This work investigated the potential of metal oxide semiconductor (MOS) gas sensors for environmental monitoring of methane. Calibrations were performed under controlled conditions in the lab, and under semi-controlled conditions in the field, using a modified head space chamber set-up. Concentrations up to ±300 ppm methane were tested. The relationship between sensor conductance and methane concentrations could be very well described using principles from adsorption theory. The adjustable parameters were background conductance G0, a sensitivity constant S and a non-ideality coefficient n, where n has a non-rational value between 0 and 1. Sensor behaviour was very different in dry air than in humid air, with the background conductance increasing approximately tenfold and sensitivity decreasing between 20 fold and 80 fold, while the non-ideality coefficient increased from ±0.4 to ±0.6. Nevertheless, at high methane concentrations comparable conductance values were recorded in dry and humid air. The standard deviation of predicted values was 1.6 μS.for the least well described dataset. Using the corresponding calibration curve, a detection limit of 11 ppm is calculated for humid ambient air. This values suggests that MOS sensor are adequately sensitive to be used for methane detection in an agricultural context.
{"title":"Evaluation of the applicability of a metal oxide semiconductor gas sensor for methane emissions from agriculture","authors":"Bastiaan Molleman , Enrico Alessi , Fabio Passaniti , Karen Daly","doi":"10.1016/j.inpa.2023.11.001","DOIUrl":"10.1016/j.inpa.2023.11.001","url":null,"abstract":"<div><div>This work investigated the potential of metal oxide semiconductor (MOS) gas sensors for environmental monitoring of methane. Calibrations were performed under controlled conditions in the lab, and under semi-controlled conditions in the field, using a modified head space chamber set-up. Concentrations up to ±300 ppm methane were tested. The relationship between sensor conductance and methane concentrations could be very well described using principles from adsorption theory. The adjustable parameters were background conductance G<sub>0</sub>, a sensitivity constant S and a non-ideality coefficient n, where n has a non-rational value between 0 and 1. Sensor behaviour was very different in dry air than in humid air, with the background conductance increasing approximately tenfold and sensitivity decreasing between 20 fold and 80 fold, while the non-ideality coefficient increased from ±0.4 to ±0.6. Nevertheless, at high methane concentrations comparable conductance values were recorded in dry and humid air. The standard deviation of predicted values was 1.6 μS.for the least well described dataset. Using the corresponding calibration curve, a detection limit of 11 ppm is calculated for humid ambient air. This values suggests that MOS sensor are adequately sensitive to be used for methane detection in an agricultural context.</div></div>","PeriodicalId":53443,"journal":{"name":"Information Processing in Agriculture","volume":"11 4","pages":"Pages 573-580"},"PeriodicalIF":7.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135454758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tobacco (Nicotiana tabacum) plants synthesize the psychoactive pyridine alkaloid nicotine, which has sparked growing interest in reducing nicotine levels through genome editing aiming at inactivating key biosynthetic genes. Although stable transformation-mediated genome editing is effective in tobacco, its polyploid nature complicates the complete knockout of genes and the segregation of transgenes from edited plants. In this study, we developed a non-transgenic genome editing method in tobacco by delivering the CRISPR/Cas machinery via an engineered negative-strand RNA rhabdovirus vector, followed by the regeneration of mutant plants through tissue culture. Using this method, we targeted six berberine bridge enzyme-like protein (BBL) family genes for mutagenesis, which are implicated in the last steps of pyridine alkaloid biosynthesis, in the commercial tobacco cultivar Hongda. We generated a panel of 16 mutant lines that were homozygous for mutations in various combinations of BBL genes. Alkaloid profiling revealed that lines homozygous for BBLa and BBLb mutations exhibited drastically reduced nicotine levels, while other BBL members played a minor role in nicotine synthesis. The decline of nicotine content in these lines was accompanied by reductions in anatabine and cotinine levels but increases in nornicotine and its derivative myosmine. Preliminary agronomic evaluation identified two low-nicotine lines with growth phenotypes comparable to those of wild-type plants under greenhouse and field conditions. Our work provides potentially valuable genetic materials for breeding low-nicotine tobacco and enhances our understanding of alkaloid biosynthesis.
