Infection-specific phosphorylation of glutamyl-prolyl tRNA synthetase induces antiviral immunity.

The mammalian cytoplasmic multi-tRNA synthetase complex (MSC) is a depot system that regulates non-translational cellular functions. Here we found that the MSC component glutamyl-prolyl-tRNA synthetase (EPRS) switched its function following viral infection and exhibited potent antiviral activity. Infection-specific phosphorylation of EPRS at Ser990 induced its dissociation from the MSC, after which it was guided to the antiviral signaling pathway, where it interacted with PCBP2, a negative regulator of mitochondrial antiviral signaling protein (MAVS) that is critical for antiviral immunity. This interaction blocked PCBP2-mediated ubiquitination of MAVS and ultimately suppressed viral replication. EPRS-haploid (Eprs+/-) mice showed enhanced viremia and inflammation and delayed viral clearance. This stimulus-inducible activation of MAVS by EPRS suggests an unexpected role for the MSC as a regulator of immune responses to viral infection.

Promises and prospects of two-dimensional transistors.

Two-dimensional (2D) semiconductors have attracted tremendous interest as atomically thin channels that could facilitate continued transistor scaling. However, despite many proof-of-concept demonstrations, the full potential of 2D transistors has yet to be determined. To this end, the fundamental merits and technological limits of 2D transistors need a critical assessment and objective projection. Here we review the promise and current status of 2D transistors, and emphasize that widely used device parameters (such as carrier mobility and contact resistance) could be frequently misestimated or misinterpreted, and may not be the most reliable performance metrics for benchmarking 2D transistors. We suggest that the saturation or on-state current density, especially in the short-channel limit, could provide a more reliable measure for assessing the potential of diverse 2D semiconductors, and should be applied for cross-checking different studies, especially when milestone performance metrics are claimed. We also summarize the key technical challenges in optimizing the channels, contacts, dielectrics and substrates and outline potential pathways to push the performance limit of 2D transistors. We conclude with an overview of the critical technical targets, the key technological obstacles to the 'lab-to-fab' transition and the potential opportunities arising from the use of these atomically thin semiconductors.

Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae).

BACKGROUND: Corydalis DC., the largest genus in the family Papaveraceae, comprises > 465 species. Complete plastid genomes (plastomes) of Corydalis show evolutionary changes, including syntenic arrangements, gene losses and duplications, and IR boundary shifts. However, little is known about the evolution of the mitochondrial genome (mitogenome) in Corydalis. Both the organelle genomes and transcriptomes are needed to better understand the relationships between the patterns of evolution in mitochondrial and plastid genomes. RESULTS: We obtained complete plastid and mitochondrial genomes from Corydalis pauciovulata using a hybrid assembly of Illumina and Oxford Nanopore Technologies reads to assess the evolutionary parallels between the organelle genomes. The mitogenome and plastome of C. pauciovulata had sizes of 675,483 bp and 185,814 bp, respectively. Three ancestral gene clusters were missing from the mitogenome, and expanded IR (46,060 bp) and miniaturized SSC (202 bp) regions were identified in the plastome. The mitogenome and plastome of C. pauciovulata contained 41 and 67 protein-coding genes, respectively; the loss of genes was a plastid-specific event. We also generated a draft genome and transcriptome for C. pauciovulata. A combination of genomic and transcriptomic data supported the functional replacement of acetyl-CoA carboxylase subunit ß (accD) by intracellular transfer to the nucleus in C. pauciovulata. In contrast, our analyses suggested a concurrent loss of the NADH-plastoquinone oxidoreductase (ndh) complex in both the nuclear and plastid genomes. Finally, we performed genomic and transcriptomic analyses to characterize DNA replication, recombination, and repair (DNA-RRR) genes in C. pauciovulata as well as the transcriptomes of Liriodendron tulipifera and Nelumbo nuicifera. We obtained 25 DNA-RRR genes and identified their structure in C. pauciovulata. Pairwise comparisons of nonsynonymous (dN) and synonymous (dS) substitution rates revealed that several DNA-RRR genes in C. pauciovulata have higher dN and dS values than those in N. nuicifera. CONCLUSIONS: The C. pauciovulata genomic data generated here provide a valuable resource for understanding the evolution of Corydalis organelle genomes. The first mitogenome of Papaveraceae provides an example that can be explored by other researchers sequencing the mitogenomes of related plants. Our results also provide fundamental information about DNA-RRR genes in Corydalis and their related rate variation, which elucidates the relationships between DNA-RRR genes and organelle genome stability.

