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Abstract Soft-shelled turtles, or Trionychia, are an enigmatic and fascinating group due to their specific morphological features and ecological adaptations. Based on mitochondrial DNA (mtDNA) and/or nuclear markers, previous studies showed the incongruent phylogenetic topologies within Trionychia (e.g., the Palea and its closely related species). In order to resolve the equivocal relationships and obtain some “genome-level” common evolutionary characters of soft-shelled turtles, in this study, we assembled and annotated the complete mitochondrial genomes of Palea steindachneri and Pelodiscus axenaria, both naturally distributed in Asia. The sizes of the two mitochondrial genomes were 16,811 bp and 17,143 bp, respectively. Typical vertebrate animal mtDNA features were observed, such as the usual gene components and arrangements (37 genes with a non-coding control region) and the A + T biased nucleotide compositions on the light strand (61.5% and 62.7%, respectively). All conserved blocks common to the vertebrates control region except for the extended terminal associated sequences (ETAS2) were found in the two soft-shelled turtles. The ω ratio averaged over all sites of each protein-coding gene (PCG) was below 1, which indicated purifying selection at the gene-wide level. However, a positive selection site at the 350-codon position in the cytb gene was detected, as estimated by Bayes empirical Bayes (BEB) analysis. Compared with the gene subsets, the mitogenomes provided the most robust phylogenetic resolution. The monophyly of the clades Amydona, Gigantaesuarochelys, and Apalonia was well supported. Topology discrepancies were observed among different datasets (e.g., the positions of Lissemys and Palea), reflecting the heterogeneous phylogenetic signals in the soft-shelled turtle mitogenomes. Precise date estimation based on Bayesian relaxed clock analyses indicated that the crown group age of extant Trionychia was approximately 115.84 Ma (95% HPD: 91.33–142.18 Ma). Paleoclimate changes, especially the Eocene − Oligocene transition, could be responsible for the speciation in these groups. Our results reiterated the necessity and effectiveness of incorporating entire mitochondrial genomes to delineate phylogenetic relationships in chelonian phylogeny studies.

Abstract The Asian giant softshell turtle Pelochelys cantorii is one of the largest aquatic turtles in China and has been designated a First Grade Protected Animal in China. To advance conservation research, a combination of Illumina short-read, PacBio long-read, and Hi-C scaffolding technologies was used to develop a high-quality chromosome-level genome assembly for P. cantorii. A total of 262.77 Gb of clean data were produced (121.6 × depth) and then the genome was assembled into 2.16 Gb with a contig N50 of 41.44 Mb and scaffold N50 length of 120.17 Mb, respectively. Moreover, about 99.98% assembly genome sequences were clustered and ordered onto 33 pseudochromosomes. Genome annotation revealed that 21,833 protein-coding genes were predicted, and 96.40% of them were annotated. This new chromosome-level assembly will be an enabling resource for genetic and genomic studies to support fundamental insight into P. cantorii biology.

IntroductionA total of 94 Propionibacterium acnes (P. acnes) isolates were obtained from a hospital in Beijing to evaluate their susceptibility to erythromycin, clarithromycin, doxycycline, and minocycline. As well as the determination of the effectiveness of P. acnes phages in vitro and in P. acnes-induced lesions mouse model.MethodsPatients with acne vulgaris (AV) were enrolled from August 2021 to October 2022. Standard methods were employed for specimen collection, culture, and identification of P. acnes. Susceptibility testing was conducted using E-strips for erythromycin, clarithromycin, minocycline, and doxycycline. Phage culture and identification followed standard procedures. A mouse model with P. acnes-induced skin lesions was established, and data was analyzed using χ2 test.ResultsThe results showed that all isolates were susceptible to minocycline and doxycycline, while 53 (56.4%) and 52 (55.3%) isolates were susceptible to erythromycin and clarithromycin, respectively. Interestingly, younger patients and those with lower acne severity exhibited reduced resistance. Phage cleavage rates ranged from 88.30 to 93.60%. Multilocus sequence typing (MLST) analysis was conducted on eight randomly selected P. acnes isolates, and the IA-2 subtype was used in experiments to address P. acnes-induced lesions in mice. Phage therapy proved effective in this model.DiscussionThis study highlights the high susceptibility of P. acnes to doxycycline and tetracycline, while erythromycin and clarithromycin exhibited elevated resistance. Additionally, P. acnes phages demonstrated high cleavage rates and potential effectiveness in treating P. acnes-induced lesions. These findings suggest promising avenues for further exploration of phage therapy in acne treatment.

