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Glycosylation is a unique posttranslational modification that dynamically shapes the surface of cells. Glycans attached to proteins or lipids in a cell or tissue are studied as a whole and collectively designated as a glycome. UniCarb-DB is a glycomic spectral library of tandem mass spectrometry (MS/MS) fragment data. The current version of the database consists of over 1500 entries and over 1000 unique structures. Each entry contains parent ion information with associated MS/MS spectra, metadata about the original publication, experimental conditions, and biological origin. Each structure is also associated with the GlyTouCan glycan structure repository allowing easy access to other glycomic resources. The database can be directly utilized by mass spectrometry (MS) experimentalists through the conversion of data generated by MS into structural information. Flexible online search tools along with a downloadable version of the database are easily incorporated in either commercial or open-access MS software. This chapter highlights UniCarb-DB online search tool to browse differences of isomeric structures between spectra, a peak matching search between user-generated MS/MS spectra and spectra stored in UniCarb-DB and more advanced MS tools for combined quantitative and qualitative glycomics.
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Glicómica , Polisacáridos , Programas Informáticos , Espectrometría de Masas en Tándem , Espectrometría de Masas en Tándem/métodos , Glicómica/métodos , Polisacáridos/química , Polisacáridos/análisis , Bases de Datos Factuales , Glicosilación , HumanosRESUMEN
Two-dimensional transition metal dichalcogenides (TMDs) are promising materials for semiconductor nanodevices owing to their flexibility, transparency, and appropriate band gaps. A variety of optoelectronic and electronic devices based on TMDs p-n diodes have been extensively investigated due to their unique advantages. However, improving their performance is challenging for commercial applications. In this study, we propose a facile and doping-free approach based on the contact engineering of a few-layer tungsten di-selenide to form a lateral p-n homojunction photovoltaic. By combining surface and edge contacts for p-n diode fabrication, the photovoltaic effect is achieved with a high fill factor of ≈0.64, a power conversion efficiency of up to ≈4.5%, and the highest external quantum efficiency with a value of ≈67.6%. The photoresponsivity reaches 283 mA/W, indicating excellent photodiode performance. These results demonstrate that our technique has great potential for application in next-generation optoelectronic devices.
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Stacking of graphene with hexagonal boron nitride (h-BN) can dramatically modify its bands from their usual linear form, opening a series of narrow minigaps that are separated by wider minibands. While the resulting spectrum offers strong potential for use in functional (opto)electronic devices, a proper understanding of the dynamics of hot carriers in these bands is a prerequisite for such applications. In this work, we therefore apply a strategy of rapid electrical pulsing to drive carriers in graphene/h-BN heterostructures deep into the dissipative limit of strong electron-phonon coupling. By using electrical gating to move the chemical potential through the "Moiré bands", we demonstrate a cyclical evolution between metallic and semiconducting states. This behavior is captured in a self-consistent model of non-equilibrium transport that considers the competition of electrically driven inter-band tunneling and hot-carrier scattering by strongly non-equilibrium phonons. Overall, our results demonstrate how a treatment of the dynamics of both hot carriers and hot phonons is essential to understanding the properties of functional graphene superlattices.
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Two-dimensional (2D) materials and their heterostructures exhibit intriguing optoelectronic properties; thus, they are good platforms for exploring fundamental research and further facilitating real device applications. The key is to preserve the high quality and intrinsic properties of 2D materials and their heterojunction interface even in production scale during the transfer and assembly process so as to apply in semiconductor manufacturing field. In this study, we successfully adopted a wet transfer existing method to separate mediator-assisted wafer-scale from SiO2/Si growing wafer for the first time with intermediate annealing to fabricate wafer-scale MoS2/h-BN and WS2/h-BN heterostructures on a SiO2/Si wafer. Interestingly, the high-quality wafer-scale 2D material heterostructure optical properties were enhanced and confirmed by Raman and photoluminescence spectroscopy. Our approach can be applied to other 2D materials and expedite mass production for industrial applications.