Formation and Transport of Secondary Contaminants Associated with Germicidal Ultraviolet Light Systems in an Occupied Classroom.

Germicidal ultraviolet light (GUV) systems are designed to control airborne pathogen transmission in buildings. However, it is important to acknowledge that certain conditions and system configurations may lead GUV systems to produce air contaminants including oxidants and secondary organic aerosols (SOA). In this study, we modeled the formation and dispersion of oxidants and secondary contaminants generated by the operation of GUV systems employing ultraviolet C 254 and 222 nm. Using a three-dimensional computational fluid dynamics model, we examined the breathing zone concentrations of chemical species in an occupied classroom. Our findings indicate that operating GUV 222 leads to an approximate increase of 10 ppb in O3 concentration and 5.2 µg·m-3 in SOA concentration compared to a condition without GUV operation, while GUV 254 increases the SOA concentration by about 1.2 µg·m-3, with a minimal impact on the O3 concentration. Furthermore, increasing the UV fluence rate of GUV 222 from 1 to 5 µW·cm-2 results in up to 80% increase in the oxidants and SOA concentrations. For GUV 254, elevating the UV fluence rate from 30 to 50 µW·cm-2 or doubling the radiating volume results in up to 50% increase in the SOA concentration. Note that indoor airflow patterns, particularly buoyancy-driven airflow (or displacement ventilation), lead to 15-45% lower SOA concentrations in the breathing zone compared to well-mixed airflow. The results also reveal that when the ventilation rate is below 2 h-1, operating GUV 254 has a smaller impact on human exposure to secondary contaminants than GUV 222. However, GUV 254 may generate more contaminants than GUV 222 when operating at high indoor O3 levels (>15 ppb). These results suggest that the design of GUV systems should consider indoor O3 levels and room ventilation conditions.

Systemic Treatment with Fas-Blocking Peptide Attenuates Apoptosis in Brain Ischemia.

Apoptosis plays a crucial role in neuronal injury, with substantial evidence implicating Fas-mediated cell death as a key factor in ischemic strokes. To address this, inhibition of Fas-signaling has emerged as a promising strategy in preventing neuronal cell death and alleviating brain ischemia. However, the challenge of overcoming the blood-brain barrier (BBB) hampers the effective delivery of therapeutic drugs to the central nervous system (CNS). In this study, we employed a 30 amino acid-long leptin peptide to facilitate BBB penetration. By conjugating the leptin peptide with a Fas-blocking peptide (FBP) using polyethylene glycol (PEG), we achieved specific accumulation in the Fas-expressing infarction region of the brain following systemic administration. Notably, administration in leptin receptor-deficient db/db mice demonstrated that leptin facilitated the delivery of FBP peptide. We found that the systemic administration of leptin-PEG-FBP effectively inhibited Fas-mediated apoptosis in the ischemic region, resulting in a significant reduction of neuronal cell death, decreased infarct volumes, and accelerated recovery. Importantly, neither leptin nor PEG-FBP influenced apoptotic signaling in brain ischemia. Here, we demonstrate that the systemic delivery of leptin-PEG-FBP presents a promising and viable strategy for treating cerebral ischemic stroke. Our approach not only highlights the therapeutic potential but also emphasizes the importance of overcoming BBB challenges to advance treatments for neurological disorders.

ACY-241, a histone deacetylase 6 inhibitor, suppresses the epithelial-mesenchymal transition in lung cancer cells by downregulating hypoxia-inducible factor-1 alpha.

Hypoxia-inducible factor-1 alpha (HIF-1α) is a transcription factor activated under hypoxic conditions, and it plays a crucial role in cellular stress regulation. While HIF-1α activity is essential in normal tissues, its presence in the tumor microenvironment represents a significant risk factor as it can induce angiogenesis and confer resistance to anti-cancer drugs, thereby contributing to poor prognoses. Typically, HIF-1α undergoes rapid degradation in normoxic conditions via oxygen-dependent degradation mechanisms. However, certain cancer cells can express HIF-1α even under normoxia. In this study, we observed an inclination toward increased normoxic HIF-1α expression in cancer cell lines exhibiting increased HDAC6 expression, which prompted the hypothesis that HDAC6 may modulate HIF-1α stability in normoxic conditions. To prove this hypothesis, several cancer cells with relatively higher HIF-1α levels under normoxic conditions were treated with ACY-241, a selective HDAC6 inhibitor, and small interfering RNAs for HDAC6 knockdown. Our data revealed a significant reduction in HIF-1α expression upon HDAC6 inhibition. Moreover, the downregulation of HIF-1α under normoxic conditions decreased zinc finger E-box-binding homeobox 1 expression and increased E-cadherin levels in lung cancer H1975 cells, consequently suppressing cell invasion and migration. ACY-241 treatment also demonstrated an inhibitory effect on cell invasion and migration by reducing HIF-1α level. This study confirms that HDAC6 knockdown and ACY-241 treatment effectively decrease HIF-1α expression under normoxia, thereby suppressing the epithelial-mesenchymal transition. These findings highlight the potential of selective HDAC6 inhibition as an innovative therapeutic strategy for lung cancer.

