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Gossypol is a yellow polyphenol naturally produced by Malvaceae plants such as cotton, which mainly exists in roots, stems, leaves, and seeds of cotton. Gossypol has animal toxicity, and long-term intake of gossypol will accumulate in livestock and cause poisoning, resulting in decreased fecundity, organ lesions, and even death of animals. The cotton output in Xinjiang is huge, accounting for more than 80% of the whole country. After cotton harvest, most of the waste cotton straws are directly crushed and returned to the field, resulting in great waste of resources. Cotton straw is rich in crude protein, cellulose, hemicellulose, and lignin, which is equivalent to common crop straw in nutritional components. However, its gossypol content exceeded the standard, which limited the application of cotton straw feed. How to achieve efficient and low-cost detoxification of gossypol has become the key factor to determining the fodder of cotton straw. The structure, properties, toxicity, detoxification technology, and detoxification mechanism of gossypol were summarized in this paper, which provided a reference for feed utilization of cotton straw. [ABSTRACT FROM AUTHOR]

Gossypium hirsutum (upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of G. hirsutum , and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly via historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species. [ABSTRACT FROM AUTHOR]

Main conclusion: The novel structural variations were identified in cotton chloroplast tRNAs and gene loss events were more obvious than duplications in chloroplast tRNAs. Transfer RNAs (tRNA) have long been believed an evolutionary-conserved molecular family, which play the key roles in the process of protein biosynthesis in plant life activities. In this study, we detected the evolutionary characteristics and phylogeny of chloroplast tRNAs in cotton plants, an economic and fibered important taxon in the world. We firstly annotated the chloroplast tRNAs of 27 Gossypium species to analyze their genetic composition, structural characteristics and evolution. Compared with the traditional view of evolutionary conservation of tRNA, some novel tRNA structural variations were identified in cotton plants. I.g., tRNAVal-UAC and tRNAIle-GAU only contained one intron in the anti-condon loop region of tRNA secondary structure, respectively. In the variable region, some tRNAs contained a circle structure with a few nucleotides. Interestingly, the calculation result of free energy indicated that the variation of novel tRNAs contributed to the stability of tRNA structure. Phylogenetic analysis suggested that chloroplast tRNAs have evolved from multiple common ancestors, and the tRNAMet seemed to be an ancestral tRNA, which can be duplicated and diversified to produce other tRNAs. The chloroplast tRNAs contained a group I intron in cotton plants, and the evolutionary analysis of introns indicated that group I intron of chloroplast tRNA originated from cyanobacteria. Analysis of gene duplication and loss events showed that gene loss events were more obvious than duplications in Gossypium chloroplast tRNAs. Additionally, we found that the rate of transition was higher than the ones of transversion in cotton chloroplast tRNAs. This study provided new insights into the structural characteristics and evolution of chloroplast tRNAs in cotton plants. [ABSTRACT FROM AUTHOR]

Key message: The DNA fragments transferred among cotton cytoplasmic genomes are highly differentiated. The wild D group cotton species have undergone much greater evolution compared with cultivated AD group. Cotton (Gossypium spp.) is one of the most economically important fiber crops worldwide. Gene transfer, nucleotide evolution, and the codon usage preferences in cytoplasmic genomes are important evolutionary characteristics of high plants. In this study, we analyzed the nucleotide sequence evolution, codon usage, and transfer of cytoplasmic DNA fragments in Gossypium chloroplast (cp) and mitochondrial (mt) genomes, including the A genome group, wild D group, and cultivated AD group of cotton species. Our analyses indicated that the differences in the length of transferred cytoplasmic DNA fragments were not significant in mitochondrial and chloroplast sequences. Analysis of the transfer of tRNAs found that trnQ and nine other tRNA genes were commonly transferred between two different cytoplasmic genomes. The Codon Adaptation Index values showed that Gossypium cp genomes prefer A/T-ending codons. Codon preference selection was higher in the D group than the other two groups. Nucleotide sequence evolution analysis showed that intergenic spacer sequences were more variable than coding regions and nonsynonymous mutations were clearly more common in cp genomes than mt genomes. Evolutionary analysis showed that the substitution rate was much higher in cp genomes than mt genomes. Interestingly, the D group cotton species have undergone much faster evolution compared with cultivated AD groups, possibly due to the selection and domestication of diverse cotton species. Our results demonstrate that gene transfer and differential nucleotide sequence evolution have occurred frequently in cotton cytoplasmic genomes. [ABSTRACT FROM AUTHOR]

