Phenotypic Identification, Genetic Characterization, and Selective Signal Detection of Huitang Duck.

The Huitang duck (HT), a long-domesticated elite local breed from Hunan Province, China, with excellent meat quality, has not had its population genetic structure and genomic selective sweeps extensively studied to date. This study measured the phenotypic characteristics of HT and conducted comparative analysis between HT and 16 different duck breeds, including wild, indigenous, and meat breeds, to characterize its population structure and genetic potential. The results revealed that HT is a dual-purpose indigenous breed with a genetic background closely related to the Youxian sheldrake and Linwu ducks. In the selective sweep analysis between HT and Linwu ducks, genes such as PLCG2, FN1, and IGF2BP2, which are associated with muscle growth and development, were identified near the 27 selection signals. The comparison between HT and Jinding ducks revealed 68 selective signals that contained important genes associated with ovarian development (GRIK4, MAP3K8, and TGIF1) and egg-laying behaviors (ERBB4). Selective sweep analysis between HT and Youxian sheldrake ducks found 93 selective regions covering genes related to both meat (IGF1R and IGFBP5) and egg-production (FOXO3 and ITPR1) traits. Our study may provide novel knowledge for exploring the population structure and genetic potential of HT, offering a theoretical basis for its breeding strategies in the future.

CytoSIP: an annotated structural atlas for interactions involving cytokines or cytokine receptors.

Therapeutic agents targeting cytokine-cytokine receptor (CK-CKR) interactions lead to the disruption in cellular signaling and are effective in treating many diseases including tumors. However, a lack of universal and quick access to annotated structural surface regions on CK/CKR has limited the progress of a structure-driven approach in developing targeted macromolecular drugs and precision medicine therapeutics. Herein we develop CytoSIP (Single nucleotide polymorphisms (SNPs), Interface, and Phenotype), a rich internet application based on a database of atomic interactions around hotspots in experimentally determined CK/CKR structural complexes. CytoSIP contains: (1) SNPs on CK/CKR; (2) interactions involving CK/CKR domains, including CK/CKR interfaces, oligomeric interfaces, epitopes, or other drug targeting surfaces; and (3) diseases and phenotypes associated with CK/CKR or SNPs. The database framework introduces a unique tri-level SIP data model to bridge genetic variants (atomic level) to disease phenotypes (organism level) using protein structure (complexes) as an underlying framework (molecule level). Customized screening tools are implemented to retrieve relevant CK/CKR subset, which reduces the time and resources needed to interrogate large datasets involving CK/CKR surface hotspots and associated pathologies. CytoSIP portal is publicly accessible at https://CytoSIP.biocloud.top , facilitating the panoramic investigation of the context-dependent crosstalk between CK/CKR and the development of targeted therapeutic agents.

Hydrogen sulfide regulates macrophage polarization and necroptosis to accelerate diabetic skin wound healing.

Hydrogen sulfide (H2S), recognized as the third gasotransmitter, plays a pivotal role in the pathophysiological processes of various diseases. Cystathionine γ-lyase (CSE) is the main enzyme for H2S production in the skin. However, effects and mechanisms of H2S in diabetic skin wound healing remain unclear. Our findings revealed a decrease in plasma H2S content in diabetic patients with skin wounds. CSE knockout (KO) diabetic mice resulted in delayed wound healing, reduced blood perfusion, and CD31 expression around the wounds. It also led to increased infiltration of inflammatory cells and M1-type macrophages, decreased collagen levels, α-smooth muscle actin (α-SMA), and proliferating cell nuclear antigen (PCNA) expression. Additionally, there were enhanced expressions of necroptosis related proteins, including receptor interacting protein kinase 1 (RIPK1), RIPK3 and mixed lineage kinase domain like protein (MLKL). In comparison, sodium hydrosulfide (NaHS), H2S donor, accelerated skin wound healing in leptin receptor deficiency (db/db) mice. This acceleration was accompanied by increased blood perfusion and CD31 expression, reduced infiltration of inflammatory cells and M1-type macrophages, elevated collagen levels, α-SMA, and PCNA expressions, and decreased necroptosis-related protein expressions together with nuclear factor-κB (NF-κB) p65 phosphorylation. In conclusion, H2S regulates macrophage polarization and necroptosis, contributing to the acceleration of diabetic skin wound healing. These findings offer a novel strategy for the treatment of diabetic skin wounds.

PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules.

Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue predominate), or regulatory (2-residue predominate) roles. Computational tools for modeling metal ions in protein structures, especially for transient, reversible, and concentration-dependent regulatory sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system for predicting zinc ion localization and environment in macromolecular structures. Compared to other predictors, PMM excels in predicting regulatory sites (median deviation of 0.34 Å), demonstrating superior accuracy in locating catalytic sites (median deviation of 0.27 Å) and structural sites (median deviation of 0.14 Å). PMM assigns a certainty score to each predicted site based on local structural and physicochemical features independent of homolog presence. Interactive validation through our server, CheckMyMetal, expands PMM's scope, enabling it to pinpoint and validates diverse functional zinc sites from different structure sources (predicted structures, cryo-EM and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top. While currently trained on zinc, the PMM workflow can easily adapt to other metals through expanded training data.

Sn(OTf)2-Catalyzed (3 + 2) Cycloaddition/Sulfur Rearrangement Reaction of Donor-Acceptor Cyclopropanes with Indoline-2-thiones.

The (3 + 2) cycloaddition/sulfur rearrangement reaction of donor-acceptor cyclopropanes bearing a single keto acceptor with indoline-2-thiones has been realized. Under the catalysis of Sn(OTf)2, a series of functionalized 3-indolyl-4,5-dihydrothiophenes were synthesized with moderate to excellent yields.

Yb(OTf)3-Catalyzed Formal (4 + 3) Cycloaddition Reactions of 3-Benzylideneindoline-2-thiones with Donor-Acceptor Cyclopropanes.

A Yb(OTf)3-catalyzed formal (4 + 3) cycloaddition reaction of donor-acceptor cyclopropanes with 3-benzylideneindoline-2-thiones as sulfur-containing 4π components has been successfully achieved. A series of functionalized 5,10-dihydro-2H-thiepino[2,3-b]indole derivatives were synthesized with good yields and moderate to good diastereoselectivity. The reaction described herein represented the inaugural (4 + 3) cycloaddition of 3-benzylideneindoline-2-thiones.

AlCl3-mediated ring-opening reactions of indoline-2-thiones with acyl cyclopropanes, bi-cyclopropanes and spirocyclic cyclopropanes.

AlCl3-mediated nucleophilic ring-opening reactions of indoline-2-thiones with various acyl cyclopropanes, bi-cyclopropanes and spirocyclic cyclopropanes were investigated. A series of ketones functionalized with indolylthio groups were synthesized in yields ranging from moderate to good. Moreover, chemical transformations of 4-indolylthio butan-1-ones to dihydro-2H-thiepino[2,3-b]indoles and sulfone were carried out to further expand both synthetic utility and structural complexity.

Responsive photonic hydrogel for colorimetric detection of formaldehyde.

Formaldehyde (FA) can damage DNA, cause liver and kidney dysfunction, and ultimately lead to malignant tumors. Therefore, it is essential to develop a method that can conveniently detect FA with high detection sensitivity. Here, a responsive photonic hydrogel was prepared by embedding three-dimensional photonic crystal (PC) into amino-functionalized hydrogel to construct a colorimetric sensing film for FA. The amino groups on the polymer chains of the photonic hydrogel reacts with FA to increase the crosslinking density of the hydrogel, resulting in its volume shrinkage and a decrease in microsphere spacing of the PC. That causes the reflectance spectra blue-shift of more than 160 nm and color change from red to cyan for the optimized photonic hydrogel, achieving the sensitive, selective and colorimetric detection of FA. The constructed photonic hydrogel shows good accuracy and reliability for practical determination of FA in air and aquatic products, providing a new strategy for designing other target analytes responsive photonic hydrogels.

A "turn-on" inverse opal photonic crystal fluorescent sensing film for detection of cysteine and its bioimaging of living cells.

