Nonlocal metasurface for dark-field edge emission

Nonlocal effects originating from interactions between neighboring meta-atoms introduce additional degrees of freedom for peculiar characteristics of metadevices, such as enhancement, selectivity, and spatial modulation. However, they are generally difficult to manipulate because of the collective responses of multiple meta-atoms. Here, we experimentally demonstrate the nonlocal metasurface to realize the spatial modulation of dark-field emission. Plasmonic asymmetric split rings (ASRs) are designed to simultaneously excite local dipole resonance and nonlocal quasi-bound states in the continuum and spatially extended modes. With one type of unit, nonlocal effects are tailored by varying array periods. ASRs at the metasurface's edge lack sufficient interactions, resulting in stronger dark-field scattering and thus edge emission properties of the metasurface. Pixel-level spatial control is demonstrated by simply erasing some units, providing more flexibility than conventional local metasurfaces. This work paves the way for manipulating nonlocal effects and facilitates applications in optical trapping and sorting at the nanoscale.

Broadband 2 × 2 multimode-interference coupler on the silicon-nitride platform

In this paper, we present the design, optimization, and implementation of a sub-wavelength grating (SWG) multi-mode interference coupler (MMI) on the silicon nitride photonic integrated circuit (PIC) platform with a significantly enhanced bandwidth compared to the conventional MMI. We extend the SWG MMI theory, previously presented for the silicon-on-insulator platform, to the Si3N4/SiO2 platform. Our approach involves an initial parameter optimization for a non-paired design, followed by a shift to a paired design that offers a smaller footprint and a broader bandwidth. The optimized SWG MMI exhibits a 1 dB bandwidth of 300 nm for both the insertion loss and power imbalance, making it a significant addition to silicon nitride photonics.

Impact of Antenatal SARS-CoV-2 Exposure on SARS-CoV-2 Neutralization Potency

A pregnancy booster dose significantly reduces the risk and severity of COVID-19, and it is widely recommended. A prospective cohort study was conducted to compare the transplacental passage of maternal antibodies from vaccination or infection during three trimesters against both the vaccine-targeted Wuhan strain and the Omicron strain of SARS-CoV-2. Maternal-infant dyads from vaccinated mothers were collected between 6 June 2022 and 20 September 2022. We analyzed 38 maternal-infant dyads from mothers who had been infected with COVID-19 and 37 from mothers without any previous infection. Pregnant women who received their last COVID-19 vaccine dose in the third trimester exhibited the highest anti-spike protein antibody levels and neutralizing potency against both the Wuhan strain and Omicron BA.2 variant in their maternal and cord plasma. Both second- and third-trimester vaccination could lead to a higher level of neutralization against the Wuhan and Omicron strains. COVID-19 infection had a negative effect on the transplacental transfer ratio of SARS-CoV-2 antibodies. A booster dose during the second or third trimester is encouraged for the maximum transplacental transfer of humoral protection against COVID-19 for infants.

High-Resolution Metalens Imaging with Sequential Artificial Intelligence Models

An analysis of the optical response of a GaN-based metalens was conducted alongside the utilization of two sequential artificial intelligence (AI) models in addressing the occasional issues of blurriness and color cast in captured images. The optical loss of the metalens in the blue spectral range was found to have resulted in the color cast of images. Autoencoder and CodeFormer sequential models were employed in order to correct the color cast and reconstruct image details, respectively. Said sequential models successfully addressed the color cast and reconstructed details for all of the allocated face image categories. Subsequently, the CIE 1931 chromaticity diagrams and peak signal-to-noise ratio analysis provided numerical evidence of the AI models' effectiveness in image reconstruction. Furthermore, the AI models can still repair the image without blue information. Overall, the integration of metalens and artificial intelligence models marks a breakthrough in enhancing the performance of full-color metalens-based imaging systems.

High-fat diet induces C-reactive protein secretion, promoting lung adenocarcinoma via immune microenvironment modulation

To understand the effects of a high-fat diet (HFD) on lung cancer progression and biomarkers, we here used an inducible mutant epidermal growth factor receptor (EGFR)-driven lung cancer transgenic mouse model fed a regular diet (RD) or HFD. The HFD lung cancer (LC-HFD) group exhibited significant tumor formation and deterioration, such as higher EGFR activity and proliferation marker expression, compared with the RD lung cancer (LC-RD) group. Transcriptomic analysis of the lung tissues revealed that the significantly changed genes in the LC-HFD group were highly enriched in immune-related signaling pathways, suggesting that an HFD alters the immune microenvironment to promote tumor growth. Cytokine and adipokine arrays combined with a comprehensive analysis using meta-database software indicated upregulation of C-reactive protein (CRP) in the LC-HFD group, which presented with increased lung cancer proliferation and metastasis; this was confirmed experimentally. Our results imply that an HFD can turn the tumor growth environment into an immune-related pro-tumorigenic microenvironment and demonstrate that CRP has a role in promoting lung cancer development in this microenvironment.

Rail Corrugation Index Development by Sound-Field Excitation on the Carriage Floor of In-Service Train

The steel rail and wheel in the railway system offer a high precision and smooth-running surface. Nevertheless, the point of contact between the rail and wheel presents a critical area that can give rise to rail corrugation. This phenomenon can potentially elevate sound and vibration levels in the vicinity considerably, necessitating advanced monitoring and assessment measures. Recently, many efforts have been directed towards utilizing in-service trains for evaluating rail corrugation, and the evaluation has primarily relied on axle-box acceleration (ABA). However, the ABA measurements require a higher threshold for vibration detection. This study introduces a novel approach to rail corrugation detection by carriage floor acceleration (CFA), aimed at lowering the detection threshold. The method capitalizes on the acceleration data sensed on the carriage floor, which is induced by the sound pressure (e.g., sound-field excitation) generated at the wheel-rail contact point. An exploration of the correlation between these datasets is undertaken by simultaneously measuring both ABA and CFA. Moreover, a pivotal aspect of this research is the development of the eigenfrequency rail corrugation index (E-RCI), a mechanism that culminates energy around specific eigenfrequencies by CFA. Through this index, a focused analysis of rail corrugation patterns is facilitated. The study further delves into the stability, repeatability, and sensitivity of the E-RCI via varied measurement scenarios. Ultimately, the CFA-based rail corrugation identification is verified, establishing its practical applicability and offering a distinct approach to detecting and characterizing rail corrugation phenomena. This study has introduced an innovative methodology for rail corrugation detection using CFA, with the principal objective of lowering the detection threshold. This approach offers an efficient measurement technique for identifying rail corrugation areas, thereby potentially reducing maintenance costs and enhancing efficiency within the railway industry.

