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The transgene toggling device is recognized as a powerful tool for gene- and cell-based biological research and precision medicine. However, many of these devices often operate in binary mode, exhibit unacceptable leakiness, suffer from transgene silencing, show cytotoxicity, and have low potency. Here, we present a novel transgene switch, SIQ, wherein all the elements for gene toggling are packed into a single vector. SIQ has superior potency in inducing transgene expression in response to tebufenozide compared with the Gal4/UAS system, while completely avoiding transgene leakiness. Additionally, the ease and versatility of SIQ make it possible with a single construct to perform transient transfection, establish stable cell lines by targeting a predetermined genomic locus, and simultaneously produce adenovirus for transduction into cells and mammalian tissues. Furthermore, we integrated a cumate switch into SIQ, called SIQmate, to operate a Boolean AND logic gate, enabling swift toggling-off of the transgene after the removal of chemical inducers, tebufenozide and cumate. Both SIQ and SIQmate offer precise transgene toggling, making them adjustable for various researches, including synthetic biology, genome engineering, and therapeutics.

Abstract Osteoporosis is a condition characterized by decreased bone mineral density (BMD) and reduced bone strength, leading to an increased risk of fractures. Here, to identify novel risk variants for susceptibility to osteoporosis-related traits, an exome-wide association study is performed with 6,485 exonic single nucleotide polymorphisms (SNPs) in 2,666 women of two Korean study cohorts. The rs2781 SNP in UBAP2 gene is suggestively associated with osteoporosis and BMD with p-values of 6.1 × 10−7 (odds ratio = 1.72) and 1.1 × 10−7 in the case-control and quantitative analyzes, respectively. Knockdown of Ubap2 in mouse cells decreases osteoblastogenesis and increases osteoclastogenesis, and knockdown of ubap2 in zebrafish reveals abnormal bone formation. Ubap2 expression is associated with E-cadherin (Cdh1) and Fra1 (Fosl1) expression in the osteclastogenesis-induced monocytes. UBAP2 mRNA levels are significantly reduced in bone marrow, but increased in peripheral blood, from women with osteoporosis compared to controls. UBAP2 protein level is correlated with the blood plasma level of the representative osteoporosis biomarker osteocalcin. These results suggest that UBAP2 has a critical role in bone homeostasis through the regulation of bone remodeling.

We investigated the impact of surface treatments on Si-based electrolyte-gated transistors (EGTs) for detecting urea. Three types of EGTs were fabricated with distinct gate electrodes (Ag, Au, Pt) using a top-down method. These EGTs exhibited exceptional intrinsic electrical properties, including a low subthreshold swing of 80 mV/dec, a high on/off current ratio of 106, and negligible hysteresis. Three surface treatment methods ((3-amino-propyl) triethoxysilane (APTES) and glutaraldehyde (GA), 11-mercaptoundecanoic acid (11-MUA), 3-mercaptopropionic acid (3-MPA)) were individually applied to the EGTs with different gate electrodes (Ag, Au, Pt). Gold nanoparticle binding tests were performed to validate the surface functionalization. We compared their detection performance of urea and found that APTES and GA exhibited the most superior detection characteristics, followed by 11-MUA and 3-MPA, regardless of the gate metal. APTES and GA, with the highest pKa among the three surface treatment methods, did not compromise the activity of urease, making it the most suitable surface treatment method for urea sensing.

In this study, we investigated the influence of quasi-one-dimensional (Quasi-1D) characteristics on the source and drain contact resistances within vertical nanowire (NW) field-effect transistors (FETs) of diminutive diameter. The top contact of the NW is segregated into two distinct regions: the first encompassing the upper surface, designated as the axial contact, and the second encircling the side surface, known as the radial contact, which is formed during the top-contact metal deposition process. Quantum confinement effects, prominent within Quasi-1D NWs, exert significant constraints on radial transport, consequently inducing a noticeable impact on contact resistance. Notably, in the radial direction, electron tunneling occurs only through quantized, discrete energy levels. Conversely, along the axial direction, electron tunneling freely traverses continuous energy levels. In a meticulous numerical analysis, these disparities in transport mechanisms unveiled that NWs with diameters below 30 nm exhibit a markedly higher radial contact resistance compared to their axial counterparts. Furthermore, an increase in the overlap length (less than 5 nm) contributes to a modest reduction in radial resistance; however, it remains consistently higher than the axial contact resistance.

