Late-stage guanine C8-H alkylation of nucleosides, nucleotides, and oligonucleotides via photo-mediated Minisci reaction.

Chemically modified nucleosi(ti)des and functional oligonucleotides (ONs, including therapeutic oligonucleotides, aptamer, nuclease, etc.) have been identified playing an essential role in the areas of medicinal chemistry, chemical biology, biotechnology, and nanotechnology. Introduction of functional groups into the nucleobases of ONs mostly relies on the laborious de novo chemical synthesis. Due to the importance of nucleosides modification and aforementioned limitations of functionalizing ONs, herein, we describe a highly efficient site-selective alkylation at the C8-position of guanines in guanosine (together with its analogues), GMP, GDP, and GTP, as well as late-stage functionalization of dinucleotides and single-strand ONs (including ssDNA and RNA) through photo-mediated Minisci reaction. Addition of catechol to assist the formation of alkyl radicals via in situ generated boronic acid catechol ester derivatives (BACED) markedly enhances the yields especially for the reaction of less stable primary alkyl radicals, and is the key to success for the post-synthetic alkylation of ONs. This method features excellent chemoselectivity, no necessity for pre-protection, wide range of substrate scope, various free radical precursors, and little strand lesion. Downstream applications in disease treatment and diagnosis, or as biochemical probes to study biological processes after linking with suitable fluorescent compounds are expected.

Tandem duplication and sub-functionalization of clerodane diterpene synthase originate the blooming of clerodane diterpenoids in Scutellaria barbata.

Scutellaria barbata is a traditional Chinese herb medicine and a major source of bioactive clerodane diterpenoids. However, barely clerodanes have been isolated from the closely related S. baicalensis. Here we assembled a chromosome-level genome of S. barbata and identified three class II clerodane diterpene synthases (SbarKPS1, SbarKPS2 and SbaiKPS1) from these two organisms. Using in vitro and in vivo assays, SbarKPS1 was characterized as a monofunctional (-)-kolavenyl diphosphate synthases ((-)-KPS), while SbarKPS2 and SbaiKPS1 produced major neo-cleroda-4(18),13E-dienyl diphosphate with small amount of (-)-KPP. SbarKPS1 and SbarKPS2 shared a high protein sequence identity and formed a tandem gene pair, indicating tandem duplication and sub-functionalization probably led to the evolution of monofunctional (-)-KPS in S. barbata. Additionally, SbarKPS1 and SbarKPS2 were primarily expressed in the leaves and flowers of S. barbata, which was consistent with the distribution of major clerodane diterpenoids scutebarbatine A and B. In contrast, SbaiKPS1 was barely expressed in any tissue of S. baicalensis. We further explored the downstream class I diTPS by functional characterizing of SbarKSL3 and SbarKSL4. Unfortunately, no dephosphorylated product was detected in the coupled assays with SbarKSL3/KSL4 and four class II diTPSs (SbarKPS1, SbarKPS2, SbarCPS2 and SbarCPS4) when a phosphatase inhibitor cocktail was included. Co-expression of SbarKSL3/KSL4 with class II diTPSs in yeast cells did not increase the yield of the corresponding dephosphorylated products, either. Together, these findings elucidated the involvement of two class II diTPSs in clerodane biosynthesis in S. barbata, while the class I diTPS is likely not responsible for the subsequent dephosphorylation step.

Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm.

As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli's genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources.

Palladium-Catalyzed C-H Olefination for Nucleic Acid Production.

The palladium-catalyzed direct C-H olefination of unprotected uridine, 2'-deoxyuridine, uridine monophosphate, and uridine analogues are described here. This protocol provides an efficient, atom-economical, and environmentally friendly method for the introduction of an alkenyl group at the C5 position of the uracil without pre-functionalization. A series of C5-alkenylated uridine analogues, including some biologically significant compounds and potential pharmaceutical candidates, were synthesized with exposed hydroxyl groups on the ribose. © 2023 Wiley Periodicals LLC. Basic Protocol 1: The reaction of uridine, 2'-deoxyuridine, and sofosbuvir for the C-H olefination with methyl acrylate Basic Protocol 2: The reaction of uridine and 2'-deoxyuridine for the C-H olefination with styrene.