LCRMP-1 is required for spermatogenesis and stabilises spermatid F-actin organization via the PI3K-Akt pathway

Long-form collapsin response mediator protein-1 (LCRMP-1) belongs to the CRMP family which comprises brain-enriched proteins responsible for axon guidance. However, its role in spermatogenesis remains unclear. Here we find that LCRMP-1 is abundantly expressed in the testis. To characterize its physiological function, we generate LCRMP-1-deficient mice (Lcrmp-1^-/-). These mice exhibit aberrant spermiation with apoptotic spermatids, oligospermia, and accumulation of immature testicular cells, contributing to reduced fertility. In the seminiferous epithelial cycle, LCRMP-1 expression pattern varies in a stage-dependent manner. LCRMP-1 is highly expressed in spermatids during spermatogenesis and especially localized to the spermiation machinery during spermiation. Mechanistically, LCRMP-1 deficiency causes disorganized F-actin due to unbalanced signaling of F-actin dynamics through upregulated PI3K-Akt-mTOR signaling. In conclusion, LCRMP-1 maintains spermatogenesis homeostasis by modulating cytoskeleton remodeling for spermatozoa release.

Design and implementation of a Si3N4 three-stigmatic-point arrayed waveguide grating with a resolving power over 17,000

To provide a solution to the issue of the non-flat focal surface in traditional Rowland AWGs, we have designed and implemented a Si₃N₄ three-stigmatic-point arrayed waveguide grating (TSP AWG) with three inputs, and a spectral resolving power over 17,000 has been achieved experimentally. The flat focal surface of this AWG can accommodate a butt-coupled detector array positioned at the output facet without any reduction of the resolving power of the edge channels. Therefore, it is particularly advantageous to some astronomical applications which require an AWG as a light-dispersing component to obtain a complete 2D spectrum. As a proof-of-concept for next generation devices, the multi-input aspect of the design accommodates multiple single-mode fibers coming into the AWG. In addition, because the device is implemented on a high-index-contrast platform (Si₃N₄/SiO₂), a compact size of ∼9.3 × 9.3 mm² is achieved.

Suppression of wetting transition on evaporative fakir droplets by using slippery superhydrophobic surfaces with low depinning force

This study experimentally investigated the evaporation and wetting transition behavior of fakir droplets on five different microstructured surfaces. Diamond-like carbon was introduced as the substrate, and the influence of varying the width, height, and pitch of the micropillars was assessed. The experimental results showed that the interfacial properties of the surfaces change the evaporation behavior and the starting point of the wetting transition. An important result of this study is the demonstration of a slippery superhydrophobic surface with low depinning force that suppresses the transition from the Cassie-Baxter state to the Wenzel state for microdroplets less than 0.37 mm in diameter, without employing large pillar height or multiscale roughness. By selecting an appropriate pillar pitch and employing tapered micropillars with small pillar widths, the solid-liquid contact at the three-phase contact line was reduced and low depinning forces were obtained. The underlying mechanism by which slippery superhydrophobic surfaces suppress wetting transitions is also discussed. The accuracy of the theoretical models for predicting the critical transition parameters was assessed, and a numerical model was developed in the surface evolver to compute the penetration of the droplet bottom meniscus within the micropillars.

Identification of Ndfip1 as a novel negative regulator for spatial memory formation associated with increased ubiquitination of Beclin 1 and PTEN

Long-term memory formation requires de novo RNA and protein synthesis. By using the differential display-polymerase chain reaction strategy, we have presently identified the Nedd4 family interacting protein 1 (Ndfip1) cDNA fragment that is differentially expressed between the slow learners and the fast learners from the water maze learning task in rats. Further, the fast learners show decreased Ndfip1 mRNA and protein expression levels than the slow learners. Spatial training similarly decreases the Ndfip1 mRNA and protein expression levels. Conversely, the Ndfip1 conditional heterozygous (cHet) mice show enhanced spatial memory performance compared to the Ndfip1flox/WT control mice. Result from co-immunoprecipitation experiment indicates that spatial training decreases the association between Ndfip1 and the E3 ubiquitin ligase Nedd4 (Nedd4-1), and we have shown that both Beclin 1 and PTEN are endogenous ubiquitination targets of Nedd4 in the hippocampus. Further, spatial training decreases endogenous Beclin 1 and PTEN ubiquitination, and increases Beclin 1 and PTEN expression in the hippocampus. On the other hand, the Becn1 conditional knockout (cKO) mice and the Pten cKO mice both show impaired spatial learning and memory performance. Moreover, the expression level of Beclin 1 and PTEN is higher in the Ndfip1 cHet mice compared with the Ndfip1flox/WT control mice. Here, we have identified Ndfip1 as a candidate novel negative regulation for spatial memory formation and this is associated with increased ubiquitination of Beclin 1 and PTEN in the hippocampus.

Selenocystine induces oxidative-mediated DNA damage via impairing homologous recombination repair of DNA double-strand breaks in human hepatoma cells

Selenocystine (SeC) has been identified as a novel compound with broad-spectrum anticancer activity. However, the effects of SeC on modifying DNA repair mechanism were less addressed. In this study, we demonstrated that SeC selectively induced cytotoxicity and genotoxicity against HepG2 hepatoma cell line. Comet assay revealed SeC-induced DNA damage in HepG2 cells, particularly in the form of DNA double strand breaks (DSBs), corroborated by the increase expression of the DSB marker, gamma-H2AX. We further demonstrated that SeC suppressed DNA homologous recombination repair, exacerbating DNA damage accumulation. Such effects on DNA damage and cell viability inhibition were alleviated by antioxidants, glutathione and Trolox, suggesting the involvement of reactive oxygen species (ROS). High levels of intracellular and mitochondrial ROS were detected in SeC-treated HepG2. In addition, SeC impaired the expression of antioxidant enzymes (superoxidase mutases and catalase), prompting the imbalance between antioxidant protection and excessive ROS formation and eliciting DSBs and cellular death. Decreased procaspase-3, 7, and 9 and Bcl-2 proteins and an increased Bax/Bcl-2 ratio, were observed after SeC treatment, but could be reversed by Torlox, confirming the action of SeC on ROS-induced apoptosis. In vivo, the xenograft tumor model of HepG2 cells validated the inhibition of SeC on tumor growth, and the induction of DSBs and apoptosis. In summary, SeC has the capability to induce ROS-dependent DNA damage and impeded DBS repair in HepG2 cells. Thus, SeC holds great promise as a therapeutic or adjuvant agent targeting DNA repair for cancer treatment.

