Extra Structures Research Articles

Formation of extra centrosomal structures is dependent on β-catenin

beta-Catenin has important roles in cell-cell adhesion and in the regulation of gene transcription. Mutations that stabilize beta-catenin are common in cancer, but it remains unclear how these mutations contribute to cancer progression. beta-Catenin is also a centrosomal component involved in centrosome separation. Centrosomes nucleate interphase microtubules and the bipolar mitotic spindle in normal cells, but their organization and function in human cancers are abnormal. Here, we show that expression of stabilized mutant beta-catenin, which mimics mutations found in cancer, results in extra non-microtubule nucleating structures that contain a subset of centrosome proteins including gamma-tubulin and centrin, but not polo-like kinase 4 (Plk4), SAS-6 or pericentrin. A transcriptionally inactive form of beta-catenin also gives rise to abnormal structures of centrosome proteins. HCT116 human colon cancer cell lines, from which the mutant beta-catenin allele has been deleted, have reduced numbers of cells with abnormal centrosome structures and S-phase-arrested, amplified centrosomes. RNAi-mediated depletion of beta-catenin from centrosomes inhibits S-phase-arrested amplification of centrosomes. These results indicate that beta-catenin is required for centrosome amplification, and mutations in beta-catenin might contribute to the formation of abnormal centrosomes observed in cancers.

Coalgebraic tensor product and homology operations

In their paper [4] Hunton and Turner set up the framework for homological algebra of coalgebraic rings and coalgebraic modules, which arise naturally in the study of ordinary and generalized homologies of infinite loop spaces. Their language has proved to be a useful tool both for describing (see eg Hunton and Turner [5] and Kashiwabara and Wilson [7]) and computing (see Kashiwabara [6]) homology of infinite loop spaces. Of course, such objects tend to get equipped with extra structures. For example the Steenrod algebra [11], the Dyer–Lashof algebra [3] or the algebra of cohomology operations for appropriate generalized cohomology theory (see Adams [1]) may act on these objects. Thus it is natural to ask if these actions can be extended to the algebraic constructions defined by Hunton and Turner, notably to the coalgebraic tensor product.

OsC6, Encoding a Lipid Transfer Protein, Is Required for Postmeiotic Anther Development In Rice

Synthesis of lipidic components in anthers, including of the pollen exine, is essential for plant male reproductive development. Plant lipid transfer proteins (LTPs) are small, abundant lipid-binding proteins that have the ability to exchange lipids between membranes in vitro. However, their biological role in male reproductive development remains less understood. Here, we report the crucial role of OsC6 in regulating postmeiotic anther development in rice (Oryza sativa). Found in monocots, OsC6 belongs to a distinct clade from previously identified LTP1 and LTP2 family members found in both dicots and monocots. OsC6 expression is mainly detectable in tapetal cells and weakly in microspores from stage 9 to stage 11 of anther development. Immunological assays indicated that OsC6 is widely distributed in anther tissues such as the tapetal cytoplasm, the extracellular space between the tapetum and middle layer, and the anther locule and anther cuticle. Biochemical assays indicated that recombinant OsC6 has lipid binding activity. Moreover, plants in which OsC6 was silenced had defective development of orbicules (i.e. Ubisch bodies) and pollen exine and had reduced pollen fertility. Furthermore, additional evidence is provided that the expression of OsC6 is positively regulated by a basic helix-loop-helix transcription factor, Tapetum Degeneration Retardation (TDR). Extra granule-like structures were observed on the inner surface of the tdr tapetal layer when the expression of OsC6 was driven by the TDR promoter compared with the tdr mutant. These data suggest that OsC6 plays a crucial role in the development of lipidic orbicules and pollen exine during anther development in rice.

Fractional quantum conductance values in Au nanoelectrodes due to hydrogen adsorption

Hydrogen adsorption in gold nanocontact electrodes in electrochemical solution is experimentally discerned. This is performed with gold nanocontact conductance histograms in an electrochemical environment in which both the electrochemical potential and the electrolyte type are varied. Different salts, acids, and hydrogen peroxide electrolytes are studied. Salts and acids exhibit at negative electrochemical potentials different fractional quantum conductance histograms peaks associated to extra stable structures due to H adsorption while these peaks do not appear for H 2O 2 where electron transfer between solution and electrodes occurs without hydrogen formation or hydrogen adsorption on the gold electrode.