Abstract The recent Coronavirus Disease 2019 (COVID‐19) outbreak strongly propels advancements in biosensor technology, leading to the emergence of novel methods for virus detection. Among them, those using nanostructured field‐effect transistors (FETs) provide an ultrasensitive approach toward point‐of‐care diagnostics. However, the application of these biosensors in analyzing biofluids has been limited by their reduced screening length in high ionic strength liquids. To address this challenge, a solution is presented involving the surface modification of FETs with a hydrogel based on star‐shaped polyethylene glycol. This hydrogel is loaded with specific antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) spike protein. By incorporating the hydrogel, the effective Debye length is effectively increased, thereby preserving the sensitivity in biofluids. The efficacy of this approach is demonstrated by employing silicon nanonet‐based FETs for the detection of viral antigens in both buffer and saliva, as well as cultured viral particle dispersions. Moreover, positive and negative patient samples are successfully differentiated, showcasing the practical application of this method. Finally, a theoretical frame is proposed to elucidate the underlying mechanism behind the preservation of sensitivity.

The sensing responses of SARS-CoV-2 spike protein using top-down-fabricated Si-based electrolyte-gated transistors (EGTs) have been investigated. An aptamer was employed as a receptor for the SARS-CoV-2 spike protein. The EGT demonstrated excellent intrinsic characteristics and higher sensitivity in the subthreshold regime compared to the linear regime. The limit of detection (LOD) was achieved as low as 0.94 pg/mL and 20 pg/mL for the current and voltage sensitivity, respectively. To analyze the sensing responses of EGT in detecting the aptamer–SARS-CoV-2 spike protein conjugate, a lumped-capacitive model with the presence of an effective dipole potential and an effective capacitance of the functionalized layer component was employed. The aptamer-functionalized EGT showed high sensitivity even in 10 mM phosphate-buffered saline (PBS) solution. These results suggest that Si-based EGTs are a highly promising method for detecting SARS-CoV-2 spike proteins.

Electrical characteristics with various program temperatures (TPGM) in three-dimensional (3-D) NAND flash memory are investigated. The cross-temperature conditions of the TPGM up to 120 °C and the read temperature (TREAD) at 30 °C are used to analyze the influence of grain boundaries (GB) on the bit line current (IBL) and threshold voltage (VT). The VT shift in the E-P-E pattern is successfully decomposed into the charge loss (ΔVT,CL) component and the poly-Si GB (ΔVT,GB) component. The extracted ΔVT,GB increases at higher TPGM due to the reduced GB potential barrier. Additionally, the ΔVT,GB is evaluated using the Technology Computer Aided Design (TCAD) simulation, depending on the GB position (XGB) and the bit line voltage (VBL).

The instability in threshold voltage (VTH) and charge distributions in noncircular cells of three-dimensional (3D) NAND flash memory are investigated. Using TCAD simulation, we aim to identify the main factors influencing the VTH of noncircular cells. The key focus is on the nonuniform trapped electron density in the charge trapping layer (CTL) caused by the change in electric field between the circular region and the spike region. There are less-trapped electron (LT) regions within the CTL of programmed noncircular cells, which significantly enhances current flow. Remarkably, more than 50% of the total current flows through these LT regions when the spike size reaches 15 nm. We also performed a comprehensive analysis of the relationship between charge distribution and VTH in two-spike cells with different heights (HSpike) and angles between spikes (θ). The results of this study demonstrate the potential to improve the reliability of next-generation 3D NAND flash memory.

The effects of carbon incorporation on the thermal stability of the interfacial TiO2 layer and the electrical characteristics of Ti/TiO2/ n-Ge contacts were investigated. The improved thermal stability and contact characteristics of Ti/TiO2/ n-Ge contacts were characterized in terms of Schottky barrier height (SBH) and specific contact resistivity ( $\rho _{c}$ ) using the Schottky diode and circular transmission line model (CTLM). The values of SBH and $\rho _{c}$ increased after the rapid thermal annealing (RTA) above 550 °C. The current density–bias voltage ( $J-V$ ) curves of the Schottky diode showed a change of contact characteristics from Ohmic-like behavior to rectifying. This thermal instability was mainly caused by the decomposition of the interfacial TiO2 layer after high-temperature annealing. The structural degradation was confirmed by transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) analyses. When carbon ions were incorporated into the interfacial TiO2 layer, the SBH and $\rho _{c}$ values showed relatively stable characteristics as the RTA temperature increased up to 600 °C. The EELS mapping showed that the diffusion of oxygen from the interfacial TiO2 layer was effectively suppressed thanks to the incorporation of carbon. Thus, the carbon incorporation can improve the thermal stability of the interfacial TiO2 layer and the metal–insulator–semiconductor contact characteristics for Ge-based device applications.