Review of Metasurfaces and Metadevices: Advantages of Different Materials and Fabrications

Flat optics, metasurfaces, metalenses, and related materials promise novel on-demand light modulation within ultrathin layers at wavelength scale, enabling a plethora of next-generation optical devices, also known as metadevices. Metadevices designed with different materials have been proposed and demonstrated for different applications, and the mass production of metadevices is necessary for metadevices to enter the consumer electronics market. However, metadevice manufacturing processes are mainly based on electron beam lithography, which exhibits low productivity and high costs for mass production. Therefore, processes compatible with standard complementary metal–oxide–semiconductor manufacturing techniques that feature high productivity, such as i-line stepper and nanoimprint lithography, have received considerable attention. This paper provides a review of current metasurfaces and metadevices with a focus on materials and manufacturing processes. We also provide an analysis of the relationship between the aspect ratio and efficiency of different materials.

Review of component designs for post-COVID-19 HVAC systems: Possibilities and challenges

The globally occurring recurrent waves of the COVID-19 pandemic, primarily caused by the transmission of aerosolized droplets from an infected person to a healthy person in the indoor environment, has led to the urgency of designing new modes of indoor ventilation. To prevent cross-contaminations due to airborne viruses, bacteria, and other pollutants in indoor environments, heating ventilation and air-conditioning (HVAC) systems need to be redesigned with anti-pandemic components. The three vital anti-pandemic components for the post-COVID-19 HVAC systems, as identified by the authors, are: a biological contaminant inactivation unit, a volatile organic compound decomposition unit, and an advanced air filtration unit. The purpose of the current article is to provide an overview of the latest research outcomes toward designing these anti-pandemic components and pointing out the future promises and challenges. In addition, the role of personalized ventilation in minimizing the risk of indoor cross-contamination by employing various air terminal devices is discussed. The authors believe that this article will encourage HVAC designers to develop effective anti-pandemic components to minimize the indoor airborne transmission.

Evaluation of gas permeability in porous separators for polymer electrolyte fuel cells: Computational fluid dynamics simulation based on micro-x-ray computed tomography images

Pore structures and gas transport properties in porous separators for polymer electrolyte fuel cells are evaluated both experimentally and through simulations. In the experiments, the gas permeabilities of two porous samples, a conventional sample and one with low electrical resistivity, are measured by a capillary flow porometer, and the pore size distributions are evaluated with mercury porosimetry. Local pore structures are directly observed with micro-x-ray computed tomography (CT). In the simulations, the effective diffusion coefficients of oxygen and the air permeability in porous samples are calculated using random walk Monte Carlo simulations and computational fluid dynamics (CFD) simulations, respectively, based on the x-ray CT images. The calculated porosities and air permeabilities of the porous samples are in good agreement with the experimental values. The simulation results also show that the in-plane permeability is twice the through-plane permeability in the conventional sample, whereas it is slightly higher in the low-resistivity sample. The results of this study show that CFD simulation based on micro-x-ray CT images makes it possible to evaluate anisotropic gas permeabilities in anisotropic porous media.

Investigation of entrance effects on particle electrophoretic behavior near a nanopore for resistive pulse sensing

Resistive pulse sensing using solid-state nanopores provides a unique platform for detecting the structure and concentration of molecules of different types of analytes in an electrolyte solution. The capture of an entity into a nanopore is subject not only to the electrostatic force but also the effect of electroosmotic flow originating from the charged nanopore surface. In this study, we theoretically analyze spherical particle electrophoretic behavior near the entrance of a charged nanopore. By investigating the effects of pore size, particle-pore distance, and salt concentration on particle velocity, we summarize dominant mechanisms governing particle behavior for a range of conditions. In the literature, the Helmholtz-Smoluchowski equation is often adopted to evaluate particle translocation by considering the zeta potential difference between the particle and nanopore surfaces. We point out that, due to the difference of the electric field inside and outside the nanopore and the influence from the existence of the particle itself, the zeta potential of the particle, however, needs to be at least 30% higher than that of the nanopore to allow the particle to enter into the nanopore when its velocity is close to zero. Accordingly, we summarize the effective salt concentrations that enable successful particle capture and detection for different pore sizes, offering direct guidance for nanopore applications.

Molecular dynamics study of water confined in MIL-101 metal-organic frameworks

Molecular dynamics simulations of water adsorbed in Material Institute Lavoisier MIL-101(Cr) metal-organic frameworks are performed to analyze the kinetic properties of water molecules confined in the framework at 298.15 K and under different vapor pressures and clarify the water adsorption mechanism in MIL-101(Cr). The terahertz frequency-domain spectra (THz-FDS) of water are calculated by applying fast Fourier transform to the configurational data of water molecules. According to the characteristic frequencies in the THz-FDS, the dominant motions of water molecules in MIL-101(Cr) can be categorized into three types: (1) low-frequency translational motion (0-0.5 THz), (2) medium-frequency vibrational motion (2-2.5 THz), and (3) high-frequency vibrational motion (>6 THz). Each type of water motion is confirmed by visualizing the water configuration in MIL-101(Cr). The ratio of the number of water molecules with low-frequency translational motion to the total number of water molecules increases with the increase in vapor pressure. In contrast, that with medium-frequency vibrational motion is found to decrease with vapor pressure, exhibiting a pronounced decrease after water condensation has started in the cavities. That with the high-frequency vibrational motion is almost independent of the vapor pressure. The interactions between different types of water molecules affect the THz-FDS. Furthermore, the self-diffusion coefficient and the velocity auto-correlation function are calculated to clarify the adsorption state of the water confined in MIL-101(Cr). To confirm that the general trend of the THz-FDS does not depend on the water model, the simulations are performed using three water models, namely, rigid SPC/E, flexible SPC/E, and rigid TIP5PEw.

Nanoconfined Electrochemical Sensing of Single Silver Nanoparticles with a Wireless Nanopore Electrode

Single entity electrochemistry (SEE) has emerged as a promising method for precise measurement and fundamental understanding of the heterogeneity of single entities. Herein, we propose the dual responsive SEE sensing of the silver nanoparticles (AgNPs) collisions through a wireless nanopore electrode (WNE). Given the high temporal resolution and low background noise features, the Faradaic and capacitive currents provide the AgNPs' collision response. The electron transfer between the AgNPs and the electrode surface is identified under a bipolar electrochemical mechanism. Compared to the ultramicroelectrode, multistep oxidation of 30 nm AgNPs is observed due to the decreased interaction of the nanoparticles to the electrode. Moreover, the nanoconfinement of WNE plays a vital role in the repeated capturing of nanoparticles from the nontunneling region into the tunneling region until a complete oxidation. As a comparison, the collision of 5 nm AgNPs with higher interaction at the electrode surface shows great decrease in the multistep events. Thus, we propose a nanoconfined interaction based SEE method which could be used for simultaneously capturing the Faradaic and capacitive response. The nanoconfined interaction based SEE method holds great promise in the better understanding of heterogeneity of single particles.