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Ambient air commonly contains carbon dioxide at concentrations greater than 400 µmol mol-1 and methane at ~ 2000 nmol mol-1; non-methane hydrocarbons are also widespread in the atmosphere at much lower concentrations. For quantification of various carbon-containing compounds in typical analytical instrument, corresponding number of reference materials are required. Therefore, the development of a method that uses a single reference material applicable to air monitoring is desired. Here, we examined a post-column reaction system combined with a gas chromatograph equipped with a flame ionization detector (FID), which involves oxidation and reduction processes after separation. To determine various carbon-containing gases by post-column reaction gas chromatography with FID (GC-r-FID) using a single reference, it is necessary to confirm a good linearity of the response with carbon concentrations originating from various carbon-containing gases. When mixtures of carbon-containing gases at three different concentrations and the calibration curve of the FID response with the concentration converted into methane were used, a single linear calibration curve (correlation coefficient > 0.9999, 18 points) was obtained over four orders of magnitudes (to ~ 5000 µmol mol-1 as methane). The applicability of GC-r-FID was confirmed by determining carbon-containing gases in air and gas seeped from the seafloor samples. Because the results were comparable to those obtained by conventional GC-FID and GC-thermal conductivity detector, typically GC-r-FID with a single reference gas should be suitable for air monitoring.
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Owing to their practical applications, two-dimensional semiconductor p-n diodes have attracted enormous attention. Over the past decade, various methods, such as chemical doping, heterojunction structures, and metallization using metals with different work functions, have been reported for fabrication of such devices. In this study, a lateral p-n junction diode is formed in tungsten diselenide (WSe2 ) using a combination of edge and surface contacts. The appearance of amorphous tungsten oxide at etched WSe2 , and the formation of a junction near the edge contact, are verified by high-resolution transmission electron microscopy. The device demonstrates high on/off ratio for both the edge and surface contacts, with respective values of 107 and 108 . The diode can achieve extremely high mobility of up to 168 cm2 V-1 s-1 and a rectification ratio of 103 . The ideality factor is 1.11 at a back gate voltage VG = 60 V at 300 K. The devices with encapsulation of hexagonal boron nitride exhibit good stability to atmospheric exposure, over a measured period of 2 months. In addition, the architecture of the contacts, which is based on a single-channel device, should be advantageous for the implementation of more complicated applications such as inverters, photodetectors, and light-emitting diodes.
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Transition metal dichalcogenides (TMDs) are of great interest owing to their unique properties. However, TMD materials face two major challenges that limit their practical applications: contact resistance and surface contamination. Herein, a strategy to overcome these problems by inserting a monolayer of hexagonal boron nitride (h-BN) at the chromium (Cr) and tungsten disulfide (WS2 ) interface is introduced. Electrical behaviors of direct metal-semiconductor (MS) and metal-insulator-semiconductor (MIS) contacts with mono- and bilayer h-BN in a four-layer WS2 field-effect transistor (FET) are evaluated under vacuum from 77 to 300 K. The performance of the MIS contacts differs based on the metal work function when using Cr and indium (In). The contact resistance is significantly reduced by approximately ten times with MIS contacts compared with that for MS contacts. An electron mobility up to ≈115 cm2 V-1 s-1 at 300 K is achieved with the insertion of monolayer h-BN, which is approximately ten times higher than that with MS contacts. The mobility and contact resistance enhancement are attributed to Schottky barrier reduction when h-BN is introduced between Cr and WS2 . The dependence of the tunneling mechanisms on the h-BN thickness is investigated by extracting the tunneling barrier parameters.
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In this study, an electrostatically induced quantum confinement structure, so-called quantum point contact, has been realized in a p-type trilayer tungsten diselenide-based van der Waals heterostructure with modified van der Waals contact method with degenerately doped transition metal dichalcogenide crystals. Clear quantized conductance and pinch-off state through the one-dimensional confinement were observed by dual-gating of split gate electrodes and top gate. Conductance plateaus were observed at a step of e2/h in addition to quarter plateaus such as 0.25 × 2e2/h at a finite bias voltage condition indicating the signature of intrinsic spin-polarized quantum point contact.
