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PLoS Genetics Dec 2023Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome...
Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.
Topics: Animals; Humans; Glioblastoma; Genome; Astacoidea; Genomics; Biological Evolution; Mutation
PubMed: 38096267
DOI: 10.1371/journal.pgen.1011085 -
Chemosphere Dec 2023This study investigated the toxicity of polyethylene microplastics (MPs; <0.02 mm) and CuSO4, alone and in combination, on the freshwater crayfish Pontastacus...
Single and combined effects of CuSO and polyethylene microplastics on biochemical endpoints and physiological impacts on the narrow-clawed crayfish Pontastacusleptodactylus.
This study investigated the toxicity of polyethylene microplastics (MPs; <0.02 mm) and CuSO4, alone and in combination, on the freshwater crayfish Pontastacus leptodactylus. In this study, the crayfish were exposed to PE-MPs (0.0, 0.5, and 1 mg L) and CuSO4·5H2O (0.0, 0.5, and 1 mg L) for a period of 28 days. Next, multi-biomarkers, including biochemical, immunological, and oxidative stress indicators were analyzed. Results showed that co-exposure to PE-MPs and CuSO4 resulted in increased aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), and decreased alkaline phosphatase (ALP), butyrylcholinesterase (BChE), and gamma-glutamyl-transferase (GGT). Triglycerides, cholesterol, glucose, and albumin content also increased. Although no significant change was observed in lysozyme and phenoloxidase activities in crayfish co-exposed to 0.5 mg L MPs and 0.5 mg L CuSO4, their activities were significantly decreased in other experimental groups. Oxidative stress parameters in hepatopancreas indicated increased superoxide dismutase (SOD), glutathione peroxidase (GPx), and in malondialdehyde (MDA) levels, but decreased catalase (CAT), glucose 6-phosphate dehydrogenase (G6PDH), and cellular total antioxidant (TAC). Results showed that the sub-chronic toxicity of CuSO4 was confirmed. The study confirmed the toxicity of CuSO4 and found that higher concentrations led to more severe effects. Co-exposure to PE-MPs and CuSO4 primarily compromised the endpoints, showing increased toxicity when both pollutants were present in higher concentrations. The activities of POX, LYZ, ALP, GGT, LDH, and CAT were suppressed by both CuSO4 and MPs. However, a synergistic increase was observed in other measured biomarkers in crayfish co-exposed to CuSO4 and MPs.
Topics: Animals; Microplastics; Polyethylene; Plastics; Astacoidea; Butyrylcholinesterase; Antioxidants; Oxidative Stress; Glucose; Biomarkers
PubMed: 37865200
DOI: 10.1016/j.chemosphere.2023.140478 -
International Journal of Molecular... Jul 2023To enhance the management and protection of crayfish genetic diversity and germplasm resources in (), a common species of () was used as a control group to compare the...
To enhance the management and protection of crayfish genetic diversity and germplasm resources in (), a common species of () was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus.
Topics: Animals; Genome, Mitochondrial; Astacoidea; Phylogeny; NAD; Sequence Analysis, DNA
PubMed: 37511042
DOI: 10.3390/ijms241411282 -
Applied Microbiology and Biotechnology Dec 2024The intestinal microbiota interacts with the host and plays an important role in the immune response, digestive physiology, and regulation of body functions. In...