Flower morphology as a predictor of pollination mode in a biotic to abiotic pollination continuum.

BACKGROUND AND AIMS: Wind pollination has evolved repeatedly in flowering plants, yet the identification of a wind pollination syndrome as a set of integrated floral traits can be elusive. Thalictrum (Ranunculaceae) comprises temperate perennial herbs that have transitioned repeatedly from insect to wind pollination while also exhibiting mixed pollination, providing an ideal system to test for evolutionary correlation between floral morphology and pollination mode in a biotic to abiotic continuum. Moreover, the lack of floral organ fusion across this genus allows testing for specialization to pollination vectors in the absence of this feature. METHODS: We expanded phylogenetic sampling in the genus from a previous study using six chloroplast loci, which allowed us to test whether species cluster into distinct pollination syndromes based on floral morphology. We then used multivariate analyses on floral traits followed by ancestral state reconstruction of the emerging flower morphotypes and determined whether these traits are evolutionarily correlated under a Bayesian framework with Brownian motion. KEY RESULTS: Floral traits fell into five distinct clusters, which were reduced to three after considering phylogenetic relatedness and were largely consistent with flower morphotypes and associated pollination vectors. Multivariate evolutionary analyses found a positive correlation between the lengths of floral reproductive structures (styles, stigmas, filaments and anthers). Shorter reproductive structures tracked insect-pollinated species and clades in the phylogeny, whereas longer structures tracked wind-pollinated ones, consistent with selective pressures exerted by biotic vs. abiotic pollination vectors, respectively. CONCLUSIONS: Although detectable suites of integrated floral traits across Thalictrum were correlated with wind or insect pollination at the extremes of the morphospace distribution, a presumed intermediate, mixed pollination mode morphospace was also detected. Thus, our data broadly support the existence of detectable flower morphotypes from convergent evolution underlying the evolution of pollination mode in Thalictrum, presumably via different paths from an ancestral mixed pollination state.

Computational design of a thermolabile uracil-DNA glycosylase of Escherichia coli.

Polymerase chain reaction (PCR) is a powerful tool to diagnose infectious diseases. Uracil DNA glycosylase (UDG) is broadly used to remove carryover contamination in PCR. However, UDG can contribute to false negative results when not inactivated completely, leading to DNA degradation during the amplification step. In this study, we designed novel thermolabile UDG derivatives by supercomputing molecular dynamic simulations and residual network analysis. Based on enzyme activity analysis, thermolability, thermal stability, and biochemical experiments of Escherichia coli-derived UDG and 22 derivatives, we uncovered that the UDG D43A mutant eliminated the false negative problem, demonstrated high efficiency, and offered great benefit for use in PCR diagnosis. We further obtained structural and thermodynamic insights into the role of the D43A mutation, including perturbed protein structure near D43; weakened pairwise interactions of D43 with K42, N46, and R80; and decreased melting temperature and native fraction of the UDG D43A mutant compared with wild-type UDG.

Development of quantitative and continuous measure for severity degree of Alzheimer's disease evaluated from MRI images of 761 human brains.

