Machine Learning-Guided Systematic Search of DNA Sequences for Sorting Carbon Nanotubes

The prerequisite of utilizing DNA in sequence-dependent applications is to search specific sequences. Developing a strategy for efficient DNA sequence screening represents a grand challenge due to the countless possibilities of sequence combination. Herein, relying on sequence-dependent recognition between DNA and single-wall carbon nanotubes (SWCNTs), we demonstrate a method for systematic search of DNA sequences for sorting single-chirality SWCNTs. Different from previously documented empirical search, which has a low efficiency and accuracy, our approach combines machine learning and experimental investigation. The number of resolving sequences and the success rate of finding them are improved from ∼102 to ∼103 and from ∼10% to >90%, respectively. Moreover, the resolving sequence patterns determined from 5-mer and 6-mer short sequences can be extended to sequence search in longer DNA subspaces

Optical Detection of Stereoselective Interactions with DNA-Wrapped Single-Wall Carbon Nanotubes

DNA-wrapped carbon nanotubes have been explored increasingly as sensitive near-infrared fluorescence probes for biomolecules. However, notably missing in previous studies is an inquiry on stereoselective interactions between DNA-wrapped carbon nanotubes and biomolecules. Here, enantiopure (+) and (−)­(6,5), and (−)­(8,3) as well as achiral (11,0) carbon nanotubes wrapped with specific resolving DNA sequences are used to demonstrate their stereoselective detection of amino acid enantiomers. Furthermore, stereoselective sensing abilities are found to be retained by dispersions containing a multitude of chiral nanotube structures. The fluorescence response profiles of six different DNA-wrapped carbon nanotube dispersions to nine standard amino acids, and their enantiomers, demonstrate that DNA-wrapped carbon nanotubes are exquisitely sensitive to the stereoconfiguration and side-chain functionality of amino acids in a manner that is dependent on both DNA sequence and nanotube chirality. Implications of our findings are discussed in the context of developing a machine learning-aided multiplexed biosensing scheme called a molecular perceptron

DataSheet1_Isorhamnetin Alleviates Airway Inflammation by Regulating the Nrf2/Keap1 Pathway in a Mouse Model of COPD.ZIP

Chronic obstructive pulmonary disease (COPD) is a severely disabling chronic lung disease characterized by persistent airway inflammation, which leads to limited expiratory airflow that deteriorates over time. Isorhamnetin (Iso) is one of the most important active components in the fruit of Hippophae rhamnoides L. and leaves of Ginkgo biloba L, which is widely used in many pulmonary disease studies because of its anti-inflammatory effects. Here, we investigated the pharmacological action of Iso in CS-induced airway inflammation and dissected the anti-inflammation mechanisms of Iso in COPD mice. A mouse model of COPD was established by exposure to cigarette smoke (CS) and intratracheal inhalation of lipopolysaccharide (LPS). Our results illustrated that Iso treatment significantly reduced leukocyte recruitment and excessive secretion of interleukin-6 (IL-6), monocyte chemoattractant protein-1 (MCP-1), and regulated upon activation, normal T-cell expressed and secreted (RANTES) in BALF of CS-induced COPD mice in a dose-dependent manner. This improved airway collagen deposition and emphysema, and further alleviated the decline in lung functions and systemic symptoms of hypoxia and weight loss. Additionally, Iso treatment obviously improves the T lymphocyte dysregualtion in peripheral blood of COPD mice. Mechanistically, Iso may degrade Keap1 through ubiquitination of p62, thereby activating the nuclear factor erythroid 2-related factor (Nrf2) pathway to increase the expression of protective factors, such as heme oxygenase-1 (HO-1), superoxide dismutase (SOD) 1, and SOD2, in lungs of CS-exposed mice, which plays an anti-inflammatory role in COPD. In conclusion, our study indicates that Iso significantly alleviates the inflammatory response in CS-induced COPD mice mainly by affecting the Nrf2/Keap1 pathway. More importantly, Iso exhibited anti-inflammatory effects comparable with Dex in COPD and we did not observe discernible side effects of Iso. The high safety profile of Iso may make it a potential drug candidate for COPD.</p

Table_6_Transcriptomic and Proteomic Analysis of Shaan2A Cytoplasmic Male Sterility and Its Maintainer Line in Brassica napus.XLSX

Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus. The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant. Transcriptomic analysis revealed differentially expressed genes (DEGs) mainly related to carbon metabolism, lipid and flavonoid metabolism, and the mitochondrial electron transport/ATP synthesis pathway. Proteomic results showed that differentially expressed proteins were mainly associated with carbohydrate metabolism, energy metabolism, and genetic information processing pathways. Importantly, nine gene ontology categories associated with anther and pollen development were enriched among down-regulated DEGs at the young bud (YB) stage, including microsporogenesis, sporopollenin biosynthetic process, and tapetal layer development. Additionally, 464 down-regulated transcription factor (TF) genes were identified at the YB stage, including some related to early anther differentiation such as SPOROCYTELESS (SPL, also named NOZZLE, NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), MYB80 (formerly named MYB103), and ABORTED MICROSPORES (AMS). These results suggested that the sterility gene in the Shaan2A mitochondrion might suppress expression of these TF genes in the nucleus, affecting early anther development. Finally, we constructed an interaction network of candidate proteins based on integrative analysis. The present study provides new insights into the molecular mechanism of Shaan2A CMS in B. napus.</p

Energy Transport in PEG Oligomers: Contributions of Different Optical Bands

The transport of high-frequency vibrational energy in linear oligomer chains can be fast and efficient if specific conditions which permit ballistic transport are satisfied. These conditions include high delocalization and slow dephasing rate of chain states. We present new experimental results probing the energy transport in linear polyethylene glycol (PEG) oligomers of 0, 4, 8, and 12 PEG units terminated with IR-active end groups, N₃ and succinimide ester. The energy transport was initiated by vibrational excitation of one of the end groups and the energy arrival to another end group was detected using dual-frequency, two-dimensional infrared spectroscopy. In addition to end-group to end-group energy transport dynamics, the end-group-to-chain-state and chain-state-to-chain-state waiting-time dynamics are reported. The results show that despite rather short lifetimes for several IR-active chain states, the end-to-end energy transport occurs with a constant and rather high speed of 5.5 Å/ps, regardless of which end group initiated the transport (N₃ or asymmetric CO stretching mode of the succinimide), which contrasts previous reports for similarly terminated alkane chains where the transport was dependent on the way it was initiated. To understand the transport mechanism, the PEG chain dispersion relations were computed, indicating that while many chain bands can contribute to the transport, most of them have short lifetimes (≤1 ps) that cannot support a ballistic regime to distances exceeding that of PEG8. However, the states of a single rocking band, at about 800–850 cm^–1, feature longer lifetimes, permitting ballistic transport via this band for 50 Å at room temperature. Theoretical modeling, based on solving the quantum Liouville equation for a density matrix for a linear chain, was performed. The modeling indicates that under directed diffusion conditions, a switch between ballistic and diffusive transport regimes can occur without abrupt changes of the transport speed. The approaches developed in this study are applicable to other chain types, in particular, those involving heteroatoms in the backbone

Image_1_Transcriptomic and Proteomic Analysis of Shaan2A Cytoplasmic Male Sterility and Its Maintainer Line in Brassica napus.JPEG

Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus. The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant. Transcriptomic analysis revealed differentially expressed genes (DEGs) mainly related to carbon metabolism, lipid and flavonoid metabolism, and the mitochondrial electron transport/ATP synthesis pathway. Proteomic results showed that differentially expressed proteins were mainly associated with carbohydrate metabolism, energy metabolism, and genetic information processing pathways. Importantly, nine gene ontology categories associated with anther and pollen development were enriched among down-regulated DEGs at the young bud (YB) stage, including microsporogenesis, sporopollenin biosynthetic process, and tapetal layer development. Additionally, 464 down-regulated transcription factor (TF) genes were identified at the YB stage, including some related to early anther differentiation such as SPOROCYTELESS (SPL, also named NOZZLE, NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), MYB80 (formerly named MYB103), and ABORTED MICROSPORES (AMS). These results suggested that the sterility gene in the Shaan2A mitochondrion might suppress expression of these TF genes in the nucleus, affecting early anther development. Finally, we constructed an interaction network of candidate proteins based on integrative analysis. The present study provides new insights into the molecular mechanism of Shaan2A CMS in B. napus.</p

DataSheet2_Isorhamnetin Alleviates Airway Inflammation by Regulating the Nrf2/Keap1 Pathway in a Mouse Model of COPD.PDF

