Developing high-resolution methods to study DNA and RNA dynamics

Nucleic acids, including DNA and RNA, are one of the most important biomacromolecules inside the cell. DNA stores genetic information, while RNA has more versatile roles including conveying and deciphering genetic information, catalyzing biological reactions, conducting post- transcriptional regulation, and even storing genetic information. To understand the functioning principles of cells and living organisms, it is very important to study DNA- and RNA-involved biochemical reactions as well as the molecular mechanisms behind them, which is quite challenging due to the small size and high metabolism rate of cells. Thanks to the technology advancement in the past several decades, we are able to develop research methods to achieve high-rate, high-resolution and high-throughput study on DNA and RNA. Here we developed several fluorescence-based high-resolution assays to study DNA and RNA dynamics in vitro and in vivo. First, we established a single molecule FRET assay to study homodimeric single-stranded binding protein (Thermus thermophilus SSB) specifically binding and protecting single-stranded DNA during DNA metabolism. With the help of specifically designed DNA constructs and total internal reflection microscopy, we discovered that homodimeric SSB showed similar one- dimensional diffusion and salt-dependent binding mode transition behavior which was confirmed for intensively studied homotetrameric SSB, suggesting that those behaviors might be universal among SSB homologues from different organisms. Second, we developed a live cell RNA labeling and imaging method based on an aptamer- fluorogen system called “Spinach”, which contains an RNA sequence that binds a fluorogen DFHBI and induces its fluorescence. We constructed a Spinach array with tandem Spinach repeats and it greatly enhanced the cellular fluorescence signal, and we could easily visualize mRNAs in the cell. We further characterized the Spinach RNA imaging method and found that either single Spinach or Spinach arrays do not affect RNA transcription, protein translation or RNA degradation. Therefore we proposed that aptamer/fluorogen imaging and aptamer array construction could be a generalizable strategy for high performance and low perturbation live cell RNA imaging. Finally, we expanded the research to gene expression regulation. Our research target, sgrS, is a bacterial small RNA that regulates several target genes at post-transcriptional level in response to sugar-phosphate stress. It is known that sgrS anneals target transcripts via basepairing interaction with the guide of Hfq protein. Nevertheless, how individual nucleotides within sgrS sequence contribute to the regulation process is not clear. Here we utilized the recently developed Sort-Seq method combining fluorescence-activated cell sorting (FACS) and high-throughput DNA sequencing to study sequence-dependent sgrS regulation on its primary target, ptsG. We constructed a target-reporter system with ptsG 5’ UTR, which is responsible for sgrS annealing, fused to GFP, whose expression level is indicated by fluorescence level and is capable of being regulated by sgrS. By introducing an sgrS random mutation library, cells show various fluorescence levels due to diverse regulation capabilities of sgrS mutants. By sorting the cells into different groups based on its fluorescence signal followed by extracting the sgrS mutation distribution among sorted groups, we could find out which mutations totally abolished sgrS function. Results showed that 2 nucleotides involved in ptsG/sgrS annealing, G176 and G178, are extremely significant; other 24 nucleotides are equally significant, but they are involved in sgrS binding by Hfq. The study suggested important nucleotides within the sgrS/ptsG annealing region, and emphasized the significance of Hfq in maintaining sgrS function

Superior High-Energy-Density Biocidal Agent Achieved with a 3D Metal−Organic Framework

17 USC 105 interim-entered record; under review.The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsami.0c12251.|17 USC 105 interim-entered record; under review.The article of record as published may be foun|d at https://doi.org/A significant number of challenges are encountered when developing biocidal agents with high throwing capacity for biosafety applications. Now a three-dimensional metal−organic framework (3D MOF) {MOF (2), [Cu(atrz)(IO3)2]n (atrz = 4,4′-azo-1,2,4-triazole)} was obtained using a postsynthetic method from MOF (1) {[Cu(atrz)3(NO3)2]n}. Benefitting from the oxygen-rich and small volume of the iodate (IO3) ligands (2.73 Å) in MOF (2) compared to the atrz ligand (7.70 Å) in MOF (1), the density of MOF (2) is 3.168 g cm−3, nearly twice that of its precursor. Its detonation velocity of 7271 ms−1 exceeds that of TNT (trinitrotoluene) and its detonation pressure of 40.6 GPa is superior to that of HMX (cyclotetramethylenetetranitramine) (1,3,5,7- tetranitro-1,3,5,7-tetrazoctane, 39.2 Gpa), which are the highest detonation properties for a biocidal agent. Its superior detonation performance results in its main product, I2, being distributed over a wide area, markedly reducing the diffusion of harmful microorganisms. This study offers novel insight not only for high-energy-density materials but also for huge potential applications as biocidal agents

