Characterization and phylogenetic analysis of the complete mitochondrial genome of Aipysurus eydouxii Gray 1849 (Elapidae: Hydrophiinae).

Hydrophiine sea snakes represent ecologically significant and species-rich marine predatory reptiles, many of which inhabit marine environments throughout their entire lifecycles. However, due to morphological variability and limited molecular phylogenetic studies, the taxonomic relationships within this group remain unclear. In this study, we present the first complete mitochondrial genome of Aipysurus sea snakes, specifically Aipysurus eydouxii Gray 1849. The mitogenome comprises 17,228 base pairs and contains a total of 37 genes , plus a putative control region. This study provides valuable genetic data that will contribute to the future taxonomic classification and ecological protection of hydrophiine sea snakes.

Comparative Analysis of Complete Mitochondrial Genomes of Five Chromodorididae Species (Nudibranchia:Doridina).

Mitochondrial genome is an important molecular marker for exploring the phylogenetic relationships of species and revealing molecular evolution. In the present study, 5 mitogenomes of Chromodorididae (Chromodoris lochi, Chromodoris colemani, Chromodoris elisabethina, Chromodoris annae and Hypselodoris whitei) were systemically investigated. The lengths of the mitogenomes sequences were 14248 bp, 14257 bp, 14252 bp, 14254 bp and 14856 bp, respectively. Most protein-coding genes (PCGs) were initiated with the common ATG codon and terminated with the TAA and TAG. We calculated Ka/Ks values for all 13 PCGs of Chromodorididae species, all ratios were less than 1, indicating selection by purification. Phylogenetic relationships were constructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all complete genomes of 50 species, primarily from the family Chromodorididae (Doridina) and 2 outgroups. This phylogenetic tree provided further additional references for the classification of the suborder Doridina. Gene rearrangement suggested a more conserved pattern of gene sequences in the superfamily Chromodoridoidea. These results and newly sequenced will contribute to a better understanding of Chromodorididae and provide reference for further phylogenetic studies.

Chromosomal-level genome assembly and annotation of the tropical sea cucumber Holothuria scabra.

Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.

MicroRNA sequencing analysis reveals immune responses in hepatopancreas of Fenneropenaeus penicillatus under white spot syndrome virus infection.

White Spot Disease is one of the most harmful diseases of the red tail shrimp, which can cause devastating economic losses due to the highest mortality up to 100% within a few days. MicroRNAs (miRNAs) are large class of small noncoding RNAs with the ability to post-transcriptionally repress the translation of target mRNAs. MiRNAs are considered to have a significant role in the innate immune response of crustaceans, particularly in relation to antiviral defense mechanisms. Numerous crustacean miRNAs have been verified to be required in host immune defense against viral infection, however, till present, the miRNAs functions of F. penicillatus defense WSSV infection have not been studied yet. Here in this study, for the first time, miRNAs involved in the F. penicillatus immune defense against WSSV infection were identified using high-throughput sequencing platform. A total of 432 miRNAs were obtained including 402 conserved miRNAs and 30 novel predicted miRNAs. Comparative analysis between the WSSV-challenged group and the control group revealed differential expression of 159 microRNAs in response to WSSV infection. Among these, 48 were up-regulated and 111 were down-regulated. Ten candidate MicroRNAs associated with immune activities were randomly selected for qRT-PCR analysis, which confirming the expression profiling observed in the MicroRNA sequencing data. As a result, most differentially expressed miRNAs were down-regulated lead to increase the expression of various target genes that mediated immune reaction defense WSSV infection, including genes related to signal transduction, Complement and coagulation cascade, Phagocytosis, and Apoptosis. Furthermore, the genes expression of the key members in Toll and Imd signaling pathways and apoptotic signaling were mediated by microRNAs to activate host immune responses including apoptosis against WSSV infection. These results will help to understand molecular defense mechanism against WSSV infection in F. penicillatus and to develop an effective WSSV defensive strategy in shrimp farming.

