Kinetic Controlled Chirality Transfer and Induction in 2D Hydrogen-Bonding Assemblies of Glycylglycine on Au(111).

Chirality transfer is of vital importance that dominates the structure and functionality of biological systems and living matters. External physical stimulations, e.g. polarized light and mechanical forces, can trigger the chirality symmetry breaking, leading to the appearance of the enantiomeric entities created from a chiral self-assembly of achiral molecule. Here, several 2D assemblies with different chirality, synthesized on Au(111) surface by using achiral building blocks - glycylglycine (digly), the simplest polypeptide are reported. By delicately tuning the kinetic factors, i.e., one-step slow/rapid deposition, or stepwise slow deposition with mild annealing, achiral square hydrogen-bond organic frameworks (HOF), homochiral rhombic HOF and racemic rectangular assembly are achieved, respectively. Chirality induction and related symmetry broken in assemblies are introduced by the handedness (H-bond configurations in principle) of the assembled motifs and then amplified to the entire assemblies via the interaction between motifs. The results show that the chirality transfer and induction of biological assemblies can be tuned by altering the kinetic factors instead of applying external forces, which may offer an in-depth understanding and practical approach to peptide chiral assembly on the surfaces and can further facilitate the design of desired complex biomolecular superstructures.

Characterization of highly polymorphic microsatellite markers for the chinese monal (Lophophorus lhuysii, Galliformes) using Illumina MiSeq sequencing.

BACKGROUND: The Chinese monal (Lophophorus lhuysii, Galliformes) is a vulnerable and endemic bird from southwestern China. To better protect this species and increase its population size, genetic markers are urgently needed for investigation and conservation of both wild and captive populations. METHODS AND RESULTS: By using next-generation sequencing, we developed and characterized markers for seven microsatellite loci of the Chinese monal. PCR examination and statistical analysis indicated that these microsatellites exhibited moderate to high levels of polymorphism, with the expected heterozygosity and polymorphic information content ranging from 0.578 to 0.858 and from 0.540 to 0.841, respectively. Cross-species genome comparison further suggests that these microsatellites are a feature of certain galliform species rather than being specific to the Chinese monal. CONCLUSION: A combination of the seven highly polymorphic loci may provide a fundamental genetic toolkit to assess genetic backgrounds and will contribute to design conservation plan, breeding management and other possible studies of the Chinese monal and other evolutionarily related species in the future.

Highly sensitive biosensor based on aptamer and hybridization chain reaction for detection of cadmium ions.

In this work, a highly sensitive biosensor for detecting cadmium ions (Cd2+ ) was developed based on a Cd2+ -specific DNA aptamer and a hybridization chain reaction (HCR). The Cd2+ aptamer (named S0) was used to recognize Cd2+ and trigger the HCR. Without Cd2+ , S0 initiated the HCR to form long nicked dsDNA structures to quench the fluorescence. Then, Cd2+ could bind with S0 to block HCR to recover fluorescence. This biosensor had high sensitivity with a detection limit of 0.36 nM and a linear range from 0 to 10 nM. Moreover, it showed a satisfactory selectivity and recovery rates.

Fluorescence determination of glyphosate based on a DNA-templated copper nanoparticle biosensor.

A rapid and convenient fluorescence glyphosate (GLYP) biosensor was developed based on DNA-templated copper nanoparticles (DNA-CuNPs). In the absence of GLYP, the DNA-CuNPs were formed through the reduction of Cu2+ by vitamin C (Vc). The DNA-CuNPs emitted intense fluorescence at 615 nm when being excited at 340 nm. In the presence of GLYP, GLYP can strongly chelate with Cu2+ by the phosphate and carboxyl groups to decrease the amount of free Cu2+. Due to the lack of free Cu2+, DNA-CuNPs cannot be formed, which caused the fluorescence to decrease. The whole detection process of this proposed GLYP biosensor can be completed within 14 min. Titration experiments showed that this biosensor had a linear relationship for GLYP in the range 1 to 18 µM with a limit of detection (LOD) of 0.47 µM. This biosensor showed obvious selectivity among other pesticides, even between GLYP and organophosphorus pesticides. This biosensor performed well for GLYP detection in real samples with recoveries of 88.0-104.0%.

Duplex-Specific Nuclease-Triggered Fluorescence Immunoassay Based on Dual-Functionalized AuNP for Acetochlor, Metolachlor, and Propisochlor.