Cherax quadricarinatus, also known as the redclaw crayfish, is native to northern Australia and southern Papua New Guinea and is an important freshwater aquaculture species in many countries. Studying the genetic structure of the current cultured population can improve the breeding plan for redclaw crayfish to better manage the hybridization and germplasm bank and promote their rational utilization; however, microsatellite resources for redclaw crayfish remain insufficient. The purpose of this study was to analyze the genetic diversity of different redclaw crayfish populations in China. After screening 18 pairs of microsatellite markers from redclaw crayfish transcriptome data, 240 samples from seven main breeding areas (Changsha, Guangzhou, Haikou, Huzhou, Jiangmen, Wuxi, and Zhanjiang) were evaluated and detected using these microsatellite markers. In total, 97 alleles were detected, of which the minimum number was two and the maximum number was twelve. The observed heterozygosity ranged from 0.258 to 0.807, with an average of 0.559, and the expected heterozygosity ranged from 0.288 to 0.815, with an average value of 0.558. The polymorphic information content values of seven populations ranged from 0.268 to 0.791, with an average of 0.511. Moreover, pairwise genetic differentiation within the population was between 0.007 and 0.031. The UPGMA clustering results showed that the Zhanjiang population stands alone on a branch, but the genetic variation between branches is very small. Meanwhile, STRUCTURE analysis further revealed that the genetic backgrounds of each population are essentially identical, with no noticeable genetic differentiation arising from geographic differences. These results provide a basic assessment of the genetic diversity of the main cultured populations of redclaw crayfish and a molecular foundation for future genetic monitoring and selective breeding research.

Immersive environments have become increasingly popular for visualizing and exploring large-scale, complex scientific data because of their key features: immersion, engagement, and awareness. Virtual reality offers numerous new interaction possibilities, including tactile and tangible interactions, gestures, and voice commands. However, it is crucial to determine the most effective combination of these techniques for a more natural interaction experience. In this paper, we present MEinVR, a novel multimodal interaction technique for exploring 3D molecular data in virtual reality. MEinVR combines VR controller and voice input to provide a more intuitive way for users to manipulate data in immersive environments. By using the VR controller to select locations and regions of interest and voice commands to perform tasks, users can efficiently perform complex data exploration tasks. Our findings provide suggestions for the design of multimodal interaction techniques in 3D data exploration in virtual reality.

In recent years, environmental DNA (eDNA) technology has become an accepted approach for investigating rare and endangered species because of its economic efficiency, high sensitivity, and non-invasiveness. The Asian giant softshell turtle (Pelochelys cantorii) is a first-class protected aquatic animal in China, and traditional resource survey methods have not identified its natural populations for many years. In this study, primers and a TaqMan probe targeting ND5 were designed, reaction conditions were optimized, a standard curve was constructed using synthetic DNA, and an eDNA quantitative PCR (qPCR) detection method was established. The eDNA detection technology for P. cantorii revealed that the number of species in the experimental pools showed a significant linear relationship with the eDNA concentration (p < 0.05). The eDNA concentration was negatively correlated with the length of time after the removal of P. cantorii and retention in the water body for 9 days. The qPCR detection method for P. cantorii eDNA established in this study can be applied to the qualitative detection of P. cantorii in water bodies, as well as to preliminary evaluation of its relative biomass. This can serve as a baseline for the investigation of natural P. cantorii population and the evaluation of its wild release effects.

In aquaculture, the traditional method for hatching Pelodiscus sinensis eggs needs further investigation. Here, we developed a medium-free incubation method for hatching P. sinensis eggs and evaluated its differences from the traditional vermiculite incubation method and the effects of light on it. We found that medium-free incubation had no significant effects on hatching success, body weight, carapace length, carapace width, plastron length, plastron width, and righting response time of P. sinensis compared with those under traditional vermiculite incubation, irrespective of thermostatic or fluctuating temperature conditions. Furthermore, light treatment significantly shortened the incubation period and negatively affected body weight, carapace length, carapace width, plastron length, and righting response time during medium-free incubation. Additionally, this study is the first to report the phenomenon of egg-hatching synchrony in P. sinensis. Overall, our results provide basic data and novel insights for improving the method for hatching P. sinensis eggs.

Abstract Multiple heavy metal pollution in mangrove wetlands is serious. Kandelia obovata seedlings were cultured in pots in which lead (Pb), zinc (Zn) and copper (Cu) were added separately and in combinations. The results showed that heavy metal stress improved the rate of root oxygen leakage, enhanced root activity, and reduced root porosity. The root under single heavy metal stress was impacted by the addition of other heavy metals, demonstrating antagonistic or synergistic effects. Iron plaque (IP) formation was improved under single Zn or Cu stress, and inhibited in binary stress of Pb + Cu. The adsorptions of IP on heavy metals in combined stress (Pb, 62–116 μg g−1; Zn, 194–207 μg g−1; Cu, 35–52 μg g−1) were higher than that in single stress (Pb, 18 μg g−1; Zn, 163 μg g−1; Cu, 22 μg g−1). K. obovata accumulated higher levels of heavy metals in root (Pb, 7–200 μg g−1; Cu, 4–78 μg g−1), compared with IP (Pb, 18–116 μg g−1; Cu, 22–52 μg g−1), stem (Pb, 3–7 μg g−1; Cu, 9–17 μg g−1), and leaf (Pb, 2–4 μg g−1; Cu, 4–7 μg g−1). Correlation analysis showed that single and binary stresses affected K. obovata, with more significant effect of trinary stress. Regression path analysis showed that multiple heavy metal stress firstly affected root, then indirectly contributed to IP formation, as well as heavy metal in IP and root; at last, heavy metal in IP directly contributed to heavy metal bioaccumulations in root.