{"title":"Development of an RNA virus vector for non-transgenic genome editing in tobacco and generation of berberine bridge enzyme-like mutants with reduced nicotine content","authors":"Haiying Xiang, Binhuan Chen, Shuo Wang, Wanli Zeng, Jiarui Jiang, Weisong Kong, Haitao Huang, Qili Mi, Shuang Ni, Qian Gao, Zhenghe Li","doi":"10.1007/s42994-024-00188-y","DOIUrl":"10.1007/s42994-024-00188-y","url":null,"abstract":"<div><p>Tobacco (<i>Nicotiana tabacum</i>) plants synthesize the psychoactive pyridine alkaloid nicotine, which has sparked growing interest in reducing nicotine levels through genome editing aiming at inactivating key biosynthetic genes. Although stable transformation-mediated genome editing is effective in tobacco, its polyploid nature complicates the complete knockout of genes and the segregation of transgenes from edited plants. In this study, we developed a non-transgenic genome editing method in tobacco by delivering the CRISPR/Cas machinery via an engineered negative-strand RNA rhabdovirus vector, followed by the regeneration of mutant plants through tissue culture. Using this method, we targeted six <i>berberine bridge enzyme-like protein</i> (<i>BBL</i>) family genes for mutagenesis, which are implicated in the last steps of pyridine alkaloid biosynthesis, in the commercial tobacco cultivar Hongda. We generated a panel of 16 mutant lines that were homozygous for mutations in various combinations of <i>BBL</i> genes. Alkaloid profiling revealed that lines homozygous for <i>BBLa</i> and <i>BBLb</i> mutations exhibited drastically reduced nicotine levels, while other <i>BBL</i> members played a minor role in nicotine synthesis. The decline of nicotine content in these lines was accompanied by reductions in anatabine and cotinine levels but increases in nornicotine and its derivative myosmine. Preliminary agronomic evaluation identified two low-nicotine lines with growth phenotypes comparable to those of wild-type plants under greenhouse and field conditions. Our work provides potentially valuable genetic materials for breeding low-nicotine tobacco and enhances our understanding of alkaloid biosynthesis.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"449 - 464"},"PeriodicalIF":4.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00188-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.aaf.2023.02.002
The present experimental investigation was executed to evaluate the combined effect of probiotic bacterium Bacillus coagulans along with herb Mentha piperita on histological architecture; and extent of DNA damage after challenge trial with pathogenic bacterium Aeromonas hydrophila in Catla catla. In this experiment, six dietary treatments in triplicate were formulated; C0, M3 and M6 in which M. piperita was supplemented at 0, 3, 6 g kg−1 of feed, while in dietary treatments CP, MP3 and MP6; supplementation of probiotic bacterium B. coagulans at the rate of 3000 CFU g−1 was done along with different inclusion level of M. piperita (0, 3, 6 g kg−1 of feed). Fishes were fed for 60 days on different dietary treatments. Growth performance, histological study and extent of DNA damage using comet assay was examined. Significantly (p < 0.05) high growth % gain in BW was observed in treatment MP6 followed by treatment M6. The histological analysis clearly revealed that dietary M. piperita without or with probiotic bacterium can protect the histoarchitecture of intestinal layers and liver even after challenge with A. hydrophila. Analysis of various comet parameters (tail length, olive moment, tail DNA, head DNA) affirmed that M. piperita supplemented diet can reduce the extent of DNA damage in fishes after challenge trial with A. hydrophila, however dietary supplementation of probiotic bacterium along with M. piperita can reduce the DNA damage up to larger extent confirming its combined protective effect of supplemented diets.