Abstract Background Host tp53 mutations are frequently found during the early stages of colitis-associated colorectal cancer (CAC), but whether such mutations induce gut microbiota dysbiosis and chronic intestinal inflammation that contributes to the development of CAC, remains unknown. Results We found that zebrafish tp53 mutant larvae exhibited elevated intestinal inflammation, by monitoring the NFκB activity in the mid-distal intestines of zebrafish larvae using an NFκB:EGFP transgenic reporter line in vivo as well as neutrophil infiltration into the intestine. This inflammation was due to dysbiotic gut microbiota with reduced diversity, revealed using both 16S rRNA amplicon sequencing and a germfree larva model. In this dysbiosis, Aeromonas spp. were aberrantly enriched as major pathobionts and exhibited the capacity for aggressive colonization in tp53 mutants. Importantly, the ex-germfree experiments supported the causality of the host tp53 mutation for inducing the inflammation. Transcriptome and high-performance liquid chromatography analyses of the host gastrointestinal tracts identified dysregulated sialic acid (SA) metabolism concomitant with increased host Neu5Gc levels as the key determinant of aberrant inflammation, which was reversed by the sialidase inhibitors oseltamivir and Philippin A. Conclusions These results demonstrate a crucial role for host tp53 in maintaining symbiosis and immune homeostasis via SA metabolism. Disturbed SA metabolism via a tp53 mutation may be exploited by specific elements of the gut microbiome, eliciting both dysbiosis and inflammation. Manipulating sialometabolism may therefore provide an efficacious therapeutic strategy for tp53 mutation-induced dysbiosis, inflammation, and ultimately, related cancers. Video Abstract

The quantitative characteristics of traps created in the bandgap-engineered tunneling oxide (BE-TOX) layer and block layer after program/erase (P/E) stress-cycling in a 3D NAND flash memory were investigated. The trap spectroscopy by charge injection and sensing technique was used to obtain the distribution of traps in these layers. In the BE-TOX layer, significant traps were generated around 1.3 eV in the nitrogen-doped layer (N1) and increased by 48% in the fresh cell after P/E stress-cycling. The H bonds in the N1 are more likely to break during the stress-cycling and create neutral $\equiv \mathrm {SiO}^{\bullet }$ traps. In the block layer, however, trap generation was negligible after stress-cycling.

Hong et al. describe a new transgene expression system, IQ-Switch, and its variants and characterize their applications in cell culture and zebrafish systems. They show that IQ-Switch system has several advantages over the previous inducible transgene expression switches, including the low toxicity, tunability of expression levels and low levels of gene silencing.

Hyperphosphorylated Tau accumulation promotes neurodegeneration in Alzheimer’s disease. Here, the authors screen a miRNA library in Drosophila and identify a conserved ubiquitin ligase that directs Tau for autophagic degradation, uncovering a potential target to treat Tau-mediated neurodegeneration.

The SARS-CoV-2 pandemic has triggered many studies worldwide in the area of biosensors, leading to innovative approaches for the quantitative assessment of COVID-19. A nanostructured field-effect transistor (FET) is one type of device shown to be ultrasensitive for virus determination. FETs can be used as transducers to analyze changes in electrical current caused by the bonding of viral molecules to the surface of the semiconducting nanomaterial layer of the FETs. Although nano-transistors require simple setups amenable to be miniaturized for point-of-care diagnostic of COVID-19, this type of sensor usually has limited sensitivity in biological fluids. The reason behind this is the shortened screening length in the presence of high ionic strength solutions. In the frame of this study, we propose a methodology consisting of the FET surface modification with a hydrogel based on the star-shaped polyethylene glycol (starPEG), which hosts specific antibodies against SARS-CoV-2 spike protein in its porous structure. The deposition of the hydrogel increases the effective Debye length, preserving the biosensor’s sensitivity. We demonstrate the capability of silicon nanonet-based FETs to detect viral antigens and cultured viral particles in phosphate-buffered saline (PBS) as well as in human-purified saliva. Finally, we discriminated between positive and negative patients’ nasopharyngeal swab samples.

We experimentally demonstrate Si-based electrolyte-gated transistors (EGTs) for detecting urea. The top-down-fabricated device exhibited excellent intrinsic characteristics, including a low subthreshold swing (SS) (~80 mV/dec) and a high on/off current ratio (~107). The sensitivity, which varied depending on the operation regime, was analyzed with the urea concentrations ranging from 0.1 to 316 mM. The current-related response could be enhanced by reducing the SS of the devices, whereas the voltage-related response remained relatively constant. The urea sensitivity in the subthreshold regime was as high as 1.9 dec/pUrea, four times higher than the reported value. The extracted power consumption of 0.3 nW was extremely low compared to other FET-type sensors.

Si-based electrolyte-gated transistors (EGTs) have been investigated to achieve high sensitivity and a low detection limit (LOD). Here, a lumped-capacitive model was applied to analyze the influence of receptor–target conjugates on the sensing performance. The voltage-related sensitivity is mainly determined by the effective dipole potential ( $V_{DP,EFF}$ ), the effective capacitance of the functionalization layer ( $C_{FN,EFF}$ ), and the total charge density in the channel ( $Q_{S}$ ) related to the operating regime. In an n-type EGT, the sensitivity is enhanced as the device is operated in the subthreshold regime with a positive $V_{DP,EFF}$ and a small $C_{FN,EFF}$ . The influence of the $V_{DP,EFF}$ and $C_{FN,EFF}$ was experimentally evaluated by detecting the peanut allergen (PA) using the fabricated n-type Si-EGTs. A higher sensitivity and a lower LOD could be achieved in the subthreshold regimes than in the linear regime. These results suggest that the proposed model is very useful to optimize the sensing characteristics of Si-based EGT for biosensing applications.