Through a 30-day experiment, this study investigated the effects of five photoperiods (0L:24D, 6L:18D, 12L:12D, 18L:6D, and 24L:0D) on the survival, enzyme activity, body color, and growth-related gene expression of redclaw crayfish (Cherax quadricarinatus) juveniles. The results showed that C. quadricarinatus juveniles under 18L:6D and 24L:0D photoperiods exhibited the highest survival rate, which was significantly higher than the survival rates of juveniles under the other three photoperiods (p < 0.05). However, the 0L:24D group had the highest final body weight and weight gain rate, significantly surpassing those of the 12L:12D, 18L:6D, and 24L:0D groups (p < 0.05). Regarding enzyme activity and hormone levels, juveniles under the 18L:6D photoperiod exhibited relatively higher activity of superoxide dismutase (SOD), acid phosphatase (ACP), and lysozyme (LZM) enzymes than those under other photoperiods, but their levels of melatonin and cortisol were relatively low. In addition, the 24L:0D group showed the highest malondialdehyde (MDA) content. Analysis of gene expression levels revealed that retinoid X receptor (RXR) and α-amylase (α-AMY) genes in C. quadricarinatus juveniles exhibited significantly higher expression levels under the 18L:6D photoperiod than those under the other four photoperiods (p < 0.05). With increasing daylight exposure, the body color of C. quadricarinatus changed from pale blue to yellow–brown. In summary, C. quadricarinatus juveniles achieved high survival rates, good growth performance, strong antioxidant stress response, and immune defense capabilities under an 18 h photoperiod. Therefore, in the industrial seedling cultivation of redclaw crayfish, it is recommended to provide 18 h of daily light. Further, the study demonstrated the ability to manipulate the body color of C. quadricarinatus through controlled artificial photoperiods. These findings provide essential technical parameters needed for the industrial cultivation of C. quadricarinatus juveniles.

Understanding tourist perceptions and the relationship between landscape features and emotional attitudes in traditional village is crucial for sustainable development. However, quantifying these perceptions over vast spatiotemporal scales is challenging. Additionally, there is a paucity of knowledge on which landscape features influence tourist perceptions within varied samples on a spatial scale. In this study, we analyzed 39,130 online reviews of 57 traditional Chinese villages from 2018 to 2023. Utilizing Word2Vec and machine learning techniques, we identified 14 key landscape feature indicators. These were quantitatively scored using expert evaluations, and their relationship to tourists’ emotional attitudes was determined through linear regression analysis. The analysis revealed that architectural elements, service facilities, convenience, and sanitation are positively associated with tourists’ emotional attitudes towards traditional villages. Contrary to expectations, the frequency of landscape feature mentions did not correlate significantly with emotional attitudes, challenging traditional assumptions about the visibility of landscape features and their impact.

Abstract Knowledge of sex determination has important implications in physiology, ecology and genetics, but the evolutionary mechanisms of sex determination systems in turtles have not been fully elucidated, due to a lack of reference genomes. Here, we generate a high-quality genome assembly of Asian yellow pond turtle (Mauremys mutica) using continuous long-read (PacBio platform), Illumina, and high-throughput chromatin conformation capture (Hi-C) technologies. The M. mutica haplotype has a genome size of 2.23 Gb with a contig N50 of 8.53 Mb and scaffold N50 of 141.98 Mb. 99.98% sequences of the total assembly are anchored to 26 pseudochromosomes. Comparative genomics analysis indicated that the lizard-snake-tuatara clade diverged from the bird-crocodilian-turtle clade at approximately 267.0–312.3 Mya. Intriguingly, positive selected genes are mostly enriched in the calcium signaling pathway and neuroactive ligand-receptor interaction, which are involved in the process of temperature-dependent sex determination. These findings provide important evolutionary insights into temperature-dependent sex determination system.

It is particularly important to improve the performance of mid-infrared (mid-IR) electro-optic (EO) modulator, which is one of the key devices that will expand the channels of optic communication, and will be utilized in optical free space communication, optical detection for gas molecules, etc. We present and theoretically design the performance of the high-speed mid-IR EO modulator based on lithium niobate on insulator (LNOI) at λ = 3 μm. We have designed, calculated, and optimized single-mode ridge waveguide, 1 × 2 multimode interference (MMI) couplers and coplanar waveguide (CPW) electrodes structures for x-cut lithium niobate. Our device with an extinction ratio greater than 40 dB, a half-wave voltage-length product is about 12 V·cm, and a EO bandwidth up to 12 GHz with interaction length of 15 mm. The performance of interaction length of 5 mm and 10 mm mid-IR EO modulator are also proposed and simulated for a compromise consideration between the EO bandwidth and driving voltage.