A "turn-on" inverse opal photonic crystal fluorescent sensing film infiltrated with a coumarin derivative is reported for the reliable and accurate detection of cysteine in human serum and fluorescence imaging of living cells. The coumarin derivative containing allyl ester specifically reacts with cysteine by ammonolysis to generate a fluorescent product whose emission wavelength is at ~ 535 nm, providing a selective fluorescence detection for cysteine. The emitted fluorescence is significantly enhanced due to the slow photon effect derived from the photonic crystal film. This is because the emission wavelength is overlapped with the blue-band edge of the photonic stopband of the selected inverse opal film. The fluorescence enhancement effect endows the prepared inverse opal film with highly sensitive detection with a limit of detection of 3.23 × 10-9 mol/L and a wide linear detection range of 1 × 10-7 - 1 × 10-3 mol/L. A fast response within 30 s toward cysteine is also achieved due to the three-dimensional interconnected macroporous structure with a high-specific surface area of the inverse opal film. The prepared inverse opal fluorescent sensing film has been successfully applied to the detection of cysteine in human serum and bioimaging of living cells. In the diluted human serum, the recoveries for the detection of cysteine were 97.92 - 107.20%, and the relative standard deviations were 2.61-9.04%, demonstrating the potential applicability of the inverse opal fluorescent sensing film to real sample analysis. The method may provide a universal strategy for constructing various photonic crystal fluorescent sensing films by using different fluorescent probes.

Ultrafine oxygenophilic nanoalloys induced by multifunctional interstitial boron for methanol oxidation reaction.

Interface construction is one of the most feasible approaches to optimize the physical and chemical properties of noble metal-based catalysts and consequently improve their catalytic performance. Herein, the design of effective reaction interfaces by bimetallic, trimetallic or polymetallic alloying has been extensively explored. In this research, metalloid boron (B) was alloyed within palladium-iridium (Pd-Ir) nanoalloy supported on nitrogen-doped graphene (NG) to promote the methanol oxidation reaction (MOR) in alkaline media. Being benefited from this, the optimum Pd7IrBx/NG catalyst exhibited enhanced EOR activity mass activity (1141.7 mA mg-1) and long-term stability (58.2 % current density retention rate after 500 cycles of cyclic voltammetry). The mechanism was further studied by electrochemical experiments and characterization, which highlighted that the multifunctional effect of electronic effect and strain effect and kinetic optimization induced by boron doping played a very positive role on MOR.

Zn-Catalyzed Regioselective and Chemoselective Reduction of Aldehydes, Ketones and Imines.

An operationally convenient Zn-catalyzed synthesis of alcohols by the reduction of aldehydes, ketones, and α,ß-unsaturated aldehydes/ketones is reported. It is a rare example of using mild and sustainable HBpin as a reductant for catalytic reduction of carbonyl compounds in the absence of acid or base as hydrolysis reagent. The reaction is upscalable and proceeds in high selectivity without the formation of boronate ester by-products, and tolerates sensitive functionalities, such as iodo, bromo, chloro, fluoro, nitro, trifluoromethyl, aminomethyl, alkynyl, and amide. The Zn(OAc)2/HBpin combination has been also proved to be chemoselective for the C=N reduction of imine analogs.

Multi-Factors Cooperatively Actuated Photonic Hydrogel Aptasensors for Facile, Label-Free and Colorimetric Detection of Lysozyme.

Responsive two-dimensional photonic crystal (2DPC) hydrogels have been widely used as smart sensing materials for constructing various optical sensors to accurately detect different target analytes. Herein, we report photonic hydrogel aptasensors based on aptamer-functionalized 2DPC poly(acrylamide-acrylic acid-N-tert-butyl acrylamide) hydrogels for facile, label-free and colorimetric detection of lysozyme in human serum. The constructed photonic hydrogel aptasensors undergo shrinkage upon exposure to lysozyme solution through multi-factors cooperative actuation. Here, the specific binding between the aptamer and lysozyme, and the simultaneous interactions between carboxyl anions and N-tert-butyl groups with lysozyme, increase the cross-linking density of the hydrogel, leading to its shrinkage. The aptasensors' shrinkage decreases the particle spacing of the 2DPC embedded in the hydrogel network. It can be simply monitored by measuring the Debye diffraction ring of the photonic hydrogel aptasensors using a laser pointer and a ruler without needing sophisticated apparatus. The significant shrinkage of the aptasensors can be observed by the naked eye via the hydrogel size and color change. The aptasensors show good sensitivity with a limit of detection of 1.8 nM, high selectivity and anti-interference for the detection of lysozyme. The photonic hydrogel aptasensors have been successfully used to accurately determine the concentration of lysozyme in human serum. Therefore, novel photonic hydrogel aptasensors can be constructed by designing functional monomers and aptamers that can specifically bind target analytes.