The extraction of nitride trap density ( $N_{t}$ ) filled with electrons emitted by thermal emission (TE) in the charge-trapping layer of 3-D NAND flash memory is demonstrated. The intercell program (IP) pattern was adopted to intentionally inject electrons into the intercell region to minimize the influence of lateral migration (LM) on the trap profiles. This was confirmed by the retention characteristics observed at 120 °C, where the charge loss is mainly caused by the TE of the trapped electrons in the nitride layer. The extracted peak value of $N_{t}$ at $E_{C}$ - $E_{T}$ value of 1.20 eV using the IP pattern was as low as $1.01\times 10^{19}$ cm−3eV−1, in the scan range of 0.96 eV to 1.27 eV. This value was 17% lower than that from the conventional adjacent cell program (P-P-P) pattern. Therefore, the IP pattern can be used in extracting trap profiles in the SiN layer in scaled 3-D NAND memories.

The initiation of translation is a highly regulated process that contributes to specific gene expression programs. Here the authors find that, in vertebrate, threonyl-tRNA synthetase (TRS) can act as a scaffold for the initiation machinery to stimulate the translation of a specific set of mRNAs.

tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.

DNA damage response (DDR) is an evolutionarily conserved mechanism by which eukaryotic cells sense DNA lesions caused by intrinsic and extrinsic stimuli, including virus infection. Although interactions between DNA viruses and DDR have been extensively studied, how RNA viruses, especially coronaviruses, regulate DDR remains unknown. A previous study showed that the porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus in the Coronaviridae family, induces DDR in infected cells. However, the underlying mechanism was unclear. This study showed that PEDV activates the ATM-Chk2 signaling, while inhibition of ATM or Chk2 dampens the early stage of PEDV infection. Additionally, we found that PEDV-activated ATM signaling correlates with intracellular ROS production. Interestingly, we showed that, unlike the typical γH2AX foci, PEDV infection leads to a unique γH2AX staining pattern, including phase I (nuclear ring staining), II (pan-nuclear staining), and III (co-staining with apoptotic bodies), which highly resembles the apoptosis process. Furthermore, we demonstrated that PEDV-induced H2AX phosphorylation depends on the activation of caspase-7 and caspase-activated DNAse (CAD), but not ATM-Chk2. Finally, we showed that the knockdown of H2AX attenuates PEDV replication. Taken together, we conclude that PEDV induces DDR through the ROS-ATM and caspase7-CAD-γH2AX signaling pathways to foster its early replication.

The highly sensitive detection of peanut allergens (PAs) using silicon-based electrolyte-gated transistors (Si-EGTs) was demonstrated. The Si-EGT was made using a top-down technique. The fabricated Si-EGT showed excellent intrinsic electrical characteristics, including a low threshold voltage of 0.7 V, low subthreshold swing of SV) showed a constant behavior from the subthreshold regime to the linear regime. The current-related sensitivity (SI) was high in the subthreshold regime and then significantly decreased as the drain current increased. The limit of detection (LOD) was calculated to be as low as 25 pg/mL based on SI characteristics, which is the lowest value reported to date in the literature for various sensor methodologies. The Si-EGT showed selective detection of PA through a non-specific control test. These results confirm that Si-EGT is a high-sensitivity and low-power biosensor for PA detection.

Effects of carbon implantation (C-imp) on the contact characteristics of Ti/Ge contact were investigated. The C-imp into Ti/Ge system was developed to reduce severe Fermi-level pinning (FLP) and to improve the thermal stability of Ti/Ge contact. The current density (J)-voltage (V) characteristics showed that the rectifying behavior of Ti/Ge contact into an Ohmic-like behavior with C-imp. The lowering of Schottky barrier height (SBH) indicated that the C-imp could mitigate FLP. In addition, it allows a lower specific contact resistivity (ρc) at the rapid thermal annealing (RTA) temperatures in a range of 450–600 °C. A secondary ion mass spectrometry (SIMS) showed that C-imp facilitates the dopant segregation at the interface. In addition, transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) mapping showed that after RTA at 600 °C, C-imp enhances the diffusion of Ge atoms into Ti layer at the interface of Ti/Ge. Thus, carbon implantation into Ge substrate can effectively reduce FLP and improve contact characteristics.