Introduction: Bone morphogenetic proteins (BMPs) play a crucial role in bone formation and differentiation. Recent RNA-Seq results suggest that BMPs may be involved in the sex differentiation of P. sinensis, yet more relevant studies about BMPs in P. sinensis are lacking.Methods: Herein, we identified BMP gene family members, analyzed the phylogeny, collinear relationship, scaffold localization, gene structures, protein structures, transcription factors and dimorphic expression by using bioinformatic methods based on genomic and transcriptomic data of P. sinensis. Meanwhile, qRT-PCR was used to verify the RNA-Seq results and initially explore the function of the BMPs in the sex differentiation of P. sinensis.Results: A total of 11 BMP genes were identified, 10 of which were localized to their respective genomic scaffolds. Phylogenetic analysis revealed that BMP genes were divided into eight subfamilies and shared similar motifs (“WII”, “FPL”, “TNHA”, “CCVP”, and “CGC”) and domain (TGF-β superfamily). The results of the sexually dimorphic expression profile and qRT-PCR showed that Bmp2, Bmp3, Bmp15l, Bmp5, Bmp6 and Bmp8a were significantly upregulated in ovaries, while Bmp2lb, Bmp7, Bmp2bl and Bmp10 were remarkable upregulated in testes, suggesting that these genes may play a role in sex differentiation of P. sinensis.Discussion: Collectively, our comprehensive results enrich the basic date for studying the evolution and functions of BMP genes in P. sinensis.

Background: Randall’s plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease.Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein–protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518.Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518.Conclusion: Randall’s plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.

Salinity stress can trigger a series of physiological changes. However, the mechanism underlying the response to acute salinity stress in Macrobrachium rosenbergii remains poorly understood. In this study, osmoregulation, physiological metabolism, antioxidant capacity, and apoptosis were examined over 96 h of acute salinity stress. Hemolymph osmolality increased with increasing salinity. After 48 h of salinity exposure, the glucose, triglycerides, total protein, and total cholesterol contents in two salinity stress groups (13 and 26‰ salinity) were significantly lower than those in the 0‰ salinity group. The highest levels of these parameters were detected at 6 h; however, superoxide dismutase (SOD), total antioxidant capacity (T-AOC), and malondialdehyde (MDA) were the lowest at 96 h in the 13‰ salinity group. The activity of immunity-related enzyme alkaline phosphatase (AKP) showed a decreasing trend with increasing salinity and remained at a low level in the 26‰ salinity group throughout the experiment. No significant differences were observed in aspartate aminotransferase (AST), alanine aminotransferase (ALT), or lysozyme (LZM) among the three treatments at 96 h. After 96 h of salinity treatments, the gill filament diameter significantly decreased, and a more pronounced terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive signal was detected in the 13‰ and 26‰ groups compared to that in the 0‰ group. Expression levels of apoptosis-related genes, including Cysteine-aspartic acid protease 3 (Caspase 3), Cysteine-aspartic acid protease 8 (Caspase 8), Cytochrome c (Cyt-c), tumor suppressor gene (P53), Nuclear factor kappa-B (NF-κB), and B cell lymphoma 2 ovarian killer (Bok) were significantly higher in the 26‰ salinity group than in the other groups at 24 h, but lower than those in the 0‰ salinity group at 96 h. Cyt-c and P53 levels exhibited a significantly positive relationship with MDA, AST, and LZM activity during salinity stress. In the 13‰ salinity group, Bok expression was significantly correlated with SOD, T-AOC, AKP, acid phosphatase, and LZM activity, whereas in the 26‰ group, the AST content was positively correlated with Caspase 8, Cyt-c, and P53 expression. A significant negative relationship was observed between Caspase 3 expression and catalase (CAT) activity. These findings provide insight into the mechanisms underlying the response to acute salinity stress and will contribute to improving M. rosenbergii aquaculture and management practices.

This research explores the cross-modal correspondence effect of ambient color on people’s taste perception in virtual reality (VR). To this end, we designed and conducted two experiments to investigate whether and how taste-congruent ambient colors in VR influence taste perception measured by four aspects: 1) taste ratings of a neutral drink; 2) taste association with virtual environments; 3) associated scenarios when immersed in these virtual environments; and 4) participants’ liking of these environments. In Experiment 1, participants adjusted the ambient light with different cross-modal-related colors in the immersive environments and reported their scaling of the Virtual Reality Sickness Questionnaire (VRSQ). Comfortable light intensity for each ambient color was obtained and color recognition problems were observed. In Experiment 2, participants tasted black tea (as the neutral drink), after being exposed to eight different virtual environments with different ambient colors. Results showed that the pink ambient color significantly increased the sweetness ratings. Differences in the color-taste association and environment liking were also observed in the ambient color conditions. Our results provide new insights into the cross-modal correspondence effect on ambient color and taste perception not found in prior work in VR scenarios.

