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1. SDEAP: a splice graph based differential transcript expression analysis tool for population data

   https://doi.org/10.1093/bioinformatics/btw513  

   Yang, Ei-Wen; Jiang, Tao (December 2016, Bioinformatics)

   Motivation: Differential transcript expression (DTE) analysis without predefined conditions is critical to biological studies. For example, it can be used to discover biomarkers to classify cancer samples into previously unknown subtypes such that better diagnosis and therapy methods can be developed for the subtypes. Although several DTE tools for population data, i.e. data without known biological conditions, have been published, these tools either assume binary conditions in the input population or require the number of conditions as a part of the input. Fixing the number of conditions to binary is unrealistic and may distort the results of a DTE analysis. Estimating the correct number of conditions in a population could also be challenging for a routine user. Moreover, the existing tools only provide differential usages of exons, which may be insufficient to interpret the patterns of alternative splicing across samples and restrains the applications of the tools from many biology studies. Results: We propose a novel DTE analysis algorithm, called SDEAP, that estimates the number of conditions directly from the input samples using a Dirichlet mixture model and discovers alternative splicing events using a new graph modular decomposition algorithm. By taking advantage of the above technical improvement, SDEAP was able to outperform the other DTE analysis methods in our extensive experiments on simulated data and real data with qPCR validation. The prediction of SDEAP also allowed us to classify the samples of cancer subtypes and cell-cycle phases more accurately. 

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2. Synthesis and Self-Assembling Properties of Carbohydrate- and Diarylethene-Based Photoswitchable Molecular Gelators

   https://doi.org/10.3390/molecules28176228  

   Aryal, Pramod; Morris, Joedian; Adhikari, Surya B.; Bietsch, Jonathan; Wang, Guijun (September 2023, Molecules)

   Carbohydrate-based low-molecular-weight gelators are interesting new materials with many potential applications. These compounds can be designed to include multiple stimuli-responsive functional groups. In this study, we designed and synthesized several chemically responsive bola-glycolipids and dimeric carbohydrate- and diarylethene-based photoswitchable derivatives. The dimeric glycolipids formed stable gels in a variety of solvent systems. The best performing gelators in this series contained decanedioic and dithienylethene (DTE) spacers, which formed gels in eight and nine of the tested solvents, respectively. The two new DTE-containing esters possessed interesting photoswitching properties and DTE derivative 7 was found to have versatile gelation properties in many solvents, including DMSO solutions at low concentrations. The gels formed by these compounds were stable under acidic conditions and tended to hydrolyze under basic conditions. Several gels were used to absorb rhodamine B and Toluidine blue from aqueous solutions. In this study, we demonstrated the rational design of molecular gelators which incorporated photoresponsive and pH responsive functions, leading to the discovery of multiple effective stimuli-responsive gelators. 

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3. Photoswitchable optoelectronic properties of 2D MoSe2/diarylethene hybrid structures

   https://doi.org/10.1038/s41598-024-57479-z  

   Park, Sewon; Ji, Jaehoon; Cunningham, Connor; Pillai, Srajan; Rouillon, Jean; Benitez-Martin, Carlos; Fang, Mengqi; Yang, Eui-Hyeok; Andréasson, Joakim; You, Jeong Ho; et al (March 2024, Scientific Reports)

   Abstract The ability to modulate optical and electrical properties of two-dimensional (2D) semiconductors has sparked considerable interest in transition metal dichalcogenides (TMDs). Herein, we introduce a facile strategy for modulating optoelectronic properties of monolayer MoSe₂with external light. Photochromic diarylethene (DAE) molecules formed a 2-nm-thick uniform layer on MoSe₂, switching between its closed- and open-form isomers under UV and visible irradiation, respectively. We have discovered that the closed DAE conformation under UV has its lowest unoccupied molecular orbital energy level lower than the conduction band minimum of MoSe₂, which facilitates photoinduced charge separation at the hybrid interface and quenches photoluminescence (PL) from monolayer flakes. In contrast, open isomers under visible light prevent photoexcited electron transfer from MoSe₂to DAE, thus retaining PL emission properties. Alternating UV and visible light repeatedly show a dynamic modulation of optoelectronic signatures of MoSe₂. Conductive atomic force microscopy and Kelvin probe force microscopy also reveal an increase in conductivity and work function of MoSe₂/DAE with photoswitched closed-form DAE. These results may open new opportunities for designing new phototransistors and other 2D optoelectronic devices. 

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4. Zirconocene‐Mediated Radical Hydrophosphination

   https://doi.org/10.1002/ejic.202300341  

   Javier‐Jiménez, Diego R.; Novas, Bryan T.; Waterman, Rory (July 2023, European Journal of Inorganic Chemistry)

   Abstract Hydrophosphination activity has been solicited from the parent and decamethyl zirconocene dichloride compounds, Cp₂ZrCl₂and Cp*₂ZrCl₂. Given recent reports of photocatalytic hydrophosphination, these compounds were irradiated in the near ultraviolet (UV) as precatalysts resulting in the successful hydrophosphination of styrene substrates and activated alkenes. Irradiation appears to induce homolysis of the Cp or Cp* ligand, resulting in radical hydrophosphination. Successful detection of this radical reactivity was achieved by monitoring for EPR signals within situirradiation, a methodology proving to be general for the determination of radical versus closed‐shell reactivity in transition‐metal photocatalysis. 

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5. Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

   https://doi.org/10.1107/S2052252523008060  

   Mitchell, Travis B.; Zhang, Xiaotong; Jerozal, Ronald T.; Chen, Yu-Sheng; Wang, SuYin; Benedict, Jason B. (November 2023, IUCrJ)

   Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novelD–Danalysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, theD–Danalysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids. 

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