Crystal structure characterization, Hirshfeld surface analysis, and DFT calculation studies of 1-(6-amino-5-nitro-naphthalen-2-yl)ethanone.

The title compound, C12H10N2O3, was obtained by the de-acetyl-ation reaction of 1-(6-amino-5-nitro-naphthalen-2-yl)ethanone in a concentrated sulfuric acid methanol solution. The mol-ecule comprises a naphthalene ring system bearing an acetyl group (C-3), an amino group (C-7), and a nitro group (C-8). In the crystal, the mol-ecules are assembled into a two-dimensional network by N⋯H/H⋯N and O⋯H/H⋯O hydrogen-bonding inter-actions. n-π and π-π stacking inter-actions are the dominant inter-actions in the three-dimensional crystal packing. Hirshfeld surface analysis indicates that the most important contributions are from O⋯H/H⋯O (34.9%), H⋯H (33.7%), and C⋯H/H⋯C (11.0%) contacts. The energies of the frontier mol-ecular orbitals were computed using density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-TZVP level of theory and the LUMO-HOMO energy gap of the mol-ecule is 3.765 eV.

Synthesis, crystal structure and Hirshfeld surface analysis of N-(6-acetyl-1-nitro-naphthalen-2-yl)acetamide.

The title compound, C14H12N2O4, was obtained from 2-acetyl-6-amino-naphthalene through two-step reactions of acetyl-ation and nitration. The mol-ecule comprises the naphthalene ring system consisting of functional systems bearing a acetyl group (C-2), a nitro group (C-5), and an acetyl-amino group (C-6). In the crystal, the mol-ecules are assembled into two-dimensional sheet-like structures by inter-molecular N-H⋯O and C-H⋯O hydrogen-bonding inter-actions. Hirshfeld surface analysis illustrates that the most important contributions to the crystal packing are from O⋯H/H⋯O (43.7%), H⋯H (31.0%), and C⋯H/H⋯C (8.5%) contacts.

Crystal structure and Hirshfeld analysis of (1aS,3aR,4aS,5aR)-15-acet-oxy-linden-7(11),8-trieno-12,8-lactone.

The structure of the title com-pound, C17H20O4 [systematic name: (1aS,3aR,4aS,5aR)-15-(acet-oxy)linden-7(11),8-trieno-12,8-lactone or (4aR,5S,5aR,6aS,6bR)-5-(acet-oxy-meth-yl)-4a,5,5a,6,6a,6b-hexa-hydro-3,6b-di-methyl-cyclo-propa[2,3]indeno-[5,6-b]furan-2(4H)-one, ent-chloranthalactone C], a natural product iso-lated from the whole plant Chloranthus japonicus Sieb., is a typical lin-den-ane-type sesquiterpenoid. The mol-ecule com-prises a bi-cyclo-[3.1.0]hexane ring (A/B system) bearing an acetoxymethyl (C-4) group, a bi-cyclo-[4.3.0]nonane ring (B/C system) containing a double bond (C-8/9) and a chiral quaternary carbon (C-10), and a 7(11)-en-12,8-olide structural moiety on the cyclo-hexan-8-ene (C ring). In the tetra-cyclic skeleton, the 1,3-cyclo-propane ring has a ß-con-figuration, and atoms H-5 and H3-14 have α- and ß-orientations, respectively. In the crystal, the mol-ecules are assembled into a two-dimensional network by weak O⋯H/H⋯O inter-actions. Hirshfeld surface analysis illustrates that the greatest contributions are from H⋯H (55.2%), O⋯H/H⋯O (34.6%) and C⋯H/H⋯C (8.9%) contacts.

The complete chloroplast genome of Carex agglomerata C. B. Clarke (Cyperaceae), an endemic species from China.