Stepped-height ridge waveguide MQW polarization mode converter monolithically integrated with sidewall grating DFB laser

We report the first demonstration of a 1555 nm stepped-height ridge waveguide polarization mode converter monolithically integrated with a side wall grating distributed-feedback (DFB) laser using the identical epitaxial layer scheme. The device shows stable single longitudinal mode (SLM) operation with the output light converted from TE to TM polarization with an efficiency of >94% over a wide range of DFB injection currents (IDFB) from 140 mA to 190 mA. The highest TM mode purity of 98.2% was obtained at IDFB=180 mA. A particular advantage of this device is that only a single step of metalorganic vapor-phase epitaxy and two steps of III-V material dry etching are required for the whole integrated device fabrication, significantly reducing complexity and cost

Regrowth-free AlGaInAs MQW polarization controller integrated with sidewall grating DFB laser

We report an AlGaInAs multiple quantum well integrated source of polarization controlled light consisting of a polarization mode converter PMC, differential phase shifter(DPS), and a side wall grating distributed-feedback DFB laser. We demonstrate an asymmetrical stepped-height ridge waveguide PMC to realize TE to TM polarization conversion and a symmetrical straight waveguide DPS to enable polarization rotation from approximately counterclockwise circular polarization to linear polarization. Based on the identical epitaxial layer scheme, all of the PMC, DPS, and DFB laser can be integrated monolithically using only a single step of metalorganic vapor phase epitaxy and two steps of III V material dry etching. For the DFB-PMC device, a high TE to TM polarization conversion efficiency 98% over a wide range of DFB injection currents is reported at 1555 nm wavelength. For the DFB-PMC-DPS device, a 60 degree rotation of the Stokes vector was obtained on the Poincar\'e sphere with a range of bias voltage from 0 V to -4.0 V at IDFB is 170 mA.Comment: arXiv admin note: text overlap with arXiv:2210.1051

Can Programming Languages Boost Each Other via Instruction Tuning?

When human programmers have mastered a programming language, it would be easier when they learn a new programming language. In this report, we focus on exploring whether programming languages can boost each other during the instruction fine-tuning phase of code large language models. We conduct extensive experiments of 8 popular programming languages (Python, JavaScript, TypeScript, C, C++, Java, Go, HTML) on StarCoder. Results demonstrate that programming languages can significantly improve each other. For example, CodeM-Python 15B trained on Python is able to increase Java by an absolute 17.95% pass@1 on HumanEval-X. More surprisingly, we found that CodeM-HTML 7B trained on the HTML corpus can improve Java by an absolute 15.24% pass@1. Our training data is released at https://github.com/NL2Code/CodeM.Comment: Work in progres

An overview of Old Tibetan synchronic phonology

Despite the importance of Old Tibetan in the Tibeto-Burman language family, little research has treated Old Tibetan synchronic phonology. This article gives a complete overview of the Old Tibetan phonemic system by associating sound values with the letters of the Tibetan alphabet and exploring the distribution of these sounds in syllable structure

Stepped-height ridge waveguide MQW polarization mode converter monolithically integrated with sidewall grating DFB laser

We report the first demonstration of a 1555 nm stepped-height ridge waveguide polarization mode converter monolithically integrated with a side wall grating distributed-feedback (DFB) laser using the identical epitaxial layer scheme. The device shows stable single longitudinal mode (SLM) operation with the output light converted from TE to TM polarization with an efficiency of >94% over a wide range of DFB injection currents (IDFB) from 140 mA to 190 mA. The highest TM mode purity of 98.2% was obtained at IDFB=180 mA. A particular advantage of this device is that only a single step of metalorganic vapor-phase epitaxy and two steps of III-V material dry etching are required for the whole integrated device fabrication, significantly reducing complexity and cost

Corrigendum: Hu H et al. (2023) Taxonomic and phylogenetic characterisations of six species of Pleosporales (in Didymosphaeriaceae, Roussoellaceae and Nigrogranaceae) from China. MycoKeys 100: 123–151. https://doi.org/10.3897/mycokeys.100.109423

Four new species, Xynobius azonius sp. nov., X. brevifemora sp. nov., X. duoferus sp. nov., and X. stipitoides sp. nov., are described and illustrated, and one species X. geniculatus (Thomson, 1895) is newly reported from South Korea. Xynobius geniculatus (Thomson, 1895) is redescribed and illustrated, and a new combination, Xynobius (Stigmatopoea) cubitalis (Fischer, 1959), comb. nov. is suggested. An identification key to the Xynobius species known from South Korea is provided