The intestinal microbiota interacts with the host and plays an important role in the immune response, digestive physiology, and regulation of body functions. In addition, it is also well documented that the intestinal microbiota of aquatic animals are closely related to their growth rate. However, whether it resulted in different sizes of crayfish in the rice-crayfish coculture model remained vague. Here, we analyzed the intestinal microbiota characteristics of crayfish of three sizes in the same typical rice-crayfish coculture field by high-throughput sequencing technology combined with quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme activity, investigating the relationship between intestinal microbiota in crayfish and water and sediments. The results showed that the dominant intestinal microbiota of crayfish was significantly different between the large size group (BS), normal size group (NS), and small size group (SS), where Bacteroides and Candidatus_Bacilloplasma contributed to the growth of crayfish by facilitating food digestion through cellulolysis, which might be one of the potential factors affecting the difference in sizes. Follow-up experiments confirmed that the activity of lipase (LPS) and protease was higher in BS, and the relative expression of development-related genes, including alpha-amylase (α-AMY), myocyte-specific enhancer factor 2a (MEF2a), glutathione reductase (GR), chitinase (CHI), and ecdysone receptor (EcR), in BS was significantly higher than that in SS. These findings revealed the intestinal microbiota characteristics of crayfish of different sizes and their potential impact on growth, which is valuable for managing and manipulating the intestinal microbiota in crayfish to achieve high productivity in practice. KEY POINTS: • Significant differences in the dominant microflora of BS, NS, and SS in crayfish. • Cellulolysis might be a potential factor affecting different sizes in crayfish. • Adding Bacteroides and Candidatus_Bacilloplasma helped the growth of crayfish.
Topics: Animals; Gastrointestinal Microbiome; Astacoidea; Microbiota; Seafood; Bacteroides; Oryza
PubMed: 38204126
DOI: 10.1007/s00253-023-12914-5 -
Proceedings of the National Academy of... Feb 2024GABA receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust...
GABA receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the "Flash and Freeze-fracture" method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.
Topics: Animals; Receptors, GABA-B; Habenula; Astacoidea; Presynaptic Terminals; Caffeine; Neurotransmitter Agents; gamma-Aminobutyric Acid
PubMed: 38346189
DOI: 10.1073/pnas.2301449121 -
Genes Dec 2023is the most widely distributed freshwater shrimp in China, with important economic value and great potential for development. The forkheadboxL2 () gene has been found...
is the most widely distributed freshwater shrimp in China, with important economic value and great potential for development. The forkheadboxL2 () gene has been found to be involved in the reproductive development of many crustaceans. To understand the role of the gene in the gonad development of , we designed CDS-specific primers for the () gene and cloned its CDS sequence using RT-PCR. The nucleotide and protein sequence information was then analyzed through bioinformatics analysis. The expression and subcellular localization of in various tissues were detected using qRT-PCR and in situ hybridization. The effects of knockdown on gonad development were investigated using RNA interference. The results showed that the CDS length of the gene was 1614 bp and encoded 537 amino acids. Protein sequence comparison and phylogenetic analysis showed that was the closest relative to Crayfish. qRT-PCR analysis indicated that the expression level of in the testis was significantly higher (>40 fold) than that in the ovary ( < 0.01). The in situ hybridization results showed that was expressed in both the cytoplasm and the nucleus of egg cells, and that the expression was strongest in egg cells at the early stage of yolk synthesis, while weak in the secondary oocytes. The positive signal was strongest in the spermatocyte nucleolus, while only a trace signal was observed in the cytoplasm. After interfering with the gene using dsRNA, the expression of in the RNA interference group was significantly lower than that in the control group, and this interference effect lasted for one week. Moreover, the gonad index of the experimental group was significantly lower than that of the control group ( < 0.05) after 10 days of cultivation following knockdown. The expression levels of the and genes, which are related to gonad development, decreased significantly after gene interference. The results suggest that the gene is involved in the growth and development of gonads, particularly in the development of testis, and is related to the early development of oocytes. This study provides a theoretical basis for the artificial breeding of .
Topics: Male; Animals; Female; Astacoidea; Phylogeny; Amino Acid Sequence; Polymerase Chain Reaction; Cloning, Molecular
PubMed: 38137012
DOI: 10.3390/genes14122190 -
Toxins Jul 2023Bacterial lipopolysaccharide (LPS) in the aquatic environment has been reported to cause diseases in red swamp crayfish (). In addition, deoxynivalenol (DON) is one of...