Macrobrachium rosenbergii is an important cultured shrimp worldwide, and its precocious puberty has led to serious economic losses. Although reproductive sterilization can avoid this problem, little is known about the molecular mechanisms underlying gonadal development and gametogenesis in M. rosenbergii. Here, we conducted transcriptome analysis of the ovaries, testes, and male/female brain tissues of M. rosenbergii to discover germ cell development-related genes. A total of 60,607 unigenes were identified, of which 20,963 unigenes could be functionally annotated. Eighteen candidate genes were identified by Venn diagram analysis, keyword, and known marker search, followed by elimination of low-expression and repetitive genes. Subsequent real-time quantitative reverse transcription polymerase chain reaction and in situ hybridization identified five genes (RAD51, vasa, SPDS, MRR, and Fem-1C) associated with germ cell development—RAD51, vasa, and SPDS were expressed in both male and female gonads, whereas Fem-1C was specifically expressed in the ovary and MRR in the testis. In the ovary, vasa, SPDS, and Fem-1C were mainly expressed in stage 1–3 oocytes, while RAD51 was expressed in stage 2–3 oocytes. In testis, vasa were significantly expressed in spermatogonia and primary spermatocytes, whereas RAD51 and SPDS were only enriched in spermatogonia and MRR in vas deferens. Our research indicates that these five genes are important germ cell development-related genes, of which RAD51, SPDS, and Fem-1C were proven to function in germ cells of this species for the first time. The discovery of these genes could help develop molecular breeding techniques to overcome precocious puberty in M. rosenbergii.

Abstract Background We reported a patient with Testicular adrenal rest tumors(TARTs) caused by congenital adrenal hyperplasia(CAH). TARTs occur frequently in CAH population with 21-hydroxylase deficiency(21-OHD). There are few reports of TARTs with 3β-hydroxysteroid dehydrogenase deficiency-2 (3β-2HSD).Furthermore,gaint TARTs are rarely mentioned in reported cases involving affected siblings. Case presentation A 14-year-old male patient was admitted by congenital adrenal hyperplasia with progressively increasing bilateral testicular masses.The Patient and his elder brother had been performed mutational and chromosome analysis and biopsy. Hormonal and anthropometric measurements were performed during endocrine treatments. We successfully performed surgery and excised two 83mm×46mm×44mm and 74mm×49mm×31mm tumors. Our pathology and immunochemistry tests have proven TARTs in patient. At first, both siblings received regular doses of hydrocortisone and fludrocortisones and tumor size regressed. During the one-year irregular intake due to Covid-19 pandemic, endocrine treatment became insensitive and tumor size slowly increased. The gene analysis reported two novel mutations C.776 C>T and C.674 T>A. The C.776 C>T is from father and has been reported. The C.674 T>A inherited from mother and cannot found in gene library and may related to TARTs. Conclusions This case illustrates inadequate hormone therapy could cause tumor enlargement. It is essential to seek for ultrasound examination once suspected scrotal mass occurred.It is necessary to adjust endocrine medicine or adopt surgery in refractory gaint TARTs. And presence of tunica vaginalis cavity may indicate the severity of TARTs in surgery.

Offspring size-number trade-off is a critical component of life-history theory and is important for further understanding the reproductive strategies of animals. The relationship between this trade-off and maternal size has been explored in several turtle species, except for the Asian yellow pond turtle, Mauremys mutica. To investigate how the maternal condition affects offspring size and number, we explored the relationships among the maternal body size and the number and size of cultured M. mutica hatchlings using a 4-year dataset. Our results showed that different females not only produced different sizes of offspring but also produced different numbers of offspring. No trade-off in egg size number was detected. According to regression analysis, we did not find that the maternal body size significantly influenced the offspring mass; however, we detected that the offspring size was significantly correlated with the clutch size and maternal age. The mean body mass of offspring increased with maternal age, and the clutch size varied significantly over four years, which was correlated with offspring size, maternal body size and age. However, the number of offspring per female increased with the maternal plastron length rather than age. Our results were inconsistent with the optimal offspring size theory in that females did not increase their offspring size but rather increased the offspring number to increase their fitness, which will also provide a basis for the efficient cultivation management of turtles.

Hibernation in turtle species is an adaptive survival strategy to colder winter conditions or food restrictions. However, the mechanisms underlying seasonal adaptions remain unclear. In the present study, we collected hemocytes from Pelochelys cantorii and compared the molecular signature of these cells between the active state and hibernation period based on single-cell RNA sequencing (scRNA-seq) analysis. We found six cell types and identified a list of new marker genes for each cell subpopulation. Moreover, several heat shock genes, including the Hsp40 family chaperone gene (DNAJ) and HSP temperature-responsive genes (HSPs), were upregulated during the hibernation period, which predicted these genes may play crucial roles in the stress response during hibernation. Additionally, compared to hemocytes in the active state, several upregulated differentially expressed immune-related genes, such as stat1, traf3, and socs6, were identified in hemocytes during the hibernation period, thus indicating the important immune function of hemocytes. Therefore, our findings provide a unified classification of P. cantorii hemocytes and identify the genes related to the stress response, thereby providing a better understanding of the adaptive mechanisms of hibernation.

