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The Xishuangbanna game fowl, a local Chinese chicken breed renowned for its athleticism, is facing extinction. Despite its significance, research on its genome assembly and resequencing remains sparse, limiting our understanding of its genetic structure and function. In this study, we assembled a chromosome-level genome using second-generation sequencing and high-throughput chromosome conformation capture (Hi-C), along with transcriptome sequencing. We also resequenced 62 individuals. The resulting assembly yielded a 1.09 gigabase (Gb) high-quality genome, 994.34 Gb of resequencing data, and 141.38 Gb of transcriptome data from 15 tissues. This comprehensive dataset provides valuable insights into the artificial selection processes shaping the breed and offers a solid foundation for further genetic and population studies., (© 2024. The Author(s).)

We perform the modulation instability analysis of the 2D and 3D nonlinear Klein-Gordon equation. The instability region depends on dispersion and wavenumbers of the plane wave. The N-breathers of the nonlinear Klein-Gordon equation are constructed directly from its 2N-solitons obtained in history. The regularity conditions of breathers are established. The dynamic behaviors of breathers of the 2D nonlinear Klein-Gordon equation are consistent with modulation instability analysis. Furthermore, by means of the bilinear method together with improved long-wave limit technique, we obtain general high order rogue waves of the 2D and 3D nonlinear Klein-Gordon equation. In particular, the first- and second-order rogue waves and lumps of the 2D nonlinear Klein-Gordon equation are investigated by using their explicit expressions. We find that their dynamic behaviors are similar to the nonlinear Schrödinger equation. Finally, the first-order rational solutions are illustrated for the 3D nonlinear Klein-Gordon equation. It is demonstrated that the rogue waves of the 2D and 3D nonlinear Klein-Gordon equation always exist by choosing dispersion and wavenumber of plane waves., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

In order to explore the unique physiological roles of gas signaling molecules and gasotransmitters in vivo, chemists have engineered a variety of gas-responsive polymers that can monitor their changes in cellular milieu, and gas-releasing polymers that can orchestrate the release of gases. These have advanced their potential applications in the field of bio-imaging, nanodelivery, and theranostics. Since these polymers are of different chain structures and properties, the morphology of their assemblies will manifest distinct transitions after responding to gas or releasing gas. In this review, we summarize the fundamental design rationale of gas-responsive and gas-releasing polymers in structure and their controlled transition in self-assembled morphology and function, as well as present some perspectives in this prosperous field. Emerging challenges faced for the future research are also discussed., (© 2024 Wiley-VCH GmbH.)

Great effort has been dedicated to the engineering of porous organic cages (POCs) in geometry and topology. Yet, harnessing these cage-like entities as premade building units to construct infinite cage-based superstructures remains elusive. In this study, we design a type of vertex-modified phosphine organic prism by a postfunctionalized approach and use it as a ditopic cage monomer to achieve an intercage supramolecular polymerization via the synergy of metal coordination and π-π dimerization. The resulting cage-by-cage polymers can further hierarchically organize into superstructures of diverse morphologies and dimensionalities, including 1D fibers, 2D lamellae, and 3D vesicles. Control over the cosolvents is capable of well regulating their structural hierarchies and self-assembled shapes. This would pave a way for the creation of cage-based supramolecular assemblies and nanomaterials.

Significant efforts have been dedicated to designing porous organic cage compounds with geometric complexity and topological diversity. However, the use of these cage molecules as premade building units for constructing infinite cage-based superstructures remains unexplored. Here, we report the use of a panel-decorated phosphine organic cage as a special monomer to achieve supramolecular polymerization, resulting in cage-by-cage noncovalent polymers through the synergy of metal-coordination and intercage π - π dimerization. At a monomer concentration of 122 mM, the average degree of polymerization reaches 17, corresponding to a molecular weight of 26 kDa. The obtained cage-based supramolecular polymers can further hierarchically self-assemble into vesicular morphologies or one-dimensional nanofiber architectures. Selective control over the cosolvents can regulate their structural hierarchy and assembled morphology. This approach paves a new way for the construction of cage-based hierarchical assemblies and materials., (© 2024 IOP Publishing Ltd.)

