Construction of a stable fluorescent sensor based on CsPbBr3/CdS core/shell quantum dots for selective and sensitive detection of tetracycline in ethanol.

The weakly bound organic ligand shells around perovskite quantum dots (QDs) are easily decomposed and cannot provide sufficient stability in polar solvents, which greatly obstructs their applications in sensing. Herein, a fluorescent sensor based on CsPbBr3/CdS core/shell QDs was developed for the detection of tetracycline (TC) in the polar solvent-ethanol. Pristine CsPbBr3 QDs were treated with cadmium diethyldithiocarbamate (Cd(DDTC)2) to form a shell on the surface at 110 °C, while extra oleylammonium bromide (OAmBr) was added to inhibit the phase transformation of CsPbBr3 into a Cs4PbBr6 impurity phase during high-temperature processing. And finally CsPbBr3/CdS core/shell QDs were successfully synthesized. The capping with the CdS inorganic shell remediated surface defects and improved the stability in ethanol without affecting the emission properties of the parent CsPbBr3 QDs. The results showed that the fluorescent sensor detected TC in the range of 0.05-25 µM with a low detection limit of 22.6 nM, whereas it had high selectivity and anti-interference ability for TC. And the fluorescence quenching mechanism of the sensor was mainly photoinduced electron transfer between TC and CsPbBr3/CdS QDs. Our research provides a unique way to improve the stability of perovskite QDs in polar solvents and applications in fluorescence detection.

Planar liquid crystal optics for axial focus shaping with an adjustable intensity and a high efficiency.

In this Letter, we report the application of planar liquid crystal (LC) devices in axial focus shaping, proving that LC diffractive optical elements (DOEs) can achieve continuous adjustment of a symmetrical axial light field by changing the ellipticity of the incident light and can flexibly and quickly achieve various axial light field designs through an axial iterative Fourier transform algorithm. The LC DOE achieves a quasi-continuous phase and an extremely high transmittance (98.6% at 1030 nm), which makes the focusing efficiency of the LC DOE with two segments of uniform focal depths as high as 84%. The experimental results demonstrate the accurate optical field shaping effect and the axial intensity adjustable ability of LC DOE, indicating potential applications in optical tomography and precision manufacturing, among others.

Characterization and Comparison of the Two Mitochondrial Genomes in the Genus Rana.

The mitochondrial genome (mitogenome) possesses several invaluable attributes, including limited recombination, maternal inheritance, a fast evolutionary rate, compact size, and relatively conserved gene arrangement, all of which make it particularly useful for applications in phylogenetic reconstruction, population genetics, and evolutionary research. In this study, we aimed to determine the complete mitogenomes of two morphologically similar Rana species (Rana hanluica and Rana longicrus) using next-generation sequencing. The entire circular mitogenome was successfully identified, with a length of 19,395 bp for R. hanluica and 17,833 bp for R. longicrus. The mitogenomes of both species contained 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and one control region; mitogenome size varied predominantly with the length of the control region. The two synonymous codon usages in 13 PCGs showed that T and A were used more frequently than G and C. The ratios of non-synonymous to synonymous substitutions of all 13 PCGs were <1 in the Rana species, indicating that the PCGs were under purifying selection. Finally, phylogenetic relationship analyses suggested that R. hanluica and R. longicrus were classified in the R. japonica group. Our study provides valuable reference material for the taxonomy of the genus Rana.

A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae.

Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches.

C-Dot-Embedded SiO2 Concentric Microspheres for Bright Fluorescent Photonic Pigments.

A simple yet powerful approach to obtain structural color is the amorphous assembly of colloidal spheres, which is also referred to as the amorphous photonic structure or photonic glasses (PGs). Additionally, the functionalization of the colloidal spheres as building blocks can further endow the resulting PGs with multifunctions. Herein, we have developed a facile strategy to prepare SiO2 colloidal spheres with concentrically embedded carbon dots (CDs). Notably, the CDs are prepared and silane-functionalized simultaneously, which enables the perfect incorporation of CDs into the Si-O network during the Stöber reaction and thus leads to the formation of a concentric SiO2/CD interlayer within the obtained SiO2 spheres. Moreover, the obtained SiO2/CD spheres can be applied as photonic pigments by assembling them into PGs, which exhibit structural color under daylight and fluorescence under UV illumination. With incorporation of carbon black, the structural color saturation and fluorescence intensity can be further manipulated. Owing to the combination of structural colored PGs and fluorescent CDs, our study can offer inspiration for color- and fluorescence-related applications such as sensing, in vivo imaging, LEDs, and anticounterfeiting.

A Comprehensive Analysis of Triplophysa labiata (Kessler, 1874) Mitogenome and Its Phylogenetic Implications within the Triplophysa Genus.

