Pub Date : 2023-11-14DOI: 10.1101/2023.11.13.566953
Subhanil Chakraborty, Subhajit Sen, Ranadhir Chakraborty
Pseudomonas aeruginosa, a Gram-negative opportunistic bacterium has emerged as a cause of life-threatening infections in topical burn wounds. Current therapeutic approaches through wound dressings and systemic medicines are far from satisfactory; multiple-antibiotic-resistance shown by pathogens contribute to failures of therapy causing mortality. This animal study was conducted to check efficacy of one Ayurveda based fermented polyherbal preparation (AP 01) against multiple antibiotic resistant Pseudomonas aeruginosa HW01 infected rat burn wounds. AP-01 was applied on artificially inflected burn wound on rat model infected with Multiple Antibiotics Resistant Pseudomonas aeruginosa to register the healing effects in terms of reduction in residual wound area percentage, presence of C-reactive protein in blood, presence of viable bacteria colony while keeping conventional antibiotics as positive control.The polyherbal preparation had reduced the infected residual burn wound area at 40.63% from the initial burn wound area within two weeks after a single intervention; whereas residual burn wound area remained much higher in case of animals left untreated and in case of the animals treated with control drug. Restoration to normalcy of serum C-reactive protein level were also achieved earlier in case of polyherbal AP-01 treated groups than other groups. Fermented formulation using components of AP-01 singly or in different combinations were never been tested earlier for topical application in infected burn-wound. The formulation AP-01 was found superior in terms of rate of healing and control of infection by multiple-antibiotic-resistant P. aeruginosa strains in burn wounds in rat model.
{"title":"Fermented polyherbal formulation ameliorates the severity of acute multiple - antibiotics - resistant Pseudomonas aeruginosa infected burn wound in rat burn model","authors":"Subhanil Chakraborty, Subhajit Sen, Ranadhir Chakraborty","doi":"10.1101/2023.11.13.566953","DOIUrl":"https://doi.org/10.1101/2023.11.13.566953","url":null,"abstract":"Pseudomonas aeruginosa, a Gram-negative opportunistic bacterium has emerged as a cause of life-threatening infections in topical burn wounds. Current therapeutic approaches through wound dressings and systemic medicines are far from satisfactory; multiple-antibiotic-resistance shown by pathogens contribute to failures of therapy causing mortality. This animal study was conducted to check efficacy of one Ayurveda based fermented polyherbal preparation (AP 01) against multiple antibiotic resistant Pseudomonas aeruginosa HW01 infected rat burn wounds. AP-01 was applied on artificially inflected burn wound on rat model infected with Multiple Antibiotics Resistant Pseudomonas aeruginosa to register the healing effects in terms of reduction in residual wound area percentage, presence of C-reactive protein in blood, presence of viable bacteria colony while keeping conventional antibiotics as positive control.The polyherbal preparation had reduced the infected residual burn wound area at 40.63% from the initial burn wound area within two weeks after a single intervention; whereas residual burn wound area remained much higher in case of animals left untreated and in case of the animals treated with control drug. Restoration to normalcy of serum C-reactive protein level were also achieved earlier in case of polyherbal AP-01 treated groups than other groups. Fermented formulation using components of AP-01 singly or in different combinations were never been tested earlier for topical application in infected burn-wound. The formulation AP-01 was found superior in terms of rate of healing and control of infection by multiple-antibiotic-resistant P. aeruginosa strains in burn wounds in rat model.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"49 14","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991304","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 : 2023-11-14DOI: 10.1101/2023.11.13.566865