[Diagnostic value of whole exome sequencing for patients with intellectual disability or global developmental delay].

OBJECTIVE: To assess the diagnostic value of whole exome sequencing (WES) for patients with intellectual disability (ID) or global developmental delay (GDD). METHODS: 134 individuals with ID or GDD who presented at Chenzhou First People's Hospital between May 2018 and December 2021 were selected as the study subjects. WES was carried out on peripheral blood samples of the patients and their parents, and candidate variants were verified by Sanger sequencing, copy number variation sequencing (CNV-seq) and co-segregation analysis. The pathogenicity of the variants was predicted based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). RESULTS: A total of 46 pathogenic single nucleotide variants (SNVs) and small insertion/deletion (InDel) variants, 11 pathogenic genomic copy number variants (CNVs), and 1 uniparental diploidy (UPD) were detected, which yielded an overall detection rate of 43.28% (58/134). The 46 pathogenic SNV/InDel have involved 62 mutation sites in 40 genes, among which MECP2 was the most frequent (n = 4). The 11 pathogenic CNVs have included 10 deletions and 1 duplication, which have ranged from 0.76 to 15.02 Mb. A loss of heterozygosity (LOH) region of approximately 15.62 Mb was detected in 15q11.2q12 region in a patient, which was validated as paternal UPD based on the result of trio-WES. The patient was ultimately diagnosed as Angelman syndrome. CONCLUSION: WES can detect not only SNV/InDel, but also CNV and LOH. By integrating family data, WES can accurately determine the origin of the variants and provide a useful tool for uncovering the genetic etiology of patients with ID or GDD.

Palladium-catalyzed C-H olefination of uridine, deoxyuridine, uridine monophosphate and uridine analogues.

The palladium-catalyzed oxidative C-H olefinations of uridine, deoxyuridine, uridine monophosphate and uridine analogues are reported herein. This protocol provides an efficient, atom-economic and environmentally friendly approach to the synthesis of biologically important C5-alkene modified uracil/uridine-containing derivatives and pharmaceutical candidates.

Grifola frondosa Polysaccharide Ameliorates Early Diabetic Nephropathy by Suppressing the TLR4/NF-κB Pathway.

Grifola frondosa is a medicinal macro-fungus with a wide range of biological activities. Polysaccharides from Grifola frondosa (PGF) play a positive role in regulating blood glucose and alleviating kidney injury. Here, we investigated the exact mechanism of action by which PGF ameliorates diabetic nephropathy. Our results showed that PGF effectively improved glucose tolerance and insulin sensitivity in streptozocin (STZ)-induced DN mice. Additionally, administration of PGF also ameliorated renal function and inflammatory response in STZ-induced DN mice. Consistent with the in vitro results, the high glucose-induced inflammatory response and apoptosis of renal tubular epithelial cells were decreased by PGF treatment. Furthermore, PGF not only suppressed the expression of TLR4, but also more effectively protected the kidney and reduced the inflammatory response when TLR4 was inhibited. All these data revealed that PGF alleviates diabetic nephropathy by blocking the TLR4/NF-κB pathway.

DO-Conv: Depthwise Over-Parameterized Convolutional Layer.

Convolutional layers are the core building blocks of Convolutional Neural Networks (CNNs). In this paper, we propose to augment a convolutional layer with an additional depthwise convolution, where each input channel is convolved with a different 2D kernel. The composition of the two convolutions constitutes an over-parameterization, since it adds learnable parameters, while the resulting linear operation can be expressed by a single convolution layer. We refer to this depthwise over-parameterized convolutional layer as DO-Conv, which is a novel way of over-parameterization. We show with extensive experiments that the mere replacement of conventional convolutional layers with DO-Conv layers boosts the performance of CNNs on many classical vision tasks, such as image classification, detection, and segmentation. Moreover, in the inference phase, the depthwise convolution is folded into the conventional convolution, reducing the computation to be exactly equivalent to that of a convolutional layer without over-parameterization. As DO-Conv introduces performance gains without incurring any computational complexity increase for inference, we advocate it as an alternative to the conventional convolutional layer. We open sourced an implementation of DO-Conv in Tensorflow, PyTorch and GluonCV at https://github.com/yangyanli/DO-Conv.