ELE restrains empty glumes from developing into lemmas

Although there is evident homology among reproductive organs when comparing Poaceae (grass) and eudicots, the identity of grass specific organs, such as lodicules, palea, lemma, and glumes has been the subject of a vast and largely inconclusive discussion. Here we provide some direct evidence to support the idea that the empty glumes of rice (Oryza sativa) are counterparts of lemmas. We show that the development of empty glumes is regulated by ELE (elongated empty glume), which belongs to a plant specific novel gene family. Mutations at the ELE locus cause elongated empty glumes, which mimic the lemmas and have the epidermal morphology of lemmas with four or five vascular bundles. As a nuclear-localized gene, ELE is specifically expressed at the empty glumes of immature spikelets, and its ectopic expression causes many floral development defects, including lemma-like palea, extra palea-like structures, elongated lodicules, extra stamens and stigmas. Our result suggests that empty glumes are lemmas of the sterile florets located at the lateral side of the rice spikelet, and ELE acts as a regulator restraining its growth to maintain its small size in wild-type plants.

Homology swapping of intrinsic secondary structural elements between cellulosomal types I and II cohesins and their effect on dockerin binding

The high-affinity cohesin–dockerin interaction dictates the suprastructural assembly of the multienzyme cellulosome complex. The interaction between these two complementary families of protein modules was found to be species-specific and type-dependent. The structure of the type II cohesin module possesses additional intrinsic secondary structural elements absent in the type I cohesin, i.e., an α-helix and two singular "β-flaps". The role of these extra secondary structures in dockerin recognition was studied in this work using gene swapping, in which corresponding homologous stretches of types I and II cohesins were interchanged. The specificity of binding of the resultant chimaeric cohesins was determined by enzyme-linked affinity assay. Several chimaeric cohesins retained dockerin recognition properties. Hence, these cohesins may undergo manipulations (insertion/deletion of peptide segments) without altering their affinity toward their counterpart dockerin, although type-dependent binding specificity cannot be converted by swapping of the additional secondary structural elements between the two cohesin types. The results further emphasize the strong affinity and plasticity between the cohesin and dockerin pair and are consistent with the known findings on specificity of the types I and II interactions. These studies provide insight into the structural and functional resilience of the cohesins and thus have direct bearing on their potential use in biotechnological applications.

Optical conductivity of multilayer graphene

The optical conductivity of graphene monolayer and multilayers are theoretically studied taking into account of the full dispersion, yielding results that are valid up to the ultraviolet region. Compared to the optical conductivity of monolayer graphene, extra peak structures appear in both the infrared and ultraviolet frequency regions for the multilayer case, which is understood as a combined effect of van Hove singularities in the energy band structures and optical transition selection rules. The number of ultraviolet peaks is equal to the number of layers. The number of infrared peaks in an even-layered graphene is equal to one half of the layer number. In odd-layered graphene, due to the existence of a monolayer-like subband, the number of infrared peaks is equal to that in the corresponding even-layered graphene with one layer less.

Lats kinase is involved in the intestinal apical membrane integrity in the nematodeCaenorhabditis elegans

The roles of Lats kinases in the regulation of cell proliferation and apoptosis have been well established. Here we report new roles for Lats kinase in the integrity of the apical membrane structure. WTS-1, the C. elegans Lats homolog, localized primarily to the subapical region in the intestine. A loss-of-function mutation in wts-1 resulted in an early larval arrest and defects in the structure of the intestinal lumen. An electron microscopy study of terminally arrested wts-1 mutant animals revealed numerous microvilli-containing lumen-like structures within the intestinal cells. The wts-1 phenotype was not caused by cell proliferation or apoptosis defects. Instead, we found that the wts-1 mutant animals exhibited gradual mislocalization of apical actin and apical junction proteins, suggesting that wts-1 normally suppresses the formation of extra apical membrane structures. Heat-shock-driven pulse-chase expression experiments showed that WTS-1 regulates the localization of newly synthesized apical actins. RNAi of the exocyst complex genes suppressed the mislocalization phenotype of wts-1 mutation. Collectively, the data presented here suggest that Lats kinase plays important roles in the integrity of the apical membrane structure of intestinal cells.