Carex agglomerata C. B. Clarke is a sedge with excellent ornamental characters, it is an important ecosystem stabilizer. Here we report the complete chloroplast genome of C. agglomerata to provide a foundation for further phylogenetic studies on the Cyperaceae. The chloroplast (cp) genome is 184,157 bp in size and consists of a large single-copy (LSC) region 106,654 bp in length, a small single-copy (SSC) region of 36,099 bp, two inverted repeats (IR) regions each 20,702 bp. The total GC content of the cp genome is 33.9% with the LSC, SSC, and IR regions 32, 32.5, and 42.9%, respectively. The cp genome contains 128 genes, including 80 protein-coding, 40 tRNA, and eight rRNA genes. The phylogenetic analysis showed C. agglomerata is in a clade with Carex neurocarpa Maxim and Carex siderosticta Hance. This study provides a basis for further phylogenetic studies of Carex.

Comprehensive analysis to identify DLEU2L/TAOK1 axis as a prognostic biomarker in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the deadliest malignant tumors that are harmful to human health. Increasing evidence has underscored the critical role of the competitive endogenous RNA (ceRNA) regulatory networks among various human cancers. However, the complexity and behavior characteristics of the ceRNA network in HCC were still unclear. In this study, we aimed to clarify a phosphatase and tensin homolog (PTEN)-related ceRNA regulatory network and identify potential prognostic markers associated with HCC. The expression profiles of three RNAs (long non-coding RNAs [lncRNAs], microRNAs [miRNAs], and mRNAs) were extracted from The Cancer Genome Atlas (TCGA) database. The DLEU2L-hsa-miR-100-5p/ hsa-miR-99a-5p-TAOK1 ceRNA network related to the prognosis of HCC was obtained by performing bioinformatics analysis. Importantly, we identified the DLEU2L/TAOK1 axis in the ceRNA by using correlation analysis, and it appeared to become a clinical prognostic model by Cox regression analysis. Furthermore, methylation analyses suggested that the abnormal upregulation of the DLEU2L/TAOK1 axis likely resulted from hypomethylation, and immune infiltration analysis showed that the DLEU2L/TAOK1 axis may have an impact on the changes in the tumor immune microenvironment and the development of HCC. In summary, the current study constructing a ceRNA-based DLEU2L/TAOK1 axis might be a novel important prognostic factor associated with the diagnosis and prognosis of HCC.

Characterization of the mitochondrial genome of Alloxiphidiopsis emarginata (Orthoptera, Tettigoniidae, Meconematinae).

The length of Alloxiphidiopsis emarginata complete mitogenome was 16,207 bp and contained the typical gene arrangement, base composition, codon usage found in other related species. The overall base composition exhibited obvious anti-G (10.6%) and AT bias (71.6%). The initiation codons of all PCGs were typical ATN (ATA/ATG/ATT), and the termination codons were TAA, TAG, or incomplete stop codon T. All tRNAs could be folded into typical cloverleaf secondary structures, except tRNASer (AGN). Phylogenetic analyses showed that A. emarginata was closer with Xizicus howardi.

The involvement of programmed cell death in inflated leaf petiole morphogenesis in Trapa pseudoincisa.

Trapa plants (Trapaceae) have an inflated leaf petiole called a spongy airbag. The aims of this study were to assess the involvement of programmed cell death (PCD) in the process of inflated leaf petiole morphogenesis. In this paper, light and transmission electron microscopy (TEM) were used to investigate cytological events and the development of inflated leaf petiole. During this process, the inflated leaf petiole of Trapa pseudoincisa L. undergoes a developmental process, changing from solid to hollow phase. Debris from the degraded cells was seldom observed in the transverse sections of leaf petioles, but some degraded cells with an abnormal morphology were observed in longitudinal sections. Cytoplasmic changes, such as disrupted vacuoles, degraded plastids, and the emergence of secondary vacuoles were observed during leaf petiole morphogenesis. In addition, gel electrophoresis and TUNEL assays were used to evaluate DNA cleavage during petiole morphogenesis. DNA internucleosomal cleavage and TUNEL-positive nuclei indicate that the typical PCD features of DNA cleavage occurred early in the process. These results revealed that PCD plays a critical role in inflated leaf petiole morphogenesis. Additionally, a trans-disciplinary systems approach is required that recognises the necessity for integration of cytological and molecular characteristics for identification of aerenchyma type.