In order to resolve the long-standing controversy surrounding the relationships within the Triplophysa genus, we conducted an extensive analysis of the complete mitogenome of Triplophysa labiata using DNBSEQ short reads. Additionally, we reconstructed the phylogeny of the Nemacheilidae family using mitogenome data. By comparing all available mitogenomes within the Triplophysa genus, we gained valuable insights into its evolutionary history. Our findings revealed that the mitogenome sequence of T. labiata is circular, spanning a length of 16,573 bp. It encompasses 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (D-loop). Among the PCGs, the start codon ATG was commonly observed, except in cox1, while the stop codons TAA/TAG/T were found in all PCGs. Furthermore, purifying selection was evident across all PCGs. Utilizing maximum likelihood (ML) methods, we employed the 13 PCGs and the concatenated nucleotide sequences of 30 Triplophysa mitogenomes to infer the phylogeny. Our results strongly supported the division of the Triplophysa genus into four primary clades. Notably, our study provides the first evidence of the close relationship between T. labiata and T. dorsalis. These findings serve as a significant foundation for future investigations into the mitogenomics and phylogeny of Nemacheilidae fishes, paving the way for further advancements in this field of research.

Mitogenomes of Eight Nymphalidae Butterfly Species and Reconstructed Phylogeny of Nymphalidae (Nymphalidae: Lepidoptera).

The Nymphalidae family of cosmopolitan butterflies (Lepidoptera) comprises approximately 7200 species found on all continents and in all habitats. However, debate persists regarding the phylogenetic relationships within this family. In this study, we assembled and annotated eight mitogenomes of Nymphalidae, constituting the first report of complete mitogenomes for this family. Comparative analysis of 105 mitochondrial genomes revealed that the gene compositions and orders were identical to the ancestral insect mitogenome, except for Callerebia polyphemus trnV being before trnL and Limenitis homeyeri having two trnL genes. The results regarding length variation, AT bias, and codon usage were consistent with previous reports on butterfly mitogenomes. Our analysis indicated that the subfamilies Limenitinae, Nymphalinae, Apaturinae, Satyrinae, Charaxinae, Heliconiinae, and Danainae are monophyletic, while the subfamily the subfamily Cyrestinae is polyphyletic. Danainae is the base of the phylogenetic tree. At the tribe level, Euthaliini in Limenitinae; Melitaeini and Kallimini in Nymphalinae; Pseudergolini in Cyrestinae; Mycalesini, Coenonymphini, Ypthimini, Satyrini, and Melanitini in Satyrinae; and Charaxini in Charaxinae are regarded as monophyletic groups. However, the tribe Lethini in Satyrinae is paraphyletic, while the tribes Limenitini and Neptini in Limenitinae, Nymphalini and Hypolimni in Nymphalinae, and Danaini and Euploeini in Danainae are polyphyletic. This study is the first to report the gene features and phylogenetic relationships of the Nymphalidae family based on mitogenome analysis, providing a foundation for future studies of population genetics and phylogenetic relationships within this family.

CDs-Peroxyfluor Conjugation for Ratiometric Fluorescence Detection of Glucose and Shortening Its Detection Time from Reaction Dynamic Perspective.

A ratiometric fluorescence probe based on the conjugation of peroxyfluor-NHS (PF) and carbon dots (CDs) was designed for selective and rapid detection of glucose. When glucose was catalytically oxidized by glucose oxidase (GOx), the product H2O2 would react with colorless and non-fluorescent peroxyfluor moiety to give the colored and fluorescent fluorescein moiety which would absorb the energy of CDs emission at 450 nm due to the Förster Resonance Energy Transfer (FRET) and generate a new emission peak at 517 nm. The reaction between PF and H2O2 was slow with a rate constant of about 2.7 × 10-4 s-1 under pseudo-first-order conditions (1 uM PF, 1 mM H2O2), which was unconducive to rapid detection. Given this, a short time detection method was proposed by studying the kinetics of the reaction between PF and H2O2. In this method, the detection time was fixed at three minutes. The linear detection of glucose could be well realized even if the reaction was partially done. As glucose concentration increased from 0.05 mM to 5 mM, the fluorescence intensity ratio (I517/I450) after 3 minutes' reaction of CDs-PF and glucose oxidation products changed linearly from 0.269 to 1.127 with the limit of detection (LOD) of 17.19 µM. In addition, the applicability of the probe in blood glucose detection was verified.

Difunctional Hydrogel Optical Fiber Fluorescence Sensor for Continuous and Simultaneous Monitoring of Glucose and pH.