Rapid kinetics, complex and diverse reaction intermediates, and difficult screening make the study of assembly mechanisms of high-nuclearity lanthanide clusters challenging. Here, we synthesize a double-cage dysprosium cluster [Dy60(H2L1)24(OAc)71(O)5(OH)3(H2O)27]·6H2O·6CH3OH·7CH3CN (Dy60) by using a multidentate chelate-coordinated diacylhydrazone ligand. Two Dy30 cages are included in the Dy60 structure, which are connected via an OAc− moiety. The core of Dy60 is composed of 8 triangular Dy3 and 12-fold linear Dy3 units. We further change the alkali added in the reaction system and successfully obtain a single cage-shaped cluster [Dy30(H2L1)12(OAc)36(OH)4(H2O)12]·2OH·10H2O·12CH3OH·13CH3CN (Dy30) with a perfect spherical cavity, which could be considered an intermediate in Dy60 formation. Time-dependent, high-resolution electrospray ionization mass spectrometry (HRESI-MS) is used to track the formation of Dy60. A possible self-assembly mechanism is proposed. We track the formation of Dy30 and the six intermediate fragments are screened. High-nuclearity lanthanide clusters can exhibit interesting properties such as magnetism, but the mechanisms by which they assemble are poorly understood. Here, the formation of two dysprosium nanoclusters containing 30 or 60 atoms is followed over time by mass spectrometry and proposed to follow a seven-step assembly mechanism. [ABSTRACT FROM AUTHOR]

Pinus L. is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms. However, our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny. Thus, we analyzed the sequences of 97 Pinus plastid genomes, including four newly sequenced genomes and 93 previously published plastomes, to explore the evolution and phylogenetic relationships in the genus Pinus. The complete chloroplast genomes of Pinus species ranged in size from 109 640 bp (P. cembra L.) to 121 976 bp (P. glabra Walter), and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms. We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983 (44%), followed by tandem repeats with 2999 (33%), and then palindromic repeats with 2126 (23%). Sixteen divergence hotspot regions were identified in Pinus plastid genomes, which could be useful molecular markers for future population genetics studies. Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus (single needle section) and Pinus (double needles section). Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous. The two subgenera subsequently split 85.86 Mya, which was largely consistent with the other molecular results based on partial DNA markers. These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes. [ABSTRACT FROM AUTHOR]

We obtained a binuclear Gd(III) complex [Gd2(L1)2(NO3)4] (1, HL1 = (E)-2-(2-(pyridin-2-ylmethyleneamino)ethoxy)ethanol) by reacting N2O2-tetradentate chelating ligand HL1 with Gd(NO3)3·6H2O at solvothermal temperature of 100 °C. Time-dependent high-resolution electrospray ionization mass spectrometry (HRESI-MS) followed the formation of 1 and revealed it's the assembly mechanism: HL1 → Gd(L1) → Gd2(L1)2. When we used the NO2-tridentate chelating ligand HL2 (HL2 = 2-(2-aminoethoxy)ethanol) under the same reaction conditions, we obtained an "hourglass-like" nonanuclear Gd(III) cluster [Gd9(L2)8(μ3-OH)8(μ4-O)2(NO3)8]·2CH3OH·H2O (2). Their assembly mechanism was proposed: HL2 → Gd(L2) → Gd2(L2)2 → Gd3(L2)3 → Gd4(L2)4 → Gd5(L2)4 → Gd9(L2)8. Most notably, when we used the NO-bidentate chelate ligand HL3 (HL3 = picolinic acid), we obtained a dodecanuclear Gd(III) cluster [Gd12(L3)8(OH)16(NO3)8(OH)4(H2O)4]·22CH3OH·25CH3CN (3) under the same reaction conditions. We found that the formation process of cluster 3 involved two different and mutually interfering self-assembly processes, namely, multitemplate-induced assembly (HL3 → Gd(L3) → Gd2(L3)2 → Gd12(L3)8) and stepwise assembly (HL3 → Gd(L3) → Gd2(L3)2 → Gd3(L3)2 → Gd4(L3)2 → Gd5(L3)2 → Gd6(L3)2 → Gd12(L3)8). [ABSTRACT FROM AUTHOR]