The failure of amyloid beta (Aβ) clearance is a major cause of Alzheimer’s disease, and the brain lymphatic systems play a crucial role in clearing toxic proteins. Recently, brain lymphatic endothelial cells (BLECs), a non-lumenized lymphatic cell in the vertebrate brain, was identified, but Aβ clearance via this novel cell is not fully understood. We established an in vivo zebrafish model using fluorescently labeled Aβ42 to investigate the role of BLECs in Aβ clearance. We discovered the efficient clearance of monomeric Aβ42 (mAβ42) compared to oligomeric Aβ42 (oAβ42), which was illustrated by the selective uptake of mAβ42 by BLECs and peripheral transport. The genetic depletion, pharmacological inhibition via the blocking of the mannose receptor, or the laser ablation of BLECs resulted in the defective clearance of mAβ42. The treatment with an Aβ disaggregating agent facilitated the internalization of oAβ42 into BLECs and improved the peripheral transport. Our findings reveal a new role of BLECs in the differential clearance of mAβ42 from the brain and provide a novel therapeutic strategy based on promoting Aβ clearance.

During chronic cold stress, thermogenic adipocytes generate heat through uncoupling of mitochondrial respiration from ATP synthesis. Recent discovery of various dietary phytochemicals, endogenous metabolites, synthetic compounds, and their molecular targets for stimulating thermogenesis has provided promising strategies to treat or prevent obesity and its associated metabolic diseases. Nuclear factor E2 p45-related factor 2 (Nrf2) is a stress response protein that plays an important role in obesity and metabolisms. However, both Nrf2 activation and Nrf2 inhibition can suppress obesity and metabolic diseases. Here, we summarized and discussed conflicting findings of Nrf2 activities accounting for part of the variance in thermogenesis and energy metabolism. We also discussed the utility of Nrf2-activating mechanisms for their potential applications in stimulating energy expenditure to prevent obesity and improve metabolic deficits.

Tauopathy refers to a group of progressive neurodegenerative diseases, including frontotemporal lobar degeneration and Alzheimer’s disease, which correlate with the malfunction of microtubule-associated protein Tau (MAPT) due to abnormal hyperphosphorylation, leading to the formation of intracellular aggregates in the brain. Despite extensive efforts to understand tauopathy and develop an efficient therapy, our knowledge is still far from complete. To find a solution for this group of devastating diseases, several animal models that mimic diverse disease phenotypes of tauopathy have been developed. Rodents are the dominating tauopathy models because of their similarity to humans and established disease lines, as well as experimental approaches. However, powerful genetic animal models using Drosophila, zebrafish, and C. elegans have also been developed for modeling tauopathy and have contributed to understanding the pathophysiology of tauopathy. The success of these models stems from the short lifespans, versatile genetic tools, real-time in-vivo imaging, low maintenance costs, and the capability for high-throughput screening. In this review, we summarize the main findings on mechanisms of tauopathy and discuss the current tauopathy models of these non-rodent genetic animals, highlighting their key advantages and limitations in tauopathy research.

Olfaction is an important neural system for survival and fundamental behaviors such as predator avoidance, food finding, memory formation, reproduction, and social communication. However, the neural circuits and pathways associated with the olfactory system in various behaviors are not fully understood. Recent advances in optogenetics, high-resolution in vivo imaging, and reconstructions of neuronal circuits have created new opportunities to understand such neural circuits. Here, we generated a transgenic zebrafish to manipulate olfactory signal optically, expressing the Channelrhodopsin (ChR2) under the control of the olfactory specific promoter, omp. We observed light-induced neuronal activity of olfactory system in the transgenic fish by examining c-fos expression, and a calcium indicator suggesting that blue light stimulation caused activation of olfactory neurons in a non-invasive manner. To examine whether the photo-activation of olfactory sensory neurons affect behavior of zebrafish larvae, we devised a behavioral choice paradigm and tested how zebrafish larvae choose between two conflicting sensory cues, an aversive odor or the naturally preferred phototaxis. We found that when the conflicting cues (the preferred light and aversive odor) were presented together simultaneously, zebrafish larvae swam away from the aversive odor. However, the transgenic fish with photo-activation were insensitive to the aversive odor and exhibited olfactory desensitization upon optical stimulation of ChR2. These results show that an aversive olfactory stimulus can override phototaxis, and that olfaction is important in decision making in zebrafish. This new transgenic model will be useful for the analysis of olfaction related behaviors and for the dissection of underlying neural circuits.

We present the fabrication and electrical characteristics of nanonet-channel (NET) low-temperature polysilicon channel (LTPS) thin-film transistors (TFTs) using a nanosphere-assisted patterning (NAP) technique. The NAP technique is introduced to form a nanonet-channel instead of the electron beam lithography (EBL) or conventional photolithography method. The size and space of the holes in the nanonet structure are well controlled by oxygen plasma treatment and a metal lift-off process. The nanonet-channel TFTs show improved electrical characteristics in terms of the ION/IOFF, threshold voltage, and subthreshold swing compared with conventional planar devices. The nanonet-channel devices also show a high immunity to hot-carrier injection and a lower variation of electrical characteristics. The standard deviation of VTH (σVTH) is reduced by 33% for a nanonet-channel device with a gate length of 3 μm, which is mainly attributed to the reduction of the grain boundary traps and enhanced gate controllability. These results suggest that the cost-effective NAP technique is promising for manufacturing high-performance nanonet-channel LTPS TFTs with lower electrical variations.