Momtaz A Shahin, Hesham A Sultan, Ali Zanaty, Zienab Mosaad, Naglaa M Hagage, Amany Adel, Karim Selim, Dalia Saied, Abdel Hafez Samir, Ahmed Erfan, Abdelsatar Arafa, Abdullah Selim, Mohammed Samy, Mahmoud M Naguib, Heba Hassan, Osama El Shazly, Zeinab A Elbade, Mahmoud Kamel, Eman Farghaly, Samah Eid, Mohamed El Shahaby, Mohamed Hammoda, Osama Mehana, Mohamed Nabeh, Ahmed Samy
Infectious bursal disease viruses (IBDVs) have a profound impact on poultry production worldwide, directly causing mortality rates of up to 100%, and indirectly through their immunosuppressive effects. Since the emergence of the antigenically modified very virulent IBDV (vvIBDV) in Egypt in late 1999, the country has experienced recurrent outbreaks with high mortality rates and typical vvIBDV gross lesions. However, a notable shift occurred in 2023, characterized by a substantial increase in reported subclinical IBDV cases exhibiting atrophied bursa and associated immunosuppression. To assess the field situation, we examined samples from 21 farms in 2023 and 18 farms from 2021 and 2022, all of which experienced IBD outbreaks based on clinical diagnosis. These samples were submitted to our laboratory for confirmatory testing and subsequently subjected to VP2-HVR sequencing. Phylogenetic analysis revealed that all samples collected in 2021 and 2022 clustered with classical virulent strains and very virulent IBDV. In 2023, one sample clustered with the Egyptian vvIBDV, while one sample clustered with classic virulent IBDV, and the remaining 2023 samples clustered with the Chinese novel variant IBDV (nVarIBDV). The alignment of deduced amino acid sequences for VP2 revealed that all Egyptian classic virulent strains were similar to the Winterfield or Leukert strains. In contrast, vvIBDV strains exhibited two out of the three typical residues found in Egyptian antigenically atypical vvIBDV, namely Y220F and G254S, but not A321T, and one sample was identical to the European vvIBDV (emerged in 1989). Meanwhile, all variant strains recognized in the present study exhibited typical residues found in variant IBDV, in addition to the three conserved amino acid residues found only in Chinese variant IBDVs. However, all Egyptian variant strains showed a mutation at position 321 (321V), which represents the most exposed part of the capsid and is known to have a massive impact on IBDV antigenicity, with the exception of one sample that had 318G instead. This report highlights the emergence of a new variant IBDV clustered with the Chinese new variant in Egypt, causing bursa atrophy and spreading subclinically in broiler farms over a wide geographic distance, resulting in massive economic losses due to immunosuppression.
{"title":"Emergence of the Novel Infectious bursal disease viruse Variant in Vaccinated Poultry Flocks in Egypt","authors":"Momtaz A Shahin, Hesham A Sultan, Ali Zanaty, Zienab Mosaad, Naglaa M Hagage, Amany Adel, Karim Selim, Dalia Saied, Abdel Hafez Samir, Ahmed Erfan, Abdelsatar Arafa, Abdullah Selim, Mohammed Samy, Mahmoud M Naguib, Heba Hassan, Osama El Shazly, Zeinab A Elbade, Mahmoud Kamel, Eman Farghaly, Samah Eid, Mohamed El Shahaby, Mohamed Hammoda, Osama Mehana, Mohamed Nabeh, Ahmed Samy","doi":"10.1101/2023.11.13.566865","DOIUrl":"https://doi.org/10.1101/2023.11.13.566865","url":null,"abstract":"Infectious bursal disease viruses (IBDVs) have a profound impact on poultry production worldwide, directly causing mortality rates of up to 100%, and indirectly through their immunosuppressive effects. Since the emergence of the antigenically modified