Electroosmotic flow: From microfluidics to nanofluidics

Electroosmotic flow (EOF), a consequence of an imposed electric field onto an electrolyte solution in the tangential direction of a charged surface, has emerged as an important phenomenon in electrokinetic transport at the micro/nanoscale. Because of their ability to efficiently pump liquids in miniaturized systems without incorporating any mechanical parts, electroosmotic methods for fluid pumping have been adopted in versatile applications—from biotechnology to environmental science. To understand the electrokinetic pumping mechanism, it is crucial to identify the role of an ionically polarized layer, the so‐called electrical double layer (EDL), which forms in the vicinity of a charged solid–liquid interface, as well as the characteristic length scale of the conducting media. Therefore, in this tutorial review, we summarize the development of electrical double layer models from a historical point of view to elucidate the interplay and configuration of water molecules and ions in the vicinity of a solid–liquid interface. Moreover, we discuss the physicochemical phenomena owing to the interaction of electrical double layer when the characteristic length of the conducting media is decreased from the microscale to the nanoscale. Finally, we highlight the pioneering studies and the most recent works on electro osmotic flow devoted to both theoretical and experimental aspects.

Joule Heating Effects on Transport-Induced-Charge Phenomena in an Ultrathin Nanopore

Transport-induced-charge (TIC) phenomena, in which the concentration imbalance between cations and anions occurs when more than two chemical potential gradients coexist within an ultrathin dimension, entail numerous nanofluidic systems. Evidence has indicated that the presence of TIC produces a nonlinear response of electroosmotic flow to the applied voltage, resulting in complex fluid behavior. In this study, we theoretically investigate thermal effects due to Joule heating on TIC phenomena in an ultrathin nanopore by computational fluid dynamics simulation. Our modeling results show that the rise of local temperature inside the nanopore significantly enhances TIC effects and thus has a significant influence on electroosmotic behavior. A local maximum of the solution conductivity occurs near the entrance of the nanopore at the high salt concentration end, resulting in a reversal of TIC across the nanopore. The Joule heating effects increase the reversal of TIC with the synergy of the negatively charged nanopore, and they also enhance the electroosmotic flow regardless of whether the nanopore is charged. These theoretical observations will improve our knowledge of nonclassical electrokinetic phenomena for flow control in nanopore systems.

Melatonin Induction of APP Intracellular Domain 50 SUMOylation Alleviates AD through Enhanced Transcriptional Activation and Aβ Degradation

The amyloid precursor protein (APP) intracellular domain (AICD) is implicated in the pathogenesis of Alzheimer’s disease (AD), but post-translational modification of AICD has rarely been studied and its role in AD is unknown. In this study, we examined the role and molecular mechanism of AICD SUMOylation in the pathogenesis of AD. We found that AICD is SUMO-modified by the SUMO E3 ligase protein inhibitor of activated STAT1 (PIAS1) in the hippocampus at Lys-43 predominantly, and that knockdown of PIAS1 decreases endogenous AICD SUMOylation. AICD SUMOylation increases AICD association with its binding protein Fe65 and increases AICD nuclear translocation. Furthermore, AICD SUMOylation increases AICD association with cyclic AMP-responsive element binding protein (CREB) and p65 and their DNA binding for transcriptional activation of neprilysin (NEP) and transthyretin (TTR), two major Aβ-degrading enzymes, respectively. Consequently, AICD SUMOylation decreases the Aβ level, Aβ oligomerization, and amyloid plaque deposits. It also rescues spatial memory deficits in APP/PS1 mice. Conversely, blockade of AICD SUMOylation at Lys-43 produces the opposite effects. Melatonin is identified as an endogenous stimulus that induces AICD SUMOylation. It also decreases the Aβ level and rescues reduction of PIAS1, NEP, and TTR expression in APP/PS1 mice. In this study, we demonstrate that AICD SUMOylation functions as a novel endogenous defense mechanism to combat AD.

Augmenting the Carbon Dioxide Uptake and Selectivity of Metal-Organic Frameworks by Metal Substitution: Molecular Simulations of LMOF-202

Metal organic frameworks (MOFs) are promising porous materials for the adsorption of CO_2. Here, we report the study of a luminescent MOF (LMOF), called LMOF-202. We have employed Grand Canonical Monte Carlo (GCMC) simulations to understand and explain the adsorption phenomena inside LMOF-202, and based on the phenomena happening at the molecular level, we have varied the metal ions in LMOF-202 to increase the CO₂ affinity and selectivity of the material. We show that the CO₂ adsorption capacity and selectivity can be increased by approximately 1.5 times at 1 bar and 298 K by changing the metal ion from Zn to Ba. We also report the feasibility of using this material to capture CO₂ from flue gas under realistic conditions (1 bar and 298 K). This work shows that LMOF-202 merits further consideration as a carbon capture adsorbent.

Dairy cattle with bovine leukaemia virus RNA show significantly increased leukocyte counts

Infection with bovine leukaemia virus (BLV), a retrovirus, causes dysfunction of the immune system and can have a marked economic impact on dairy industries due to decreased milk production and reduced lifespan in affected dairy cattle. The presence of proviral DNA has been the major diagnostic indicator of BLV infection. However in the course of BLV infection, the viral genome can be dormant, without detectable gene expression, resulting in limited impact on infected animals. At present, there is limited knowledge regarding haematological indices in dairy cattle that could indicate activation of the BLV genome and suggest reactivated BLV infection. In this study, BLV infection and BLV genome reactivation were evaluated based on the presence of BLV DNA and BLV env gene transcripts, respectively. BLV RNA transcription was confirmed. Among 93 whole blood samples obtained from asymptomatic dairy cattle, the prevalence of BLV proviral DNA and transcripts was 93.5% (n = 87/93) and 83.9% (n = 78/93), respectively. Between groups with and without BLV, the mean counts of white blood cells and lymphocytes in whole blood were significantly associated with the presence of BLV RNA (P < 0.05), but not with BLV proviral DNA. These results shed light on the activation status of the BLV genome and should be taken into account when evaluating the possible impact of BLV on cattle.