Abstract Background DYRK1A maps to the Down syndrome critical region at 21q22. Mutations in this kinase-encoding gene have been reported to cause microcephaly associated with either intellectual disability or autism in humans. Intellectual disability accompanied by microcephaly was recapitulated in a murine model by overexpressing Dyrk1a which mimicked Down syndrome phenotypes. However, given embryonic lethality in homozygous knockout (KO) mice, no murine model studies could present sufficient evidence to link Dyrk1a dysfunction with autism. To understand the molecular mechanisms underlying microcephaly and autism spectrum disorders (ASD), we established an in vivo dyrk1aa KO model using zebrafish. Methods We identified a patient with a mutation in the DYRK1A gene using microarray analysis. Circumventing the barrier of murine model studies, we generated a dyrk1aa KO zebrafish using transcription activator-like effector nuclease (TALEN)-mediated genome editing. For social behavioral tests, we have established a social interaction test, shoaling assay, and group behavior assay. For molecular analysis, we examined the neuronal activity in specific brain regions of dyrk1aa KO zebrafish through in situ hybridization with various probes including c-fos and crh which are the molecular markers for stress response. Results Microarray detected an intragenic microdeletion of DYRK1A in an individual with microcephaly and autism. From behavioral tests of social interaction and group behavior, dyrk1aa KO zebrafish exhibited social impairments that reproduce human phenotypes of autism in a vertebrate animal model. Social impairment in dyrk1aa KO zebrafish was further confirmed by molecular analysis of c-fos and crh expression. Transcriptional expression of c-fos and crh was lower than that of wild type fish in specific hypothalamic regions, suggesting that KO fish brains are less activated by social context. Conclusions In this study, we established a zebrafish model to validate a candidate gene for autism in a vertebrate animal. These results illustrate the functional deficiency of DYRK1A as an underlying disease mechanism for autism. We also propose simple social behavioral assays as a tool for the broader study of autism candidate genes.

DYRK1A is a major causative gene in Down syndrome (DS). Reduced incidence of solid tumors such as neuroblastoma in DS patients and increased vascular anomalies in DS fetuses suggest a potential role of DYRK1A in angiogenic processes, but in vivo evidence is still scarce. Here, we used zebrafish dyrk1aa mutant embryos to understand DYRK1A function in cerebral vasculature formation. Zebrafish dyrk1aa mutants exhibited cerebral hemorrhage and defects in angiogenesis of central arteries in the developing hindbrain. Such phenotypes were rescued by wild-type dyrk1aa mRNA, but not by a kinase-dead form, indicating the importance of DYRK1A kinase activity. Chemical screening using a bioactive small molecule library identified a calcium chelator, EGTA, as one of the hits that most robustly rescued the hemorrhage. Vascular defects of mutants were also rescued by independent modulation of calcium signaling by FK506. Furthermore, the transcriptomic analyses supported the alterations of calcium signaling networks in dyrk1aa mutants. Together, our results suggest that DYRK1A plays an essential role in angiogenesis and in maintenance of the developing cerebral vasculature via regulation of calcium signaling, which may have therapeutic potential for DYRK1A-related vascular diseases.

The microbiota–gut–brain axis (MGBA) is a bidirectional signaling pathway mediating the interaction of the microbiota, the intestine, and the central nervous system. While the MGBA plays a pivotal role in normal development and physiology of the nervous and gastrointestinal system of the host, its dysfunction has been strongly implicated in neurological disorders, where intestinal dysbiosis and derived metabolites cause barrier permeability defects and elicit local inflammation of the gastrointestinal tract, concomitant with increased pro-inflammatory cytokines, mobilization and infiltration of immune cells into the brain, and the dysregulated activation of the vagus nerve, culminating in neuroinflammation and neuronal dysfunction of the brain and behavioral abnormalities. In this topical review, we summarize recent findings in human and animal models regarding the roles of the MGBA in physiological and neuropathological conditions, and discuss the molecular, genetic, and neurobehavioral characteristics of zebrafish as an animal model to study the MGBA. The exploitation of zebrafish as an amenable genetic model combined with in vivo imaging capabilities and gnotobiotic approaches at the whole organism level may reveal novel mechanistic insights into microbiota–gut–brain interactions, especially in the context of neurological disorders such as autism spectrum disorder and Alzheimer’s disease.