BACKGROUND: Alzheimer's disease affects profoundly the quality of human behavior and cognition. The very broad distribution of its severity across various human subjects requires the quantitative diagnose of Alzheimer's disease beyond the conventional tripartite classification of cohorts such as cognitively normal (CN), mild cognitive impairment (MCI), Alzheimer's disease (AD). The unfolding of such broad distributions by the quantitative and continuous degree of AD severity is necessary for the precise diagnose in the cross-sectional study of different stages in AD. RESULTS: We conducted the massive reanalysis on MRI images of 761 human brains based on the accumulated bigdata of Alzheimer's Disease Neuroimaging Initiative. The score matrix of cortical thickness profile at cortex points of subjects was constructed by statistically learning the cortical thickness data of 761 human brains. We also developed a new and simple algebraic predictor which provides the quantitative and continuous degree of AD severity of subjects along the scale from 0 for fully CN to 1 for fully AD state. The mathematical measure of a new predictor for the degree of AD severity is presented based on a covariance correlation matrix of cortical thickness profile between human subjects. One can remove the uncertainty in the determination of different stages in AD by the quantitative degree of AD severity and thus go far beyond the tripartite classification of cohorts. CONCLUSIONS: We unfold the nature of broad distribution of AD severity of subjects even within a given cohort by the scale from 0 for fully CN to 1 for fully AD state. The quantitative and continuous degree of AD severity developed in this study would be a good practical measure for diagnosing the different stages in AD severity.

Gene loss, genome rearrangement, and accelerated substitution rates in plastid genome of Hypericum ascyron (Hypericaceae).

BACKGROUND: Comparative genomic analysis exhibits dynamic evolution of plastid genome (plastome) in the clusioid clade of Malpighiales, which comprise five families, including multiple inversions and gene losses. Little is known about the plastome evolution in Hypericaceae, a large family in the clade. Only the plastome of one species, Cratoxylum cochinchinense, has been published. RESULTS: We generated a complete plastome sequence for Hypericum ascyron, providing the first complete plastome from the tribe Hypericeae (Hypericaceae). The H. ascyron plastome exhibits dynamic changes in gene and intron content, structure, and sequence divergence compared to the C. cochinchinense plastome from the tribe Cratoxyleae (Hypericaceae). Transcriptome data determined the evolutionary fate of the missing plastid genes infA, rps7, rps16, rpl23, and rpl32 in H. ascyron. Putative functional transfers of infA, rps7, and rpl32 were detected to the nucleus, whereas rps16 and rpl23 were substituted by nuclear-encoded homologs. The plastid rpl32 was integrated into the nuclear-encoded SODcp gene. Our findings suggested that the transferred rpl32 had undergone subfunctionalization by duplication rather than alternative splicing. The H. ascyron plastome rearrangements involved seven inversions, at least three inverted repeat (IR) boundary shifts, which generated gene relocations and duplications. Accelerated substitution rates of plastid genes were observed in the H. ascyron plastome compared with that of C. cochinchinense plastid genes. The higher substitution rates in the accD and clpP were correlated with structural change, including a large insertion of amino acids and losses of two introns, respectively. In addition, we found evidence of positive selection of the clpP, matK, and rps3 genes in the three branches related to H. ascyron. In particular, the matK gene was repeatedly under selection within the family Hypericaceae. Selective pressure in the H. ascyron matK gene was associated with the loss of trnK-UUU and relocation into the IR region. CONCLUSIONS: The Hypericum ascyron plastome sequence provides valuable information for improving the understanding of plastome evolution among the clusioid of the Malpighiales. Evidence for intracellular gene transfer from the plastid to the nucleus was detected in the nuclear transcriptome, providing insight into the evolutionary fate of plastid genes in Hypericaceae.

Fiber-Based Electrochemical Biosensors for Monitoring pH and Transient Neurometabolic Lactate.

Developing tools that are able to monitor transient neurochemical dynamics is important to decipher brain chemistry and function. Multifunctional polymer-based fibers have been recently applied to monitor and modulate neural activity. Here, we explore the potential of polymer fibers comprising six graphite-doped electrodes and two microfluidic channels within a flexible polycarbonate body as a platform for sensing pH and neurometabolic lactate. Electrodes were made into potentiometric sensors (responsive to pH) or amperometric sensors (lactate biosensors). The growth of an iridium oxide layer made the fiber electrodes responsive to pH in a physiologically relevant range. Lactate biosensors were fabricated via platinum black growth on the fiber electrode, followed by an enzyme layer, making them responsive to lactate concentration. Lactate fiber biosensors detected transient neurometabolic lactate changes in an in vivo mouse model. Lactate concentration changes were associated with spreading depolarizations, known to be detrimental to the injured brain. Induced waves were identified by a signature lactate concentration change profile and measured as having a speed of ∼2.7 mm/min (n = 4 waves). Our work highlights the potential applications of fiber-based biosensors for direct monitoring of brain metabolites in the context of injury.