very virulent IBDV (vvIBDV) in Egypt in late 1999, the country has experienced recurrent outbreaks with high mortality rates and typical vvIBDV gross lesions. However, a notable shift occurred in 2023, characterized by a substantial increase in reported subclinical IBDV cases exhibiting atrophied bursa and associated immunosuppression. To assess the field situation, we examined samples from 21 farms in 2023 and 18 farms from 2021 and 2022, all of which experienced IBD outbreaks based on clinical diagnosis. These samples were submitted to our laboratory for confirmatory testing and subsequently subjected to VP2-HVR sequencing. Phylogenetic analysis revealed that all samples collected in 2021 and 2022 clustered with classical virulent strains and very virulent IBDV. In 2023, one sample clustered with the Egyptian vvIBDV, while one sample clustered with classic virulent IBDV, and the remaining 2023 samples clustered with the Chinese novel variant IBDV (nVarIBDV). The alignment of deduced amino acid sequences for VP2 revealed that all Egyptian classic virulent strains were similar to the Winterfield or Leukert strains. In contrast, vvIBDV strains exhibited two out of the three typical residues found in Egyptian antigenically atypical vvIBDV, namely Y220F and G254S, but not A321T, and one sample was identical to the European vvIBDV (emerged in 1989). Meanwhile, all variant strains recognized in the present study exhibited typical residues found in variant IBDV, in addition to the three conserved amino acid residues found only in Chinese variant IBDVs. However, all Egyptian variant strains showed a mutation at position 321 (321V), which represents the most exposed part of the capsid and is known to have a massive impact on IBDV antigenicity, with the exception of one sample that had 318G instead. This report highlights the emergence of a new variant IBDV clustered with the Chinese new variant in Egypt, causing bursa atrophy and spreading subclinically in broiler farms over a wide geographic distance, resulting in massive economic losses due to immunosuppression.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"48 21","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991317","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 : 2023-11-14DOI: 10.1101/2023.11.14.567104
Yoko K Takada, Jessica Yu, Xiaojin Ye, Chun-Yi Wu, Brunie H Felding, Masaaki Fujita, yoshikazu takada
VEGF-A is a key cytokine in tumor angiogenesis and a major therapeutic target for cancer. VEGF165 is the predominant isoform and is the most potent angiogenesis stimulant. VEGFR2/KDR domains 2 and 3 (D2D3) bind to the N-terminal domain (NTD, residues 1-110) of VEGF165. Since removal of the heparin-binding domain (HBD, residues 111-165) markedly reduced the mitogenic activity of VEGF165, it has been proposed that the HBD plays a critical role in the mitogenicity of VEGF165. Integrin αvβ3 has been shown to bind to VEGF165, but the role of integrin αvβ3 in VEGF165 signaling are unclear. Here we describe that αvβ3 specifically bound to the isolated HBD, but not to the NTD. We identified several critical amino acid residues in HBD for integrin binding (Arg-123, Arg-124, Lys-125, Lys-140, Arg-145, and Arg-149) by docking simulation and mutagenesis, and generated full-length VEGF165 that is defective in integrin binding by including mutations in the HBD. The full-length VEGF165 mutant defective in integrin binding (R123A/R124A/K125A/K140A/R145A/R149A) was defective in ERK1/2 phosphorylation, integrin β3 phosphorylation, and KDR phosphorylation, although the mutation did not affect KDR binding to VEGF165. We propose a model in which VEGF165 induces KDR (through NTD)-VEGF165 (through HBD)-integrin αvβ3 ternary complex formation on the cell surface and this process is critically involved in potent mitogenicity of VEGF165.