The complete chloroplast genome sequence of Echinocodon Lobophyllus (Campanulaceae) revealed by next-generation sequencing and phylogenetic implication.

The complete chloroplast genome sequence of Echinocodon lobophyllus was determined by Illumina pair-end sequencing. The results showed that the complete plastid genome was 169,419 bp in length, containing a large single copy (LSC) of 85,599 bp and a small single copy (SSC) of 8054 bp, which were separated by a pair of 37,883 bp inverted repeats (IRs). A total of 109 unique genes were annotated, including 75 protein coding genes, 30 tRNA genes, and 4 rRNA genes. Among these genes, 16 genes contained one or two introns. The overall GC contents of the plastid genome were 38.4%. A maximum likelihood phylogenetic analysis showed that E. lobophyllus and Codonopsis minima formed one clade at the base of the phylogenetic tree of Campanulaceae with a high support value.

The complete chloroplast genome sequence of Fargesia qinlingensis (Poaceae): an endemic to China.

The complete chloroplast genome of Fargesia qinlingensis (Poaceae) has been reconstructed from the whole-genome Illumina sequencing data. The complete chloroplast genome sequence of F. qinlingensis obtained in this study was 139,640 bp in length, with a large single copy (LSC) region of 83,220 bp, a small single copy (SSC) region of 12,826 bp, separated by two inverted repeat (IR) regions of 21,797 bp each. The GC content was 38.9%, and in the LSC, SSC, and IR regions were 37.0%, 33.2%, and 44.2%, respectively. A total of 130 genes were annotated, including 83 protein-coding genes (PCGs), 39 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The result of the phylogenetic analysis showed that F. qinlingensis was more closely related to the species of F. denudata.

Complete mitochondrial genome of Xiphidiopsis (Xiphidiopsis) gurneyi (Orthoptera, Tettigoniidae, Meconematinae).

Xiphidiopsis (Xiphidiopsis) gurneyi belongs to Meconematinae. The complete mitochondrial genome of X. (X.) gurneyi was sequenced by the next-generation sequencing (NGS) technology. The total length of the mitogenome was 16,225 bp and contains the typical gene arrangement, base composition, codon usage found in Meconematinae species. Phylogenetic tree was constructed based on concatenated datasets of PCGs and rRNAs of X. (X.) gurneyi and 19 Tettigoniidae species to assess their phylogenic relationship. Phylogenetic analysis showed that X. (X.) gurneyi was more closely related to the genus of Xizicus.

Leaf-shape remodeling: programmed cell death in fistular leaves of Allium fistulosum.

Some species of Allium in Liliaceae have fistular leaves. The fistular lamina of Allium fistulosum undergoes a process from solid to hollow during development. The aims were to reveal the process of fistular leaf formation involved in programmed cell death (PCD) and to compare the cytological events in the execution of cell death to those in the unusual leaf perforations or plant aerenchyma formation. In this study, light and transmission electron microscopy were used to characterize the development of fistular leaves and cytological events. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assays and gel electrophoresis were used to determine nuclear DNA cleavage during the PCD. The cavity arises in the leaf blade by degradation of specialized cells, the designated pre-cavity cells, in the center of the leaves. Nuclei of cells within the pre-cavity site become TUNEL-positive, indicating that DNA cleavage is an early event. Gel electrophoresis revealed that DNA internucleosomal cleavage occurred resulting in a characteristic DNA ladder. Ultrastructural analysis of cells at the different stages showed disrupted vacuoles, misshapen nuclei with condensed chromatin, degraded cytoplasm and organelles and emergence of secondary vacuoles. The cell walls degraded last, and residue of degraded cell walls aggregated together. These results revealed that PCD plays a critical role in the development of A. fistulosum fistular leaves. The continuous cavity in A. fistulosum leaves resemble the aerenchyma in the pith of some gramineous plants to improve gas exchange.