Restoring Wnt6 signaling ameliorates behavioral deficits in MeCP2 T158A mouse model of Rett syndrome

The methyl-CpG-binding protein 2 gene, MECP2, is an X chromosome-linked gene encoding the MeCP2 protein, and mutations of MECP2 cause Rett syndrome (RTT). Previous study has shown that re-expression of SUMO-modified MeCP2 in Mecp2-null neurons rescues synaptic and behavioral deficits in Mecp2 conditional knockout mice, whereas about 12-fold decrease in Wnt6 mRNA level was found in MeCP2K412R sumo-mutant mice. Here, we examined the role of Wnt6 in MeCP2 T158A mouse model of RTT. Results show that lentiviral delivery of Wnt6 to the amygdala ameliorates locomotor impairment and social behavioral deficits in these animals. MeCP2 T158A mice show decreased level of GSK-3β phosphorylation and increased level of β-catenin phosphorylation. They also show reduced level of MeCP2 SUMOylation. These alterations were also restored by lenti-Wnt6 transduction. Further, both BDNF and IGF-1 expressions are decreased in MeCP2 T158A mice. Overexpression of Wnt6 increases Bdnf and Igf-1 promoter activity in HEK293T cells in a dose-dependent manner. Lenti-Wnt6 transduction to the amygdala similarly increases the mRNA level and protein expression of BDNF and IGF-1 in MeCP2 T158A mice. Moreover, environmental enrichment (EE) similarly ameliorates the locomotor and social behavioral deficits in MeCP2 T158A mice. One of the mechanisms underlying EE is mediated through enhanced MeCP2 SUMOylation and increased Wnt6 expression in these animals by EE.

Water Filling and Emptying Kinetics in Two-Dimensional Hexagonal Mesoporous Silica of the Same Pore Diameter but Different Pore Lengths

The effect of pore length on the water filling and emptying rates was studied using mesoporous silica (MPS) with same pore diameter but different pore lengths. The pore diameter of the synthesized MPS was ∼8 nm, whereas the average pore lengths were 460, 1,770, and 4000 nm. The gravimetric method was employed to record the time course of the adsorbed mass of water in MPS at 298 K and 1 atm. In both the filling and emptying processes, the relaxation curves (time course of adsorbed mass of water per unit mass of sample) were not significantly related to the pore length. This independence of the initial adsorption and desorption rates on the pore length suggests that the surface of the MPS aggregates is the bottleneck in the overall adsorption and desorption processes and that the initial mass flux in each nanopore is inversely proportional to the pore length. Furthermore, because the relaxation times to reach the equilibrium state were independent of the pore length, the mass flux of water uptake, release, and transport probably increase with an increase in the pore length during the entire adsorption and desorption processes. A transport model to describe these phenomena was proposed.

Galectin-3 promotes Aβ oligomerization and Aβ toxicity in a mouse model of Alzheimer's disease

Amyloid-β (Aβ) oligomers largely initiate the cascade underlying the pathology of Alzheimer's disease (AD). Galectin-3 (Gal-3), which is a member of the galectin protein family, promotes inflammatory responses and enhances the homotypic aggregation of cancer cells. Here, we examined the role and action mechanism of Gal-3 in Aβ oligomerization and Aβ toxicities. Wild-type (WT) and Gal-3-knockout (KO) mice, APP/PS1;WT mice, APP/PS1;Gal-3^+/- mice and brain tissues from normal subjects and AD patients were used. We found that Aβ oligomerization is reduced in Gal-3 KO mice injected with Aβ, whereas overexpression of Gal-3 enhances Aβ oligomerization in the hippocampi of Aβ-injected mice. Gal-3 expression shows an age-dependent increase that parallels endogenous Aβ oligomerization in APP/PS1 mice. Moreover, Aβ oligomerization, Iba1 expression, GFAP expression and amyloid plaque accumulation are reduced in APP/PS1;Gal-3^+/- mice compared with APP/PS1;WT mice. APP/PS1;Gal-3^+/- mice also show better acquisition and retention performance compared to APP/PS1;WT mice. In studying the mechanism underlying Gal-3-promoted Aβ oligomerization, we found that Gal-3 primarily co-localizes with Iba1, and that microglia-secreted Gal-3 directly interacts with Aβ. Gal-3 also interacts with triggering receptor expressed on myeloid cells-2, which then mediates the ability of Gal-3 to activate microglia for further Gal-3 expression. Immunohistochemical analyses show that the distribution of Gal-3 overlaps with that of endogenous Aβ in APP/PS1 mice and partially overlaps with that of amyloid plaque. Moreover, the expression of the Aβ-degrading enzyme, neprilysin, is increased in Gal-3 KO mice and this is associated with enhanced integrin-mediated signaling. Consistently, Gal-3 expression is also increased in the frontal lobe of AD patients, in parallel with Aβ oligomerization. Because Gal-3 expression is dramatically increased as early as 3 months of age in APP/PS1 mice and anti-Aβ oligomerization is believed to protect against Aβ toxicity, Gal-3 could be considered a novel therapeutic target in efforts to combat AD.

Protein inhibitor of activated STAT1 Ser503 phosphorylation-mediated Elk-1 SUMOylation promotes neuronal survival in APP/PS1 mice

BACKGROUND AND PURPOSE

Protein inhibitor of activated STAT1 (PIAS1) is phosphorylated by IKKα at Ser⁹⁰ in a PIAS1 E3 ligase activity-dependent manner. Whether PIAS1 is also phosphorylated at other residues and the functional significance of these additional phosphorylation events are not known. The transcription factor Elk-1 remains SUMOylated under basal conditions, but the role of Elk-1 SUMOylation in brain is unknown. Here, we examined the functional significance of PIAS1-mediated Elk-1 SUMOylation in Alzheimer's disease (AD) using the APP/PS1 mouse model of AD and amyloid β (Aβ) microinjections in vivo.

EXPERIMENTAL APPROACH

Novel phosphorylation site(s) on PIAS1 were identified by LC-MS/MS, and MAPK/ERK-mediated phosphorylation of Elk-1 demonstrated using in vitro kinase assays. Elk-1 SUMOylation by PIAS1 in brain was determined using in vitro SUMOylation assays. Apoptosis in hippocampus was assessed by measuring GADD45α expression by western blotting, and apoptosis of hippocampal neurons in APP/PS1 mice was assessed by TUNEL assay.

KEY RESULTS

Using LC-MS/MS, we identified a novel MAPK/ERK-mediated phosphorylation site on PIAS1 at Ser⁵⁰³ and showed this phosphorylation determines PIAS1 E3 ligase activity. In rat brain, Elk-1 was SUMOylated by PIAS1, which decreased Elk-1 phosphorylation and down-regulated GADD45α expression. Moreover, lentiviral-mediated transduction of Elk-1-SUMO1 reduced the number of hippocampal apoptotic neurons in APP/PS1 mice.