Metabolic mapping of rat forebrain and midbrain during delay and trace eyeblink conditioning

While the essential neural circuitry for delay eyeblink conditioning has been largely identified, much of the neural circuitry for trace conditioning has yet to be determined. The major difference between delay and trace conditioning is a time gap between the presentation of the conditioned stimulus (CS) and the unconditioned stimulus (US) during trace conditioning. It is this time gap, which accounts for the additional memory component and may require extra neural structures, including hippocampus and prefrontal cortex. A metabolic marker of energy use, radioactively labeled glucose analog, was used to compare differences in glucose analog uptake between delay, trace, and unpaired experimental groups (rats, Long-Evans), to identify possible new areas of involvement within forebrain and midbrain. Here, we identify increased 2-DG uptake for the delay group compared to the unpaired group in various areas including: the medial geniculate nuclei (MGN), the amygdala, cingulate cortex, auditory cortex, medial dorsal thalamus, and frontal cortices. For the trace group, compared to the unpaired group, there was an increase in 2-DG uptake for the medial orbital frontal cortex and the medial MGN. The trace group also exhibited more increases lateralized to the right hemisphere, opposite to the side of US delivery, in various areas including: CA1, subiculum, presubiculum, perirhinal cortex, ventral and dorsal MGN, and the basolateral and central amygdala. While some of these areas have been identified as important for delay or trace conditioning, some new structures have been identified such as the orbital frontal cortex for both delay and trace groups.

Persistence-based handle and tunnel loops computation revisited for speed up

Loops in surfaces associated with topological features such as handles and tunnels are important entities in many applications including surface parameterization, feature identification, and topological simplification. Recently, a persistent homology based algorithm has been proposed to compute them. The algorithm has several advantages including its simplicity, combinatorial nature and independence from computing other extra structures. In this paper, we propose changes to this loop computation algorithm based on some novel observations. These changes reduce the computation time of the algorithm dramatically. In particular, our experimental results show that the suggested changes achieve considerable speed up for large data sets without sacrificing loop qualities.

Molting interferes with web decorating behavior in Argiope keyserlingi (Araneae, Araneidae)

Abstract Various orb weaving spiders decorate their webs with extra silk structures. In the araneid genus Argiope, these web decorations consist of flimsy aciniform silk threads arranged in zig zag shaped bands. The adaptive value of these structures is still unclear and controversy over a suite of possible functional explanations persists: the high variation of web decoration adds further uncertainty. Web decorations can differ in shape, size, and frequency across species and even within species. Physiological processes may influence individual variation in web decorating behavior. Molting events are major physiological transitions combined with fundamental alterations of the metabolic state of the spiders. For gaining new insights into possible proximate mechanisms driving web decorating behavior, we observed subadult Argiope keyserlingi Karsch 1878 females in the laboratory and registered the individual variation of web decorations associated with the maturity molt under laboratory conditions. We found...

Two proposals for the inclusion of directory information in the last-level private caches of glueless shared-memory multiprocessors

In glueless shared-memory multiprocessors where cache coherence is usually maintained using a directory-based protocol, the fast access to the on-chip components (caches and network router, among others) contrasts with the much slower main memory. Unfortunately, directory-based protocols need to obtain the sharing status of every memory block before coherence actions can be performed. This information has traditionally been stored in main memory, and therefore these cache coherence protocols are far from being optimal. In this work, we propose two alternative designs for the last-level private cache of glueless shared-memory multiprocessors: the lightweight directory and the SGluM cache. Our proposals completely remove directory information from main memory and store it in the home node’s L2 cache, thus reducing both the number of accesses to main memory and the directory memory overhead. The main characteristics of the lightweight directory are its simplicity and the significant improvement in the execution time for most applications. Its drawback, however, is that the performance of some particular applications could be degraded. On the other hand, the SGluM cache offers more modest improvements in execution time for all the applications by adding some extra structures that cope with the cases in which the lightweight directory fails.

Experimental and Numerical Analysis of Strain in High-Strength $\hbox{Nb}_{3}\hbox{Sn}$ Magnets

We have developed a high-strength Ta-reinforced conductor for high-magnetic-field magnets. In our previous work, it was demonstrated that the Ta-reinforced conductor had good characteristics against mechanical stress and strain. In this study, we made a 2-D calculation code for a stress-strain analysis, and derived the stress and strain of the magnet using some physical values such as the Young's modulus of the conductors, magnet dimensions and so on. According to the calculation results of some model magnets, the Ta-reinforced conductor could be used without extra support structures. Hence, the conductors are fit for high-magnetic-field and large-scale magnets such as NMR and SMES magnets.