Symmetry Dictated Grain Boundary State in a Two-Dimensional Topological Insulator.

Grain boundaries (GBs) are ubiquitous in solids and have been of central importance in understanding the nature of polycrystals. In addition to their classical roles, topological insulators (TIs) offer a chance to realize GBs hosting distinct topological states that can be controlled by their crystal symmetries. However, such roles of crystalline symmetry in two-dimensional (2D) TIs have not been definitively measured yet. Here, we present the first direct evidence of a symmetry-enforced metallic state along a GB in 1T'-MoTe2, a prototypical 2D TI. Using scanning tunneling microscopy, we show a metallic state along a GB with nonsymmorphic lattice symmetry and its absence along another boundary with symmorphic symmetry. Our atomistic simulations demonstrate in-gap Weyl semimetallic states for the former, whereas they demonstrate gapped states for the latter, explaining our observation well. The observed metallic state, tightly linked to its crystal symmetry, can be used to create a stable conducting nanowire inside TIs.

Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes.

Caprifoliaceae s.l. plastid genomes (plastomes) show that one inversion and two inverted repeat boundary shifts occurred in the common ancestor of this family, after which the plastomes are generally conserved. This study reports plastome sequences of five additional species, Fedia cornucopiae, Valeriana fauriei, and Valerianella locusta from the subfamily Valerianoideae, as well as Dipsacus japonicus and Scabiosa comosa from the subfamily Dipsacoideae. Combined with the published plastomes, these plastomes provide new insights into the structural evolution of plastomes within the family. Moreover, the three plastomes from the subfamily Valerianoideae exhibited accelerated nucleotide substitution rates, particularly at synonymous sites, across the family. The patterns of accD sequence divergence in the family are dynamic with structural changes, including interruption of the conserved domain and increases in nonsynonymous substitution rates. In particular, the Valeriana accD gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the Valeriana accD gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the clpP gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded rps15, and a potential functional gene transfer to the nucleus was confirmed.

Refractory Dry Eye Syndrome after Transconjunctival Excision of the Palpebral Lobe of the Lacrimal Gland.

The aim of the present study was to report two cases of refractory dry eye syndrome (DES) after transconjunctival excision of the palpebral lobe of the lacrimal gland. A 25-year-old female patient with a chief complaint of a palpable mass in both upper eyelids visited our medical center. Preoperative orbital computer tomography showed high-attenuation lesions in both lacrimal glands. Incisional biopsy of the lacrimal gland palpebral lobe via transconjunctival incision was performed in January 2019. At 1 month after the biopsy, a lack of tears and persistent corneal erosions were found in both eyes. Artificial tears, punctal occlusion, autologous serum eye drops, and therapeutic contact lenses were applied in an attempt to control the dry eye symptoms. The patient continues to suffer from intractable DES at 2.5 years after the procedure. The second case involved a 52-year-old female patient who visited our medical center with a chief complaint of a palpable mass in both upper eyelids. Bilateral orbital tumors were diagnosed with preoperative magnetic resonance imaging. An incisional biopsy of the lacrimal gland was performed. Immunoglobulin G4-related dacryoadenitis was confirmed through lacrimal palpebral lobe incisional biopsy. Intractable DES and corneal erosion of her left eye persisted thereafter. A transconjunctival incision is an effective approach for minimizing postoperative scars and is suitable for the biopsy of tumors that are visible through the conjunctiva. After a biopsy of the palpebral lobe of the main lacrimal glands, the secretion of reflex tears decreases due to damage to the secreting ducts of the main lacrimal glands. However, total tear secretion can be maintained by basal tear secretion from the accessory lacrimal glands. In this report, we describe two cases of refractory DES due to decreased total tear secretion, although only the palpebral lobes of the main lacrimal glands were biopsied.

Magnetothermal Multiplexing for Selective Remote Control of Cell Signaling.

Magnetic nanoparticles have garnered sustained research interest for their promise in biomedical applications including diagnostic imaging, triggered drug release, cancer hyperthermia, and neural stimulation. Many of these applications make use of heat dissipation by ferrite nanoparticles under alternating magnetic fields, with these fields acting as an externally administered stimulus that is either present or absent, toggling heat dissipation on and off. Here, we motivate and demonstrate an extension of this concept, magnetothermal multiplexing, in which exposure to alternating magnetic fields of differing amplitude and frequency can result in selective and independent heating of magnetic nanoparticle ensembles. The differing magnetic coercivity of these particles, empirically characterized by a custom high amplitude alternating current magnetometer, informs the systematic selection of a multiplexed material system. This work culminates in a demonstration of magnetothermal multiplexing for selective remote control of cellular signaling in vitro.