The most effective way to understand reaction mechanisms and kinetics is to identify the reaction intermediates and determine the possible reaction patterns. The influencing factors that must be considered in the self-assembly of clusters are the type of ligand, metal ion, coordination anion and the pH of the solution. However, changes in ligand substituents resulting in different self-assembly processes to obtain different types of structures are still very rare, especially with –H and –CH3 substituents, which do not exert significant steric hindrance effects. In this study, planar mononuclear Ni(L1)2 (L1 = 2-ethoxy-6-(iminomethyl)phenol) was dissolved in methanol and combined with Dy(NO3)3·6H2O for 48 h at room temperature to obtain a butterfly-like Ni2Dy2 cluster ([Dy2Ni2(L1)4(CH3O)2(NO3)4], 1). The Dy(III) ions in cluster 1 are in an O8N coordination environment, and the Ni(II) ions are in an O5N coordination environment. High-resolution electrospray ionization mass spectrometry (HRESI-MS) was used to track species changes during the formation of cluster 1. Six key intermediate fragments were screened, and the self-assembly mechanism was proposed as Ni(L1)2 → HL1 + NiL1 → DyL1/Ni(L1)2′ → DyNi(L1)2 → Dy2Ni2(L1)4. Through this assembly mechanism, we found that Ni(L1)2 was first cleaved into HL1 + NiL1 and then further assembled to obtain 1. Another butterfly-like tetranuclear heterometallic cluster ([Dy2Ni2(L2)4(CH3O)2(NO3)4], 2) was obtained using planar mononuclear Ni(L2)2 (L2 = (E)-2-ethoxy-6-((methylimino)methyl)phenol) with –CH3 substitution on the nitrogen atom under the same reaction conditions. The structural analysis of cluster 2 showed that the Dy(III) ions are in an O9 coordination environment, and the Ni(II) ions are in an O4N2 coordination environment. HRESI-MS was used to trace species changes during the formation of 2, and the assembly mechanism was proposed as Ni(L2)2 → DyNi(L2)2 → Dy2Ni(L2)2 → Dy2Ni2(L2)4. Analysis of the assembly mechanism of 2 showed that Ni(L2)2 was twisted during the reaction, and its coordination point was exposed to capture the Dy(III) ions. Finally, Dy(NO3)3·6H2O was replaced with NaN3 to obtain a [Ni2Na2(L2)4(N3)4] cluster (3) under the same reaction conditions and verify the above-mentioned torsion step. HRESI-MS was also used to trace the assembly process, and the assembly mechanism was proposed as Ni(L2)2 → NiNa(L2)2 → NiNa2(L2)2 → Ni2Na2(L2)4. Herein, the effect of interference from substitution and the regulation self-assembly process were discovered in the formation of 3d–4f heterometallic clusters, and different types of coordination clusters were obtained. [ABSTRACT FROM AUTHOR]