CONCLUSIONS AND IMPLICATIONS

MAPK/ERK-mediated phosphorylation of PIAS1 at Ser⁵⁰³ determines PIAS1 E3 ligase activity. Moreover, PIAS1 mediates SUMOylation of Elk-1, which functions as an endogenous defence mechanism against Aβ toxicity in vivo. Targeting Elk-1 SUMOylation could be considered a novel therapeutic strategy against AD.

Thermodynamic Stability Analysis of Microbubbles Confined in a Liquid Droplet

A thermodynamic stability analysis of microbubbles in an enclosed volume of a volatile liquid-noncondensable gas solution was performed. The stability conditions for the formation of the bubbles and the relationship between the equilibrium bubble radius and the equilibrium bubble number were investigated. The calculation results show that even if the saturation vapor pressure of a volatile liquid is higher than the pressure of the liquid phase, stable noncondensable gas bubbles appear in a closed system. Under such a condition, if the initial pressure of the noncondensable gas, which is proportional to the total number of moles of a noncondensable gas in the system, increases, stable bubbles appear at a lower temperature. At a fixed parameter of h₀, which is defined as the ratio of the saturation vapor pressure of the volatile liquid minus the pressure in the liquid phase to the initial pressure of the noncondensable gas, the equilibrium bubble radius increases with a decrease of the equilibrium bubble number.

Theory of Transport-Induced-Charge Electroosmotic Pumping toward Alternating Current Resistive Pulse Sensing

In this work, we study transport-induced-charge electroosmosis toward alternating current resistive pulse sensing for the next generation of biomedical applications. Transport-induced-charge electroosmosis, being a new class of electrokinetic phenomenon, occurs as a salt concentration gradient works in synergy with an electric field in ultrathin nanopores. Apart from the conventional electric double layer-governed electroosmotic flow in which the flow behavior is subject to the surface charge, it is found that the transport-induced-charge electroosmotic flow behaves independently of surface charge magnitude but can be linearly regulated by the bulk salt concentration bias. The reversal of the electric field simultaneously inverses the induced charge allowing the establishment of a unidirectional flow under the application of a periodic alternating current field. This unique phenomenon permits continuous water and nanoparticles pumping through a two-dimensional material nanopore in spite of the reversal of the electric field. Built upon this mechanism, we propose a theoretical prototype of alternating current resistive pulse sensing in a two-dimensional nanopore system.

Molecular simulations of water adsorption and transport in mesopores with varying hydrophilicity arrangements

The adsorption and transport of water in an open cylindrical mesopore with two different inner surface arrangements of hydrophilicities were examined by molecular simulations. The first model has a weak hydrophilic surface at both entrances of the pore and a stronger hydrophilic surface in the mid-section. The second pore has stronger hydrophilic surfaces at the entrances and weaker in the middle region. The simulation results show that the water adsorption isotherms obtained from Grand Canonical Monte Carlo simulations and pore filling curves acquired from Grand Canonical Molecular Dynamics simulations change depending on the arrangement of the strong and weak hydrophilic surfaces. In the first model, water condensation focuses on the mid-section forming a liquid bridge or a film, which creates a concave meniscus accelerating subsequent adsorption within the pore. Two bridges form in the entrance regions, where a cavity naturally occurs in between the films, in the second model. The different filling and emptying mechanisms clearly change the adsorption-desorption characteristics for the two pore types, but the second type generally showed faster transitions overall. Flux and meniscus analysis also reveals a circulating flow at the menisci of the interfaces within the pore. The results are expected to be valuable in understanding the effects of interior surface modification of nanopores in future applications.

Effect of lower-energy, higher-fiber diets on pigs divergently selected for residual feed intake when fed higher-energy, lower-fiber diets

Residual feed intake (RFI) is the difference between observed and predicted feed intake of an animal, based on growth and maintenance requirements. In Yorkshire pigs, divergent selection for increased (Low RFI) and decreased (High RFI) RFI was carried out over 10 generations (G) while feeding a corn- and soybean-meal-based, higher-energy, lower-fiber (HELF) diet. In G8 to G10, representing 4 replicates, barrows and gilts (n = 649) of the RFI lines were fed the HELF diet and a diet incorporating coproducts that were lower in energy and higher in dietary fiber (LEHF). The diets differed in ME, 3.32 vs. 2.87 Mcal/kg, and in neutral detergent fiber (NDF), 9.4% vs. 25.9%, respectively. The impact of the LEHF diet on 1) performance and growth, 2) diet digestibility, 3) genetic parameter estimates, and 4) responses to selection for RFI, when fed the HELF, was assessed. In general, the LEHF diet reduced the performance of both lines. When fed the HELF diet, the Low RFI pigs had lower (P < 0.05) ADFI (-12%), energy intake (-12%), ADG (-6%), and backfat depth (-12%); similar (P > 0.05) loin muscle area (LMA; +5%); and greater (P < 0.05) feed efficiency (i.e., 8% higher G:F and 7% lower RFI) than the High RFI line. These patterns of line differences were still present under the LEHF diet but differences for ADFI (-11%), energy intake (-10%), G:F (+2%), and RFI (-6%) were reduced compared to the HELF diet. Apparent total tract digestibility (ATTD) of the HELF and LEHF diets was assessed using 116 barrows and gilts from G8. When fed the HELF diet, ATTD of DM, GE, N, and NDF were similar between lines (P ≥ 0.27), but when fed the LEHF diet, the Low RFI pigs had greater digestibility (7%, 7%, 10%, and 32%) than the High RFI line (P ≤ 0.04). To measure responses to selection for RFI and estimate genetic parameters, data from all 10 generations were used (HELF; n = 2,310; LEHF, n = 317). Heritability estimates of performance traits ranged from 0.19 to 0.63, and genetic correlations of traits between diets were high and positive, ranging from 0.87 (RFI) to 0.99 (LMA). By G10, RFI in the Low RFI line was 3.86 and 1.50 genetic SD lower than in the High RFI line when fed the HELF and LEHF diets, respectively. Taken together, the results of this study demonstrate that responses to selection for RFI when fed a HELF diet are not fully realized when pigs are fed an extremely LEHF diet. Thus, feeding diets that differ from those used for selection may not maximize genetic potential for feed efficiency.