It is significant for people with diabetes to know their body's real-time glucose level, which can guide the diagnosis and treatment. Therefore, it is necessary to research continuous glucose monitoring (CGM) as it gives us real-time information about our health condition and its dynamic changes. Here, we report a novel hydrogel optical fiber fluorescence sensor segmentally functionalized with fluorescein derivative and CdTe QDs/3-APBA, which can continuously monitor pH and glucose simultaneously. In the glucose detection section, the complexation of PBA and glucose will expand the local hydrogel and decrease the fluorescence of the quantum dots. The fluorescence can be transmitted to the detector by the hydrogel optical fiber in real time. As the complexation reaction and the swelling-deswelling of the hydrogel are all reversible, the dynamic change of glucose concentration can be monitored. For pH detection, the fluorescein attached to another segment of the hydrogel exhibits different protolytic forms when pH changes and the fluorescence changes correspondingly. The significance of pH detection is compensation for pH errors in glucose detection because the reaction between PBA and glucose is sensitive to pH. The emission peaks of the two detection units are 517 nm and 594 nm, respectively, so there is no signal interference between them. The sensor can continuously monitor glucose in 0-20 mM and pH in 5.4-7.8. The advantages of this sensor are multi-parameter simultaneous detection, transmission-detection integration, real-time dynamic detection, and good biocompatibility.

Mitochondrial genome of Leocrates chinensis Kinberg, 1866 (Annelida: Hesionidae).

We report the complete mitochondrial genome of Leocrates chinensis Kinberg, 1866 - the type species of the genus. It is 15061 bp long, and contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), and 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that L. chinensis was placed as sister to Sirsoe methanicola (BS = 100) of the same family Hesionidae.

Complete Mitogenome of the Triplophysa bombifrons: Comparative Analysis and Phylogenetic Relationships among the Members of Triplophysa.

In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes.

Genomic insight into the nocturnal adaptation of the black-crowned night heron (Nycticorax nycticorax).

BACKGROUND: The black-crowned night heron (Nycticorax nycticorax) is an ardeid bird successfully adapted to the nocturnal environment. Previous studies had indicated that the eyes of the night herons have evolved several specialized morphological traits favoring nocturnal vision. However, the molecular mechanisms of the nocturnal vision adaptation of night herons remained inattentions. In this study, the whole genome of N. nycticorax was sequenced and comparative analyses were performed on the vision-related and olfactory receptor (OR) genes to understand the molecular mechanisms of the visual and olfactory adaptation of night herons. RESULTS: The results indicated that a number of vision genes were under positive or relaxed selection in N. nycticorax, whereas a number of other vision genes were under relaxed or intensified selection in the boat-billed heron (Cochlearius cochlearius), which suggested that the two species adapt to nocturnality with different genetic mechanisms. The different selections acting on vision genes are probably associated with the enlargement of eye size and the enhancement of visual sensitivity in night herons. The analyses on olfactory receptor (OR) genes indicated that the total number of OR genes in the genomes of N. nycticorax and C. cochlearius were about half those in the little egret (Egretta garzetta), whereas the diversity of their OR genes was not remarkably different. Additionally, the number of expressed OR genes in the transcriptomes of N. nycticorax was also fewer than that in E. garzetta. These results suggest a reduced olfactory capability in night herons compared with E. garzetta. CONCLUSIONS: Our results provided evidence that several vision genes of the night herons were subjected to different natural selections, which can contribute to a better understanding of the genetic mechanisms of visual adaptions of the night heron. In addition, the finding of the reduced number of total and expressed OR genes in night herons may reflect a trade-off between olfaction and vision.

De Novo Whole-Genome Sequencing and Assembly of the Yellow-Throated Bunting (Emberiza elegans) Provides Insights into Its Evolutionary Adaptation.

Yellow-throated bunting is a small migratory songbird unique to the Palearctic region. However, the genetic studies of this species remain limited, with no nuclear genomic sequence reported to date. In this study, the genomic DNA from the bird was sequenced in long reads using Nanopore sequencing technology. Combining short-read sequencing, the genome was well-assembled and annotated. The final length of the assembly is approximately 1.14 Gb, with a scaffold N50 of 28.94 Mb. About 15,868 protein-coding genes were predicted, and 16.62% of the genome was identified as having repetitive elements. Comparative genomic analysis showed numerous expanded gene families and positively selected genes significantly enriched in those KEGG pathways that are associated with migratory behavior adaptation and immune response. Here, this newly generated de novo genome of the yellow-throated bunting using long reads provide the research community with a valuable resource for further studies of population genetic diversity and genome evolution in this species.

Complete mitochondrial genomes of Papilio nephelus chaon and Papilio epycides (Lepidoptera: Papilionidae: Papilioninae) and phylogenetic analysis.

