A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis.

BACKGROUND: The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis. RESULTS: The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers. CONCLUSIONS: These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.

Genome Identification and Expression Profiles in Response to Nitrogen Treatment Analysis of the Class I CCoAOMT Gene Family in Populus.

Lignin is essential for the characteristics and quality of timber. Nitrogen has significant effects on lignin contents in plants. Nitrogen has been found to affect wood quality in plantations and lignin content in plants. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is an important methyltransferase in lignin biosynthesis. However, the classification of woody plant CCoAOMT gene family members and the regulation mechanism of nitrogen are not clear. Bioinformatics methods were used to predict the members, classification, and transcriptional distribution of the CCoAOMT gene family in Populus trichocarpa. The results showed that there were five PtCCoAOMTs identified, and they could be divided into three sub-groups according to their structural and phylogenetic features. The results of tissue expression specificity analysis showed that: PtCCoAOMT1 was highly expressed in roots and internodes; PtCCoAOMT2 was highly expressed in roots, nodes, and internodes, PtCCoAOMT3 was highly expressed in stems; PtCCoAOMT4 was highly expressed in young leaves, and, PtCCoAOMT5 was highly expressed in roots. Different forms and concentrations of nitrogen had varying effects on the expression patterns of genes in different plant tissue types. The results of real-time PCR showed that the expression levels of PtCCoAOMT1 and PtCCoAOMT2 in stems increased significantly under different forms of nitrogen. PtCCoAOMT3 and PtCCoAOMT4 were induced by nitrate nitrogen in upper stems and lower leaves, respectively. PtCCoAOMT4 and PtCCoAOMT5 were induced by different concentrations of nitrate nitrogen in lower stems and roots, respectively. These results could provide valuable information for revealing the differences between functions and expression patterns of the various CCoAOMT gene family members under different forms and concentrations of exogenous nitrogen in poplar.

The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination.

BACKGROUND: Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear. RESULTS: In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events. CONCLUSIONS: Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.

Legacy and novel perfluoroalkyl substances in raw and cooked squids: Perspective from health risks and nutrient benefits.

Perfluoroalkyl substance (PFAS) existed ubiquitously in the environment and could be ingested unconsciously with food which posed a disease risk to human health. Swordtip squid (Uroteuthis edulis) is one of the most popular and highly consumed seafood worldwide, with wide distribution and abundant biomass. Therefore, it is of great importance to the health of the public by reducing the health risks of squid consumption while preserving the benefits of squid to humans. In this study, the PFAS and fatty acids in squids were tested from the southeast coastal regions of China, a major habitat for squids. Relative higher concentrations of PFAS in squid were found in the subtropical zone of southern China (mean: 15.90 ng/g·dw) compared to those of the temperate zone of northern China (mean: 11.77 ng/g·dw). The digestive system had high tissue/muscle ratio (TMR) values, and the pattern of TMR among the same carbon-chain PFAS was similar. Cooking methods have a significant contribution to eliminating PFAS (in squids). PFAS were transferred from squids to other mediums after cooking, so juice and oil should be poured out to minimize PFAS exposure into body. The result showed that squids can be regarded as a healthy food by health benefits associated with fatty acids. Estimated daily intake (EDI) had the highest level in Korea via consuming squids through cooking processes compared with other countries. Based on the assessment of the hazard ratios (HRs), there was a high exposure risk of perfluoropentanoic acid (PFPeA) via taking squids for human health. This research provided the theoretical guidance of aquatic product processing in improving nutrition and reducing harmful substances.

Cooking methods effectively alter perfluoroalkyl substances and nutrients in cultured and wild bullfrogs.

The ubiquitous distribution of perfluoroalkyl substances (PFASs) poses a threat to the health of aquatic organisms and humans. Bullfrogs are considered a popular aquatic food product in South China, providing high protein and tasty cuisine; however bullfrogs have been shown to contain significant concentrations of PFASs. However, the risk-benefit ratios of PFASs and nutrient contents in cooked bullfrogs are not well understood. PFASs and nutrients were investigated in raw and cooked specimens of cultured and wild bullfrogs in this study. Novel PFASs showed higher detection levels and accumulation in wild bullfrogs than in cultured bullfrogs. Potential factors such as fat and fatty acid ratio affected PFASs accumulation in different tissues and by different cooking methods of bullfrogs. All cooking methods can reduce PFASs in edible tissues while significantly enhancing the nutritive value index (NVI) compared to raw bullfrogs. Steaming was the most effective way to reduce PFASs (rate of reduction was over 66%) and resulted in a lower risk of contributing to arteriosclerosis than other cooking methods assessed by atherogenicity index (AI) values. Cultured bullfrogs instead of wild bullfrogs were recommended for human consumption, and steaming was regarded as a better cooking method in terms of risk-benefit concerns. Overall, this work provides quantitative analysis of cooking methods that alter PFASs and nutrients in bullfrogs.