A new deaminase, TadA8e, was recently evolved in the laboratory. TadA8e catalyzes DNA deamination over 1,000 times faster than ABE7.10. We developed a high-efficiency adenine base editor, rABE8e (rice ABE8e), combining monomeric TadA8e, bis-bpNLS and codon optimization. rABE8e had substantially increased editing efficiencies at NG-protospacer adjacent motif (PAM) and NGG-PAM target sequences compared with ABEmax. For most targets, rABE8e exhibited nearly 100% editing efficiency and high homozygous substitution rates in the specific editing window, especially at Positions A5 and A6. The ability to rapidly generate plant materials with homozygous base substitutions will benefit gene function research and precision molecular breeding., (© 2021 Institute of Botany, Chinese Academy of Sciences.)

We report for the first time that the imidate radical can be efficiently added to glycals to generate glycosyl radicals, based on which a general, toxic-reagent-free synthesis of C -glycosides of 2-deoxy-2-amino sugars has been developed. Complementary to previous strategies, the reaction is 1,2- trans -stereoselective and could use aryl alkenes as substrates. The late-stage functionalization and density functional theory calculations are reported.

Endothelial progenitor cells (EPCs), widely existing in bone marrow and peripheral blood, are involved in the repair of injured vascular endothelium and angiogenesis which are important to diabetic mellitus (DM) patients with vascular complications. The number and the function of EPCs are related to the advanced glycation end products (AGEs) generated in DM patients. Lycopene (Lyc) is an identified natural antioxidant that protects EPCs under the microenvironment of AGEs from damage. However, the underlying mechanism remains unclear. To investigate the effect of Lyc on EPCs, we isolated EPCs from DM rat bone marrow and determined cell proliferation, cell cycle,apoptosis and autophagy of EPCs. The present study showed that 10μg/mL Lyc improved cell proliferation and had low cytotoxicity in the presence of AGEs. In addition, Lyc rescued S phase of the cell cycle arrest, reduced apoptosis rate and decreased autophagic reaction including ROS and mitochondrial membrane potential (MMP) of EPCs. Moreover, Lyc combined use of autophagy inhibitors, 3-MA, had better protective effects. Taken together, our data suggests that Lyc promotes EPCs survival and protect EPCs from apoptosis and oxidative autophagy induced by AGEs, further remaining the number and function of EPCs. This study provides new insights into Lyc protective mechanism of AGEs-induced oxidative autophagy in EPCs from DM patients and offers a new therapy for DM vascular complications., (Copyright © 2017 Elsevier Masson SAS. All rights reserved.)

Background/objectives: The objectives of this study were to investigate the effects of lycopene on the migration, adhesion, tube formation capacity, and p38 mitogen-activated protein kinase (p38 MAPK) activity of endothelial progenitor cells (EPCs) cultivated with high glucose (HG) and as well as explore the mechanism behind the protective effects of lycopene on peripheral blood EPCs., Materials/methods: Mononuclear cells were isolated from human peripheral blood by Ficoll density gradient centrifugation. EPCs were identified after induction of cellular differentiation. Third generation EPCs were incubated with HG (33 mmol/L) or 10, 30, and 50 µg/mL of lycopene plus HG. MTT assay and flow cytometry were performed to assess proliferation and apoptosis of EPCs. EPC migration was assessed by MTT assay with a modified boyden chamber. Adhesion assay was performed by replating EPCs on fibronectin-coated dishes, after which adherent cells were counted. In vitro vasculogenesis activity was assayed by Madrigal network formation assay. Western blotting was performed to analyze protein expression of both phosphorylated and non-phosphorylated p38 MAPK., Results: The proliferation, migration, adhesion, and in vitro vasculogenesis capacity of EPCs treated with 10, 30, and 50 µg/mL of lycopene plus HG were all significantly higher comapred to the HG group (P < 0.05). Rates of apoptosis were also significantly lower than that of the HG group. Moreover, lycopene blocked phosphorylation of p38 MAPK in EPCs (P < 0.05). To confirm the causal relationship between MAPK inhibition and the protective effects of lycopene against HG-induced cellular injury, we treated cells with SB203580, a phosphorylation inhibitor. The inhibitor significantly inhibited HG-induced EPC injury., Conclusions: Lycopene promotes proliferation, migration, adhesion, and in vitro vasculogenesis capacity as well as reduces apoptosis of EPCs. Further, the underlying molecular mechanism of the protective effects of lycopene against HG-induced EPC injury may involve the p38 MAPK signal transduction pathway. Specifically, lycopene was shown to inhibit HG-induced EPC injury by inhibiting p38 MAPKs.