Programmed cell death: a mechanism for the lysigenous formation of secretory cavities in leaves of Dictamnus dasycarpus.

The formation of secretory cavities in Rutaceae has been the subject of great interest. In this study, cytological events that are involved in the lysigenous formation of the secretory cavities in the leaves of Dictamnus dasycarpus are characterized by an interesting pattern of programmed cell death (PCD). During the developmental process, clusters of cells from a single protoepidermal cell embark on different trajectories and undergo different cell death fates: the cell walls of the secretory cells have characteristics of thinning or complete breakdown, while the sheath cells present a predominantly thick-walled feature. A DAPI assay shows deformed nuclei that are further confirmed to be TUNEL-positive. Gel electrophoresis indicates that DNA cleavage is random and does not result in ladder-like DNA fragmentation. Ultrastructurally, several remarkable features of PCD have been determined, such as misshapen nuclei with condensed chromatin and a significantly diffused membrane, degenerated mitochondria and plastids with disturbed membrane systems, multivesicular bodies, plastolysomes, vacuole disruption and lysis of the center secretory cell. Cytological evidence and Nile red stains exhibit abundant essential oils accumulated in degenerated outer secretory cells after the dissolution of the center secretory cell. In addition, explanations of taxonomic importance and the relationship between PCD and oil droplet accumulation in the secretory cavities are also discussed.

Laticiferous canal formation in fruits of Decaisnea fargesii: a programmed cell death process?

Programmed cell death (PCD), a topic of abiding interest, remodels plants at the cell, tissue, and organ levels involving various developmental processes of plants. The aim of this study is to provide a morphological characterization of evidence of PCD involvement in the laticiferous canal formation in fruit of Decaisnea fargesii. Several ultrastructural features of PCD have been observed including disintegration of vacuole and plasma membranes, cell wall degeneration, degenerated cytoplasm, abundant membrane structures and flocculent material, mitochondria and misshapen nuclei coupled with degraded plastids in vacuoles, and nuclei enveloped by rubber granule. In D. fargesii, the nuclei of the secretory epidermal cells become TUNEL-positive from the sunken stage to the late expanding stage, then DAPI-negative during the mature stage, indicating an early event of deoxyribonucleic acid (DNA) cleavage and a late event of complete DNA degeneration. Gel electrophoresis indicates that DNA cleavage is random and does not result in the laddering pattern indicating multiples of internucleosomal units. During the PCD of secretory epidermal cells, the rubber granules continue to be synthesized and accumulated in the secretory epidermal cells despite nuclear degradation. The PCD's role in laticiferous canal formation suggests that PCD may play important roles in gland development of plants.

Ultrastructure and secretion of secretory canals in vegetative organs of Bupleurum chinense DC.

The development of secretory canals in vegetative organs of Bupleurum chinense DC. and the accumulation of essential oils were investigated by transmission electron microscopy (TEM) analysis. The secretion mechanism of the essential oil was also discussed. The results indicate that the plastid, ground substances of cytoplasm and mitochondria took part in the biosynthesis of oil or oil precursor. The endoplasmic reticulum involved in the transport of essential oil to the secretory lumen. At latter stages of development of secretory cells, numerous different sized vesicles fused with the plasmalemma along the boundary between two neighbor secretory cells and secreted the substance into the wall. Thus, the wall between two neighbor secretory cells near the lumen became loosely structured. Then, the wall lined the lumen near two neighbor secretory cells extruded numerous grey vesicles with various sizes on the side facing the lumen, and released these vesicles into the lumen. As a result, the manner of secretion in secretory canals of Bupleurum chinense DC. appeared to be exocytosis.