Trapping Structural Coloration by a Bioinspired Gyroid Microstructure in Solid State

In theory, gyroid photonic crystals in butterfly wings exhibit advanced optical properties as a result of their highly interconnected microstructures. Because of the difficulties in synthesizing artificial gyroid materials having periodicity corresponding to visible wavelengths, human-made visible gyroid photonic crystals are still unachievable by self-assembly. In this study, we develop a physical approach-trapping of structural coloration (TOSC)-through which the visible structural coloration of an expanded gyroid lattice in a solvated state can be preserved in the solid state, thereby allowing the fabrication of visible-wavelength gyroid photonic crystals. Through control over the diffusivity and diffusive distance for solvent evaporation, the single-molecular-weight gyroid block copolymer photonic crystal can exhibit desired structural coloration in the solid state without the need to introduce any additives, namely, evapochromism. Also, greatly enhanced reflectivity is observed arising from the formation of porous gyroid nanochannels, similar to those in butterfly wings. As a result, TOSC facilitates the fabrication of the human-made solid gyroid photonic crystal featuring tunable and switchable structural coloration without the synthesis to alter the molecular weight. It appears to be applicable in the fields of optical communication, energy, light-emission, sensors, and displays.

Thermal dependence of nanofluidic energy conversion by reverse electrodialysis

The thermal dependence of salinity-gradient-driven energy conversion by reverse electrodialysis using a mesoporous silica thin film with pores ca. 2-3 nm in diameter was studied in a temperature range of 293-333 K. As the temperature increases, the surface charge density of mesopores increases owing to an increase in the zeta potential of the pore walls, which in turn increases the concentration of counter-ions in the electrical double layer. The ion mobility also increases with increasing temperature owing to a decrease in the liquid viscosity. As a result, the temperature increase improves the ion conductance of mesopores both in the surface-charge-governed regime at low ion concentrations and in the bulk regime at high ion concentrations. However, further increases in temperature induce bubble nucleation. In particular, in highly concentrated salt solutions, hydrophobic patches appear on the pore surfaces because of the salting-out effect and mask the surface charge. The weakened polarity in mesopores allows more co-ions to enter them, decreasing the potential difference across the film, resulting in a serious deterioration of the energy conversion efficiency. The thermal dependence of the performance characteristics of mesoporous-silica-based nanofluidic devices was also evaluated.

Galectin-3 Negatively Regulates Hippocampus-Dependent Memory Formation through Inhibition of Integrin Signaling and Galectin-3 Phosphorylation

Galectin-3, a member of the galectin protein family, has been found to regulate cell proliferation, inhibit apoptosis and promote inflammatory responses. Galectin-3 is also expressed in the adult rat hippocampus, but its role in learning and memory function is not known. Here, we found that contextual fear-conditioning training, spatial training or injection of NMDA into the rat CA1 area each dramatically decreased the level of endogenous galectin-3 expression. Overexpression of galectin-3 impaired fear memory, whereas galectin-3 knockout (KO) enhanced fear retention, spatial memory and hippocampal long-term potentiation. Galectin-3 was further found to associate with integrin α3, an association that was decreased after fear-conditioning training. Transfection of the rat CA1 area with small interfering RNA against galectin-3 facilitated fear memory and increased phosphorylated focal adhesion kinase (FAK) levels, effects that were blocked by co-transfection of the FAK phosphorylation-defective mutant Flag-FAKY397F. Notably, levels of serine-phosphorylated galectin-3 were decreased by fear conditioning training. In addition, blockade of galectin-3 phosphorylation at Ser-6 facilitated fear memory, whereas constitutive activation of galectin-3 at Ser-6 impaired fear memory. Interestingly galectin-1 plays a role in fear-memory formation similar to that of galectin-3. Collectively, our data provide the first demonstration that galectin-3 is a novel negative regulator of memory formation that exerts its effects through both extracellular and intracellular mechanisms.

Manipulation of Protein Translocation through Nanopores by Flow Field Control and Application to Nanopore Sensors

The control of biomolecule translocation through nanopores is important in nanopore protein detection. Improvement in current nanopore molecule control is desired to enhance capture rates, extend translocation times, and ensure the effective detection of various proteins in the same solutions. We present a method that simultaneously resolves these issues through the use of a gate-modulated conical nanopore coupled with solutions of varying salt concentration. Simulation results show that the presence of an induced reverse electroosmotic flow (IREOF) results in inlet flows from the two ends of the nanopore centerline entering into the nanopore in opposite directions, which simultaneously elevates the capture rate and immobilizes the protein in the nanopore, thus enabling steady current blockage measurements for a range of proteins. In addition, it is shown that proteins with different size/charge ratios can be trapped by a gate modulation intensified flow field at a similar location in the nanopore in the same solution conditions.

Electrokinetics of the silica and aqueous electrolyte solution interface: Viscoelectric effects

The manipulation of biomolecules, fluid and ionic current in a new breed of integrated nanofluidic devices requires a quantitative understanding of electrokinetics at the silica/water interface. The conventional capacitor-based electrokinetic Electric Double Layer (EDL) models for this interface have some known shortcomings, as evidenced by a lack of consistency within the literature for the (i) equilibrium constants of surface silanol groups, (ii) Stern layer capacitance, (iii) zeta (ζ) potential measured by various electrokinetic methods, and (iv) surface conductivity. In this study, we consider how the experimentally observable viscoelectric effect - that is, the increase of the local viscosity due to the polarisation of polar solvents - affects electrokinetcs at the silica/water interface. Specifically we consider how a model that considers viscoelectric effects (the VE model) performs against two conventional electrokinetic models, namely the Gouy-Chapman (GC) and Basic Stern capacitance (BS) models, in predicting four fundamental electrokinetic phenomena: electrophoresis, electroosmosis, streaming current and streaming potential. It is found that at moderate to high salt concentrations (>5×10(-3)M) predictions from the VE model are in quantitative agreement with experimental electrokinetic measurements when the sole additional adjustable parameter, the viscoelectric coefficient, is set equal to a value given by a previous independent measurement. In contrast neither the GS nor BS models is able to reproduce all experimental data over the same concentration range using a single, robust set of parameters. Significantly, we also show that the streaming current and potential in the moderate to high surface charge range are insensitive to surface charge behaviour (including capacitances) when viscoelectric effects are considered, in difference to models that do not consider these effects. This strongly questions the validity of using pressure based electrokinetic experiments to measure surface charge characteristics within this experimentally relevant high pH and moderate to high salt concentration range. At low salt concentrations (<5×10(-3)M) we find that there is a lack of consistency in previously measured channel conductivities conducted under similar solution conditions (pH, salt concentration), preventing a conclusive assessment of any model suitability in this regime.

Control of the Metal-Insulator Transition at Complex Oxide Heterointerfaces through Visible Light

The coupling of the localized surface plasmon resonance of Au nanoparticles is utilized to deliver a visible-light stimulus to control conduction at the LaAlO3 /SrTiO3 interface. A giant photoresponse and the controllable metal-insulator transition are characterized at this heterointerface. This study paves a new route to optical control of the functionality at the heterointerfaces.