Chronic obstructive pulmonary disease (COPD) is a severely disabling chronic lung disease characterized by persistent airway inflammation, which leads to limited expiratory airflow that deteriorates over time. Isorhamnetin (Iso) is one of the most important active components in the fruit of Hippophae rhamnoides L. and leaves of Ginkgo biloba L, which is widely used in many pulmonary disease studies because of its anti-inflammatory effects. Here, we investigated the pharmacological action of Iso in CS-induced airway inflammation and dissected the anti-inflammation mechanisms of Iso in COPD mice. A mouse model of COPD was established by exposure to cigarette smoke (CS) and intratracheal inhalation of lipopolysaccharide (LPS). Our results illustrated that Iso treatment significantly reduced leukocyte recruitment and excessive secretion of interleukin-6 (IL-6), monocyte chemoattractant protein-1 (MCP-1), and regulated upon activation, normal T-cell expressed and secreted (RANTES) in BALF of CS-induced COPD mice in a dose-dependent manner. This improved airway collagen deposition and emphysema, and further alleviated the decline in lung functions and systemic symptoms of hypoxia and weight loss. Additionally, Iso treatment obviously improves the T lymphocyte dysregualtion in peripheral blood of COPD mice. Mechanistically, Iso may degrade Keap1 through ubiquitination of p62, thereby activating the nuclear factor erythroid 2-related factor (Nrf2) pathway to increase the expression of protective factors, such as heme oxygenase-1 (HO-1), superoxide dismutase (SOD) 1, and SOD2, in lungs of CS-exposed mice, which plays an anti-inflammatory role in COPD. In conclusion, our study indicates that Iso significantly alleviates the inflammatory response in CS-induced COPD mice mainly by affecting the Nrf2/Keap1 pathway. More importantly, Iso exhibited anti-inflammatory effects comparable with Dex in COPD and we did not observe discernible side effects of Iso. The high safety profile of Iso may make it a potential drug candidate for COPD.</p

Table_7_Transcriptomic and Proteomic Analysis of Shaan2A Cytoplasmic Male Sterility and Its Maintainer Line in Brassica napus.XLSX

Cytoplasmic male sterility (CMS) lines are widely used for hybrid production in Brassica napus. The Shaan2A CMS system is one of the most important in China and has been used for decades; however, the male sterility mechanism underlying Shaan2A CMS remains unknown. Here, we performed transcriptomic and proteomic analysis, combined with additional morphological observation, in the Shaan2A CMS. Sporogenous cells, endothecium, middle layer, and tapetum could not be clearly distinguished in Shaan2A anthers. Furthermore, Shaan2A anther chloroplasts contained fewer starch grains than those in Shaan2B (a near-isogenic line of Shaan2A), and the lamella structure of chloroplasts in Shaan2A anther wall cells was obviously aberrant. Transcriptomic analysis revealed differentially expressed genes (DEGs) mainly related to carbon metabolism, lipid and flavonoid metabolism, and the mitochondrial electron transport/ATP synthesis pathway. Proteomic results showed that differentially expressed proteins were mainly associated with carbohydrate metabolism, energy metabolism, and genetic information processing pathways. Importantly, nine gene ontology categories associated with anther and pollen development were enriched among down-regulated DEGs at the young bud (YB) stage, including microsporogenesis, sporopollenin biosynthetic process, and tapetal layer development. Additionally, 464 down-regulated transcription factor (TF) genes were identified at the YB stage, including some related to early anther differentiation such as SPOROCYTELESS (SPL, also named NOZZLE, NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), MYB80 (formerly named MYB103), and ABORTED MICROSPORES (AMS). These results suggested that the sterility gene in the Shaan2A mitochondrion might suppress expression of these TF genes in the nucleus, affecting early anther development. Finally, we constructed an interaction network of candidate proteins based on integrative analysis. The present study provides new insights into the molecular mechanism of Shaan2A CMS in B. napus.</p

Titanocene Lewis Acid Complexes with Diversified N,O-Ligands: Selectivity toward Three-Component Friedel–Crafts Reactions of Indoles

Titanocene complexes by N,O-ligands were rationally designed and tuned for selective three-component aza-Friedel–Crafts reactions of indoles, aldehydes, and unmodified aniline. The combination of Cp2TiCl2 and 8-hydroxyquinoline favored the synthesis of the mono aza-Friedel–Crafts adducts, whereas Cp2TiCl2 combined with anthranilic acid overwhelmingly formed bis-indoles. 1H NMR titration experiments, mass spectroscopy, X-ray crystal structure analyses, and control experiments showed that the reaction of Cp2TiCl2 with 8-hydroxyquinoline resulted in a half-sandwich complex [CpTiCl­(C9H6NO)2] (I), in which the Lewis acidity was enhanced via fine-tuning steric and electronic properties of the Ti (IV) center, facilitating mono aza-Friedel–Crafts reaction of indoles, aldehydes, and aniline; in contrast, when anthranilic acid reacted with the same Ti­(IV) precursor, a bis-ligand sandwich complex Cp2Ti­[(o-NH2)­PhCOO]2 (II) was obtained, in which both Lewis acidity of titanium and cooperation with amino groups promoted further transformation of indoles into bis-indole adducts