{"title":"The heparin-binding domain of VEGF165 directly binds to integrin αvβ3 and plays a critical role in signaling.","authors":"Yoko K Takada, Jessica Yu, Xiaojin Ye, Chun-Yi Wu, Brunie H Felding, Masaaki Fujita, yoshikazu takada","doi":"10.1101/2023.11.14.567104","DOIUrl":"https://doi.org/10.1101/2023.11.14.567104","url":null,"abstract":"VEGF-A is a key cytokine in tumor angiogenesis and a major therapeutic target for cancer. VEGF165 is the predominant isoform and is the most potent angiogenesis stimulant. VEGFR2/KDR domains 2 and 3 (D2D3) bind to the N-terminal domain (NTD, residues 1-110) of VEGF165. Since removal of the heparin-binding domain (HBD, residues 111-165) markedly reduced the mitogenic activity of VEGF165, it has been proposed that the HBD plays a critical role in the mitogenicity of VEGF165. Integrin αvβ3 has been shown to bind to VEGF165, but the role of integrin αvβ3 in VEGF165 signaling are unclear. Here we describe that αvβ3 specifically bound to the isolated HBD, but not to the NTD. We identified several critical amino acid residues in HBD for integrin binding (Arg-123, Arg-124, Lys-125, Lys-140, Arg-145, and Arg-149) by docking simulation and mutagenesis, and generated full-length VEGF165 that is defective in integrin binding by including mutations in the HBD. The full-length VEGF165 mutant defective in integrin binding (R123A/R124A/K125A/K140A/R145A/R149A) was defective in ERK1/2 phosphorylation, integrin β3 phosphorylation, and KDR phosphorylation, although the mutation did not affect KDR binding to VEGF165. We propose a model in which VEGF165 induces KDR (through NTD)-VEGF165 (through HBD)-integrin αvβ3 ternary complex formation on the cell surface and this process is critically involved in potent mitogenicity of VEGF165.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"50 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991457","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 : 2023-11-14DOI: 10.1101/2023.11.13.566818
Maria João Ferreira, Jessy Silva, Hidenori Takeuchi, Takamasa Suzuki, Tetsuya Higashiyama, Sílvia Vieira de Almeida Coimbra
In Angiosperms, the continuation of plant species is intricately dependent on the funiculus multifaceted role in nutrient transport, mechanical support, and dehiscence of seeds. SEEDSTICK (STK) is a MADS-box transcription factor involved in seed size and dehiscence, and one of the few genes identified as affecting funiculus growth. Given the importance of the funiculus to a correct seed development, allied with previous phenotypic observations of stk mutants, we performed a transcriptomic analysis of stk funiculi, using RNA-sequencing, to infer on the deregulated networks of genes. The generated dataset of differentially expressed genes was enriched with cell wall biogenesis, cell cycle, sugar metabolism and transport terms, all in accordance with stk phenotype. We selected eight differentially expressed genes involved with abscission, seed development or novel functions in stk funiculus, such as hormones/secondary metabolites transport, for transcriptome validation using qPCR and/or promoter reporter lines. Overall, the analysis performed in this study allowed delving into the STK-network established in Arabidopsis funiculus, fulfilling a literature gap. Simultaneously, our findings reinforced the reliability of the transcriptome, and identified processes and new candidate genes that will enable a better understanding on the role of this sporophytic structure and how seed development may be affected by it.
{"title":"Transcriptomic landscape of<i>seedstick</i>in<i>Arabidopsis thaliana</i>funiculus after fertilisation","authors":"Maria João Ferreira, Jessy Silva, Hidenori Takeuchi, Takamasa Suzuki, Tetsuya Higashiyama, Sílvia Vieira de Almeida Coimbra","doi":"10.1101/2023.11.13.566818","DOIUrl":"https://doi.org/10.1101/2023.11.13.566818","url":null,"abstract":"In Angiosperms, the continuation of plant species is intricately dependent on the funiculus multifaceted role in nutrient transport, mechanical support, and dehiscence of seeds. SEEDSTICK (STK) is a MADS-box transcription factor involved in seed size and dehiscence, and one of the few genes identified as affecting funiculus growth. Given the importance of the funiculus to a correct seed development, allied with previous phenotypic observations of stk