ALBERT

Description: Journal of Proteome Research DOI: 10.1021/acs.jproteome.6b00138

Description: We present a numerical study on phononic band gaps and resonances occurring at the edge of a semi-infinite two-dimensional (2D) phononic crystal plate. The edge supports localized edge waves coupling to evanescent phononic plate modes that decay exponentially into the semi-infinite phononic crystal plate. The band-gap range and the number of edge-wave eigenmodes can be tailored by tuning the distance between the edge and the semi-infinite 2D phononic lattice. As a result, a phononic band gap for simultaneous edge waves and plate waves is created, and phononic cavities beside the edge can be built to support high-frequency edge resonances. We design an L3 edge cavity and analyze its resonance characteristics. Based on the band gap, high quality factor and strong confinement of resonant edge modes are achieved. The results enable enhanced control over acoustic energy flow in phononic crystal plates, which can be used in designing micro and nanoscale resonant devices and coupling of edge resonances to other types of phononic or photonic crystal cavities.

Description: Using light-emitting diodes (LEDs) for visible light communication has become an alternative choice of radio source due to channel crowding of the radio-frequency (RF) signal. The modulation bandwidth of LEDs is usually limited by the spontaneous carrier lifetime in multiple quantum wells. Here, sub-GHz modulation of GaN-based LED employing photonic crystal (PhC) nanostructure is demonstrated. The guided photonic modes of the LEDs are modulated by the RF signal. Both carrier lifetime of lower- and higher-order modes are studied in time-resolved photoluminescence (TRPL) at room temperature. The f - 3 dB - J curve of the PhC LED exhibits a higher bandwidth than the typical LED structure. At 11.41 kA/cm 2 , the optical −3-dB bandwidth ( f - 3 dB ) up to 234 MHz of the PhC LED (PhCLED) is achieved. Our studies on TRPL at different wavelengths and frequency response at different injection current densities conclude that the higher operation speed is attributed to faster radiative carrier recombination of extracted guided modes from the PhC nanostructure.

Description: MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase ( http://miRTarBase.mbc.nctu.edu.tw/ ) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.

Description: Background: Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 min and 12 h. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. Results: A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found that most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signals, such as auxin and ABA signaling. While comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested many downstream proteins of BR signaling are induced by phosphorylation via various kinases, not through transcriptional regulation. Conclusions: Through a large-scale dynamic profile of phosphoproteome coupled with bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified in our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.

Description: Background: Complete or partial trisomy 10q involves a duplication of 10q, or the long arm of chromosome 10. Distal 10q trisomy is a well-recognized and defined but rare genetic syndrome in which duplication of distal segments of 10q results in a pattern of malformations. Although abnormal chromosome phenotypes are commonly detected by visualization of chromosomes by traditional cytogenetic techniques, this approach is marginal in both diagnostic sensitivity and potential for biological interpretation, thus making implementation of advanced techniques and analysis methods an important consideration in a health service.Case presentationThe present study describes the case of a Taiwanese boy from healthy parents with mental, growth, and psychomotor retardations. Additional clinical features included facial dysmorphism, microcephaly, brain atrophy, camptodactyly, and—as the first reported case—bilateral renal atrophy with chronic kidney disease stage 2 and the presence of a renal cyst in one kidney. A novel 21.8 Mb copy number variation region in chromosome region 10q23.1–10q25.1 was verified by array-comparative genomic hybridization in combination with quantitative real-time polymerase chain reaction. Subsequently, 200 protein-coding genes were identified in this copy number variation region and analyzed for their biological meaning using the database for annotation, visualization and integrated discovery. Conclusion: According to the result of gene functional enrichment analysis using database for annotation, visualization and integrated discovery, the Wnt signaling pathway is the most pertinent to the gene content in the copy number variation region. A change in the expression levels of some Wnt signaling pathway components and of NFKB2 and PTEN genes due to a gain in their gene copy number may be associated with the patient’s clinical outcomes including brain atrophy, bilateral renal atrophy with chronic kidney disease stage 2, a renal cyst in one kidney, and growth retardation.

Description: Analytical Chemistry DOI: 10.1021/ac503325c