Development of a non-programmable sperm cryopreservation technique in dwarf surfclams Mulinia lateralis–a potential model species for bivalve research

Sperm cryopreservation technique has been published in many farmed bivalve species. One of the key factors preventing its application in aquaculture and/or cryobanking is the knowledge gap on the performance of resultant progeny at late developmental stages and subsequent generations. An effective strategy to overcome these challenges is to use a model species with a short generation interval, such as the dwarf surfclam Mulinia lateralis (three months). This study evaluated the parameters key to the development of a non-programmable sperm cryopreservation technique in this species, with a D-stage larval rate similar to control being achieved when the sperm were cryopreserved under the conditions (cryoprotectant agent: 8% dimethyl sulfoxide; equilibration period: 10 min; rack height: 4 cm; thawing temperature: 60°C and sperm to egg ratio: 1100:1) optimized. This technique is the most common method applied in bivalve and the results from this study were all within the ranges published for other bivalve species, indicating this species would be an ideal bivalve model species for addressing cryopreservation evaluation issues that need a long extended time to collect data and/or challenging field experiments

Impact of Ocean Acidification on the Energy Metabolism and Antioxidant Responses of the Yesso Scallop (Patinopecten yessoensis)

Ocean acidification (OA), which is caused by increasing levels of dissolved CO2 in the ocean, is a major threat to marine ecosystems. Multiple lines of scientific evidence show that marine bivalves, including scallops, are vulnerable to OA due to their poor capacities to regulate extracellular ions and acid-based status. However, the physiological mechanisms of scallops responding to OA are not well understood. In this study, we evaluated the effects of 45 days of exposure to OA (pH 7.5) on the energy metabolism and antioxidant capability of Yesso scallops. Some biochemical markers related to energy metabolism (e.g., content of glycogen and ATP, activity of ATPase, lactate dehydrogenase, glutamate oxaloacetate transaminase, and glutamate-pyruvate transaminase), antioxidant capacity (e.g., reactive oxygen species level, activity of superoxide dismutase, and catalase) and cellular damage (e.g., lipid peroxidation level) were measured. Our results demonstrate that the effects of the reduced pH (7.5) on scallops are varied in different tissues. The energy reserves are mainly accumulated in the adductor muscle and hepatopancreas. Yesso scallops exhibit energy modulation by increasing lactate dehydrogenase activities to stimulate anaerobic metabolism. The highly active Na+/K+-ATPase and massive ATP consumption in the mantle and gill indicate that a large amount of energy was allocated for the ion regulation process to maintain the acid-base balance in the reduced-pH environment. Moreover, the increase in the reactive oxygen species level and the superoxide dismutase and catalase activities in the gill and adductor muscle, indicate that oxidative stress was induced after long-term exposure to the reduced-pH environment. Our findings indicate that the effects of OA are tissue-specific, and physiological homeostasis could be modulated through different mechanisms for Yesso scallops

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Mulinia lateralis, a small bivalve, is a promising model organism to facilitate studies of mollusc development. However, because of the lack of published genomic and transcriptomic resources, integrated research on the formation of larval shells in this species, which is a representative developmental process of molluscs and of great importance for larva survival, is hindered. In this study, the blastula, gastrula, trochophore larva, and D-shaped larva of M. lateralis were utilized for generating a comprehensive full-length transcriptome through Pacific BioSciences (PacBio) isoform sequencing (Iso-seq) and Illumina RNA-Seq. A total of 238,919 full-length transcripts with an average length of 3,267 bp and 121,424 annotated genes were obtained. Illumina RNA-Seq data analysis showed that 4,512, 10,637, and 17,829 differentially expressed genes (DEGs) were obtained between the two adjacent developmental stages. Functional annotation and enrichment analysis revealed the specific function of genes in shell biomineralization during different developmental stages. Twelve genes that may be involved in the formation of the larval shell of M. lateralis were identified, including insoluble shell matrix protein-encoding gene 1 (ISMP1), ISMP2, ISMP5, chitin synthase, tyrosinase, chitin-binding protein, collagen and pu14 involved in shell matrix deposition, and carbonic anhydrase, solute carrier family 4 member 8 (slc4a8), EF-hand, and a calmodulin coding gene C-2442 participated in ion transportation. In addition, calcium ion binding function, calcium signaling pathway, and endocrine and other factor-regulated calcium reabsorption pathways were significantly enriched. Weighted gene correlation network analysis (WGCNA) identified two modules related to biomineralization and larval shell formation, and slc4a8 and ring finger protein 41 (rnf41) were key hub genes that may be involved in this process. Moreover, it could be implied that the process of ion transport occurs earlier than the deposition of the shell matrix. This work provided a clear view of the transcriptome for M. lateralis and will be valuable in elucidating the mechanisms of larval shell formation as well as other developmental processes in molluscs