本实验研究旨在评估益生菌凝结芽孢杆菌和薄荷对猫鼬病原菌嗜水气单胞菌挑战试验后的组织学结构和 DNA 损伤程度的综合影响。在该实验中，共制定了六种一式三份的膳食处理：C0、M3 和 M6，其中蒌草的添加量分别为 0、3 和 6 g kg-1 饲料，而在 CP、MP3 和 MP6 膳食处理中，在添加不同水平的蒌草（0、3 和 6 g kg-1 饲料）的同时，还添加了 3000 CFU g-1 的益生菌凝结球菌。鱼类在不同的饮食处理下被喂养了 60 天。采用彗星试验对鱼类的生长性能、组织学研究和 DNA 损伤程度进行了检测。观察到 MP6 处理的体重增长百分比显著高于 M6 处理（p < 0.05）。组织学分析清楚地表明，即使在受到嗜水青虫的挑战后，不添加益生菌或添加益生菌的膳食中的蒌蒿能保护肠道层和肝脏的组织结构。对各种彗星参数（尾长、橄榄时刻、尾部 DNA、头部 DNA）的分析表明，补充瓜子黄酮的膳食可以减少鱼类在受到蚜蝇绥氏菌挑战后的 DNA 损伤程度，但在补充瓜子黄酮的同时补充益生菌可以在更大程度上减少 DNA 损伤，这证实了补充膳食的综合保护作用。
{"title":"Dietary administration of probiotic Bacillus coagulans and Mentha piperita can protect histological architecture and DNA damage in Catla catla (Hamilton, 1822)","authors":"","doi":"10.1016/j.aaf.2023.02.002","DOIUrl":"10.1016/j.aaf.2023.02.002","url":null,"abstract":"<div><div>The present experimental investigation was executed to evaluate the combined effect of probiotic bacterium <em>Bacillus coagulans</em> along with herb <em>Mentha piperita</em> on histological architecture; and extent of DNA damage after challenge trial with pathogenic bacterium <em>Aeromonas hydrophila</em> in <em>Catla catla</em>. In this experiment, six dietary treatments in triplicate were formulated; C0, M3 and M6 in which <em>M. piperita</em> was supplemented at 0, 3, 6 g kg<sup>−1</sup> of feed, while in dietary treatments CP, MP3 and MP6; supplementation of probiotic bacterium <em>B. coagulans</em> at the rate of 3000 CFU g<sup>−1</sup> was done along with different inclusion level of <em>M. piperita</em> (0, 3, 6 g kg<sup>−1</sup> of feed). Fishes were fed for 60 days on different dietary treatments. Growth performance, histological study and extent of DNA damage using comet assay was examined. Significantly (<em>p</em> < 0.05) high growth % gain in BW was observed in treatment MP6 followed by treatment M6. The histological analysis clearly revealed that dietary <em>M. piperita</em> without or with probiotic bacterium can protect the histoarchitecture of intestinal layers and liver even after challenge with <em>A. hydrophila</em>. Analysis of various comet parameters (tail length, olive moment, tail DNA, head DNA) affirmed that <em>M. piperita</em> supplemented diet can reduce the extent of DNA damage in fishes after challenge trial with <em>A. hydrophila</em>, however dietary supplementation of probiotic bacterium along with <em>M. piperita</em> can reduce the DNA damage up to larger extent confirming its combined protective effect of supplemented diets.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"9 6","pages":"Pages 948-956"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86798169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.aaf.2023.04.008
Myostatin is a member of the TGF-β superfamily and functions as a negative regulator for skeletal muscle development and growth. It has become the most targeted gene in aquaculture that used for selective breeding. Previous studies involved in genome editing in several fish species confirmed that CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) system was highly efficient with lower off-target effect, however, no reports were raised in Culter alburnus. In this study, we employed CRISPR/Cas9 gene editing system to successfully disrupt mstn gene by co-injection with Cas9 protein and the targeted sgRNA in C. alburnus. Various Indel mutations were obtained with 82% knockout efficiency in the F0 generation by PCR sequencing. In addition, mutations in mstn that induced by CRISPR/Cas9 were detected in the F1 generation by individually mating the wild-type female with the F0 generation of mstn-KO male at sexual maturity. More importantly, the body weight and length were significantly elevated in mstn± group when compared to those of the control. As expected in mstn± group, the expression level of mstn was sharply reduced, whereas a slight increase was observed in two growth-related genes (myod and myog). Moreover, higher numbers of muscle fibers were observed in mstn± group, meaning that growth performance in mstn± individuals might be represented by increasing the number of muscle fibers. Taken together, our current study successfully obtained a site-specific modification of mstn using CRISPR/Cas9 technology, and these results provided a new insight for facilitating topmouth culter genetic studies and breeding.