Bacterial lipopolysaccharide (LPS) in the aquatic environment has been reported to cause diseases in red swamp crayfish (). In addition, deoxynivalenol (DON) is one of the primary mycotoxins found in aquaculture. However, the potential synergistic toxic effects of LPS and DON on crayfish are yet to be fully elucidated. In this study, crayfish were exposed to LPS (1 mg kg), DON (3 mg kg), and their combination (1 mg kg LPS + 3 mg kg DON, L+D) for a duration of six days. Co-exposure to LPS and DON exhibited the lowest survival rate compared to the control or individual treatments with LPS or DON alone. In the initial stage of the experiment, the combined treatment of LPS and DON showed a more pronounced up-regulation of antioxidant and immune-related enzymes in the sera compared to the other treatment groups, with a fold change ranging from 1.3 to 15. In addition, the (L+D) treatment group showed a down-regulation of immune-related genes, as well as Toll pathway-related genes in the hepatopancreas compared to LPS or DON. Moreover, the (L+D) treatment group demonstrated a 100% incidence of histopathological changes in the hepatopancreas, which were significantly more severe compared to the other three groups. In conclusion, our study provides physiological and histopathological evidence that the co-exposure to LPS and DON exerted synergistic toxic effects on crayfish. The observed effects could potentially hinder the development of the crayfish aquaculture industry in China.
Topics: Animals; Antioxidants; Astacoidea; Lipopolysaccharides; Immunity
PubMed: 37624236
DOI: 10.3390/toxins15080479 -
Scientific Reports Jul 2023In this study, we experimentally evaluated how the feeding behaviour of marbled crayfish Procambarus virginalis is influenced by cues from conspecifics and the round...
In this study, we experimentally evaluated how the feeding behaviour of marbled crayfish Procambarus virginalis is influenced by cues from conspecifics and the round goby Neogobius melanostomus, a fish predator, in tanks that permitted chemical communication but not visual recognition. We used four experimental groups with different combinations in two sub-tanks. The first sub-tank always contained a crayfish and prey (40 individuals of the water louse Asellus aquaticus). The other sub-tanks were set up as follows: (i) empty, serving as a control (C); (ii) with a conspecific crayfish (Cr); (iii) with a round goby (G) to simulate predator-only odour; and (iv) a round goby and three small conspecific crayfish (G + Cr) to simulate the presence of a predator and/or the alarm odour. Two sub-treatments were defined for the fourth group, categorised as 'injured' or 'not injured' depending on whether prey crayfish were visibly injured or not, respectively. We observed a significant decline in the consumption of water lice in the G and G + Cr treatments compared to the C and Cr treatments (up to 47% on average). There were no significant differences in consumption between the G and G + Cr treatments, or C and Cr treatments. No significant differences in food consumption parameters were detected between sub-treatments with 'injured' and 'not injured' conspecific crayfish. Knowledge of modifications in the feeding behaviour of marbled crayfish in the presence of round goby (and fish predators in general) is essential for ecologists attempting to understand the changes and impacts occurring in invaded freshwater ecosystems.
Topics: Animals; Ecosystem; Astacoidea; Cues; Fishes; Perciformes; Water; Predatory Behavior
PubMed: 37507522
DOI: 10.1038/s41598-023-39406-w -
Journal of Invertebrate Pathology Nov 2023The parasitic oomycete Aphanomyces astaci is the causative agent of crayfish plague, a devastating disease for European freshwater crayfish. Species specific...