Flexible fiber-based optoelectronics for neural interfaces.

Neurological and psychiatric conditions pose an increasing socioeconomic burden on our aging society. Our ability to understand and treat these conditions relies on the development of reliable tools to study the dynamics of the underlying neural circuits. Despite significant progress in approaches and devices to sense and modulate neural activity, further refinement is required on the spatiotemporal resolution, cell-type selectivity, and long-term stability of neural interfaces. Guided by the principles of neural transduction and by the materials properties of the neural tissue, recent advances in neural interrogation approaches rely on flexible and multifunctional devices. Among these approaches, multimaterial fibers have emerged as integrated tools for sensing and delivering of multiple signals to and from the neural tissue. Fiber-based neural probes are produced by thermal drawing process, which is the manufacturing approach used in optical fiber fabrication. This technology allows straightforward incorporation of multiple functional components into microstructured fibers at the level of their macroscale models, preforms, with a wide range of geometries. Here we will introduce the multimaterial fiber technology, its applications in engineering fields, and its adoption for the design of multifunctional and flexible neural interfaces. We will discuss examples of fiber-based neural probes tailored to the electrophysiological recording, optical neuromodulation, and delivery of drugs and genes into the rodent brain and spinal cord, as well as their emerging use for studies of nerve growth and repair.

Vertical MoS2 Double-Layer Memristor with Electrochemical Metallization as an Atomic-Scale Synapse with Switching Thresholds Approaching 100 mV.

Atomically thin two-dimensional (2D) materials-such as transition metal dichalcogenide (TMD) monolayers and hexagonal boron nitride (hBN)-and their van der Waals layered preparations have been actively researched to build electronic devices such as field-effect transistors, junction diodes, tunneling devices, and, more recently, memristors. Two-dimensional material memristors built in lateral form, with horizontal placement of electrodes and the 2D material layers, have provided an intriguing window into the motions of ions along the atomically thin layers. On the other hand, 2D material memristors built in vertical form with top and bottom electrodes sandwiching 2D material layers may provide opportunities to explore the extreme of the memristive performance with the atomic-scale interelectrode distance. In particular, they may help push the switching voltages to a lower limit, which is an important pursuit in memristor research in general, given their roles in neuromorphic computing. In fact, recently Akinwande et al. performed a pioneering work to demonstrate a vertical memristor that sandwiches a single MoS2 monolayer between two inert Au electrodes, but it could neither attain switching voltages below 1 V nor control the switching polarity, obtaining both unipolar and bipolar switching devices. Here, we report a vertical memristor that sandwiches two MoS2 monolayers between an active Cu top electrode and an inert Au bottom electrode. Cu ions diffuse through the MoS2 double layers to form atomic-scale filaments. The atomic-scale thickness, combined with the electrochemical metallization, lowers switching voltages down to 0.1-0.2 V, on par with the state of the art. Furthermore, our memristor achieves consistent bipolar and analogue switching, and thus exhibits the synapse-like learning behavior such as the spike-timing dependent plasticity (STDP), the very first STDP demonstration among all 2D-material-based vertical memristors. The demonstrated STDP with low switching voltages is promising not only for low-power neuromorphic computing, but also from the point of view that the voltage range approaches the biological action potentials, opening up a possibility for direct interfacing with mammalian neuronal networks.

Common Repository of FBS Proteins (cRFP) To Be Added to a Search Database for Mass Spectrometric Analysis of Cell Secretome.

We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search of cell secretomes. cRFP is a small supplementary sequence list of highly abundant fetal bovine serum proteins added to the reference database in use. The aim behind using cRFP is to prevent the contaminant FBS proteins from being misidentified as other proteins in the reference database, just as we would use cRAP (common Repository of Adventitious Proteins) to prevent contaminant proteins present either by accident or through unavoidable contacts from being misidentified as other proteins. We expect it to be widely used in experiments where the proteins are obtained from serum-free media after thorough washing of the cells, or from a complex media such as SILAC, or from extracellular vesicles directly.

Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae).