{"title":"CRISPR/Cas9-mediated mutation of Mstn confers growth performance in Culter alburnus juveniles","authors":"","doi":"10.1016/j.aaf.2023.04.008","DOIUrl":"10.1016/j.aaf.2023.04.008","url":null,"abstract":"<div><div>Myostatin is a member of the TGF-β superfamily and functions as a negative regulator for skeletal muscle development and growth. It has become the most targeted gene in aquaculture that used for selective breeding. Previous studies involved in genome editing in several fish species confirmed that CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) system was highly efficient with lower off-target effect, however, no reports were raised in <em>Culter alburnus</em>. In this study, we employed CRISPR/Cas9 gene editing system to successfully disrupt <em>mstn</em> gene by co-injection with Cas9 protein and the targeted sgRNA in <em>C. alburnus</em>. Various Indel mutations were obtained with 82% knockout efficiency in the F0 generation by PCR sequencing. In addition, mutations in <em>mstn</em> that induced by CRISPR/Cas9 were detected in the F1 generation by individually mating the wild-type female with the F0 generation of <em>mstn</em>-KO male at sexual maturity. More importantly, the body weight and length were significantly elevated in <em>mstn</em> <sup><em>±</em></sup> group when compared to those of the control. As expected in <em>mstn</em> <sup><em>±</em></sup> group, the expression level of <em>mstn</em> was sharply reduced, whereas a slight increase was observed in two growth-related genes (<em>myod</em> and <em>myog</em>). Moreover, higher numbers of muscle fibers were observed in <em>mstn</em> <sup><em>±</em></sup> group, meaning that growth performance in <em>mstn</em> <sup><em>±</em></sup> individuals might be represented by increasing the number of muscle fibers. Taken together, our current study successfully obtained a site-specific modification of <em>mstn</em> using CRISPR/Cas9 technology, and these results provided a new insight for facilitating topmouth culter genetic studies and breeding.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"9 6","pages":"Pages 900-907"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75635969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.aaf.2023.05.010
Simvastatin (SIM), a commonly prescribed drug for lowering serum-lipid, has been detected in many aquatic environments. Exposure to high concentrations of SIM in rats and aquatic organisms resulted in toxicity to hepatocytes and negative effects on development. However, there is a paucity of studies on the effects of long-term exposure to low concentrations of SIM on aquaculture species. This study aimed to analyze the effects of environmentally relevant concentrations (0.1 μg/L and 1 μg/L) of SIM exposure for two months on developing Mozambique tilapias. Surprisingly, the growth of male tilapias was enhanced after a 2-month SIM exposure. The analysis of testis histology revealed that after the SIM exposure, the development of the testis was delayed, and sperm production was reduced. Sequencing of testis transcriptomes showed that the exposure to SIM altered the expression of many genes related to the development of testes and spermatogenesis. These data suggest that a 2-month exposure to environmentally relevant concentrations of increases the growth of male tilapias by inhibiting sexual development of males.