Biomechanical feasibility of non-locking system in patient-specific mandibular reconstruction using fibular free flaps.

Mandibular reconstruction with free fibular flaps is frequently used to restore segmental defects. The osteosythesis, including locking and non-locking plate/screw systems, is essential to the mandibular reconstruction. Compared with the non-locking system that requires good adaption between plate and bone, the locking system appears to present a better performance by locking the plate to fixation screws. However, it also brings about limitations on screw options, a higher risk of screw failure, and difficulties in screw placement. Furthermore, its superiority is undermined by the advancing of patient-specific implant design and additive manufacturing. A customized plate can be designed and fabricated to accurately match the mandibular contour for patient-specific mandibular reconstruction. Consequently, the non-locking system seems more practicable with such personalized plates, and its biomechanical feasibility ought to be estimated. Finite element analyses of mandibular reconstruction assemblies were conducted for four most common segmental mandibular reconstructions regarding locking and non-locking systems under incisal biting and right molars clenching, during which the influencing factor of muscles' capacity was introduced to simulate the practical loadings after mandibular resection and reconstruction surgeries. Much higher, somewhat lower, and similar maximum von Mises stresses are separately manifested by the patient-specific mandibular reconstruction plate (PSMRP), fixation screws, and reconstructed mandible with the non-locking system than those with the locking system. Equivalent maximum displacements are identified between PSMRPs, fixation screws, and reconstructed mandibles with the non-locking and locking system in all four reconstruction types during two masticatory tasks. Parallel maximum and minimum principal strain distributions are shared by the reconstructed mandibles with the non-locking and locking system in four mandibular reconstructions during both occlusions. Conclusively, it is feasible to use the non-locking system in case of patient-specific mandibular reconstruction with fibular free flaps based on the adequate safety, comparable stability, and analogous mechanobiology it presents compared with the locking system in a more manufacturable and economical way.

MicroRNA sequencing analysis reveals injury-induced immune responses of Scylla paramamosain against cheliped autotomy.

During pond culture or intensive culture system of crabs (mainly Eriocheir sinensis, Portunus trituberculatus and Scylla paramamosain), high-density farming has typically contributed to a higher limb autotomy level in juvenile animals, especially in S. paramamosain which has a high level of cannibalism. Due to the high limb autotomy level, the survival and growth rates in S. paramamosain farming are restricted, which limit the growth of the mud crab farming industry. MicroRNAs (miRNAs) are small noncoding RNAs that regulate a series of biological processes including innate immune responses by post-transcriptional suppression of their target genes. MiRNAs are believed to be crucial for innate immune process of host wound healing. Many miRNAs have been verified to be required in host immune responses to repair wound and to defense pathogen after tissue damage. However, to our best knowledge, the miRNAs functions of crustacean innate immune reactions against injury induced by limb autotomy have not been studied yet. Here in this study, for the first time, miRNAs involved in the S. paramamosain immune reactions against injury induced by cheliped autotomy were obtained by high-throughput sequencing. A total of 575 miRNAs (518 known miRNAs and 57 novel predicted miRNAs) were obtained, of which 141 differentially expressed microRNAs (93 up-regulated microRNAs and 48 down-regulated microRNAs) were revealed to be modified against cheliped autotomy, and the qPCR results of randomly selected miRNAs confirmed the expression patterns in the miRNAs sequencing data. Numerous immune-related target genes associated with innate immune system were mediated by miRNAs to induce host humoral immune and cellular immune defense to minimize acute physical damage. Furthermore, the genes expression in hemolymph coagulation and melanization pathways, as well as Toll and Imd signaling pathways were mediated by miRNAs to activate host immune responses including melanization and antimicrobial peptides for rapid wound healing and killing invaded pathogens. These results will help to understand injury-induced immune responses in crabs and to develop an effective control strategy of autotomy rate in crabs farming.

Integration of transcriptomic and metabolomic analyses reveal the molecular responses of the mud crab Scylla paramamosain to infection by an undescribed endoparasite Portunion sp.