MgI2-Catalyzed Nucleophilic Ring-Opening Reactions of Donor-Acceptor Cyclopropanes with Indoline-2-thiones.

MgI2-catalyzed nucleophilic ring-opening reactions of donor-acceptor cyclopropanes with indoline-2-thiones as easy-to-handle sulfur nucleophiles were investigated. A series of functionalized γ-indolylthio butyric acid derivatives were synthesized in good to excellent yields under mild reaction conditions. Furthermore, the thioether functionalized ring-opening products could be transformed to sulfone and methionine analogues.

Xylem-Inspired Polyimide/MXene Aerogels with Radial Lamellar Architectures for Highly Sensitive Strain Detection and Efficient Solar Steam Generation.

Polyimide aerogels with mechanical robustness, great compressibility, excellent antifatigue properties, and intriguing functionality have captured enormous attention in diverse applications. Here, enlightened by the xylem parenchyma of dicotyledonous stems, a radially architectured polyimide/MXene composite aerogel (RPIMX) with reversible compressibility is developed by combining the interfacial enhancing strategy and radial ice-templating method. The strong interaction between MXene flakes and polymer can glue the MXene to form continuous lamellae, the ice crystals grow preferentially along the radial temperature gradient can effectively constrain the lamellae to create a biomimetic radial lamellar architecture. As a result, the nature-inspired RPIMX composite aerogel with centrosymmetric lamellar structure and oriented channels manifests excellent mechanical strength, electrical conductivity, and water transporting capability along the longitudinal direction, endowing itself with intriguing applications for accurate human motion monitoring and efficient photothermal evaporation. These exciting properties make the biomimetic RPIMX aerogels promising candidates for flexible piezoresistive sensors and photothermal evaporators.

Analysis of crosstalk in spectral beam combining of diode laser bar.

Spectral beam combining (SBC) of laser diodes has been proven to be an effective method to improve beam brightness. The crosstalk between different emitters in the SBC system will significantly affect the beam-combining efficiency and output beam properties without effective control. The interfering factors of the crosstalk beam intensity in semiconductor laser SBC have been theoretically analyzed, and experiments have been built to carry out the SBC of a semiconductor laser bar with a high filling factor of 80%. It is found that by adding an inverted Kepler telescope, reducing the focal length of the transmission lens or increasing the spacing of the grating and the output coupling mirror, the crosstalk can be suppressed. In an experiment of beam combining with five emitters, the ratio of the first-order crosstalk peak energy to that of the central beam spot is about 0.34 when the spacing of the grating and the output coupling mirror is 50 mm and the focal length of the transmission lens is 200 mm. The ratio decreases to 0.035 when the spacing of the grating and the output coupling mirror is 200 mm. With the addition of an inverted Kepler telescope with a magnification of 2, the ratio decreases to 0.085. In addition, the ratio decreases to 0.07 when the focal length of the transmission lens is 80 mm.

Synthesis of acyloxy-2H-azirine and sulfonyloxy-2H-azirine derivatives via a one-pot reaction of ß-enamino esters, PIDA and carboxylic acid or sulfonic acid.

PIDA mediated oxidative acyloxylation/azirination and sulfonyloxylation/azirination of ß-enamino esters were investigated. A series of functionalized acyloxy-2H-azirine and sulfonyloxy-2H-azirine derivatives was synthesized in moderate to good yields. This represents the first oxidative sulfonyloxylation/azirination of ß-enamino esters with PIDA and sulfonic acid for access to sulfonyloxy-2H-azirine. Hypervalent iodine reagents enable cascade C-O/C-N bond formation. Furthermore, a possible reaction pathway was proposed based on the experimental results.

Ascorbic acid functionalized anti-aggregated Au nanoparticles for ultrafast MEF and SERS detection of tartrazine: an ultra-wide piecewise linear range study.