Given the great harm of pesticide residues to the environment and public health, exploring ultrasensitive and low-cost methods for their quantitative analysis becomes intensely necessary. Herein, we proposed a double-functionalized gold nanoparticle (AuNP) probe as a signal amplification immunoassay for the detection of acetochlor (ATC), metolachlor, and propisochlor. The AuNP was modified with IgG and fluorophore-labeled duplex DNA by a polyadenine-based freezing method. The quenched fluorescence can be effectively recovered via duplex-specific nuclease (DSN) with excellent cleaving activity. This approach provided limits of detection (LODs) down to 0.03 ng/mL for ATC, 0.10 ng/mL for metolachlor, 0.14 ng/mL for propisochlor, and 0.08 ng/mL for their mixture. The average recoveries of ATC, metolachlor, and propisochlor were 93.0-106.6% from a corn sample, which are in good agreement with the commercial kit (R2 = 0.9995). This "turn-off" fluorescence immunoassay presents considerable potential in the analysis of chloroacetamide herbicide due to its simple process of probe preparing and ultrahigh sensitivity.

A label-free ratiometric method to detect Hg2+ based on structural change of DNA.

In this work, a simple ratiometric method has been designed to detect Hg2+ based on the structural change between double-stranded DNA (dsDNA) and its G-quadruplex structure. When Hg2+ was added, the designed G-quadruplex structure could change into the corresponding dsDNA by forming the T-Hg2+ -T mismatch. This kind of variation resulted in a decrease in the fluorescence of the G-quadruplex/N-methyl mesoporphyrin IX (NMM) complex and an increase in the fluorescence from the dsDNA/SYBR Green I (SG I) pair. The secondary excitation wavelength of SG I was used to excite NMM and SG I simultaneously. The titration experiment indicated that the new method had a linear response within 0.7-2.5 µM Hg2+ with a limit of detection of 9.3 nM. Because using the T-Hg2+ -T mismatch to recognize Hg2+ was very specific, the selectivity of the new method was also satisfactory. The recoveries ranged from 92.8% to 110.2% suggested that this new method could achieve a potential application for Hg2+ detection in real environmental samples.

Pb2+ as a Substrate and a Cofactor of a Porphyrin Metalation DNAzyme.

We herein report a DNAzyme named T30695 (sequence: (G3 T)4 ) that can catalyze Zn2+ insertion into three different porphyrins in the presence of Pb2+ as a cofactor. Meanwhile, T30695 with Pb2+ alone was found to cause a shift in both the fluorescence and UV-vis spectra of protoporphyrin IX (PPIX), thus suggesting that metalation of Pb2+ was also achieved at room temperature. From kinetic measurements, the reaction required two Pb2+ ions; this is consistent with one being a cofactor and the other being a substrate. No previous reports inserted Pb2+ into porphyrins by using DNAzymes or protein-based enzymes. This reaction was most significantly inhibited in the presence of K+ followed by Na+ and Li+ , suggesting the importance of the Pb2+ -stabilized G-quadruplex. When Pb2+ is inserted into PPIX, its emission blue shifts from 635 to 590 nm, thus allowing simple ratiometric fluorescent sensing with a detection limit of 1.2 nM Pb2+ .

Noninvasive KRAS mutation estimation in colorectal cancer using a deep learning method based on CT imaging.

BACKGROUND: The detection of Kirsten rat sarcoma viral oncogene homolog (KRAS) gene mutations in colorectal cancer (CRC) is key to the optimal design of individualized therapeutic strategies. The noninvasive prediction of the KRAS status in CRC is challenging. Deep learning (DL) in medical imaging has shown its high performance in diagnosis, classification, and prediction in recent years. In this paper, we investigated predictive performance by using a DL method with a residual neural network (ResNet) to estimate the KRAS mutation status in CRC patients based on pre-treatment contrast-enhanced CT imaging. METHODS: We have collected a dataset consisting of 157 patients with pathology-confirmed CRC who were divided into a training cohort (n = 117) and a testing cohort (n = 40). We developed an ResNet model that used portal venous phase CT images to estimate KRAS mutations in the axial, coronal, and sagittal directions of the training cohort and evaluated the model in the testing cohort. Several groups of expended region of interest (ROI) patches were generated for the ResNet model, to explore whether tissues around the tumor can contribute to cancer assessment. We also explored a radiomics model with the random forest classifier (RFC) to predict KRAS mutations and compared it with the DL model. RESULTS: The ResNet model in the axial direction achieved the higher area under the curve (AUC) value (0.90) in the testing cohort and peaked at 0.93 with an input of 'ROI and 20-pixel' surrounding area. AUC of radiomics model in testing cohorts were 0.818. In comparison, the ResNet model showed better predictive ability. CONCLUSIONS: Our experiments reveal that the computerized assessment of the pre-treatment CT images of CRC patients using a DL model has the potential to precisely predict KRAS mutations. This new model has the potential to assist in noninvasive KRAS mutation estimation.