Portunion is a rare endoparasitic isopod genus, recently observed inhabiting the hemocoel of the commercially important mud crab, Scylla paramamosain. For better understanding of the host-parasite interaction between S. paramamosain and Portunion sp., the metabolomic and transcriptomic changes in the hemolymph of the S. paramamosain were analyzed. We detected a total of 143 and 126 differentially accumulated metabolites in the positive and negative modes, respectively. Pathways related to amino acids and vitamin synthesis, such as Aminoacyl-tRNA biosynthesis, Tyrosine metabolism, Cysteine and methionine metabolism, Vitamin B6 metabolism, and Biotin metabolism were significantly enriched. Based on the transcriptomic data, a total of 942 differentially expressed genes were identified, of which 25 and 36 were significantly related to the immune system and metabolic pathways, respectively. Based on the metabolomic and transcriptomic data, 90 correlated metabolite-gene pairs were selected to build a regulatory network. Common significantly enriched pathways, including Starch and sucrose metabolism, Metabolism of xenobiotics by cytochrome P450, Aminoacyl-tRNA biosynthesis, Nitrogen metabolism, and Galactose metabolism were detected. On the basis of our analysis, the endoparasite Portunion sp. places a heavy metabolic burden on the host, particularly with respect to fundamental resources, such as amino acids, vitamins, carbohydrates, and lipids. In summary, these data provide an overview of the global metabolic and transcriptomic changes of the S. paramamosain resulting from Portunion sp. infection.

Structural Elucidation of a Glucan from Trichaster palmiferus by Its Degraded Products and Preparation of Its Sulfated Derivative as an Anticoagulant.

Echinoderms have been attracting increasing attention for their polysaccharides, with unique chemical structure and enormous potential for preparing drugs to treat diseases. In this study, a glucan (TPG) was obtained from the brittle star Trichaster palmiferus. Its structure was elucidated by physicochemical analysis and by analyzing its low-molecular-weight products as degraded by mild acid hydrolysis. The TPG sulfate (TPGS) was prepared, and its anticoagulant activity was investigated for potential development of anticoagulants. Results showed that TPG consisted of a consecutive α1,4-linked D-glucopyranose (D-Glcp) backbone together with a α1,4-linked D-Glcp disaccharide side chain linked through C-1 to C-6 of the main chain. The TPGS was successfully prepared with a degree of sulfation of 1.57. Anticoagulant activity results showed that TPGS significantly prolonged activated partial thromboplastin time, thrombin time, and prothrombin time. Furthermore, TPGS obviously inhibited intrinsic tenase, with an EC50 value of 77.15 ng/mL, which was comparable with that of low-molecular-weight heparin (LMWH) (69.82 ng/mL). TPGS showed no AT-dependent anti-FIIa and anti-FXa activities. These results suggest that the sulfate group and sulfated disaccharide side chains play a crucial role in the anticoagulant activity of TPGS. These findings may provide some information for the development and utilization of brittle star resources.

Characterization and phylogenetic analysis of the complete mitogenome of sea cucumber Stichopus ocellatus (Massin, Zulfigar, Hwai & Boss, 2002) (Aspidochirotida: Stichopodidae).

Stichopus ocellatus, known as eye-spotted sea cucumber, is a commercially important Stichopodidae holothuroid in Indo-Pacific region for its valuable nutrition and medicinal ingredients. However, because the taxonomic analyses based on morphological characters and molecular data within Aspidochirotida are limited, the deep-level evolutionary relationships of Aspidochirotida are still poorly understood. Here, for providing better insight of future evolutionary and taxonomic classification of Stichopodidae, we report the first complete mitogenome of S. ocellatus along with 37 annotated and characterized mitochondrial genes, and the phylogenetic analysis based on mitogenome data reveals sister relationship between S. ocellatus and S. monotuberculatus.

Deaminative-cleaved S. monotuberculatus fucosylated glycosaminoglycan: Structural elucidation and anticoagulant activity.

