicle docking and fusion processes. Additional factors such as munc18c and tomosyn were reported to be negative regulators of the SNARE complex assembly involved in GLUT4 vesicle fusion. However, despite numerous investigations, the positive regulators have not been adequately clarified.RESEARCH DESIGN AND METHODS— We determined the intracellular localization of DOC2b by confocal immunoflorescent microscopy in 3T3-L1 adipocytes. Interaction between DOC2b and syntaxin-4 was assessed by the yeast two-hybrid screening system, immunoprecipitation, and in vitro glutathione S-transferase (GST) pull-down experiments. Cell surface externalization of GLUT4 and glucose uptake were measured in the cells expressing DOC2b constructs or silencing DOC2b.RESULTS— Herein, we show that DOC2b, a SNARE-related protein containing double C2 domains but lacking a transmembrane region, is translocated to the plasma membrane upon insulin stimulation and directly associates with syntaxin-4 in an intracellular Ca2+-dependent manner. Furthermore, this process is essential for triggering GLUT4 vesicle fusion. Expression of DOC2b in cultured adipocytes enhanced, while expression of the Ca2+-interacting domain mutant DCO2b or knockdown of DOC2b inhibited, insulin-stimulated glucose uptake.CONCLUSIONS— These findings indicate that DOC2b is a positive SNARE regulator for GLUT4 vesicle fusion and mediates insulin-stimulated glucose transport in adipocytes.

Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR

The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum

Autophagy is the engulfment of cytosol and organelles by double-membrane vesicles termed autophagosomes. Autophagosome formation is known to require phosphatidylinositol 3-phosphate (PI(3)P) and occurs near the endoplasmic reticulum (ER), but the exact mechanisms are unknown. We show that double FYVE domain–containing protein 1, a PI(3)P-binding protein with unusual localization on ER and Golgi membranes, translocates in response to amino acid starvation to a punctate compartment partially colocalized with autophagosomal proteins. Translocation is dependent on Vps34 and beclin function. Other PI(3)P-binding probes targeted to the ER show the same starvation-induced translocation that is dependent on PI(3)P formation and recognition. Live imaging experiments show that this punctate compartment forms near Vps34-containing vesicles, is in dynamic equilibrium with the ER, and provides a membrane platform for accumulation of autophagosomal proteins, expansion of autophagosomal membranes, and emergence of fully formed autophagosomes. This PI(3)P-enriched compartment may be involved in autophagosome biogenesis. Its dynamic relationship with the ER is consistent with the idea that the ER may provide important components for autophagosome formation.

The Tyrosine Phosphorylation of Munc18c Induces a Switch in Binding Specificity from Syntaxin 4 to Doc2β

Glucose-stimulated insulin secretion is mediated by syntaxin 4-based SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes and the Sec1/Munc18 protein Munc18c. Our laboratory recently reported that Munc18c-syntaxin 4 complexes are further regulated by the competitive binding of the double C2 domain protein Doc2beta to Munc18c, although the underlying mechanism for this is unknown. Because the Doc2beta binding region of Munc18c contained residue Tyr-219 and this residue becomes phosphorylated in response to glucose stimulation, we hypothesized that the mechanism would involve Munc18c phosphorylation. Coimmunoprecipitation analyses using detergent lysates prepared from pervanadate-treated MIN6 beta cells revealed that the tyrosine phosphorylation of Munc18c corresponded to a 60% decrease in Munc18c-syntaxin 4 association with a coordinate 2-fold increase in Munc18c-Doc2beta binding. In vitro binding assays identified syntaxin 4 residues 118-194 as sufficient to confer its interaction with Munc18c; residues 118-194 contain the Hc alpha-helix and flexible linker region controlling transition of syntaxins between closed and open conformations. When overexpressed in MIN6 cells, this Hc-linker region functioned as a competitive inhibitor of endogenous syntaxin 4-Munc18c binding, increased syntaxin 4 binding to VAMP2, and significantly enhanced glucose-stimulated secretion. Molecular modeling of these new interactions yielded the predictions 1) that Tyr-219 of Munc18c remains buried under basal conditions in a conformation that is favorable for interaction with "closed" syntaxin 4 and 2) that stimulation leads to changes in syntaxin 4 contacts to facilitate exposure of Munc18c Tyr-219 for phosphorylation and Doc2beta binding.

AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay

Given the frequent occurrence of false negatives in yeast genetic assays, it is both interesting and practical to address the possible mechanisms of false negatives and, more important, to turn false negatives into true positives. We recently developed a modified yeast one-hybrid system (MY1H) useful for investigation of simultaneous protein–protein and protein:DNA interactions in vivo. We coexpressed the basic helix–loop–helix/Per-Arnt-Sim (bHLH/PAS) domains of aryl hydrocarbon receptor (AhR) and aryl hydrocarbon receptor nuclear translocator (Arnt)—namely NAhR and NArnt, respectively—which are known to form heterodimers and bind the cognate xenobiotic response element (XRE) sequence both in vitro and in vivo, as a positive control in the study of XRE-binding proteins in the MY1H system. However, we observed negative results, that is, no positive signal detected from binding of the NAhR/NArnt heterodimer and XRE site. We demonstrate that by increasing the copy number of XRE sites integrated into the yeast genome and using double GAL4 activation domains, the NAhR/NArnt heterodimer forms and specifically binds the cognate XRE sequence, an interaction that is now clearly detectable in the MY1H system. This methodology may be helpful in troubleshooting and correcting false negatives that arise from unproductive transcription in yeast genetic assays.