DYRK1A is important in neuronal development and function, and its excessive activity is considered a significant pathogenic factor in Down syndrome and Alzheimer's disease. Thus, inhibition of DYRK1A has been suggested to be a new strategy to modify the disease. Very few compounds, however, have been reported to act as inhibitors, and their potential clinical uses require further evaluation. Here, we newly identify CX-4945, the safety of which has been already proven in the clinical setting, as a potent inhibitor of DYRK1A that acts in an ATP-competitive manner. The inhibitory potency of CX-4945 on DYRK1A (IC50=6.8 nM) in vitro was higher than that of harmine, INDY or proINDY, which are well-known potent inhibitors of DYRK1A. CX-4945 effectively reverses the aberrant phosphorylation of Tau, amyloid precursor protein (APP) and presenilin 1 (PS1) in mammalian cells. To our surprise, feeding with CX-4945 significantly restored the neurological and phenotypic defects induced by the overexpression of minibrain, an ortholog of human DYRK1A, in the Drosophila model. Moreover, oral administration of CX-4945 acutely suppressed Tau hyperphosphorylation in the hippocampus of DYRK1A-overexpressing mice. Our research results demonstrate that CX-4945 is a potent DYRK1A inhibitor and also suggest that it has therapeutic potential for DYRK1A-associated diseases.

Rhus verniciflua Stokes (RVS) has been used as a traditional herbal medicine for its various biological activities including anti-adipogenic effects. Activity-guided separation led to the identification of the anti-adipogenic functions of butein. Butein, a novel anti-adipogenic compound, robustly suppressed lipid accumulation and inhibited expression of adipogenic markers. Molecular studies showed that activated transforming growth factor-β (TGF-β) and suppressed signal transducer and activator of transcription 3 (STAT3) signaling pathways were mediated by butein. Analysis of the temporal expression profiles suggests that TGF-β signaling precedes the STAT3 in the butein-mediated anti-adipogenic cascade. Small interfering RNA-mediated silencing of STAT3 or SMAD2/3 blunted the inhibitory effects of butein on adipogenesis indicating that an interaction between two signaling pathways is required for the action of butein. Upon butein treatments, stimulation of TGF-β signaling was still preserved in STAT3 silenced cells, whereas regulation of STAT3 signaling by butein was significantly impaired in SMAD2/3 silenced cells, further showing that TGF-β acts upstream of STAT3 in the butein-mediated anti-adipogenesis. Taken together, the present study shows that butein, a novel anti-adipogenic compound from RVS, inhibits adipocyte differentiation through the TGF-β pathway followed by STAT3 and peroxisome proliferator-activated receptor γ signaling, further implicating potential roles of butein in TGF-β- and STAT3-dysregulated diseases.

SUMMARY Neurofibromatosis type 1 (NF1) is a common, dominantly inherited genetic disorder that results from mutations in the neurofibromin 1 (NF1) gene. Affected individuals demonstrate abnormalities in neural-crest-derived tissues that include hyperpigmented skin lesions and benign peripheral nerve sheath tumors. NF1 patients also have a predisposition to malignancies including juvenile myelomonocytic leukemia (JMML), optic glioma, glioblastoma, schwannoma and malignant peripheral nerve sheath tumors (MPNSTs). In an effort to better define the molecular and cellular determinants of NF1 disease pathogenesis in vivo, we employed targeted mutagenesis strategies to generate zebrafish harboring stable germline mutations in nf1a and nf1b, orthologues of NF1. Animals homozygous for loss-of-function alleles of nf1a or nf1b alone are phenotypically normal and viable. Homozygous loss of both alleles in combination generates larval phenotypes that resemble aspects of the human disease and results in larval lethality between 7 and 10 days post fertilization. nf1-null larvae demonstrate significant central and peripheral nervous system defects. These include aberrant proliferation and differentiation of oligodendrocyte progenitor cells (OPCs), dysmorphic myelin sheaths and hyperplasia of Schwann cells. Loss of nf1 contributes to tumorigenesis as demonstrated by an accelerated onset and increased penetrance of high-grade gliomas and MPNSTs in adult nf1a+/−; nf1b−/−; p53e7/e7 animals. nf1-null larvae also demonstrate significant motor and learning defects. Importantly, we identify and quantitatively analyze a novel melanophore phenotype in nf1-null larvae, providing the first animal model of the pathognomonic pigmentation lesions of NF1. Together, these findings support a role for nf1a and nf1b as potent tumor suppressor genes that also function in the development of both central and peripheral glial cells as well as melanophores in zebrafish.

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

We report the electrical characteristics and pH responses of a Si-nanonet ion-sensitive field-effect transistor with ultra-thin parylene-H as a gate sensing membrane. The fabricated device shows excellent DC characteristics: a low subthreshold swing of 85 mV/dec, a high current on/off ratio of ~107 and a low gate leakage current of ~10−10 A. The low interface trap density of 1.04 × 1012 cm−2 and high field-effect mobility of 510 cm2V−1s−1 were obtained. The pH responses of the devices were evaluated in various pH buffer solutions. A high pH sensitivity of 48.1 ± 0.5 mV/pH with a device-to-device variation of ~6.1% was achieved. From the low-frequency noise characterization, the signal-to-noise ratio was extracted as high as ~3400 A/A with the lowest noise equivalent pH value of ~0.002 pH. These excellent intrinsic electrical and pH sensing performances suggest that parylene-H can be promising as a sensing membrane in an ISFET-based biosensor platform.