Analysis of the energy source at the early stage of poplar seed germination: verification of Perl's pathway.

Adenosine triphosphate (ATP) is produced at the early stage of seed germination and provides the energy for metabolism. The source of ATP in seeds may be Perl's pathway, but this has not yet been confirmed. In this study, using germinating seeds of poplar as the experimental materials, the transcript levels of genes related to Perl's pathway were determined by real-time PCR. The activities of enzymes in Perl's pathway were also determined. The results were verified by comparison with RNA-Seq and metabolomics data. The results showed that there were high transcript levels of some genes encoding malate dehydrogenase (MDH), phosphoenolpyruvate carboxykinase (PEPCK), pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH), and pyruvate kinase (PK) at the early stage of germination (0.75 h). The enzymes MDH, PEPCK, PK, PDC, and ADH showed peaks in activity at around 0.75 h and 6 h during germination. The oxaloacetate concentration was high in poplar seeds at the early stage of germination. This study provides experimental data showing that Perl's pathway participates in supplying energy during the early stages of poplar seed germination, and lays the foundation for further studies on the complex metabolic processes that function during seed germination.

Toll-like receptor 4 promotes high glucose-induced catabolic and inflammatory responses in chondrocytes in an NF-κB-dependent manner.

Diabetes is an independent risk factor for knee osteoarthritis (OA), and hyperglycaemia-induced inflammation is considered to play an important role in their connection. The Toll-like receptor 4 (TLR4) regulates inflammatory responses in several pathological conditions including diabetes and OA. However, its role in diabetes-associated OA is poorly understood. In this study, we found that TLR4 expression was higher in OA cartilage from patients with type 2 diabetes mellitus (T2DM) than that from non-T2DM patients. Similarly, its expression was induced in primary mouse chondrocytes treated with high glucose, which suggests that TLR4 upregulation in T2DM-associated OA cartilage may originate from hyperglycaemia stimulation. We further discovered that TLR4 promoted high glucose-induced catabolic and inflammatory responses in chondrocytes, and mechanistically, these effects could be explained by the exacerbated activation of the transcription factor nuclear factor kappa B (NF-κB) pathway, since its inhibition by Bay 11-7082 abrogated TLR4 effects on high glucose-treated chondrocytes. Taken together, these findings may reveal a promotive role of TLR4 in regulating hyperglycaemia-induced catabolism and inflammation in T2DM-associated OA, and also implicate that TLR4 inhibition might be of therapeutic significance in treating T2DM-associated OA.

Unidirectionally thoracoscopic resection of lingual segment of the left upper pulmonary lobe.

A patient with adenocarcinoma in situ was reported to undergo unidirectionally thoracoscopic resection of lingual segment of the left upper pulmonary lobe and lymphadenectomy in the order of the lingual segmental vein, the lingual segmental bronchus, the lingual segmental artery, and the pulmonary tissues of the lingual segment in turn. As the concepts of adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) are defined in the latest international classification of lung adenocarcinoma, pulmonary segmentectomy has been initially used in some multi-center clinical studies to treat these early lung cancer lesions. Pulmonary segmentectomy is currently one of the most minimally invasive lung surgeries, with its unique technical essentials different from those of pulmonary lobectomy. Some studies have shown that pulmonary segmentectomy for early lung cancer, especially for tumors with a diameter of less than 2 cm can achieve a similar long-term survival rate as pulmonary lobectomy, yet its effectiveness and safety should be confirmed in further large-scale prospective studies.

Unidirectionally progressive resection of left upper pulmonary lobe under video-assisted thoracoscopy.

The case is a nodule in the upper left lobe, and intraoperative frozen section pathological diagnosis on the removed nodule confirmed well differentiated mucinous adenocarcinoma. Unidirectionally progressive resection of the left upper pulmonary lobe under video-assisted thoracoscopy is selected as the surgical method. Right below the operation hole, surgeons gradually advanced in one direction, and dissociated and divided in such order: the upper left pulmonary vein, the upper left lobe bronchus, the upper left pulmonary arterial branches and the fissures. Endoscopic linear cutters and hem-o-lok clip applicator were used to deal with the blood vessels, bronchus, and under-differentiated fissures. At last, the removed upper left lobe was put into a size eight sterile glove and taken out through the main operation hole. General anesthesia with double-lumen endotracheal intubation is used. The patient took a 90 degree decubitus on his contralateral side. The surgeons were on the ventral side of the patient, and operated with endoscope apparatus under the monitor.