{"title":"Simvastatin enhanced growth and altered testis transcriptome profiles of male tilapias","authors":"","doi":"10.1016/j.aaf.2023.05.010","DOIUrl":"10.1016/j.aaf.2023.05.010","url":null,"abstract":"<div><div>Simvastatin (SIM), a commonly prescribed drug for lowering serum-lipid, has been detected in many aquatic environments. Exposure to high concentrations of SIM in rats and aquatic organisms resulted in toxicity to hepatocytes and negative effects on development. However, there is a paucity of studies on the effects of long-term exposure to low concentrations of SIM on aquaculture species. This study aimed to analyze the effects of environmentally relevant concentrations (0.1 μg/L and 1 μg/L) of SIM exposure for two months on developing Mozambique tilapias. Surprisingly, the growth of male tilapias was enhanced after a 2-month SIM exposure. The analysis of testis histology revealed that after the SIM exposure, the development of the testis was delayed, and sperm production was reduced. Sequencing of testis transcriptomes showed that the exposure to SIM altered the expression of many genes related to the development of testes and spermatogenesis. These data suggest that a 2-month exposure to environmentally relevant concentrations of increases the growth of male tilapias by inhibiting sexual development of males.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"9 6","pages":"Pages 893-899"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88996577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.ocsci.2024.09.003
Congcong Ma , Li Zhang , Lei Wang , Qingde Huang , Qianchun Deng , Fenghong Huang , Jiqu Xu
Walnut oil (WO), known for abundant polyunsaturated fatty acids and an array of bioactive substances such as tocopherols, phytosterols, squalene, melatonin, and polyphenols, which is endowed with numerous health advantages. The primary objective of this research was to ascertain the impact of WO on cognitive deficits in learning and memory impairment mice caused by scopolamine (SCOP). The Morris water maze and the step-down avoidance test were utilized to assess the memory and learning capabilities. WO notably counteracted the detrimental effects of SCOP on learning and memory in the Morris water maze, as indicated by a reduction in escape latency and swimming distance. Likewise, WO administration led to a notably reduced number of errors in training trial and an increased latency in testing trial when compared to the SCOP group in the step-down avoidance test,. Moreover, WO activated the cholinergic system of the brain by upregulating choline acetyltransferase activity and reducing acetylcholinesterase activity. These results suggest that WO has the potential to protect against memory decline in mice, offering a promising strategy for the prevention of memory-related disorders.
核桃油（WO）以丰富的多不饱和脂肪酸和一系列生物活性物质（如生育酚、植物甾醇、角鲨烯、褪黑激素和多酚）而闻名，具有众多健康优势。本研究的主要目的是确定 WO 对东莨菪碱（SCOP）导致的学习和记忆障碍小鼠认知缺陷的影响。研究采用了莫里斯水迷宫和降阶回避测试来评估小鼠的记忆和学习能力。在莫里斯水迷宫中，WO明显抵消了SCOP对学习和记忆的不利影响，这表现在逃逸潜伏期和游泳距离的缩短上。同样，在降阶回避测试中，与 SCOP 组相比，施用 WO 可显著减少训练试验中的错误次数，增加测试试验中的潜伏期。此外，WO 还能通过上调胆碱乙酰转移酶活性和降低乙酰胆碱酯酶活性来激活大脑的胆碱能系统。这些结果表明，WO 具有防止小鼠记忆力衰退的潜力，为预防记忆相关疾病提供了一种很有前景的策略。
{"title":"Ameliorative effect of walnut oil against cognitive impairment in alzheimers type dementia in rodent","authors":"Congcong Ma , Li Zhang , Lei Wang , Qingde Huang , Qianchun Deng , Fenghong Huang , Jiqu Xu","doi":"10.1016/j.ocsci.2024.09.003","DOIUrl":"10.1016/j.ocsci.2024.09.003","url":null,"abstract":"<div><div>Walnut oil (WO), known for abundant polyunsaturated fatty acids and an array of bioactive substances such as tocopherols, phytosterols, squalene, melatonin, and polyphenols, which is endowed with numerous health advantages. The primary objective of this research was to ascertain the impact of WO on cognitive deficits in learning and memory impairment mice caused by scopolamine (SCOP). The Morris water maze and the step-down avoidance test were utilized to assess the memory and learning capabilities. WO notably counteracted the detrimental effects of SCOP on learning and memory in the Morris water maze, as indicated by a reduction in escape latency and swimming distance. Likewise, WO administration led to a notably reduced number of errors in training trial and an increased latency in testing trial when compared to the SCOP group in the step-down avoidance test,. Moreover, WO activated the cholinergic system of the brain by upregulating choline acetyltransferase activity and reducing acetylcholinesterase activity. These results suggest that WO has the potential to protect against memory decline in mice, offering a promising strategy for the prevention of memory-related disorders.