Salinity is a crucial factor influencing the growth, development, immunity, and reproduction of aquatic organisms; however, little is known about the molecular mechanism of the response to salinity challenge in larvae of the giant freshwater prawn Macrobrachium rosenbergii. Herein, larvae cultured in three treatment groups with salinities of 10, 13, and 16‰ (S10, S13, and S16) were collected, and then transcriptome analysis was conducted by RNA-seq. A total of 6,473, 3,830 and 3,584 differentially expressed genes (DEGs) were identified in the S10 vs. S13 comparison, S10 vs. S16 comparison and S13 vs. S16 comparison, respectively. These genes are involved in osmoregulation, energy metabolism, molting, and the immune response. qPCR analysis was used to detect the expression patterns of 16 DEGs to verify the accuracy of the transcriptome data. Protein–protein interaction (PPI) analysis for DEGs and microsatellite marker screening were also conducted to reveal the molecular mechanism of salinity regulation. Together, our results will provide insight into the molecular genetic basis of adaptation to salinity challenge for larvae of M. rosenbergii.

The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6–251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3–54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.

To understand the genetic structure of the protected turtle species Pelochelys cantorii we used transcriptome data to design more than 30,000 tri- and tetranucleotide repeat microsatellite primer pairs, of which 230 pairs were used for laboratory experiments. After two screenings, only 10 microsatellite markers with good specificity, high amplification efficiency, and polymorphisms were obtained. Using the selected primers, two multiplex PCR systems were established to compare and analyze the genetic diversity of artificially assisted breeding generations from four parents (two females and two males) continuously bred over two years. A total of 25 alleles were detected among the 10 microsatellite loci of the offspring. The polymorphism information content (PIC) was 0.313–0.674, with an average of 0.401, among which two loci were highly polymorphic (PIC ≥ 0.5). The number of alleles was 2–5 and the number of effective alleles was 1.635–3.614. The observed heterozygosity was 0.341–0.813, with an average of 0.582, whereas the average expected heterozygosity was 0.389–0.725, with an average of 0.493. Moreover, on the basis of Nei’s genetic distance and the Bayesian clustering algorithm, the 182 offspring were divided into two subgroups, and the results corresponded to the two maternal lines. This is the first study to investigate the molecular markers of P. cantorii, and the results obtained can be used to protect genetic resources and provide a genetic basis for the design of population recovery plans.

China is a major country in turtle cultivation and has a long history of artificial breeding of turtles. In this study, a census and statistical analysis of artificially domesticated aquatic turtles in 15 provinces of China were conducted. The results showed that 29 species were aquatic turtles native to China, accounting for approximately 9% of the world’s total, and a large number of exotic aquatic turtles are also domesticated in China. The present situation of artificial breeding and protection of aquatic turtles in major provinces of China is shown, and existing problems are also put forward, with suggestions for the protection and management of aquatic turtles.

Gonadal cell lines possess the abilities of self-renewal and differentiation, being used as an efficient tool to analyzing the genes’ functions involved in sex differentiation and gametogenesis. Although some significant achievements have been obtained in the gonadal cells’ culture or manipulation across multiple phyla including teleost and mammals, there is limited study on gonadal cell manipulation in turtles. In this study, we established a new ovarian cell line from the young Asian yellow pond turtle (Mauremys mutica), which exhibited a normal diploid karyotype with high alkaline phosphatase activity. The cell line, designated as YTO2, was then characterized through the analysis of gene expression profiles. The transcriptome analysis and the reverse transcription polymerase chain reaction (RT-PCR) showed that the cells expressed germline genes such as tdrd7, nanos1, klf5, igtb1, hsd17b4 and rad51. Moreover, the immunostaining showed that the germ cell markers, Tdrd7 and Rad51 proteins, were detected predominant in cytoplasm of perinuclear region, while proliferation marker, PCNA, was dominantly observed in the nuclei of cultured cells. Intriguingly, the cells could respond to the retinoic acid induction with significantly increasing the expression level of some meiosis genes, including vasa, dazl, figla, and dmc1. Furthermore, YTO2 cells could be efficiently transfected with the pHBAd-BHG-EGFP adenovirus and properly expressed the exogenous genes. To sum up, an ovarian cell line of the Asian yellow pond turtle had been established and could be stably propagated under in vitro culture condition, as well as being capable of efficiently expressing the exogenous gene tdrd7. This cell line would provide a valuable tool to elaborate the molecular mechanisms behind germ cells development, differentiation and oogenesis in the turtle, even in reptiles.