N-Methylbenzimidazole-2-methanol (L) and Ln(NO3)3·6H2O are dissolved in a mixed solvent of methanol and acetonitrile and then reacted at 80 °C to obtain [Ln3(L)5(NO3)4] (Ln3, Ln = Gd, Tb). In Ln3, three L− are located in the same plane as the three Ln3+ ions, and the other two L− are located above and below the plane, respectively. Two of the four NO3− ions are respectively coordinated with two Ln3+, and the other two are coordinated with one Ln3+ ion, which results in the asymmetry of the above-described triangular shape Ln3. When the Ln3 single crystal was tested by Electrospray Ionization Mass Spectrometry, the main frame [Ln3L5(NO3)3]+ was found to be stable, only one NO3−ion was lost. As the energy of the ion source increases, we observe the gradual fragmentation of the triangular shape Ln3, and propose that the fragmentation mechanism is: Ln3L5 → Ln3L4 → Ln2L4 → Ln2L3 → Ln2L2 → LnL. This provides the basis for the assembly of triangular shaped Ln3 clusters. For the first time, the magnetocaloric effect (MCE) of triangular Gd3 clusters was studied and it exhibited a large MCE of 10.65 J kg−1 K−1 at 7 K for ΔH = 5 T. [ABSTRACT FROM AUTHOR]

The formation of high-nuclearity clusters of lanthanide usually involves many complicated self-assembly processes. Thus, tracking the formation process is extremely difficult and research on the assembly mechanism is very rare. In this study, a Dy-exclusive nanocluster containing vertex-sharing [Dy4(μ3-OH)4] cubanes, denoted as [Dy12(L)8(OH)16(CH3O)8(H2O)8]·(CH3O)4 (Dy12, L = quinoline-2-carboxylate), was designed and synthesized from L and DyCl3·6H2O. Eight quinoline-2-carboxylate ligands were encapsulated on the periphery of the Dy12 cluster, which served to stabilize the core. The high stability of the Dy12 cluster core was further confirmed by high-resolution electrospray-ionization mass spectrometry (HRESI-MS). With increased ion-source energy, only CH3O− and OH− bridging ligands were replaced inside the Dy12 cluster. Notably, eight intermediate fragments were successfully observed from the Dy12 cluster formation by time-dependent HRESI-MS. First, ligand L captured Dy3+ to give Dy1, which further formed Dy2 through μ2-O bridging. The Dy12 cluster was constructed in one step with four Dy2 and four Dy3+ as templates: L → Dy1→ Dy2→ Dy12. Moreover, a series of Dy3–Dy6 fragment peaks with relatively weak intensities were observed, and an alternative stepwise-assembly route was proposed: L → Dy1→ Dy2→ Dy3→ Dy4→ Dy5→ Dy6→ Dy12. On comparing the two different assembly methods, the multitemplate guided assembly formed Dy12 was found to be dominant. To the best of our knowledge, this study was the first to propose the involvement of two self-assembly mechanisms in the construction of lanthanide clusters, as further confirmed by HRESI-MS. Magnetic studies further showed that Dy12 clusters exhibited field-induced single-molecule magnet behavior. [ABSTRACT FROM AUTHOR]

Metal nanoclusters have a certain rigidity due to their specific coordination patterns and shapes; thus, they face extreme difficulty in folding into a specific direction to form a double‐helix structure and in further interconnecting to form metal–helix frameworks (MHFs). To date, no MHFs have been produced by the formation of heterometallic clusters. Selecting the appropriate "bonding molecules" to bond metal nanoclusters in a specific multiple direction is one of the most effective strategies for designing synthetic MHFs. In this study, we realized for the first time the control of different orientations of μ3‐NO3− to join heterometallic clusters (Cu10Dy2) and subsequently form a left‐handed double helix chain, which further joins to form MHFs. In the structure of the MHFs, four different directions of bridging μ3‐NO3− exist, three of which are involved in the linkage of the double‐helix chain. Each μ3‐NO3− is connected to three adjacent Cu10Dy2. Herein, we extend a new method for designing synthetic double‐helix structures and MHFs, thereby further laying the foundation for the development of similar DNA double‐helix structures and nucleic acid secondary structures in vitro. [ABSTRACT FROM AUTHOR]