</div></div>","PeriodicalId":34095,"journal":{"name":"Oil Crop Science","volume":"9 4","pages":"Pages 234-239"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142662057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genetic epistasis is a fundamental concept in genetics that describes how interactions between genes determine phenotypic traits. To enhance students' understanding and practical application of genetic epistasis, this experiment is designed and conducted using gene mutations in the adenine biosynthesis pathway of Saccharomyces cerevisiae (baker's yeast). S. cerevisiae is a classic model organism for genetic teaching experiments. In its adenine biosynthesis pathway, a mutation in the ADE2 gene leads to the accumulation of the intermediate 5'-phosphoribosylaminoimidazole (AIR), causing the cells to appear red. However, if a gene upstream of ADE2 in the adenine biosynthesis pathway (such as ADE8) is defective, the red phenotype of yeast will disappear. Conversely, a defect in a gene downstream of ADE2 (such as ADE1) does not alter the red phenotype. Therefore, ADE8 is epistatic to ADE2. In this experiment, the CRISPR-Cas9 genome editing technology is employed, allowing students to perform single knockout of ade2Δ, as well as double knockouts of ade2Δade8Δ and ade2Δade1Δ in S. cerevisiae. By observing the phenotypic changes in yeast mutants from white to red and back to white, students gain a profound understanding of the basic genetic theory of how genes determine phenotypes and the concept of epistasis in gene interactions. This experiment also enables students to master fundamental yeast genetic techniques, significantly enhancing their ability to design and conduct experiments in real research environments. This is of great significance for their future research work and academic development.
{"title":"Design and practice of educational experiments on genetic epistasis.","authors":"Yi Shi, Yao Yu, Yi-Lin Lü, Hong Lü","doi":"10.16288/j.yczz.24-248","DOIUrl":"10.16288/j.yczz.24-248","url":null,"abstract":"<p><p>Genetic epistasis is a fundamental concept in genetics that describes how interactions between genes determine phenotypic traits. To enhance students' understanding and practical application of genetic epistasis, this experiment is designed and conducted using gene mutations in the adenine biosynthesis pathway of <i>Saccharomyces cerevisiae</i> (baker's yeast). <i>S. cerevisiae</i> is a classic model organism for genetic teaching experiments. In its adenine biosynthesis pathway, a mutation in the <i>ADE2</i> gene leads to the accumulation of the intermediate 5'-phosphoribosylaminoimidazole (AIR), causing the cells to appear red. However, if a gene upstream of <i>ADE2</i> in the adenine biosynthesis pathway (such as <i>ADE8</i>) is defective, the red phenotype of yeast will disappear. Conversely, a defect in a gene downstream of <i>ADE2</i> (such as <i>ADE1</i>) does not alter the red phenotype. Therefore, <i>ADE8</i> is epistatic to <i>ADE2.</i> In this experiment, the CRISPR-Cas9 genome editing technology is employed, allowing students to perform single knockout of <i>ade2</i>Δ, as well as double knockouts of <i>ade2</i>Δ<i>ade8</i>Δ and <i>ade2</i>Δ<i>ade1</i>Δ in <i>S. cerevisiae</i>. By observing the phenotypic changes in yeast mutants from white to red and back to white, students gain a profound understanding of the basic genetic theory of how genes determine phenotypes and the concept of epistasis in gene interactions. This experiment also enables students to master fundamental yeast genetic techniques, significantly enhancing their ability to design and conduct experiments in real research environments. This is of great significance for their future research work and academic development.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 11","pages":"958-970"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Innate immune responses play a crucial role in maintaining homeostasis, their initiation closely related to pattern recognition receptors or damage-associated molecules on the surface of innate immune cells. CD209, a pattern recognition receptor on the surface of macrophages or dendritic cells, plays an important role in immune functions. However, the impact of CD209 on innate immune cells such as macrophages or neutrophils in vivo remains unclear. In this study, through multiple sequence alignment and phylogenetic tree construction, three genes homologous to human CD209 were found in zebrafish. These are cd209(Ensembl ID:ENSDARG00000029461), zgc:174904(Ensembl ID:ENSDARG00000059049) and si:dkey-187I7.2(Ensembl ID: ENSDARG00000096624).Compared to the cd209 and si:dkey-187i8.2 genes in the Ensembl database, zgc:174904 is more similar to human CD209 in sequence. Using whole-mount in situ hybridization and fluorescence co-localization experiments, it was found that zgc:174904 is mainly expressed in macrophages. Further morpholino knockdown experiments showed that knocking down zgc:174904 leads to an upregulation of M1-type macrophage-related genes and a decrease in the number of mature neutrophils, indicating that zgc:174904 is functionally more similar to CD209. These findings not only reveal the potential role of CD209 in regulating macrophage function and neutrophil development but also provide significant insights for research into the mechanisms of innate immunity.