Wrap attack activates web-decorating behavior in Argiope spiders

Various orb-weaving spiders add extra silk structures—“web decorations”—to their webs. The adaptive value of these web decorations is still unclear, and the suite of functional hypotheses remains controversial. Spiders in the genus Argiope decorate their webs with densely woven zigzag ribbons made of fibrous aciniform silk. This type of silk is also used by the spiders for “wrap attacks” to immobilize the prey by wrapping it with a dense silk cover. Previous studies suggested that the spiders use accumulated excess silk for building web decorations due to a constant secretion in the aciniform glands. We test if this hypothesis holds for 3 species, which construct different types of web decorations: linear in Argiope bruennichi, irregular in Argiope sector, and cruciate in Argiope keyserlingi. We show that depletion of aciniform silk has a stimulating effect on web-decorating behavior in 3 species of Argiope. The aciniform glands apparently readily overcompensated experimentally induced silk losses, and so silk depletion may result in the activation of the according glands. We suggest that the aciniform gland activation might be an important mechanism for Argiope’s wrap attack to ensure sufficient wrapping of silk under high prey density and repeated wrapping events. The web decorations might function as a mechanism to maintain high gland activity, thereby maximizing the efficiency of the wrap attack strategy of Argiope.

Cell‐permeant cytoplasmic blue fluorophores optimized for in vivo two‐photon microscopy with low‐power excitation

Because of the spreading of nonlinear microscopies in biology, there is a strong demand for specifically engineered probes in these applications. Herein, we report on the imaging properties in living cells and nude mice brains of recently developed water soluble blue fluorophores that show efficient diffusion through cell membranes and blood-brain barriers. They are characterized by two-photon absorption cross-sections of 100-150 Goeppert-Mayer range in the near IR and fluorescence efficiencies of up to 72% in water. They were found to stain homogeneously the cytoplasm of cultured living cells within minutes. Moreover, their diffusion times and fluorescence characteristics in the cytoplasm suggest a hydrophobic association with intracellular membranes. Their intracellular fluorescent decays were found to be almost mono-exponential, a very favorable feature for fluorescence lifetime imaging. Two photon images of living cells were obtained with a good signal to noise ratio using laser powers in the sub-milliwatt range. This allows continuous imaging without significant photobleaching for tens of minutes. In addition, these fluorophores allowed in vivo three-dimensional two-photon imaging of mice cortex vasculatures and extra vasculature structures, with no sign of toxicity.

Overexpressing Centriole-Replication Proteins In Vivo Induces Centriole Overduplication and De Novo Formation

SummaryBackgroundCentrosomes have important roles in many aspects of cell organization, and aberrations in their number and function are associated with various diseases, including cancer. Centrosomes consist of a pair of centrioles surrounded by a pericentriolar matrix (PCM), and their replication is tightly regulated. Here, we investigate the effects of overexpressing the three proteins known to be required for centriole replication in Drosophila—DSas-6, DSas-4, and Sak.ResultsBy directly observing centriole replication in living Drosophila embryos, we show that the overexpression of GFP-DSas-6 can drive extra rounds of centriole replication within a single cell cycle. Extra centriole-like structures also accumulate in brain cells that overexpress either GFP-DSas-6 or GFP-Sak, but not DSas-4-GFP. No extra centrioles accumulate in spermatocytes that overexpress any of these three proteins. Most remarkably, the overexpression of any one of these three proteins results in the rapid de novo formation of many hundreds of centriole-like structures in unfertilized eggs, which normally do not contain centrioles.ConclusionsOur data suggest that the levels of centriolar DSas-6 determine the number of daughter centrioles formed during centriole replication. Overexpression of either DSas-6 or Sak can induce the formation of extra centrioles in some tissues but not others, suggesting that centriole replication is regulated differently in different tissues. The finding that the overexpression of DSas-4, DSas-6, or Sak can rapidly induce the de novo formation of centriole-like structures in Drosophila eggs suggests that this process results from the stabilization of centriole-precursors that are normally present in the egg.

A new fast algorithm for computing the distance between two disjoint convex polygons based on Voronoi diagram

Computing the distance between two convex polygons is often a basic step to the algorithms of collision detection and path planning. Now, the lowest time complexity algorithm takes O(logm+logn) time to compute the minimum distance between two disjoint convex polygons P and Q, where n and m are the number of the polygons’ edges respectively. This paper discusses the location relations of outer Voronoi diagrams of two disjoint convex polygons P and Q, and presents a new O(logm+logn) algorithm to compute the minimum distance between P and Q. The algorithm is simple and easy to implement, and does not need any preprocessing and extra data structures.

Theoretical Study on the Structure and the Frequency of Isomers of the Naphthalene Dimer.