Spats1 (spermatogenesis-associated, serinerich 1) has been characterized as a male-biased gene which acts an important role in the germ cell differentiation of mammals. Nevertheless, the function of Spats1 in the Chinese soft-shelled turtle (P. sinensis) has not yet been reported. To initially explore the expression of Spats1 in P. sinensis and its response to sex steroid treatment, we cloned the CDS of Spats1 for the first time and analyzed its expression profile in different tissues, including the testes in different seasons. The Spats1 cDNA fragment is 1201 base pairs (bp) in length and contains an open reading frame (ORF) of 849 bp, which codes for 283 amino acids. Spats1 mRNA was highly expressed in the testes (p < 0.01) and barely detectable in other tissues. In P. sinensis, the relative expression of Spats1 also responsive to seasonal changes in testis development. In summer (July) and autumn (October), Spats1 gene expression was significantly higher in the testes than in other seasons (p < 0.05). Spats1 mRNA was found to be specifically expressed in germ cells by chemical in situ hybridization (CISH), and it was mainly located in primary spermatocytes (Sc1), secondary spermatocytes (Sc2) and spermatozoa (St). Spats1 expression in embryos was not significantly changed after 17α-methyltestosterone (MT)and 17β-estradiol (E2) treatment. In adults, MT significantly induced Spats1 expression in male P. sinensis. However, the expression of Spats1 in testes was not responsive to E2 treatment. In addition, the expression of Spats1 in females was not affected by either MT or E2 treatment. These results imply that Spats1 is a male-specific expressed gene that is mainly regulated by MT and is closely linked to spermatogenesis and release in P. sinensis.

The striped catfish, Pangasianodon hypophthalmus (Sauvage 1878), belongs to the family Pangasiidae, is an important economic freshwater species. We determined the complete mitogenome of the Pangasianodon hypophthalmus through sanger method. The complete mitochondrial genome of Pangasianodon hypophthalmus was a circular molecule of 16,469 bp with a total GC content of 44% which contains 37 genes, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNAs genes. Phylogenetic analysis showed that Pangasianodon hypophthalmus clustered together with other Pangasianodon species and was closely related to Pangasius larnaudii, both species belonged to Pangasianodon genus.

Objective: To investigate the value of high-frame rate vector flow imaging technique (V flow) in evaluating the hemodynamic changes of carotid stenosis caused by atherosclerotic plaques.Methods and Materials: In this prospective study, patients with stenosis rate (diameter) ≥30% caused by carotid atherosclerotic plaques were included. Degrees of carotid stenosis were graded according to North American Symptomatic Carotid Endarterectomy Trial criteria: moderate (30–69%) or severe (70–99%). Mindray Resona 7s ultrasound machine with a linear array transducer (3–11 MHz) was used for ultrasound examinations. The mean WSS value of carotid arteries was measured at the proximal, narrowest region and distal of carotid stenosis. The mean WSS values were correlated with peak systolic velocity (PSV) measured by color Doppler flow imaging and stenosis degree detected by digital subtraction angiography (DSA). The vector arrows and flow streamline detected by V flow dynamic imaging were analyzed. Imaging findings of DSA in carotid arteries were used as the gold standard.Results: Finally, 51 patients were included. V flow measurements were performed successfully in 17 patients (100%) with moderate-grade stenosis and in 30 patients (88.2%) with severe-grade stenosis. Dynamic V flow imaging showed yellow or red vectors at the stenotic segment, indicating fast speed blood flow (up to 260.92 cm/s). Changes of streamlines were detected in the stenotic segment. The mean WSS value measured at the narrowest region of the carotid artery had a moderately positive correlation with stenosis degree (r = 0.58, P < 0.05) and PSV value (r = 0.54, P < 0.05), respectively. Significant difference was detected in mean WSS value at the narrowest region of the carotid artery between severe carotid stenosis (1.47 ± 0.97 Pa) and moderate carotid stenosis (0.96 ± 0.44 Pa) (P < 0.05).Conclusion: The hemodynamic changes detected by V flow of the carotid stenosis might be a potential non-invasive imaging tool for assessing the degree of carotid stenosis.

In aquaculture, the Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important species with remarkable gender dimorphism in its growth patterns. However, the underlying molecular mechanisms of this phenomenon have not been elucidated well. Here, we conducted a whole-transcriptome analysis of the female and male gonads of P. sinensis. Overall, 7833 DE mRNAs, 619 DE lncRNAs, 231 DE circRNAs, and 520 DE miRNAs were identified. Some “star genes” associated with sex differentiation containing dmrt1, sox9, and foxl2 were identified. Additionally, some potential genes linked to sex differentiation, such as bmp2, ran, and sox3, were also isolated in P. sinensis. Functional analysis showed that the DE miRNAs and DE ncRNAs were enriched in the pathways related to sex differentiation, including ovarian steroidogenesis, the hippo signaling pathway, and the calcium signaling pathway. Remarkably, a lncRNA/circRNA–miRNA–mRNA interaction network was constructed, containing the key genes associated with sex differentiation, including fgf9, foxl3, and dmrta2. Collectively, we constructed a gender dimorphism profile of the female and male gonads of P. sinensis, profoundly contributing to the exploration of the major genes and potential ncRNAs involved in the sex differentiation of P. sinensis. More importantly, we highlighted the potential functions of ncRNAs for gene regulation during sex differentiation in P. sinensis as well as in other turtles.