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Two-dimensional (2D) molybdenum disulphide (MoS2) transition metal dichalcogenides (TMDs) have great potential for use in optical and electronic device applications; however, the performance of MoS2is limited by its crystal quality, which serves as a measure of the defects and grain boundaries in the grown material. Therefore, the high-quality growth of MoS2crystals continues to be a critical issue. In this context, we propose the formation of high-quality MoS2crystals via the flux method. The resulting electrical properties demonstrate the significant impact of crystal morphology on the performance of MoS2field-effect transistors. MoS2made with a relatively higher concentration of sulphur (a molar ratio of 2.2) and at a cooling rate of 2.5 °C h-1yielded good quality and optimally sized crystals. The room-temperature and low-temperature (77 K) electrical transport properties of MoS2field-effect transistors (FETs) were studied in detail, with and without the use of a hexagonal boron nitride (h-BN) dielectric to address the mobility degradation issue due to scattering at the SiO2/2D material interface. A maximum field-effect mobility of 113 cm2V-1s-1was achieved at 77 K for the MoS2/h-BN FET following high-quality crystal formation by the flux method. Our results confirm the achievement of large-scale high-quality crystal growth with reduced defect density using the flux method and are key to achieving higher mobility in MoS2FET devices in parallel with commercially accessible MoS2crystals.
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Magnetic force microscopy (MFM) is utilized to characterize the magnetic moment in nanostructured plant leaf-derived graphene quantum dot clusters (GQDCs). The MFM signal reveals that the magnetic response of the GQDCs depends on the height and width of the GQDCs. However, individual GQDs, and smaller clusters with widths of less than 20 nm, have not shown any observable magnetic signal. Importantly, experimental analyses suggest that the magnetic signal of GQDCs distributed in a plane can be effectively detected at room temperature. These results could pave the way for future graphene-based magnetic storage media and spin manipulation quantum devices.
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Glycans serve important roles in signaling events and cell-cell communication, and they are recognized by lectins, viruses and bacteria, playing a variety of roles in many biological processes. However, there was no system to organize the plethora of glycan-related data in the literature. Thus GlyTouCan (https://glytoucan.org) was developed as the international glycan repository, allowing researchers to assign accession numbers to glycans. This also aided in the integration of glycan data across various databases. GlyTouCan assigns accession numbers to glycans which are defined as sets of monosaccharides, which may or may not be characterized with linkage information. GlyTouCan was developed to be able to recognize any level of ambiguity in glycans and uniquely assign accession numbers to each of them, regardless of the input text format. In this manuscript, we describe the latest update to GlyTouCan in version 3.0, its usage, and plans for future development.
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Biología Computacional/métodos , Bases de Datos Factuales , Polisacáridos/clasificación , Programas Informáticos , Humanos , Cooperación Internacional , Internet , Polisacáridos/análisis , Polisacáridos/química , Terminología como AsuntoAsunto(s)
Carbohidratos/química , Carbohidratos/fisiología , Glicómica , Internet , Bases de Datos FactualesRESUMEN
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
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Disciplinas de las Ciencias Biológicas , Biología Computacional , Web Semántica , Minería de Datos , Metadatos , Reproducibilidad de los ResultadosRESUMEN
Although semiconductor to metal phase transformation of MoTe2 by high-density laser irradiation of more than 0.3 MW cm-2 has been reported, we reveal that the laser-induced-metal (LIM) phase is not the 1T' structure derived by a polymorphic-structural phase transition but consists instead of semi-metallic Te induced by photo-thermal decomposition of MoTe2. The technique is used to fabricate a field effect transistor with a Pd/2H-MoTe2/LIM structure having an asymmetric metallic contact, and its contact properties are studied via scanning gate microscopy. We confirm that a Schottky barrier (a diffusion potential) is always formed at the Pd/2H-MoTe2 boundary and obstacles a carrier transport while an Ohmic contact is realized at the 2H-MoTe2/LIM phase junction for both n- and p-type carriers.