The complete mitochondrial genome (mitogenome) sequences of Papilio nephelus chaon and Papilio epycides were sequenced by Illumina and analyzed in this study. They are 15,287 bp and 15,012 bp in size, respectively, and contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 AT-rich control region (CR). The phylogenetic relationships of 56 species in the Papilionidae were inferred based on concatenated nucleotide sequences by using Maximum Likelihood with the selected best-fit model GTR + F+R6. The phylogenetic analysis showed that P. nephelus chaon and P. epycides were located in the genus Papilio. This study provides a basis for further study on mitogenome and phylogenetics of the Papilionidae.

The complete mitochondrial genome of snailfish Liparis tanakae Gilbert & Burke, 1912 (Perciformes: Cottioidei: Liparidae).

Mitochondrial genome is maternal inheritance that provides higher resolution in taxonomic and phylogenetic research. The absence of complete mitogenome becomes an obstacle to further research. Here, we reported the complete mitogenome of Liparis tanakae Gilbert & Burke, 1912 (Perciformes: Cottioidei: Liparidae), which has a length of 17,860 bp. It comprised 39 genes, including 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 control region (D-loop). The 23 tRNAs in this mitogenome included two tRNA-Ala genes on the light strand. Maximum-likelihood (ML) phylogenetic analysis based on 14 available mitogenomes of 10 species in suborder Cottioidei confirmed L. tanakae as monophyletic with other snailfishes. This study would provide important genetic resources and could be useful for evolutionary analysis.

Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris.

Background: The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved. Methods: Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results: We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.

Classification of gastric cancerous tissues by a residual network based on optical coherence tomography images.

Optical coherence tomography (OCT) is a noninvasive, radiation-free, and high-resolution imaging technology. The intraoperative classification of normal and cancerous tissue is critical for surgeons to guide surgical operations. Accurate classification of gastric cancerous OCT images is beneficial to improve the effect of surgical treatment based on the deep learning method. The OCT system was used to collect images of cancerous tissues removed from patients. An intelligent classification method of gastric cancerous tissues based on the residual network is proposed in this study and optimized with the ResNet18 model. Four residual blocks are used to reset the model structure of ResNet18 and reduce the number of network layers to identify cancerous tissues. The model performance of different residual networks is evaluated by accuracy, precision, recall, specificity, F1 value, ROC curve, and model parameters. The classification accuracies of the proposed method and ResNet18 both reach 99.90%. Also, the model parameters of the proposed method are 44% of ResNet18, which occupies fewer system resources and is more efficient. In this study, the proposed deep learning method was used to automatically recognize OCT images of gastric cancerous tissue. This artificial intelligence method could help promote the clinical application of gastric cancerous tissue classification in the future.

The complete chloroplast genome of Calohypnum plumiforme (Wilson) (hypanceae, bryophyta).

Calohypnum plumiforme is a widely distributed moss in East Asia. In this study, Illumina sequencing data was used to assemble the complete chloroplast genome of C. plumiforme. The length of the circular genome is 124,037 bp. It contains a total of 121 genes, including 81 protein-coding, 36 tRNA, and 4 rRNA genes. The GC content of the chloroplast genome of C. plumiforme is 29.07%. The phylogenetic analysis suggested that C. plumiforme is sister to Calliergonella cuspidata. This study provides important sequence information for species identification and its phylogenetic relationship in the Bryopsida.

Complete mitochondrial genome of Parnassius glacialis (Lepidoptera: Papilionidae).

Parnassius glacialis is a butterfly species distributed in China, Korea, Japan. The complete P. glacialis mitochondrial genome was assembled using Illumina sequencing data. The mitogenome is 15,353 bp long and contains 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. A phylogenetic analysis of P. glacialis and 14 related Papilionidae species indicated that P. glacialis is clustered with other Parnassius species. This study generated useful genetic information for future studies on the taxonomy, phylogeny, and evolution of Papilionidae species.

The complete chloroplast genome sequence of Michelia amoena Q.F.Zheng et M.M.Lin.

Michelia amoena Q.F.Zheng et M.M.Lin is classified in Magnoliaceae and has a high economic value. Herein, we report the complete chloroplast genome of M. amoena using Illumina sequence data. The chloroplast genome is 160,088 bp in length and contains a large single copy (LSC) region of 88,118 bp and a small single-copy (SSC) region of 18,798 bp separated by two inverted repeat (IR) regions of 26,586 bp each. It contained a total of 131 genes, with an overall GC content of 39.26%. The phylogenetic analysis showed that M. amoena is closely related to Michelia figo. This study provides important sequence information for species identification and its phylogenetic relationship in the Magnoliaceae.