BACKGROUND: Lychnis kiusiana Makino is an endangered perennial herb native to wetland areas in Korea and Japan. Despite its conservational and evolutionary significance, population genetic resources are lacking for this species. Next-generation sequencing has been accepted as a rapid and cost-effective solution for the identification of microsatellite markers in nonmodel plants. RESULTS: Using Illumina HiSeq 2000 sequencing technology, we assembled 67,498,600 reads into 91,900 contigs and identified 11,403 microsatellite repeat motifs in 9563 contigs. A total of 4510 microsatellite-containing transcripts had Gene Ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 124 pathways with significant scores. Many microsatellites in the L. kiusiana leaf transcriptome were linked to genes involved in the plant response to light intensity, salt stress, temperature stimulus, and nutrient and water deprivation. A total of 12,486 single-nucleotide polymorphisms (SNPs) were identified on transcripts harboring microsatellites. The analysis of nucleotide substitution rates for 2389 unigenes indicated that 39 genes were under strong positive selection. The primers of 6911 microsatellites were designed, and 40 of 50 selected primer pairs were consistently and successfully amplified from 51 individuals. Twenty-five of these were polymorphic, and the average number of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to 0.827, respectively, and locus-specific FIS estimates ranged from - 0.116 to 0.290. Eleven of the 25 primer pairs were successfully amplified in three additional species of Lychnis: 56% in L. wilfordii, 64% in L. cognata and 80% in L. fulgens. CONCLUSIONS: The transcriptomic SSR markers of Lychnis kiusiana provide a valuable resource for understanding the population genetics, evolutionary history, and effective conservation management of this species. Furthermore, the identified microsatellite loci linked to the annotated genes should be useful for developing functional markers of L. kiusiana. The developed markers represent a potentially valuable source of transcriptomic SSR markers for population genetic analyses with moderate levels of cross-taxon portability.

Multifunctional Fibers as Tools for Neuroscience and Neuroengineering.

Multifunctional devices for modulation and probing of neuronal activity during free behavior facilitate studies of functions and pathologies of the nervous system. Probes composed of stiff materials, such as metals and semiconductors, exhibit elastic and chemical mismatch with the neural tissue, which is hypothesized to contribute to sustained tissue damage and gliosis. Dense glial scars have been found to encapsulate implanted devices, corrode their surfaces, and often yield poor recording quality in long-term experiments. Motivated by the hypothesis that reducing the mechanical stiffness of implanted probes may improve their long-term reliability, a variety of probes based on soft materials have been developed. In addition to enabling electrical neural recording, these probes have been engineered to take advantage of genetic tools for optical neuromodulation. With the emergence of optogenetics, it became possible to optically excite or inhibit genetically identifiable cell types via expression of light-sensitive opsins. Optogenetics experiments often demand implantable multifunctional devices to optically stimulate, deliver viral vectors and drugs, and simultaneously record electrophysiological signals from the specified cells within the nervous system. Recent advances in microcontact printing and microfabrication techniques have equipped flexible probes with microscale light-emitting diodes (µLEDs), waveguides, and microfluidic channels. Complementary to these approaches, fiber drawing has emerged as a scalable route to integration of multiple functional features within miniature and flexible neural probes. The thermal drawing process relies on the fabrication of macroscale models containing the materials of interest, which are then drawn into microstructured fibers with predefined cross-sectional geometries. We have recently applied this approach to produce fibers integrating conductive electrodes for extracellular recording of single- and multineuron potentials, low-loss optical waveguides for optogenetic neuromodulation, and microfluidic channels for drug and viral vector delivery. These devices allowed dynamic investigation of the time course of opsin expression across multiple brain regions and enabled pairing of optical stimulation with local pharmacological intervention in behaving animals. Neural probes designed to interface with the spinal cord, a viscoelastic tissue undergoing repeated strain during normal movement, rely on the integration of soft and flexible materials to avoid injury and device failure. Employing soft substrates, such as parylene C and poly-(dimethylsiloxane), for electrode and µLED arrays permitted stimulation and recording of neural activity on the surface of the spinal cord. Similarly, thermally drawn flexible and stretchable optoelectronic fibers that resemble the fibrous structure of the spinal cord were implanted without any significant inflammatory reaction in the vicinity of the probes. These fibers enabled simultaneous recording and optogenetic stimulation of neural activity in the spinal cord. In this Account, we review the applications of multifunctional fibers and other integrated devices for optoelectronic probing of neural circuits and discuss engineering directions that may facilitate future studies of nerve repair and accelerate the development of bioelectronic medical devices.