Carbon nanotubes in electrochemical, colorimetric, and fluorimetric immunosensors and immunoassays: a review.

This review (with 126 references) summarizes the progress that has been made in the use of carbon nanotubes (CNTs) in immunoassays and immunosensors. Following an introduction into the field, a first large section covers functional group-modified CNTs as carriers for antibodies (with subsections on CNTs modified with amino, carboxy and by various other materials). The next section treats CNTs coupled with inorganic or organic materials as active components (with the use of nanoparticles such as Fe3O4, ZnO, gold) or with indium tin oxide (ITO), NiCoBP, ionic liquids, TiO2 nanosheets, metal clusters; chitosan, polystyrene, polydopamine, graphene, or enzymes. Another section discusses the synergistic effects of CNTs with metals, metal ions, and organic/inorganic materials. Several Tables are presented that give an overview on the wealth of methods and materials. A concluding section summarizes the current status, addresses current challenges, and gives an outlook on potential future trends. Graphical abstract Schematic presentation of the roles of carbon nanotubes (CNTs) in immunosensors and immunoassays. (I) Functional group-modified CNTs as carriers for antibody; (II) CNTs coupled with metal or organic materials as active component; and (III) Synergistic effects of CNTs with other materials to improve the parameters of immunosensors.

Acidic conditions induce the accumulation of orange Monascus pigments during liquid-state fermentation of Monascus ruber M7.

The influence of pH on the biosynthesis of orange Monascus pigments (OMPs) in Monascus ruber M7 was investigated. Under acidic fermentation conditions, pigment mixtures predominantly rich in OMPs were obtained. HPLC analysis revealed the presence of four orange components (O1-O4) and four yellow components (Y1-Y4) in the mixtures, and the dominant ones were O1 and O3, which accounted for 56.0% to 75.9% of the total pigments in the pH range 3-6. Subsequently, O1 and O3 were identified by LC-DAD-ESI/MS as Rubropunctatin and Monascorubrin, respectively. The yield of OMPs was observed to be inversely dependent on pH. At pH 3, large amounts of OMPs with high purity (79.1%) were accumulated. A real-time quantitative PCR analysis revealed that the expression of genes related to the biosynthesis of OMPs in M. ruber M7 was upregulated at acidic pH as compared to neutral pH, and the variation in the level of expression of these genes with pH was consistent with the production of OMPs. These results indicated that the large accumulation of OMPs under acidic condition involved the acidic pH-induced transcription of genes related to the biosynthesis of OMPs. These results would contribute towards the development of an efficient technology for large-scale production of OMPs.

Signal amplification in immunoassays by using noble metal nanoparticles: a review.

This review (with 147 references) summarizes the state of the art in methods for signal amplification in immunoassays by using noble metal nanoparticles (MeNPs). Following an introduction into the field, a first large section covers MeNPs as signal tracers. The next sections describes the use of MeNPs as carriers for biomolecules, and of doped, decorated or functionalized MeNPs. A next large section covers MeNPs as used in aggregation-based assays that result in a change of color or dynamic light scattering (DLS). This is followed by a discussion of MeNPs that undergo etching, size reduction, or growth and thereby change color and DLS, with subsections on methods based on etching, particle growth or particle formation. We then rview methods where MeNPs acts as catalysts (enzyme mimics), with subsections on MeNPs and on doped or composed MeNPs. A final large section discusses the synergies of MeNPs or multiple signal amplification strategies in immunoassays. Several Tables are presented that give an overview on the wealth of methods and materials. A concluding section summarizes the current status, addresses current challenges, and gives an outlook on potential future trends. Graphical AbstractNoble metal nanoparticles have been widely used as essential components of signal amplification strategies to enhance the sensitivity of the immunoassays. This review summarizes various signal amplification strategies using metal NPs serving as (a) signal tracers, (b) carriers, (c) aggregators, (d) enzyme mimics, (e) in growth or etching of NPs, and (f) in synergistic effects.

Determination of Kanamycin by High Performance Liquid Chromatography.