Molecular cloning and characterization of PtrLAR3, a gene encoding leucoanthocyanidin reductase from Populus trichocarpa, and its constitutive expression enhances fungal resistance in transgenic plants

The flavonoid-derived proanthocyanidins (PAs) are one class of the major defence phenolics in poplar leaves. Transcriptional activation of PA biosynthetic genes, resulting in PA accumulation in leaves, was detected following infection by the fungal Marssonina brunnea f.sp. multigermtubi using digital gene expression analysis. In order to study PA biosynthesis and its induction by fungi, a putative leucoanthocyanidin reductase gene, PtrLAR3, was isolated from Populus trichocarpa. Sequence comparison of PtrLAR3 with other known leucoanthocyanidin reductase proteins revealed high amino acid sequence similarity. Semi-quantitative reverse-transcription (RT) PCR and quantitative real-time PCR analysis demonstrated that PtrLAR3 was expressed in various tissues and the highest level of expression was observed in roots. Overexpression of PtrLAR3 in Chinese white poplar (Populus tomentosa Carr.) led to a significant plant-wide increase in PA levels. In vitro assays showed that crude leaf extracts from 35S:PtrLAR3 transformants were able to inhibit significantly the hyphal growth of M. brunnea f.sp. multigermtubi compared to the extracts from control plants. The transgenic 35S:PtrLAR3 poplar plants displayed a significant (P < 0.05) reduction in their disease symptoms compared with the control. RT-PCR analysis showed that PtrLAR3 expression was up-regulated in all transformants. These results suggested that constitutive expression of endogenous PtrLAR3 could be exploited to improve resistance to fungal pathogens in poplar

Integrated Profiling of MicroRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma

Background: With the advent of second-generation sequencing, the expression of gene transcripts can be digitally measured with high accuracy. The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC) using massively parallel sequencing technology. Methodology: The expression of mRNAs and miRNAs were analyzed in tumor tissues and matched normal adjacent tissues obtained from 10 ccRCC patients without distant metastases. In a prevalence screen, some of the most interesting results were validated in a large cohort of ccRCC patients. Principal Findings: A total of 404 miRNAs and 9,799 mRNAs were detected to be differentially expressed in the 10 ccRCC patients. We also identified 56 novel miRNA candidates in at least two samples. In addition to confirming that canonical cancer genes and miRNAs (including VEGFA, DUSP9 and ERBB4; miR-210, miR-184 and miR-206) play pivotal roles in ccRCC development, promising novel candidates (such as PNCK and miR-122) without previous annotation in ccRCC carcinogenesis were also discovered in this study. Pathways controlling cell fates (e. g., cell cycle and apoptosis pathways) and cell communication (e. g., focal adhesion and ECM-receptor interaction) were found to be significantly more likely to be disrupted in ccRCC. Additionally, the results of the prevalence screen revealed that the expression of a miRNA gene cluster located on Xq27.3 was consistently downregulated in at least 76.7% of similar to 50 ccRCC patients. Conclusions: Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC

Comparative mRNA and microRNA Expression Profiling of Three Genitourinary Cancers Reveals Common Hallmarks and Cancer-Specific Molecular Events

Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or therapeutic applications

A Systematic Analysis on DNA Methylation and the Expression of Both mRNA and microRNA in Bladder Cancer