In this study, a tin monoselenide (SnSe)-based all-optical modulator is firstly demonstrated with high tuning efficiency, broad bandwidth, and fast response time. The SnSe nanoplates are deposited in the microfiber knot resonator (MKR) on MgF2 substrate and change its transmission spectra by the external laser irradiation. The SnSe nanoplates and the microfiber are fabricated using the liquid-phase exfoliation method and the heat-flame taper-drawing method, respectively. Due to the strong absorption and enhanced light–matter interaction of the SnSe nanoplates, the largest transmitted power tunability is approximately 0.29 dB/mW with the response time of less than 2 ms. The broad tuning bandwidth is confirmed by four external pump lights ranging from ultraviolet to near-infrared. The proposed SnSe-coated microfiber resonator holds promising potential for wide application in the fields of all-optical tuning and fiber sensors.

The giant freshwater prawn (GFP) is one of the most critical crustacean species cultured in Southeast Asia. Investigation of the genetic structure of current commercial stocks allows GFP breeding programs to better manage crosses and germplasm banks as well as to promote the rational use of GFP. The objective of the study was to characterize genetic diversity in diverse prawn populations with emphasis on those cultured in China. Seventeen microsatellite loci, including 12 novel loci derived from GFP transcriptome data, were screened to assess genetic diversity in one wild (Myanmar) and six cultured populations (i.e., four Chinese (Zhejiang, Guangxi, and Guangdong A and B), one Malaysian, and one Thai population). The results showed that the number of alleles per locus ranged from 3 to 18. The mean observed heterozygosity (0.363 ± 0.048) was less than the expected heterozygosity (0.637 ± 0.048). The mean values of polymorphism information content among the seven populations were >0.5 (ranging from 0.110 to 0.915). These cultured populations exhibited reduced genetic diversity when compared with that of the wild population. Pair-wise genetic differentiation ranged from 0.006 to 0.131 within the seven populations. The dendrogram of the genetic distance shows that the six cultured populations were distributed on the same major branch, suggesting that they have are genetically close, whereas the wild population was distributed on an independent branch. The results provide a basic assessment of genetic diversity in some available stocks and lay a foundation for future research efforts toward genetic monitoring and selective breeding.

Projections are well-known techniques that help the visual exploration of high-dimensional data by creating depictions thereof in a low-dimensional space. While projections that target the 2D space have been studied in detail both quantitatively and qualitatively, 3D projections are far less well understood, with authors arguing both for and against the added-value of a third visual dimension. We fill this gap by first presenting a quantitative study that compares 2D and 3D projections along a rich selection of datasets, projection techniques, and quality metrics. To refine these insights, we conduct a qualitative study that compares the preference of users in exploring high-dimensional data using 2D vs. 3D projections, both without and with visual explanations. Our quantitative and qualitative findings indicate that, in general, 3D projections bring only limited added-value atop of the one provided by their 2D counterparts. However, certain 3D projection techniques can show more structure than their 2D counterparts, and can stimulate users to further exploration. All our datasets, source code, and measurements are made public for ease of replication and extension.

The employee-organisation relationship between academics and universities is a critical issue in higher education (HE) human resource management. Previous studies have mainly investigated the segmentation between full-time and part-time academics, or academics working in different countries. However, few studies have explored academics' perceptions of their relationship with universities under the recent tenure-track reform in the Chinese HE system. Drawing on psychological contract theory, this qualitative study explores how academics perceive their relationships with their university. Through interviews with 21 tenure-track academics at a Chinese university, this study found four types of psychological relationships: (1) high-risk with high-yield, (2) optimistic trust, (3) mutual benefit, and (4) content and satisfied. Among the four types, tenure-track academics' expectations of universities are diversified. These findings suggest that universities should pay more attention to understanding academics' perceived employee-organisation relationship and their corresponding expectations to improve managerial efficiency.

An ion-exchange chromatography method with visible light detection was developed for the simultaneous determination of chloride, bromide, and iodide in foodstuffs. They were separated by means of low pressure ion-exchange chromatography using 4.0mM sodium carbonate solution as the eluent and a low pressure ion-exchange chromatography column as the separation column. The detection limits of chloride, bromide and iodide were 0.011 mg/l, 0.002 mg/l, and 0.023 mg/l, respectively. The relative standard deviations (RSDs) of the peak area were smaller than 2.9%. The recoveries were between 98.61% and 105.65%. Unlike the traditional methods, this validated method is inexpensive and stable.

In order to control the pollution by anionic surfactants in seawater, a simple, accurate and sensitive reverse flow injection (rFIA) spectrophotometric method for the determination of anionic surfactants in seawater is suggested in this paper. Sodium dodecylbenzenesulfonate (LAS) was selected as the reference anionic surfactant. The method is based on the ion associate formed between LAS and Ethyl Violet. The absorbance of the complex is measured by optical detector at 585 nm. Chemical factors and rFIA variables affecting the system are also discussed. Under the optimal conditions, the linear range of this method was 25.0-400.0 μg/l; the detection limit was 2.4 μg/l; the relative standard deviation was 0.38%. This method is suitable for automatic and continuous analysis, and was successfully applied to determine the content of anionic surfactants in seawater.