mutants, we performed a transcriptomic analysis of stk funiculi, using RNA-sequencing, to infer on the deregulated networks of genes. The generated dataset of differentially expressed genes was enriched with cell wall biogenesis, cell cycle, sugar metabolism and transport terms, all in accordance with stk phenotype. We selected eight differentially expressed genes involved with abscission, seed development or novel functions in stk funiculus, such as hormones/secondary metabolites transport, for transcriptome validation using qPCR and/or promoter reporter lines. Overall, the analysis performed in this study allowed delving into the STK-network established in Arabidopsis funiculus, fulfilling a literature gap. Simultaneously, our findings reinforced the reliability of the transcriptome, and identified processes and new candidate genes that will enable a better understanding on the role of this sporophytic structure and how seed development may be affected by it.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991610","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 : 2023-11-14DOI: 10.1101/2023.11.14.567063
Thai Q Dao, Colleen Drapek, Alexander M Jones, Samuel Leiboff
Plant hormones are small molecules which elicit profound physiological responses. Although plant hormone biosynthesis and response genes have been critical for agricultural improvement, it has been difficult to experimentally compare hormone biology across species because of complex phenotypic outputs. We used transient expression of genetic hormone sensors and transcriptomics to quantify tissue-specific gibberellic acid (GA) and auxin responses across tissues and genotypes in cereal crops. We found that the FRET-based GPS2 biosensor detects exogenous GA treatments in maize, barley, sorghum, and wheat, in both vegetative and floral tissues. Measuring GPS2 output across GA dosages revealed tissue- and genotype-specific differences in GA sensor response. We observed marked differences in maize vs barley leaves and floral tissues and an unexpected drop in GPS2 output in the maize d1 GA biosynthesis mutant after GA treatment, likely reflecting differences in bioactive GA content, GA transport, and mechanisms of GA response. We then used RNAseq to measure transcriptional responses to GA treatment in leaves from maize wildtype, d1, and barley as well as floral tissues from maize and barley for a cross-tissue, cross-genotype, and cross-species GA-response comparison. After orthology prediction and analysis of within- and cross-species GO-term enrichment, we identified core sets of GA-responsive genes in each species as well as maize-barley orthogroups. Our analysis suggests that downregulation of GA-INSENSITIVE DWARF1 (GID1) and upregulation of α-Expansin1 (EXPA1) orthologs comprises a universal GA-response mechanism that is independent of GA biosynthesis, and identifies F-Box proteins, hexokinase, and AMPK/SNF1 protein kinase orthologs as unexpected cross-tissue, cross-genotype, and cross-species GA-responsive genes. We then compared the transient expression of the DR5, DR5v2, and DII-mDII auxin reporters in barley and maize and find that although DR5 did not respond to exogenous auxin in barley, DR5v2 responded to auxin treatment with a similar magnitude as in maize. Both species display auxin-mediated DII degradation that requires the 26S proteasome.
{"title":"Comparing hormone dynamics in cereal crops via transient expression of hormone sensors","authors":"Thai Q Dao, Colleen Drapek, Alexander M Jones, Samuel Leiboff","doi":"10.1101/2023.11.14.567063","DOIUrl":"https://doi.org/10.1101/2023.11.14.567063","url":null,"abstract":"Plant hormones are small molecules which elicit profound physiological responses. Although plant hormone biosynthesis and response genes have been critical for agricultural improvement, it has been difficult to experimentally compare hormone biology across species because of complex phenotypic outputs. We used transient expression of genetic hormone sensors and transcriptomics to quantify tissue-specific gibberellic acid (GA) and auxin responses across tissues and genotypes in cereal crops. We found that the FRET-based GPS2 biosensor detects exogenous GA treatments in maize, barley, sorghum, and wheat, in both vegetative and floral tissues. Measuring GPS2 output across GA dosages revealed