The parasitic oomycete Aphanomyces astaci is the causative agent of crayfish plague, a devastating disease for European freshwater crayfish. Species specific quantitative real-time PCR (qPCR) can offer rapid detection of the pathogen. However, the well established A. astaci qPCR assay recommended by the World Organization for Animal Health (WOAH) amplifies the recently described Aphanomyces fennicus. Consequently, false-positive results may occur. This calls for the improvement of the established species specific A. astaci qPCR assay in order to avoid amplifying A. fennicus while screening for A. astaci. We developed an improved species specific A. astaci qPCR assay and validated the assay across three laboratories, using established procedures including different qPCR master mixes for each respective laboratory. Genomic DNA from A. astaci, A. fennicus and closely related Aphanomyces spp. was analysed and compared with both the improved and established assay. Additionally, DNA from crayfish tissue and environmental samples were analysed with both assays. The improved assay showed similar sensitivity with the established assay for all sample types, while proving highly specific for A. astaci avoiding amplification of A. fennicus and the other tested Aphanomyces spp. Environmental DNA (eDNA) samples collected at River Lierelva in Norway amplified with the established assay, but not with the improved assay indicating false positive. We were able to sequence a 530 bp fragment of the ITS region from these eDNA samples and the consensus sequence showed 99.9-100 % pairwise identity with A. fennicus and 97.2-98 % pairwise identity with A. astaci, suggesting that the occurrence of A. fennicus is not limited to Finland, where it was first discovered.
Topics: Animals; Aphanomyces; DNA; Real-Time Polymerase Chain Reaction; Norway; Astacoidea; DNA, Environmental
PubMed: 37863282
DOI: 10.1016/j.jip.2023.108008 -
Scientific Reports Dec 2023This study investigated the dietary effects of coated L-ascorbic acid (LA) on growth, feed utilization, survival, serum biochemical indices, immunity, antioxidant...
Effects of L-ascorbic acid on growth, non-specific immunity, antioxidant capacity, and intestinal and hepatopancreatic histology of red swamp crayfish, Procambarus clarkii.
This study investigated the dietary effects of coated L-ascorbic acid (LA) on growth, feed utilization, survival, serum biochemical indices, immunity, antioxidant capacity, and intestinal and hepatopancreatic histology of the pre-adult red swamp crayfish. Four isoproteinous and isolipidic diets were formulated to contain several LA levels as 0, 1300, 1600, and 1900 mg/kg and designated as control (LA0), LA13, LA16, and LA19, respectively. However, the analyzed LA concentrations in diets were 0.00, 199.57, 360.45, and 487.50 mg/kg in LA0, LA13, LA16, and LA19, respectively. Triplicate treatments of crayfish (21.60 ± 0.14 g) were fed the test diets and reared in fiberglass tanks with a density of 20 individuals per each for eight weeks. Results revealed that all LA treatments had significantly enhanced growth performance compared to the control. Of interest, the LA16 treatment recorded the highest final tank biomass, biomass gain, total feed intake, condition factor, and muscle yield among the other treatments. The tank feed conversion ratio was significantly decreased in LA treatments compared to the control. Moreover, dietary LA16 and LA19 had significantly higher survival rates (93.3%) compared to (85.0%) in the LA0 group. All dietary doses of LA significantly increased serum parameters (total protein, albumin, globulin, lysozyme activity) and respiratory burst activity compared to the LA0 treatment. Dietary LA16 significantly boosted the hepatopancreatic antioxidant capacity, manifested by decreased malondialdehyde concentrations, increased catalase, superoxide dismutase, and glutathione peroxidase enzyme activities, and reduced glutathione content compared to the LA-free diet. A normal histoarchitecture of the hepatopancreatic tubules was found in all LA treatments except with some minor degenerative changes in the tubular lumen, and hepatopancreatic cells associated with enlarged nuclei were found in the LA19. However, normal intestinal histoarchitecture was found in all treatments with no recorded intestinal lesions. Of interest, the polynomial regression performed on the analyzed LA concentrations suggested that 380 mg/kg would be suitable to provide maximal biomass gain for pre-adult crayfish. In conclusion, results revealed that coated LA could enhance the growth, immunity, and antioxidant capacity of pre-adult red swamp crayfish, suggesting its potential as a functional and necessary micronutrient for crayfish diets.
Topics: Animals; Humans; Antioxidants; Astacoidea; Dietary Supplements; Immunity, Innate; Ascorbic Acid; Diet; Animal Feed
PubMed: 38052930
DOI: 10.1038/s41598-023-48609-0