Access to benzene-modified 2nd generation strigolactams and GR24 by merging C-H olefination with decarboxylative Giese cyclization.

Herein, we reported an efficient and general synthetic route to assemble benzene-modified 2nd generation strigolactams and GR24. The key features of this synthesis include a palladium-catalyzed ortho-selective olefination of the commercially available substituted N-Boc phenylalanine and a decarboxylative Giese radical cyclization. The bioactivities of these compounds to stimulate the seed germination of Orobanche aegyptiaca parasitic weed were also analysed. 2nd generation strigolactam 15f derived from para-OMe phenylalanine showed superior bioactivity to the original unsubstituted 15b.

Engineering a Smart Nanofluidic Sensor for High-Performance Peroxynitrite Sensing through a Spirocyclic Ring Open/Close Reaction Strategy.

Peroxynitrite (ONOO-) is an important reactive oxygen/nitrogen species that participates in a range of physiological and pathological processes by modulating ion flux through biological channels. Inspired by a ONOO--regulated K+ channel in vivo, herein, we describe the construction of a smart ONOO--driven nanosensor using a spirocyclic ring open/close reaction approach. The prepared nanosensor possessed a prominent ONOO- selectivity and sensitivity and rapid response (∼90 s) owing to the specific reaction between ONOO- and ligands on the nanosensor surface with a high ion rectification ratio (∼10) and ion gating ratio (∼4). Moreover, this nanosensor system also exhibits excellent stability and recyclability. Thus, these results will provide a new direction for the design of nanochannel-based sensors for future practical and biological applications.

Construction of a Smart Nanofluidic Sensor through a Redox Reaction Strategy for High-Performance Carbon Monoxide Sensing.

Carbon monoxide (CO), an important gas signaling molecule, demonstrated various physiological and pathological functions by regulating the ion flux of biological channels. Herein, inspired by the CO-regulated K+ channel in vivo, we propose a smart CO-responsive nanosensor through the redox reaction strategy. Such nanosensor demonstrated an outstanding CO specificity and selectivity with high ion rectification (∼9) as well as excellent stability and recyclability. Therefore, these results will provide a new direction for the design of nanochannel-based sensors for future practical and biological applications.

Ligand-Free, Quinoline N-Assisted Copper-Catalyzed Nitrene Transfer Reaction To Synthesize 8-Quinolylsulfimides.

An efficient copper-catalyzed, quinolyl N-directed nitrene transfer reaction to 8-quinolylsulfides was described. A variety of 8-quinolylsulfimides with different functional groups were synthesized in moderate to high yields. The obtained 8-quinolylsulfimides were proved to be promising novel type of bidentate ligands in Pd(II)-catalyzed allylic alkylation.

Selecting precise reference normal tissue samples for cancer research using a deep learning approach.

BACKGROUND: Normal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer or cancer subtype. The recent GTEx project has profiled samples from healthy individuals, providing an excellent resource for this field, yet the feasibility of using GTEx samples as the reference remains unanswered. METHODS: We analyze RNA-Seq data processed from the same computational pipeline and systematically evaluate GTEx as a potential reference resource. We use those cancers that have adjacent normal tissues in TCGA as a benchmark for the evaluation. To correlate tumor samples and normal samples, we explore top varying genes, reduced features from principal component analysis, and encoded features from an autoencoder neural network. We first evaluate whether these methods can identify the correct tissue of origin from GTEx for a given cancer and then seek to answer whether disease expression signatures are consistent between those derived from TCGA and from GTEx. RESULTS: Among 32 TCGA cancers, 18 cancers have less than 10 matched adjacent normal tissue samples. Among three methods, autoencoder performed the best in predicting tissue of origin, with 12 of 14 cancers correctly predicted. The reason for misclassification of two cancers is that none of normal samples from GTEx correlate well with any tumor samples in these cancers. This suggests that GTEx has matched tissues for the majority cancers, but not all. While using autoencoder to select proper normal samples for disease signature creation, we found that disease signatures derived from normal samples selected via an autoencoder from GTEx are consistent with those derived from adjacent samples from TCGA in many cases. Interestingly, choosing top 50 mostly correlated samples regardless of tissue type performed reasonably well or even better in some cancers. CONCLUSIONS: Our findings demonstrate that samples from GTEx can serve as reference normal samples for cancers, especially those do not have available adjacent tissue samples. A deep-learning based approach holds promise to select proper normal samples.