Stichopus monotuberculatus is a tropical sea cucumber species and used as a folk medicine and tonic food. In this study, a fucosylated glycosaminoglycan (SmFG), the depolymerized SmFG (dSmFG) and its oligosaccharide fractions were prepared. The SmFG and its depolymerized products were comprised of a chondroitin-sulfate-E backbone, and various sulfated fucose side chains, including an unusual disaccharide side chain connected to the C-3 position of D-glucuronic acid (GlcA) or GlcA-ol. A peeling reaction occurred during the deaminative depolymerization process. The dSmFG and its fractions showed strong anticoagulant activity by selectively inhibiting intrinsic tenase complex, and had no anti-factor IIa, Xa and VIIa activity. The anticoagulant activity reduced with the decrease of molecular weight, and the unusual branch and novel reducing end may enhance the anticoagulant activity. These findings can provide significant information for development and utilization of depolymerized products from SmFG in food and pharmaceutical industries.

Biomechanical validation of structural optimized patient-specific mandibular reconstruction plate orienting additive manufacturing.

BACKGROUND AND OBJECTIVE: Owing to the unexpected in vivo fracture failure of the original design, structural optimized patient-specific mandibular reconstruction plates (PSMRPs) were created to boost the biomechanical performance of bridging segmental bony defect in the mandibular reconstruction after tumor resection. This work aimed to validate the biomechanical benefit of the structural optimized PSMRPs relative to the original design and compare the biomechanical performance between PSMRP1 with generic contour customization and PSMRP2 with a tangent arc upper margin in mandibular angle region. METHODS: Finite Element Analysis (FEA) was used to evaluate the biomechanical behavior of mandibular reconstruction assemblies (MRAs) concerning these two structural optimized PSMRPs by simulating momentary left group clenching and incisal clenching tasks. Bonded contact was set between mandibular bone and fixation screws and between PSMRP and fixation screws in the MRA, while the frictionless connection was allocated between mandibular bone and PSMRP. The loads were applied on four principal muscles, including masseter, temporalis, lateral and medial pterygoid, whose magnitudes along the three orthogonal directions. The mandibular condyles were retrained in all three directions, and either the left molars or incisors area were restrained from moving vertically. RESULTS: The peak von Mises stresses of structural optimized PSMRPs (264 MPa, 296 MPa) were way lower than that of the initial PSMRP design (393 MPa), with 33 and 25% reduction during left group clenching. The peak magnitude of von Mises stress, minimum principal stress, and maximum principal strain of PSMRP1 (264 MPa, 254 MPa; -297 MPa, -285 MPa; 0.0020, 0.0020) was lower than that of PSMRP2 (296 MPa, 286 MPa; -319 MPa, -306 MPa; 0.0022, 0.0020), while the peak maximum principal stress of PSMRP1 (275 MPa, 257 MPa) was higher than that of PSMRP2 (254 MPa, 235 MPa) during both left group clenching and incisal clenching tasks. CONCLUSIONS: The structural optimized PSMRPs reveal their biomechanical advantage compared with the original design. The PSMRP1 presents better biomechanical performance to the patient-specific mandibular reconstruction than PSMRP2 as a result of its superior safety, preferable flexibility, and comparable stability. The PSMRP2 provides biomechanical benefit in reducing the maximum tension than PSMRP1, indicated by lower peak maximum principal stress, through tangent arc upper margin in mandibular angle region.

Physicochemical Properties and Anticoagulant Activity of Purified Heteropolysaccharides from Laminaria japonica.