Tartrazine, as a synthetic food colorant, is harmful to health upon excessive intake. In this study, we developed a simple, sensitive and ultrafast method to detect tartrazine effectively. Specifically, we successfully used ascorbic acid-functionalized anti-aggregated Au nanoparticles (AuNPs) as enhanced substrates to detect tartrazine in drinks using metal enhanced fluorescence (MEF) and surface-enhanced Raman scattering (SERS) piecewise linearly. The fluorescence intensity and Raman signals of the tartrazine solution enhanced after the addition of AuNPs. There was a good linear correlation between the fluorescence intensity and the concentration of tartrazine from 2.0 µM to 40.0 µM, and the limit of detection (LoD) was 15.4 nM. In addition, the Raman intensity also increased linearly with an increase in the concentration of tartrazine in a wide range (1.0 × 10-5 µM to 1.0 × 10-1 µM) and a lower LoD (0.8 pM) was achieved compared with the results from the fluorescence technique. Both fluorescence and SERS can immediately detect tartrazine in drinks after the substrate was mixed with analytes. Hence, the as-prepared anti-aggregated AuNPs as substrate material achieved a highly sensitive, selective and ultrafast detection of tartrazine via fluorescence and Raman techniques in a wide detection range, providing a novel strategy for the detection of food additives.

Theoretical and experimental research on crosstalk in spectral beam combining of a laser diode bar with a high fill factor.

Spectral beam combining is an important way to improve the brightness of semiconductor laser beams. For a spectral beam combining system, crosstalk between different emitters would cause the deterioration of beam quality and the reduction of beam combining efficiency, especially for the laser diode bar with a high fill factor. In this paper, an analysis model of the spectral beam combining system with crosstalk is established. The most important advantage of this model is that it can analyze the spectral distribution of the combined beam and also give a relatively good estimation for the beam quality parameters, such as beam size and far-field divergence angle. This model is verified by the experimental results. Furthermore, based on the theoretical model, a method for eliminating crosstalk is developed. By introducing a spatial filter inside the grating external cavity, the crosstalk between different emitters is blocked in the far field, and the beam quality is improved. In the experiment of beam combining of five emitters, after crosstalk is eliminated, the divergence angle of the combined laser beam is reduced from 10.09 to 4.73 mrad, the beam parameter product is reduced from 2.95 to 0.91 mm⋅mrad, and the power of the main lobe is improved from 1.77 to 2 W.

virusMED: an atlas of hotspots of viral proteins.

Metal binding sites, antigen epitopes and drug binding sites are the hotspots in viral proteins that control how viruses interact with their hosts. virusMED (virus Metal binding sites, Epitopes and Drug binding sites) is a rich internet application based on a database of atomic interactions around hotspots in 7041 experimentally determined viral protein structures. 25306 hotspots from 805 virus strains from 75 virus families were characterized, including influenza, HIV-1 and SARS-CoV-2 viruses. Just as Google Maps organizes and annotates points of interest, virusMED presents the positions of individual hotspots on each viral protein and creates an atlas upon which newly characterized functional sites can be placed as they are being discovered. virusMED contains an extensive set of annotation tags about the virus species and strains, viral hosts, viral proteins, metal ions, specific antibodies and FDA-approved drugs, which permits rapid screening of hotspots on viral proteins tailored to a particular research problem. The virusMED portal (https://virusmed.biocloud.top) can serve as a window to a valuable resource for many areas of virus research and play a critical role in the rational design of new preventative and therapeutic agents targeting viral infections.

Surface engineering of copper sulfide-titania-graphitic carbon nitride ternary nanohybrid as an efficient visible-light photocatalyst for pollutant photodegradation.

Advanced photocatalyst is a key for photocatalytic water purification in the environmental pollutant remediation. In this study, graphitic carbon nitride (g-CN) modified by CuS and TiO2 ternary nanohybrid (CuS-TiO2-g-CN) with close interfacial contact among CuS, TiO2 and g-CN was fabricated through a facile and green method. Compared to the binary g-CN-based counterparts, the CuS-TiO2-g-CN possesses multiple photo-generated charge transfers owing to the synergistic action of CuS, TiO2 and g-CN. And hence the separation efficiency of photo-generated electron-hole pairs can be improved for the CuS-TiO2-g-CN. The optical and photoelectrochemical measurements prove that the CuS-TiO2-g-CN has narrower band gap energy and higher transient photocurrent density than those of g-CN and TiO2-g-CN. Therefore, the CuS-TiO2-g-CN shows notably higher photocatalytic activity and stability towards the degradation of Rhodamine B (RhB) than g-CN and TiO2-g-CN under visible-light irradiation. Moreover, a possible visible-light photocatalytic mechanism of CuS-TiO2-g-CN for degrading RhB was also proposed on the basis of the experimental results and literature reports.