The organic ligands 5,7-dibromo-2-methyl-8-quinolinol (L1), 1,10-phenanthroline (L2), and 5,7-dichloro-2-methyl-8-quinolinol (L3) were used to react with Dy(NO3)3·6H2O under solvothermal conditions at 80 °C to obtain the complexes [Dy(L1)3(H2O)] (1), [Dy(L2)2(NO3)3] (2), and [Dy(L3)3(H2O)] (3), respectively. The reaction of L1 and L2 with lanthanide(iii) nitrate salts in the presence of triethylamine as a base afforded four mononuclear complexes, namely, [Ln(L1)2(L2)(NO3)] [Ln = Dy (4), Ho (5), Er (6), and Tb (7)]. Complexes 1 and 2 emitted yellow-green and red light under excitation with light of a certain wavelength. Interestingly, 4–7 exhibited a superimposition of the luminescence of 1 and 2. To our knowledge, this is the first example of the use of different organic light-emitting ligands to adjust the fluorescence of Ln(iii) complexes. Moreover, the series of complexes [Ln(L3)2(L2)(NO3)] [Ln = Dy (8), Ho (9), Er (10), and Tb (11)] were also obtained under the same conditions by replacing L1 with L3. In the way that was expected, 8–11 exhibited a superimposition of the luminescence of 2 and 3. Density functional theory (DFT) calculations of electron cloud density showed that the electron cloud densities of complexes 4 and 8 are mainly concentrated in the quinoline rings. Furthermore, analysis of the molecular ion peaks of complexes 4–11 obtained by electrospray mass spectrometry (ESI-MS) showed that only the 1,10-phenanthroline ligand was discovered to dissociate in the solution state. Magnetic measurements of the Dy-containing complexes revealed features of field-induced single-ion magnet behavior. [ABSTRACT FROM AUTHOR]

Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A-G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium. [ABSTRACT FROM AUTHOR]

Two polymorphs of supramolecular isomers, a discrete dimer and a zig-zag chain, having the same chemical composition, [Mn(Hbit)Cl2] (Hbit=1-methyl-2-(1H-1,2,3-triazol-4-yl)-1H-benzo[d]imidazole), were obtained solvothermally in a one-pot synthesis. The isomers differ in a number of ways: orange blocks versus pale-yellow needles, triclinic P1 versus orthorhombic Pbcn, double µ2-Cl versus alternate single and triple µ2-Cl, coordination number 5 versus 6, and antiparallel versus parallel near-neighbor orientation of Hbit. The packing in each case is driven by the supramolecular interactions, H-bonds (N--H…Cl, C--H…Cl) and π…π overlaps, calculated to be in the range 20-36 kcalmol-1. Calculations gave a difference of only 2 kcalmol-1 in favor of the dimer, which confirms with the observation of principally the dimer at short reaction time. ESI-MS spectra of the dissolved crystals reveal the same fragments with similar distributions. The presence of two fragments at m/z 286.96 [MnIV(Hbit)Cl-2H]+ and 323.94 [MnIII (Hbit)Cl2]+ indicates that [Mn(Hbit)Cl2] is the building unit in both cases; thus, the different orientations of the ligands lead to the two polymorphs stabilized by the respective supramolecular interactions. Importantly, the chain form represents the first example with alternate single and triple µ2-Cl bridges. The magnetic interactions are weakly antiferromagnetic in both cases, with J in the range 0.07-0.34 cm-1; however, high-field EPR analysis reveals moderate magneto-anisotropy with D=0.26(1) cm-1, E=0.06(1) cm-1 and D=0.17(1) cm-1, E=0.03(1) cm-1, respectively. [ABSTRACT FROM AUTHOR]

Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family. [ABSTRACT FROM AUTHOR]