Laminaria japonica is widely consumed as a key food and medicine. Polysaccharides are one of the most plentiful constituents of this marine plant. In this study, several polysaccharide fractions with different charge numbers were obtained. Their physicochemical properties and anticoagulant activities were determined by chemical and instrumental methods. The chemical analysis showed that Laminaria japonica polysaccharides (LJPs) and the purified fractions LJP0, LJP04, LJP06, and LJP08 mainly consisted of mannose, glucuronic acid, galactose, and fucose in different mole ratios. LJP04 and LJP06 also contained minor amounts of xylose. The polysaccharide fractions eluted by higher concentration of NaCl solutions showed higher contents of uronic acid and sulfate group. Biological activity assays showed that LJPs LJP06 and LJP08 could obviously prolong the activated partial thromboplastin time (APTT), indicating that they had strong anticoagulant activity. Furthermore, we found that LJP06 exerted this activity by inhibiting intrinsic factor Xase with higher selectivity than other fractions, which may have negligible bleeding risk. The sulfate group may play an important role in the anticoagulant activity. In addition, the carboxyl group and surface morphology of these fractions may affect their anticoagulant activities. The results provide information for applications of L. japonica polysaccharides, especially LJP06 as anticoagulants in functional foods and therapeutic agents.

Weighted gene co-expression network analysis of embryos and first instar larvae of the horseshoe crab Tachypleus tridentatus uncovers development gene networks.

Horseshoe crabs are marine chelicerates that have existed on Earth for about 450 million years, and they are often used as an experimental model for studying marine invertebrate embryology. In this study, we performed transcriptome gene expression profiling of four continuous embryonic stages (Stages 18-21) and first instar larvae of Tachypleus tridentatus. A mean of 50,742,995 high-quality clean reads was obtained from each library. We then conducted weighted gene co-expression network analysis (WGCNA) for 13,698 genes with fragments per kilobase of exon per million mapped fragments values >5. We identified 17 modules, six of which likely play critical roles in development. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes was performed on the biologically significant modules. We found that several pathways, such as hedgehog signaling pathway, VEGF signaling pathway, dorso-ventral axis formation, may be involved in the embryonic development process of T. tridentatus. We also identified hub genes that were highly connected in the six critical modules. This is the first study to apply WGCNA to horseshoe crabs to identify hub genes that may play critical roles in development, and our results provide new insight into the mechanisms underlying early development in horseshoe crabs.

Transcriptome analysis reveals potential key immune genes of Hong Kong oyster (Crassostrea hongkongensis) against Vibrio parahaemolyticus infection.

Hong Kong oyster (Crassostrea hongkongensis) is one of the main species of economic shellfish cultivated in the coastal areas of southern China. The cultivation of this shellfish may be adversely impacted by Vibrio parahaemolyticus, a harmful pathogenic bacterium for many mariculture species, as it usually exists on the surface of Hong Kong oysters. Although previous studies have discovered that oysters rely on non-specific immune system to fight pathogen invasion, the genes corresponding to the complex immune system against Vibrio is still not fully elucidated. Therefore, we conducted a transcriptome analysis on the gill from Hong Kong oysters at two time points (i.e., 12 h and 24 h after V. parahaemolyticus or PBS challenge) to identify potential immune genes against V. parahaemolyticus infection. A total of 61779 unigenes with the average length of 1221 bp were obtained, and the annotation information of 39917 unigenes were obtained from Nr, SwissProt, KEGG and COG/KOG. After a pairwise comparison between V. parahaemolyticus or PBS challenge at the two time points, three groups of differentially expressed genes induced by V. parahaemolyticus were captured and analyzed. GO and KEGG analyses showed that multiple immune-related genes played an important role in pathogen infection, including HSP70, PCDP3 and TLR4. Furthermore, genes annotation indicated that LITAF, TNFSF10, Duox2 and big defensin family are also involved in immune regulation. Our study provides a reference for further exploration the molecular mechanism that defenses the pathogen infection regarding the identified immune-related genes in Hong Kong oysters.

Preclinical study of additive manufactured plates with shortened lengths for complete mandible reconstruction: Design, biomechanics simulation, and fixation stability assessment.