{"title":"Identification and functional characterization of CD209 homologous genes in zebrafish.","authors":"Xiao-Jun Yang, Zhen-Han Huang, Wei Liu, Wen-Qing Zhang, Zhi-Bin Huang","doi":"10.16288/j.yczz.24-181","DOIUrl":"10.16288/j.yczz.24-181","url":null,"abstract":"<p><p>Innate immune responses play a crucial role in maintaining homeostasis, their initiation closely related to pattern recognition receptors or damage-associated molecules on the surface of innate immune cells. CD209, a pattern recognition receptor on the surface of macrophages or dendritic cells, plays an important role in immune functions. However, the impact of CD209 on innate immune cells such as macrophages or neutrophils <i>in vivo</i> remains unclear. In this study, through multiple sequence alignment and phylogenetic tree construction, three genes homologous to human CD209 were found in zebrafish. These are <i>cd209</i>(Ensembl ID:ENSDARG00000029461), <i>zgc:174904</i>(Ensembl ID:ENSDARG00000059049) and <i>si:dkey-187I7.2</i>(Ensembl ID: ENSDARG00000096624).Compared to the <i>cd209</i> and <i>si:dkey-187i8.2</i> genes in the Ensembl database, <i>zgc:174904</i> is more similar to human CD209 in sequence. Using whole-mount <i>in situ</i> hybridization and fluorescence co-localization experiments, it was found that <i>zgc:174904</i> is mainly expressed in macrophages. Further morpholino knockdown experiments showed that knocking down <i>zgc:174904</i> leads to an upregulation of M1-type macrophage-related genes and a decrease in the number of mature neutrophils, indicating that <i>zgc:174904</i> is functionally more similar to CD209. These findings not only reveal the potential role of CD209 in regulating macrophage function and neutrophil development but also provide significant insights for research into the mechanisms of innate immunity.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 11","pages":"947-957"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.aaf.2023.03.005
The community stability of coral reefs and fish is the focus of ecological monitoring of coral reefs. Among them, the realization of effective metrics of variations in reef fish communities (i.e., the combined communities of coral reefs and fish) is important for analyzing the stability of communities as well as maintaining the ecological balance of coral reefs. Based on coral reef and fish data collected at St. John's Island from 2004 to 2010, this study proposes a symbiotic graph modeling method to express the biological relationships of reef fish communities, and a Pyramid Match graph kernel method for fusing Attributes (PMA) to quantify community fluctuations to measure interannual variability of communities. The results showed that the community similarity was low in 2006, 2007, and 2008. The total coral cover rate in the study area decreased by 32.04% from 2006 to 2007 and increased by 24% in 2008. The total number of fish fell from 3780 in 2006 to 2596 in 2007 and rose to 6249 in 2008. Among them, the proportion of herbivorous fish decreased to 30.84% in 2007. Furthermore, we have combined the Louvain algorithm with the proposed PMA method to effectively identify the regions that should be prioritized for protection. Experiments were conducted on real datasets with good results, demonstrating the potential of the proposed method to assist in the analysis of community stability and identification of priority conservation areas.