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We use transient electrical measurements to investigate the details of self-heating and charge trapping in graphene transistors encapsulated in hexagonal boron nitride (h-BN) and operated under strongly nonequilibrium conditions. Relative to more standard devices fabricated on SiO2 substrates, encapsulation is shown to lead to an enhanced immunity to charge trapping, the influence of which is only apparent under the combined influence of strong gate and drain electric fields. Although the precise source of the trapping remains to be determined, one possibility is that the strong gate field may lower the barriers associated with native defects in the h-BN, allowing them to mediate the capture of energetic carriers from the graphene channel. Self-heating in these devices is identified through the observation of time-dependent variations of the current in graphene and is found to be described by a time constant consistent with expectations for nonequilibrium phonon conduction into the dielectric layers of the device. Overall, our results suggest that h-BN-encapsulated graphene devices provide an excellent system for implementations in which operation under strongly nonequilibrium conditions is desired.
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The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.
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Biología Computacional/métodos , Glicómica/métodos , Glicoproteínas/metabolismo , Polisacáridos/metabolismo , Animales , Biología Computacional/normas , Bases de Datos Factuales/normas , Bases de Datos Factuales/estadística & datos numéricos , Humanos , Espectrometría de Masas/métodos , Estándares de ReferenciaRESUMEN
A high-precision analytical system to observe the variations in the amount fractions of atmospheric oxygen with a very small uncertainty was developed. The system comprises a magneto-pneumatic oxygen analyzer and three automatic pressure controllers. The drift of the analyzer's signal intensity can be reduced when the amount fractions of oxygen in the sample and reference gases are similar because the temperature coefficient of the analyzer linearly depends on the difference between these amount fractions. The repeatability of oxygen determination and the long-term stability of the system were tested to assess the applicability of the analyzer to field-based measurements for continuous atmospheric observations. The standard deviation of the average for 10-min measurements in the 5-day long-term stability test was 0.7 µmol mol-1 after a temperature correction. This indicates that the system can continuously measure the amount fractions of oxygen in the atmosphere for a few days without interruption for any calibration and/or compensation for the signal drift.
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Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.
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Bases de Datos de Compuestos Químicos , Glicómica/métodos , Polisacáridos/química , Glicómica/normas , Polisacáridos/clasificaciónRESUMEN
GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) was proposed during the early stages of the GlyTouCan project. GlyTouCan uses WURCS as its base representation for glycans because existing formats were insufficient in their flexibility to represent any and all glycans universally. Therefore, in order to obtain WURCS strings for existing or new glycan structures, conversion tools or glycan structure editors that can export WURCS became necessary. GlycanBuilder was an obvious choice to extend due to its wide usage by the community. However, GlycanBuilder was limited because it was originally developed to support mammalian glycans. It also did not support the newly proposed monosaccharide symbol standard called Symbol Nomenclature for Glycans (SNFG). Therefore in this work, we implemented a new version of GlycanBuilder to greatly increase its usability. The glycan rendering system was refactored so that cyclic glycans, nested repeating units, monosaccharide compositions and cross-linked glycan structures can be represented. Both import and export utilities for WURCS were also implemented and SNFG symbols were incorporated to allow glycans to be exported as graphics using the latest glycan symbol nomenclature. This new version of GlycanBuilder called "GlycanBuilder2", is able to support a wide variety of ambiguous glycans, including structures containing monosaccharides from bacteria and plants. These glycans can also be displayed using the new SNFG symbols. This tool can aid researchers in communicating about the complex, diverse, and ambiguous structures of glycans more rapidly. Moreover, the new GlycanBuilder can now easily output WURCS sequences from glycans drawn on the canvas. Most importantly, because GlyTouCan employs WURCS as the basic format for registration and searching of glycan information, a wider variety of glycans can now be readily registered and queried in GlyTouCan.
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Glicómica/métodos , Polisacáridos/química , Secuencia de Carbohidratos , Gráficos por ComputadorRESUMEN
A flake of monolayer graphene was sandwiched between boron nitride sheets. Temperature dependent Shubnikov-de Haas measurements were performed to access how this technique influences the electronic properties of the graphene sample. The maximum mobility found in this configuration was approximately 105 cm2 Vs -1. From the phase of the oscillations a Berry phase ß of 1/2 was obtained indicating the presence of Dirac fermions. We obtained Fermi velocities around [Formula: see text] m s-1 which imply hopping energies close to 2.5 eV. Furthermore, the carrier lifetime is typically higher than that found in graphene supported by SiO2, reaching values higher than 700 fs.