BACKGROUND: A combination of short titanium plates fabricated using additive manufacturing (AM) provides multiple advantages for complete mandible reconstruction, such as the minimisation of inherent implant deformation formed during AM and the resulting clinical impact, as well as greater flexibility for surgical operation. However, the biomechanical feasibility of this strategy is still unclear, and therefore needs to be explored. METHOD: Three different combinations of short mandible reconstruction plates (MRPs) were customised considering implant deformation during the AM process. The resulting biomechanical performance was analysed by finite element analysis (FEA) and compared to a conventional single long MRP. RESULTS: The combination of a long plate and a short plate (Design 3 [LL61 mm/RL166 mm]) shows superior biomechanical properties to the conventional single long plate (Design 1 [TL246 mm]) and reveals the most reliable fixation stability among the three designs with short plates. Compared to conventional Design 1, Design 3 provides higher plate safety (maximum tensile stress on plates reduced by 6.3%), lower system fixation instability (relative total displacement reduced by 41.4%), and good bone segment stability (bone segment dislocation below 42.1 µm) under masticatory activities. CONCLUSIONS: Preclinical evidence supports the biomechanical feasibility of using short MRPs for complete mandible reconstruction. Furthermore, the results could also provide valuable information when treating other large-sized bone defects using short customised implants, expanding the potential of AM for use in implant applications.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Actinopyga lecanora (Jaeger, 1833) (Holothuriida: Holothuriidae).

The white-bottomed sea cucumber, Actinopyga lecanora, is a valuable inshore fisheries resource which is famous for its high nutrition and pharmacological compounds. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in the genus Actinopyga have not been completely resolved yet. Moreover, there remains a complex of cryptic species within Actinopyga, many of which are incorrectly assigned within the family Holothuriidae. In this study, we report the complete mitochondrial genome of A. lecanora. The mitogenome has 15,568 base pairs (63.40% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study offers useful mitogenome data for future phylogenetic and taxonomic classification of Holothuriidae.

Biomechanical comparison of locking and non-locking patient-specific mandibular reconstruction plate using finite element analysis.

Patient-specific mandibular reconstruction plate (PSMRP), as one of the patient-specific implants (PSIs), offers a host of benefits to mandibular reconstruction. Due to the limitation of fabricating screw hole threads in the PSMRP, 3D printed PSMRP is applied to the non-locking system directly in the mandibular reconstruction with bone graft regardless of the locking system. Since the conventional manual-bending reconstruction plate (CMBRP) provides better fixation in the locking system, it needs to be validated whether the locking PSMRP performs better than the non-locking PSMRP in the patient-specific mandibular reconstruction. Thereupon, the purpose of this study was to compare the biomechanical behavior between the locking and non-locking PSMRP. Finite element analysis (FEA) was used to conduct the biomechanical comparison between the locking PSMRP and non-locking PSMRP by simulating the momentary incisal clenching through static structural analysis. Mandible was reconstructed through the virtual surgical planning, and subsequently a 3D model of mandibular reconstruction assembly, including reconstructed mandible, PSMRP, and fixation screws, was generated and meshed for the following FEA simulations. In the form of equivalent von Mises stress, equivalent elastic strain, and total deformation, the locking PSMRP demonstrated its higher strengths of preferable safety, desirable flexibility, and anticipated stability compared with the non-locking PSMRP, indicated by much lower maximum stress, lower maximum strain and equivalent displacement. Locking PSMRP/screw system provides a better fixation effect to the patient-specific mandibular reconstruction than the non-locking one as a result of its productive fixation nature. FEA plays a paramount role in pre-validating the design of PSMRP through the biomechanical behavior evaluation in static structural analysis.

The first complete mitochondrial genome of macroparasite Crassicauda magna (Nematoda: Spirurida) from Neophocoena sunameri in ningbo, China.

Members of the genus Crassicauda (Nematoda: Spirurida) are macroparasites infect the body tissues of whales and dolphins. However, limited information is available on morphological descriptions and phylogenetic studies of the worms. In present study, we report the first complete mitochondrial genome of Crassicauda magna from Neophocoena sunameri in Ningbo, Zhejiang Provence, China. The mitogenome has 13,605 base pairs (74.97% A + T content) and is made up of a total of 36 genes (12 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs). This study will provide useful molecular information for addressing taxonomic and evolutionary issues in Crassicauda sp..