The ubiquitin (Ub)-conjugating enzyme, Ubc13, has been known to be involved in error-free DNA damage tolerance (or post-replication repair) via catalyzing Lys63-linked polyubiquitin chains formation together with a Ubc variant. However, its functions remain largely unknown in plant species, especially in monocotyledons. In this study, we cloned a Ub-conjugating enzyme, OsUbc13, that shares the conserved domain of Ubc with AtUBC13B in Oryza sativa L., which encodes a protein of 153 amino acids; the deduced sequence shares high similarities with other homologs. Real-time quantitative polymerase chain reaction (PCR) indicated that OsUbc13 transcripts could be detected in all tissues examined, and the expression level was higher in palea, pistil, stamen, and leaf, and lower in root, stem, and lemma; the expression of OsUbc13 was induced by low temperature, methylmethane sulfate (MMS), and H(2)O(2), but repressed by mannitol, abscisic acid (ABA), and NaCl. OsUbc13 was probably localized in the plasma and nuclear membranes. About 20 proteins, which are responsible for the positive yeast two-hybrid interaction of OsUbc13, were identified. These include the confirmed OsVDAC (correlated with apoptosis), OsMADS1 (important for development of floral organs), OsB22EL8 (related to reactive oxygen species (ROS) scavenging and DNA protection), and OsCROC-1 (required for formation of Lys63 polyubiquitylation and error-free DNA damage tolerance). The molecular characterization provides a foundation for the functional study of OsUbc13.

Using an environmental technology assessment system, we put forward the evaluation index system for treatment technology of the typical odor pollution sources in the petroleum refining process, which has been applied in the assessment of the industrial technology. And then the best available techniques are selected for emissions of gas refinery sewage treatment plant, headspace gas of acidic water jars, headspace gas of cold coke jugs/intermediate oil tank/dirty oil tank, exhaust of oxidative sweetening, and vapors of loading and unloading oil.

We report new types of matter rogue waves of a spinor (three-component) model of the Bose-Einstein condensate governed by a system of three nonlinearly coupled Gross-Pitaevskii equations. The exact first-order rational solutions containing one free parameter are obtained by means of a Darboux transformation for the integrable system where the mean-field interaction is attractive and the spin-exchange interaction is ferromagnetic. For different choices of the parameter, there exists a variety of different shaped solutions including two peaks in bright rogue waves and four dips in dark rogue waves. Furthermore, by utilizing the relation between the three-component and the one-component versions of the nonlinear Schrödinger equation, we can devise higher-order rational solutions, in which three components have different shapes. In addition, it is noteworthy that dark rogue wave features disappear in the third-order rational solution.

The aggravation process of oasisization leads to changes of land use type in oasis rim. In order to discuss the effects of different land use types on soil properties and soil quality, the four land use types located Cele oasis rim in south margin of Tarim Basin, which are the cotton field, orchard, and Caligonum mongolicum Turcz land use type reclaimed by people and nature state land use type covered by Alhagi sparsifolia SHAP, were selected as study object. The relative soil quality index (RI) and the soil quality synthesis index (SQI) were used to analyse the changes of soil quality between four land use types within 0-20 cm, 2040 cm, 40-60 cm soil depth, respectively. Meantime, the fractal theory was used to analyse the particle-size distribution (PSD) property of top soil under different land use types. The results indicated that there was a significant difference in the soil organic matter and total nitrogen in same soil depth between four land use types; the order ranked according to RI was same to the order ranked according to SQI in each soil depth between four land use types. The cotton field and orchard have an obviously positive effect on soil quality of the top soil, however, the soil quality of Alhagi sparsifolia SHAP land use type was gradually increasing along with the increasing soil depth. The soil properties and soil quality of Caligonum mongolicum Turcz land use type were at the lowest level according to the comparison results among all land use types, and the calculation results of PSD fractal dimension also indicated the Caligonum mongolicum Turcz land use type had the worst ability on maintaining soil fine fractions.

Based on the 2005-2007 experimental data in Cele oasis in the southern margin of Tarim Basin of Xinjiang, the soil quality of four typical types of farmland with different utilization intensity, i.e., farmland with high input, farmland with normal input, newly reclaimed farmland, and farmland in oasis' interior, was analyzed and assessed by using sustainable yield index, soil improvement index, and soil quality synthesis index. Among the farmlands, there were significant differences in the contents of soil organic matter, available nitrogen, and available phosphorus. Newly reclaimed farmland had the lowest level of soil quality, while the farmland in oasis' interior had relatively higher soil quality. This study could help the reasonable exploitation and utilization of farmlands in Cele oasis, and the protection of local farmland eco-environment.