{"title":"Stability analysis of reef fish communities based on symbiotic graph model","authors":"","doi":"10.1016/j.aaf.2023.03.005","DOIUrl":"10.1016/j.aaf.2023.03.005","url":null,"abstract":"<div><div>The community stability of coral reefs and fish is the focus of ecological monitoring of coral reefs. Among them, the realization of effective metrics of variations in reef fish communities (i.e., the combined communities of coral reefs and fish) is important for analyzing the stability of communities as well as maintaining the ecological balance of coral reefs. Based on coral reef and fish data collected at St. John's Island from 2004 to 2010, this study proposes a symbiotic graph modeling method to express the biological relationships of reef fish communities, and a Pyramid Match graph kernel method for fusing Attributes (PMA) to quantify community fluctuations to measure interannual variability of communities. The results showed that the community similarity was low in 2006, 2007, and 2008. The total coral cover rate in the study area decreased by 32.04% from 2006 to 2007 and increased by 24% in 2008. The total number of fish fell from 3780 in 2006 to 2596 in 2007 and rose to 6249 in 2008. Among them, the proportion of herbivorous fish decreased to 30.84% in 2007. Furthermore, we have combined the Louvain algorithm with the proposed PMA method to effectively identify the regions that should be prioritized for protection. Experiments were conducted on real datasets with good results, demonstrating the potential of the proposed method to assist in the analysis of community stability and identification of priority conservation areas.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"9 6","pages":"Pages 1007-1017"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72851961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.aaf.2023.04.005
The biofloc technology (BFT) offers benefits in improving feed utilization and reducing the feed conversion ratio compared to the recirculating aquaculture system (RAS). In this study, high-throughput 16S rRNA gene sequencing was employed to investigate and compare the bacterial communities in these aquaculture systems and the gut microbiota of grass carp reared in them. We observed a significant distinction between the microbial communities of the aquaculture systems and the intestinal microbiota of grass carp. The genera cetobacterium and bacillus were more abundant in the BFT system, accounting for only 0.05% and 0.25% in the RAS. Our study also demonstrated that BFT could influence the intestinal microorganisms of grass carp (Ctenopharyngodon Idella) by reducing the relative abundance of burkholderia-caballeronia-paraburkholderia and increasing that of cetobacterium. Based on bugBase community predictions, the potential pathogenicity in BFT and grass carp intestine was lower than in RAS. Regarding gene expression in the grass carp intestine, immunosuppressive genes showed higher expression, while pro-inflammatory genes exhibited lower expression in grass carp reared in BFT. Furthermore, the final average length and weight of grass carp in the BFT system were significantly higher than those in the RAS. This study provides valuable insights into gut microbiome ecology in relation to two grass carp aquaculture systems, which could be effectively applied in grass carp management to promote health and improve water quality.
{"title":"Effects of biological flocculation technology (BFT) on water quality dynamics and immune response of grass carp (Ctenopharyngodon idella)","authors":"","doi":"10.1016/j.aaf.2023.04.005","DOIUrl":"10.1016/j.aaf.2023.04.005","url":null,"abstract":"<div><div>The biofloc technology (BFT) offers benefits in improving feed utilization and reducing the feed conversion ratio compared to the recirculating aquaculture system (RAS). In this study, high-throughput 16S rRNA gene sequencing was employed to investigate and compare the bacterial communities in these aquaculture systems and the gut microbiota of grass carp reared in them. We observed a significant distinction between the microbial communities of the aquaculture systems and the intestinal microbiota of grass carp. The genera <em>cetobacterium</em> and <em>bacillus</em> were more abundant in the BFT system, accounting for only 0.05% and 0.25% in the RAS. Our study also demonstrated that BFT could influence the intestinal microorganisms of grass carp (<em>Ctenopharyngodon Idella</em>) by reducing the relative abundance of <em>burkholderia</em>-<em>caballeronia</em>-<em>paraburkholderia</em> and increasing that of <em>cetobacterium</em>. Based on bugBase community predictions, the potential pathogenicity in BFT and grass carp intestine was lower than in RAS. Regarding gene expression in the grass carp intestine, immunosuppressive genes showed higher expression, while pro-inflammatory genes exhibited lower expression in grass carp reared in BFT. Furthermore, the final average length and weight of grass carp in the BFT system were significantly higher than those in the RAS. This study provides valuable insights into gut microbiome ecology in relation to two grass carp aquaculture systems, which could be effectively applied in grass carp management to promote health and improve water quality.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"9 6","pages":"Pages 921-928"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90102894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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