Organophosphine-Catalyzed [4C+X] Annulations.

In recent years, there have been extraordinary developments of organophosphine-catalyzed reactions. This includes progress in the area of [4C+X] annulations, which are of particular interest due to their potential for the rapid construction of 5⁻8-membered cyclic products. In this short overview, we summarize the remarkable progress, emphasizing reaction mechanisms and key intermediates involved in the processes. The discussion is classified according to the type of electrophilic reactants that acted as C4 synthons in the annulation process, in the order of α-alkyl allenoates, γ-alkyl allenoates, α-methyl allene ketones, ß'-OAc allenoate, δ-OAc allenoate, activated dienes and cyclobutenones.

E-Selective synthesis of vinyl sulfones via silver-catalyzed sulfonylation of styrenes.

An efficient and highly E-selective protocol for the synthesis of vinyl sulfones is described. This simple protocol demonstrates the first synthesis of vinyl sulfones via a silver-catalyzed C-S bond coupling reaction. In addition, the success of the reaction was found to be critically dependent on the use of TEMPO as the additive.

Gold-Catalyzed Enantioselective Annulations.

In the past decade, there have been many extraordinary advances in the development of gold-catalyzed enantioselective annulations, such as cycloadditions, cyclizations, cycloisomerizations, and tandem annulations, which are of particular interest owing to their potential for rapid construction of optically active hetero- and carbocyclic molecules. This Review summarizes the methods to construct chiral cyclic compounds by gold-catalyzed enantioselective annulations reported since 2005. The Review is organized according to the general annulation types catalyzed by chiral gold complexes or chiral gold salts, which have four main types (cycloadditions, cyclizations of C-C multiple bonds with tethered nucleophiles, cycloisomerization or cyclization of enynes, and tandem annulations), as well as some other strategies. The general reaction mechanisms of each subcategory, key intermediates for some unusual transformations, and the application of several novel ligands and chiral gold salts are also discussed.

A Tool-Free Calibration Method for Turntable-Based 3D Scanning Systems.

Turntable-based 3D scanners are popular but require calibration of the turntable axis. Existing methods for turntable calibration typically make use of specially designed tools, such as a chessboard or criterion sphere, which users must manually install and dismount. In this article, the authors propose an automatic method to calibrate the turntable axis without any calibration tools. Given a scan sequence of the input object, they first recover the initial rotation axis from an automatic registration step. Then they apply an iterative procedure to obtain the optimized turntable axis. This iterative procedure alternates between two steps: refining the initial pose of the input scans and approximating the rotation matrix. The performance of the proposed method was evaluated on a structured light-based scanning system.

Design, synthesis, and application of a chiral sulfinamide phosphine catalyst for the enantioselective intramolecular Rauhut-Currier reaction.

A novel class of chiral sulfinamide phosphine catalysts (Xiao-Phos) are reported, which can be easily prepared from inexpensive commercially available starting materials. The Xiao-Phos catalysts showed good performance in enantioselective intramolecular Rauhut-Currier reactions, generating α-methylene-γ-butyrolactones in high yields with up to 99% ee under mild conditions. Moreover, kinetic resolution and parallel kinetic resolution were also observed with the use of two different substituted racemic precursors.

Amino acid derived phosphine-catalyzed enantioselective 1,4-dipolar spiroannulation of cyclobutenones and isatylidenemalononitrile.

Cyclobutenones have been explored as a new type of chiral 1,4-dipole four-carbon synthon, which readily undergoes organophosphine-mediated C-C bond cleavage and asymmetric intermolecular 1,4-dipolar spiroannulation with isatylidenemalononitrile in the presence of amino acid-derived chiral phosphine catalyst to furnish enantioenriched 3-spirocyclohexenone 2-oxindoles in good yield with up to 87% ee. To our knowledge, this is the first example of asymmetric transformation of cyclobutenones and the phosphine-catalyzed asymmetric 1,4-dipolar cycloaddition consisting of C-C bond activation is unprecedented.