A silver nanoparticle is one of the representative engineered nanomaterials with excellent optical, electrical, antibacterial properties. Silver nanoparticles are being increasingly used for medical products, water filters, and cosmetics, etc. However, silver nanoparticles are known to cause adverse effects on the ecosystem and human health. To utilize silver nanoparticles with minimized negative effects, it is important to understand the behavior of silver nanoparticles released to the environment. In this study, we compared toxicity behaviors of citrate-stabilized silver nanoparticles with polyethylene glycol coated silver nanoparticles in two different ionic environments, which are aquatic environments for developing zebrafish embryo. Depending on the composition of the ionic environment, citrate-stabilized silver nanoparticles and polyethylene glycol coated silver nanoparticles exhibited different behaviors in dissolution, aggregation, or precipitation, which governed the toxicity of silver nanoparticles on zebrafish embryos.

BackgroundValvular heart surgery (VHS) utilizing cardiopulmonary bypass (CPB) is inevitably associated with ischemic-reperfusion injury, which is known to depend on oxygen tension during reperfusion. The aim of this study was to evaluate the effect of arterial oxygen tension during reperfusion on myocardial recovery in patients undergoing VHS.MethodsFifty-six patients undergoing isolated VHS were randomly exposed to an oxygen fraction of 0.7 (hyperoxic group, n = 28) or 0.5 (normoxic group, n = 28) during reperfusion. All patients received an oxygen fraction of 0.7 during CPB. In the normoxic group, the oxygen fraction was lowered to 0.5 from the last warm cardioplegia administration to 1 minute after aortic unclamping, and was then raised back to 0.7. Hemodynamic data were measured after induction of anesthesia, weaning from CPB, and sternum closure. The frequency of cardiotonic medications used during and after weaning from CPB, and the short-term outcomes during the hospital stay were also assessed.ResultsThe frequency of vasopressin and milrinone use during weaning from CPB, but not norepinephrine, was significantly less in the normoxic group. The post-operative cardiac enzyme levels and short-term outcomes were not different between the groups.ConclusionsNormoxic reperfusion from the last cardioplegia administration to 1 minute after aortic unclamping in patients undergoing VHS resulted in significantly less frequent use of vasopressin and inotropics during weaning from CPB than hyperoxic reperfusion, although it did not affect the post-operative myocardial enzyme release or short-term prognosis.

Phase change random access memory (PCRAM) devices exhibit a steady increase in resistance in the amorphous phase upon aging and this resistance drift phenomenon directly affects the device reliability. A stress relaxation model is used here to study the effect of a device encapsulating layer material in addressing the resistance drift phenomenon in PCRAM. The resistance drift can be increased or decreased depending on the biaxial moduli of the phase change material (YPCM) and the encapsulating layer material (YELM) according to the stress relationship between them in the drift regime. The proposed model suggests that the resistance drift can be effectively reduced by selecting a proper material as an encapsulating layer. Moreover, our model explains that reducing the size of the phase change material (PCM) while fully reset and reducing the amorphous/crystalline ratio in PCM help to improve the resistance drift, and thus opens an avenue for highly reliable multilevel PCRAM applications.

MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify miRNAs in pepper extensively from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on a bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. Northern blot analysis was used to validate further the expression of representative miRNAs and to analyze their tissue-specific or developmental stage-specific expression patterns. Moreover, we computationally predicted miRNA targets, many of which were experimentally confirmed using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR-396 was a domain rearranged methyltransferase, the major de novo methylation enzyme, involved in RNA-directed DNA methylation in plants. This work provides the first reliable draft of the pepper miRNA transcriptome. It offers an expanded picture of pepper miRNAs in relation to other plants, providing a basis for understanding the functional roles of miRNAs in pepper.

A wide variety of mesenchymal lesions, benign and malignant tumors can involve the vulvovaginal region. However, it is not easy to make a list for differential diagnoses by imaging modalities or gross findings. Angiomyofibroblastoma (AMFB) is a rare, benign mesenchymal tumor. Most cases of AMFB occur in the female genital tract. We reported a case of a 20-year-old female patient with AMFB on the anterior vaginal wall. The patient visited emergency clinic because of sudden vaginal bleeding that progressively increased. Ultrasound and magnetic resonance imaging revealed an approximately 7.7×5.0 cm mass between the cervix and vaginal wall. Incision was made at the anterior vaginal wall and local excision was performed under general anesthesia. She was discharged without complications and vaginal structure was well recovered. In addition, we reviewed other mesenchymal tumors of the female genitalia for their differential diagnosis. [ABSTRACT FROM AUTHOR]