Kanamycin is an aminoglycoside antibiotic widely used in treating animal diseases caused by Gram-negative and Gram-positive infections. Kanamycin has a relatively narrow therapeutic index, and can accumulate in the human body through the food chain. The abuse of kanamycin can have serious side-effects. Therefore, it was necessary to develop a sensitive and selective analysis method to detect kanamycin residue in food to ensure public health. There are many analytical methods to determine kanamycin concentration, among which high performance liquid chromatography (HPLC) is a common and practical tool. This paper presents a review of the application of HPLC analysis of kanamycin in different sample matrices. The different detectors coupled with HPLC, including Ultraviolet (UV)/Fluorescence, Evaporative Light Scattering Detector (ELSD)/Pulsed Electrochemical Detection (PED), and Mass Spectrometry, are discussed. Meanwhile, the strengths and weaknesses of each method are compared. The pre-treatment methods of food samples, including protein precipitation, liquid-liquid extraction (LLE), and solid-phase extraction (SPE) are also summarized in this paper.

Simple and Label-Free Fluorescent Detection of Melamine Based on Melamine⁻Thymine Recognition.

In the past few years, melamine has been illegally added into dairy products to increase the apparent crude protein levels. If humans or animals drink the milk adulteration of melamine, it can form insoluble melamine⁻cyanurate crystals in their kidneys which causes kidney damage or even death. In the present work, we constructed a simple and label-free fluorescent method for melamine detection based on melamine-thymine recognition. SYBR Green I was utilized as a reporter for this method as it did not require any modification or expensive equipment. In the absence of melamine, polythymine DNA was digested by Exo I, which caused a decrease in the fluorescence signal. In the presence of melamine, the polythymine DNA was able to fold into a double chain structure, however this was done with the help of T-melamine-T mismatches to prevent degradation. Then, the SYBR Green I combined with the double-stranded DNA to result in an intense fluorescence signal. The limit of detection in this method was 1.58 µM, which satisfied the FDA standards. This method also had a good linear relationship within the range of 10⁻200 µM. In addition, this new method has a good selectivity to distinguish melamine from the component of milk. As a result, we developed a simple and highly selectivity method for melamine detection.

Trichothecenes: immunomodulatory effects, mechanisms, and anti-cancer potential.

Paradoxically, trichothecenes have both immunosuppressive and immunostimulatory effects. The underlying mechanisms have not been fully explored. Early studies show that dose, exposure timing, and the time at which immune function is assessed influence whether trichothecenes act in an immunosuppressive or immunostimulatory fashion. Recent studies suggest that the immunomodulatory function of trichothecenes is also actively shaped by competing cell-survival and death-signaling pathways. Autophagy may also promote trichothecene immunosuppression, although the mechanism may be complicated. Moreover, trichothecenes may generate an "immune evasion" milieu that allows pathogens to escape host and vaccine immune defenses. Some trichothecenes, especially macrocyclic trichothecenes, also potently kill cancer cells. T-2 toxin conjugated with anti-cancer monoclonal antibodies significantly suppresses the growth of thymoma EL-4 cells and colon cancer cells. The type B trichothecene diacetoxyscirpenol specifically inhibits the tumor-promoting factor HIF-1 in cancer cells under hypoxic conditions. Trichothecin markedly inhibits the growth of multiple cancer cells with constitutively activated NF-κB. The type D macrocyclic toxin Verrucarin A is also a promising therapeutic candidate for leukemia, breast cancer, prostate cancer, and pancreatic cancer. The anti-cancer activities of trichothecenes have not been comprehensively summarized. Here, we first summarize the data on the immunomodulatory effects of trichothecenes and discuss recent studies that shed light on the underlying cellular and molecular mechanisms. These mechanisms include autophagy and major signaling pathways and their crosstalk. Second, the anti-cancer potential of trichothecenes and the underlying mechanisms will be discussed. We hope that this review will show how trichothecene bioactivities can be exploited to generate therapies against pathogens and cancer.

Ratiometric fluorescence and absorbance dual-model immunoassay based on 2,3-diaminophenazine and carbon dots for detecting Aflatoxin B1.

In this work, a dual-model immunoassay for detecting Aflatoxin B1 (AFB1) was developed based on 2,3-diaminophenazine (DAP) and carbon dots (CDs). Under the catalysis of horseradish peroxidase (HRP), the o-phthalylenediamine (OPD) was oxidized to DAP which had a yellow color and intense fluorescence. The color changes form colorless to yellow was used to design absorbance model immunoassay. Meanwhile, the absorption spectrum of DAP overlapped with the emission spectrum of CDs which caused the fluorescence of CDs to be quenched. The fluorescence changes of DAP and CDs were used to develop ratiometric fluorescence immunoassay. The dual-model immunoassay showed excellent sensitivity with the limits of detection (LODs) of 0.013 ng/mL for fluorescence mode and 0.062 ng/mL for absorbance mode. Meanwhile, both models exhibited great selectivity for AFB1. Additionally, the recovery rates suggested the proposed dual-model immunoassay had great potential in actual samples detection.