Glutamate Stimulates Local Protein Synthesis in the Axons of Rat Cortical Neurons by Activating α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors and Metabotropic Glutamate Receptors

Glutamate is the principal excitatory neurotransmitter in the mammalian CNS. By analyzing the metabolic incorporation of azidohomoalanine, a methionine analogue, in newly synthesized proteins, we find that glutamate treatments up-regulate protein translation not only in intact rat cortical neurons in culture but also in the axons emitting from cortical neurons before making synapses with target cells. The process by which glutamate stimulates local translation in axons begins with the binding of glutamate to the ionotropic AMPA receptors and metabotropic glutamate receptor 1 and members of group 2 metabotropic glutamate receptors on the plasma membrane. Subsequently, the activated mammalian target of rapamycin (mTOR) signaling pathway and the rise in Ca(2+), resulting from Ca(2+) influxes through calcium-permeable AMPA receptors, voltage-gated Ca(2+) channels, and transient receptor potential canonical channels, in axons stimulate the local translation machinery. For comparison, the enhancement effects of brain-derived neurotrophic factor (BDNF) on the local protein synthesis in cortical axons were also studied. The results indicate that Ca(2+) influxes via transient receptor potential canonical channels and activated the mTOR pathway in axons also mediate BDNF stimulation to local protein synthesis. However, glutamate- and BDNF-induced enhancements of translation in axons exhibit different kinetics. Moreover, Ca(2+) and mTOR signaling appear to play roles carrying different weights, respectively, in transducing glutamate- and BDNF-induced enhancements of axonal translation. Thus, our results indicate that exposure to transient increases of glutamate and more lasting increases of BDNF would stimulate local protein synthesis in migrating axons en route to their targets in the developing brain.

Vertical split-ring resonator based anomalous beam steering with high extinction ratio

Metasurfaces created artificially with metal nanostructures that are patterned on surfaces of different media have shown to possess “unusual” abilities to manipulate light. Limited by nanofabrication difficulties, so far most reported works have been based on 2D metal structures. We have recently developed an advanced e-beam process that allowed for the deposition of 3D nanostructures, namely vertical split-ring resonators (VSRRs), which opens up another degree of freedom in the metasurface design. Here we explore the functionality of beam steering with phase modulation by tuning only the vertical dimension of the VSRRs and show that anomalous steering reflection of a wide range of angles can be accomplished with high extinction ratio using the finite-difference-time-domain simulation. We also demonstrate that metasurfaces made of 3D VSRRs can be made with roughly half of the footprint compared to that of 2D nano-rods, enabling high density integration of metal nanostructures.

Plasmon coupling in vertical split-ring resonator metamolecules

The past decade has seen a number of interesting designs proposed and implemented to generate artificial magnetism at optical frequencies using plasmonic metamaterials, but owing to the planar configurations of typically fabricated metamolecules that make up the metamaterials, the magnetic response is mainly driven by the electric field of the incident electromagnetic wave. We recently fabricated vertical split-ring resonators (VSRRs) which behave as magnetic metamolecules sensitive to both incident electric and magnetic fields with stronger induced magnetic dipole moment upon excitation in comparison to planar SRRs. The fabrication technique enabled us to study the plasmon coupling between VSRRs that stand up side by side where the coupling strength can be precisely controlled by varying the gap in between. The resulting wide tuning range of these resonance modes offers the possibility of developing frequency selective functional devices such as sensors and filters based on plasmon coupling with high sensitivity.

Detection of indoxyl sulfate levels in dogs and cats suffering from naturally occurring kidney diseases

Indoxyl sulfate (IS), a protein-bound uraemic toxin, has been found to accumulate in the serum of people with renal diseases and is associated with free radical induction, nephrotoxicity cardiovascular toxicity, and osteoblast cytotoxicity. Although IS has been studied in humans and in experimental models, the role of IS in dogs and cats with kidney disease has not been investigated. A high performance liquid chromatography system was applied to detect plasma IS concentrations in non-azotaemic animals (63 dogs, 16 cats) and in animals with renal azotaemia (66 dogs, 69 cats). The IS levels of azotaemic animals were significantly higher (P <0.01) than those of non-azotaemic animals (median [IQR] 20.4 (9.5) mg/L vs. 7.2 (8.8) mg/L for dogs; median [IQR] 21 (18.9) mg/L vs. 14.8 (12.3) mg/L for cats). The IS level was significantly correlated with blood urea nitrogen, serum creatinine and phosphate concentrations. Dogs with acute kidney injury had significantly higher IS levels (P <0.01) than those with chronic kidney diseases (CKD) (median [IQR] 57.7 (40.8) mg/L vs. 17.7 (25.1) mg/L). When CKD was graded using the International Renal Interest Society (IRIS) staging system, IS levels were correlated with CKD severity in both dogs and cats. The IS concentration is directly related to loss of renal function. Further studies are necessary to determine whether measurement of IS provides any additional diagnostic or prognostic information in dogs and cats with kidney disease.

Improving protein order-disorder classification using charge-hydropathy plots

Background

The earliest whole protein order/disorder predictor (Uversky et al., Proteins, 41: 415-427 (2000)), herein called the charge-hydropathy (C-H) plot, was originally developed using the Kyte-Doolittle (1982) hydropathy scale (Kyte & Doolittle., J. Mol. Biol, 157: 105-132(1982)). Here the goal is to determine whether the performance of the C-H plot in separating structured and disordered proteins can be improved by using an alternative hydropathy scale.

Results

Using the performance of the CH-plot as the metric, we compared 19 alternative hydropathy scales, with the finding that the Guy (1985) hydropathy scale (Guy, Biophys. J, 47:61-70(1985)) was the best of the tested hydropathy scales for separating large collections structured proteins and intrinsically disordered proteins (IDPs) on the C-H plot. Next, we developed a new scale, named IDP-Hydropathy, which further improves the discrimination between structured proteins and IDPs. Applying the C-H plot to a dataset containing 109 IDPs and 563 non-homologous fully structured proteins, the Kyte-Doolittle (1982) hydropathy scale, the Guy (1985) hydropathy scale, and the IDP-Hydropathy scale gave balanced two-state classification accuracies of 79%, 84%, and 90%, respectively, indicating a very substantial overall improvement is obtained by using different hydropathy scales. A correlation study shows that IDP-Hydropathy is strongly correlated with other hydropathy scales, thus suggesting that IDP-Hydropathy probably has only minor contributions from amino acid properties other than hydropathy.

Conclusion

We suggest that IDP-Hydropathy would likely be the best scale to use for any type of algorithm developed to predict protein disorder.