The structures of the naphthalene monomer and dimer were investigated with performing vibrational analysis. The MP2 optimization showed that the naphthalene monomer has a nonplanar geometry in the 6-31G, 6-31G*, 6-31+G*, and 6-311G basis sets, while it has a planar geometry in the 6-31G*(0.25) and Dunning's correlation consistent basis sets. The MP2/cc-pVDZ calculation showed the presence of the four stable isomers, which were part of the isomers in the previous MP2/6-31G* calculation (Walsh, T. R. Chem. Phys. Lett. 2002, 363, 45). The presence of extra structures in the MP2/6-31G* calculation is attributed to a poor description of the potential energy surface, which is evident from the nonplanar structure of the monomer in the MP2/6-31G* calculation. The relative stability among the isomers in the MP2/cc-pVDZ calculation without counterpoise correction was maintained in both the single-point calculation at the MP2/aug-cc-pVDZ//MP2/cc-pVDZ level and the counterpoise-corrected optimization at the MP2/cc-pVDZ level. The relative stability among the isomers suggested an enhancement of the π-π interaction in the structure with lower symmetry, which could be explained using a molecular-orbital model. The vibrational analysis in MP2/cc-pVDZ without the counterpoise correction suggested that the isomers of the naphthalene dimer were distinguishable by the observation of the infrared spectrum in the low-frequency region (150-600 cm(-)(1)).

Three‐Dimensional Image Integration: A First Experience with Guidance of Atrial Fibrillation Ablations

Editorial Comment The treatment of atrial fibrillation (AF) can be challenging, with a rate control strategy not being optimal for all patients and antiarrhythmic drugs frequently ineffective and possessing serious adverse effects. A fluoroscopic or electroanatomic catheter-based approach is rapidly becoming one of the preferred treatments of AF. 1-3 However, success rates are still not ideal and complications due to damage of extra thoracic structures remain a problem. 1 Also of concern is the significant ionizing radiation exposure during the prolonged fluoroscopy required to delineate the complex anatomy of the left atrium and pulmonary veins, even with advanced techniques to minimize exposure. Total fluoroscopy duration for AF ablations is typically 8-fold higher than atrioventricular nodal reentrant tachycardia ablations, averaging over 60 minutes of fluoroscopy time, with radiation exposure in the 1.0‐1.5 Gy range. 4 One of the major promises of using integratedmodality navigation systems such as this for AF ablation is faster, more accurate catheter navigation, reduced complications, and diminished fluoroscopy use. In view of the complex and variable anatomy of cardiac structures and pulmonary veins, many of which remain invisible to fluoroscopy, the addition of further, more accurate imaging modalities are likely to improve ablation success and safety. 5,6 While three-dimensional (3D) mapping techniques using magnetic or electrical localizing systems in the modern electrophysiology laboratory are extremely useful and are currently in widespread clinical use, they require catheter manipulation to identify geometry and do not provide independent anatomic information. Both magnetic resonance (MR) imaging 7,8 and computed tomography (CT) scanning 9,10 have been shown prior to be suitable for delineating the left atrial anatomy and assisting with catheter navigation. However, it is not yet clear which imaging modality is superior for mapping of the left atrium and other cardiac structures; certainly navigation and imaging systems that allow the use of either format will be advantageous.

Structural and Mutational Analysis of Trypanosoma brucei Prostaglandin H2 Reductase Provides Insight into the Catalytic Mechanism of Aldo-ketoreductases

Trypanosoma brucei prostaglandin F2alpha synthase is an aldo-ketoreductase that catalyzes the reduction of prostaglandin H2 to PGF2alpha in addition to that of 9,10-phenanthrenequinone. We report the crystal structure of TbPGFS.NADP+.citrate at 2.1 angstroms resolution. TbPGFS adopts a parallel (alpha/beta)8-barrel fold lacking the protrudent loops and possesses a hydrophobic core active site that contains a catalytic tetrad of tyrosine, lysine, histidine, and aspartate, which is highly conserved among AKRs. Site-directed mutagenesis of the catalytic tetrad residues revealed that a dyad of Lys77 and His110, and a triad of Tyr52, Lys77, and His110 are essential for the reduction of PGH2 and 9,10-PQ, respectively. Structural and kinetic analysis revealed that His110, acts as the general acid catalyst for PGH2 reduction and that Lys77 facilitates His110 protonation through a water molecule, while exerting an electrostatic repulsion against His110 that maintains the spatial arrangement which allows the formation of a hydrogen bond between His110 and C11 that carbonyl of PGH2. We also show Tyr52 acts as the general acid catalyst for 9,10-PQ reduction, and thus we not only elucidate the catalytic mechanism of a PGH2 reductase but also provide an insight into the catalytic specificity of AKRs.