Ratiometric fluorescence immunoassay based on silver nanoclusters and calcein-Ce3+ for detecting ochratoxin A.

Ochratoxin A (OTA), a dangerous mycotoxin, is found in many crops. It is essential to create sensitive OTA detection techniques to ensure food safety. Based on the principle of p-nitrophenol (PNP) quenched the fluorescence of bovine serum albumin silver nanocluster (BSA-AgNCs) through an internal filtering effect, and phosphate activated fluorescence of calcein-Ce3+ system, a ratiometric fluorescence immunoassay for OTA detection was developed. In this strategy, the value of F518/F640 was used as a signal for response of OTA concentration. The detection range of this strategy was 0.625-25 ng/mL, the limit of detection (LOD) was 0.04 ng/mL. This new immunoassay offered a brand-new platform for detecting OTA.

Fine-grained recognition of bitter gourd maturity based on Improved YOLOv5-seg model.

Bitter gourd, being perishable, requires timely harvesting. Delayed harvesting can result in a substantial reduction in fruit quality. while premature harvesting leads to underdeveloped fruit and decreased yields, the continuous flowering pattern in bitter gourd underscores the significance of accurately assessing fruit growth and ensuring timely harvesting for subsequent fruit setting and development. The current reliance on the experience of production personnel represents a substantial inefficiency. We present an improved real-time instance segmentation model based on YOLOv5-seg. The utilization of dynamic snake convolution enables the extraction of morphological features from the curved and elongated structure of bitter gourd. Diverse branch blocks enhance feature space diversity without inflating model size and inference time, contributing to improved recognition of expansion stages during bitter gourd growth. Additionally, the introduction of Focal-EIOU loss accurately locates the boundary box and mask, addressing sample imbalances in the L2 stage. Experimental results showcase remarkable accuracy rates of 99.3%, 93.8%, and 98.3% for L1, L2, and L3 stages using mAP@0.5. In comparison, our model outperforms other case segmentation models, excelling in both detection accuracy and inference speed. The improved YOLOv5-seg model demonstrates strong performance in fine-grained recognition of bitter gourd during the expansion stage. It efficiently segments bitter gourd in real-time under varying lighting and occlusion conditions, providing crucial maturity information. This model offers reliable insights for agricultural workers, facilitating precise harvesting decisions.

Development of DNA Biosensors Based on DNAzymes and Nucleases.

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

DSIL-DDI: A Domain-Invariant Substructure Interaction Learning for Generalizable Drug-Drug Interaction Prediction.

Drug-drug interactions (DDIs) trigger unexpected pharmacological effects in vivo, often with unknown causal mechanisms. Deep learning methods have been developed to better understand DDI. However, learning domain-invariant representations for DDI remains a challenge. Generalizable DDI predictions are closer to reality than source domain predictions. For existing methods, it is difficult to achieve out-of-distribution (OOD) predictions. In this article, focusing on substructure interaction, we propose DSIL-DDI, a pluggable substructure interaction module that can learn domain-invariant representations of DDIs from source domain. We evaluate DSIL-DDI on three scenarios: the transductive setting (all drugs in test set appear in training set), the inductive setting (test set contains new drugs that were not present in training set), and OOD generalization setting (training set and test set belong to two different datasets). The results demonstrate that DSIL-DDI improve the generalization and interpretability of DDI prediction modeling and provides valuable insights for OOD DDI predictions. DSIL-DDI can help doctors ensuring the safety of drug administration and reducing the harm caused by drug abuse.

MnO2 nanosheets-triggered oxVB1 fluorescence immunoassay for detection zearalenone.

In this study, an alkaline phosphatase (ALP)-mediated fluorescence immunoassay for detecting zearalenone (ZEN) was established based on the oxVB1 fluorescence signal modulated by MnO2 nanosheets (MnO2 NS). As the ALP-antibody content increased, more 2-phosphoascorbic acid (AAP) was hydrolyzed to ascorbic acid (AA) which destroyed the MnO2 NS rapidly. In the lack of MnO2 NS, VB1 cannot be oxidized to oxVB1 for emitting fluorescence. On the contrary, the fluorescence of oxVB1 recovered slowly with the decrease of the ALP-antibody concentration. In the optimization condition, the detection limit of this method was 15.5 pg mL-1. Moreover, the recovery of ZEN in real samples ranged from 94.24 % to 108.26 %, which indicated the remarkable accuracy and reliability of this approach. Meanwhile, the proposal of this fluorescence immunoassay provided a new possibility for detecting other targets by replacing antibodies and antigens.