Background: DNA methylation aberration and microRNA (miRNA) deregulation have been observed in many types of cancers. A systematic study of methylome and transcriptome in bladder urothelial carcinoma has never been reported. Methodology/Principal Findings: The DNA methylation was profiled by modified methylation-specific digital karyotyping (MMSDK) and the expression of mRNAs and miRNAs was analyzed by digital gene expression (DGE) sequencing in tumors and matched normal adjacent tissues obtained from 9 bladder urothelial carcinoma patients. We found that a set of significantly enriched pathways disrupted in bladder urothelial carcinoma primarily related to "neurogenesis" and "cell differentiation" by integrated analysis of -omics data. Furthermore, we identified an intriguing collection of cancer-related genes that were deregulated at the levels of DNA methylation and mRNA expression, and we validated several of these genes (HIC1, SLIT2, RASAL1, and KRT17) by Bisulfite Sequencing PCR and Reverse Transcription qPCR in a panel of 33 bladder cancer samples. Conclusions/Significance: We characterized the profiles between methylome and transcriptome in bladder urothelial carcinoma, identified a set of significantly enriched key pathways, and screened four aberrantly methylated and expressed genes. Conclusively, our findings shed light on a new avenue for basic bladder cancer research

MicroRNA-150 predicts a favorable prognosis in patients with epithelial ovarian cancer, and inhibits cell invasion and metastasis by suppressing transcriptional repressor ZEB1.

MicroRNA (miR)-150 has been reported to be dramatically downregulated in human epithelial ovarian cancer (EOC) tissues and patients' serum compared to normal controls. This study aimed to investigate clinical significance and molecular mechanisms of miR-150 in EOC. In the current study, quantitative real-time PCR analysis showed that miR-150 was significantly downregulated in human EOC tissues compared to normal tissue samples. Then, we demonstrated the significant associations of miR-150 downregulation with aggressive clinicopathological features of EOC patients, including high clinical stage and pathological grade, and shorter overall and progression-free survivals. More importantly, the multivariate analysis identified miR-150 expression as an independent prognostic biomarker in EOC. After that, luciferase reporter assays demonstrated that Zinc Finger E-Box Binding Homeobox 1 (ZEB1), a crucial regulator of epithelial-to-mesenchymal transition (EMT), was a direct target of miR-150 in EOC cells. Moreover, we found that the ectopic expression of miR-150 could efficiently inhibit cell proliferation, invasion and metastasis by suppressing the expression of ZEB1. Furthermore, we also observed a significantly negative correlation between miR-150 and ZEB1 mRNA expression in EOC tissues (rs = -0.45, P<0.001). In conclusion, these findings offer the convincing evidence that aberrant expression of miR-150 may play a role in tumor progression and prognosis in patients with EOC. Moreover, our data reveal that miR-150 may function as a tumor suppressor and modulate EOC cell proliferation, and invasion by directly and negatively regulating ZEB1, implying the re-expression of miR-150 might be a potential therapeutic strategy for EOC

Experimental investigation on application potential of phase change assisted direct ventilation cooling system for Gui'an data center

© 2024 Published by Elsevier Ltd. This is the accepted manuscript version of an article which has been published in final form at https://doi.org/10.1016/j.applthermaleng.2024.123932Cooling technology using phase change material (PCM) assisted direct ventilation has demonstrated significant energy-saving potential for data centers in regions with large temperature differences between day and night. However, research on this technology in data centers remains limited. This article presents the design of a novel phase change ventilation device (PCVD) utilizing PCM, and experimental studies are conducted to analyze both the charging and discharging process of the device. The study examines the influence of four control parameters, such as inlet temperature, inlet air speed, the number and thickness of phase change plates (PCP), on the cooling performance and evaluates its applicability in data centers. The results indicate that: (1) The device is capable of reducing air temperature by 1.15-2.23℃ within 8 hrs. (2) The cooling effect of a 3 cm thick PCP is 0.2-0.5℃ greater than that of a 2 cm thick PCP. (3) The temperature difference between the inlet and outlet of the PCVD increases as the inlet temperature and number of PCP increase, but decreases with the air inlet speed increases. (4) In Gui'an, from June to September, the average usage time of PCM-assisted direct ventilation can exceed 300 h, resulting in nearly 70% reduction in mechanical cooling consumption.Peer reviewe