tissue- and genotype-specific differences in GA sensor response. We observed marked differences in maize vs barley leaves and floral tissues and an unexpected drop in GPS2 output in the maize d1 GA biosynthesis mutant after GA treatment, likely reflecting differences in bioactive GA content, GA transport, and mechanisms of GA response. We then used RNAseq to measure transcriptional responses to GA treatment in leaves from maize wildtype, d1, and barley as well as floral tissues from maize and barley for a cross-tissue, cross-genotype, and cross-species GA-response comparison. After orthology prediction and analysis of within- and cross-species GO-term enrichment, we identified core sets of GA-responsive genes in each species as well as maize-barley orthogroups. Our analysis suggests that downregulation of GA-INSENSITIVE DWARF1 (GID1) and upregulation of α-Expansin1 (EXPA1) orthologs comprises a universal GA-response mechanism that is independent of GA biosynthesis, and identifies F-Box proteins, hexokinase, and AMPK/SNF1 protein kinase orthologs as unexpected cross-tissue, cross-genotype, and cross-species GA-responsive genes. We then compared the transient expression of the DR5, DR5v2, and DII-mDII auxin reporters in barley and maize and find that although DR5 did not respond to exogenous auxin in barley, DR5v2 responded to auxin treatment with a similar magnitude as in maize. Both species display auxin-mediated DII degradation that requires the 26S proteasome.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"44 19","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991615","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 : 2023-11-14DOI: 10.1101/2023.11.14.567012
Gebrehaweria Kidane Reda, Sawadi Fransisco Ndunguru, Brigitta Csernus, Gabriella Gulyas, Renata Knop, Csaba Szabo, Levente Czegledi, Adam Z. Lendvai
Resources are needed for growth, reproduction and survival, and organisms must trade-off limited resources among competing processes. Nutritional availability in organisms is sensed and monitored by nutrient-sensing pathways that can trigger physiological changes or alter gene expression. Previous studies have proposed that one such signalling pathway, the mechanistic target of rapamycin (mTOR), underpins a form of adaptive plasticity when individuals encounter constraints in their energy budget. Despite the fundamental importance of this process in evolutionary biology, how nutritional limitation is regulated through the expression of genes governing this pathway and its consequential effects on fitness remains understudied, particularly in birds. We used dietary restriction to simulate resource depletion and examined its effects on body mass, reproduction and gene expression in Japanese quails (Coturnix japonica). Quails were subjected to ad libitum (ADL) feeding or 20%, 30%, and 40% restriction levels for two weeks. All restricted groups exhibited reduced body mass, whereas reductions in the number and mass of eggs were observed only under more severe restrictions. Dietary restriction led to decreased expression of mTOR and insulin-like growth factor 1 (IGF1), whereas the ribosomal protein S6 kinase 1 (RPS6K1) and autophagy-related genes (ATG9A and ATG5) were upregulated. The pattern in which mTOR respond to restriction was similar to what has been seen in body mass. Regardless of the treatment, proportionally higher reproductive investment was associated with individual variation in mTOR expression. These findings reveal the connection between dietary intake and the expression of mTOR and related genes in this pathway.
生长、繁殖和生存都需要资源，生物必须在竞争过程中权衡有限的资源。生物体内的营养可用性是通过营养感应途径感知和监测的，这些途径可以触发生理变化或改变基因表达。先前的研究已经提出，当个体在能量预算中遇到限制时，雷帕霉素(mTOR)的机制靶标(mechanistic target of rapamycin)这一信号通路支持一种形式的适应性可塑性。尽管这一过程在进化生物学中具有根本的重要性，但营养限制是如何通过控制这一途径的基因表达来调节的，以及它对适应性的影响仍未得到充分的研究，特别是在鸟类中。本研究以日本鹌鹑为研究对象，采用饮食限制模拟资源耗竭，研究其对日本鹌鹑体重、繁殖和基因表达的影响。鹌鹑分别饲喂20%、30%和40%限制水平的自由采食(ADL) 2周。所有受限制的组都表现出体重减少，而只有在更严格的限制下才观察到鸡蛋数量和质量的减少。饮食限制导致mTOR和胰岛素样生长因子1 (IGF1)表达降低，而核糖体蛋白S6激酶1 (RPS6K1)和自噬相关基因(ATG9A和ATG5)表达上调。mTOR对限制的反应模式与在体重中所看到的相似。无论治疗方式如何，比例较高的生殖投资与mTOR表达的个体差异相关。这些发现揭示了膳食摄入与mTOR及其相关基因表达之间的联系。
{"title":"Dietary restriction and life-history trade-offs: insights into mTOR pathway regulation and reproductive investment in birds","authors":"Gebrehaweria Kidane Reda, Sawadi Fransisco Ndunguru, Brigitta Csernus, Gabriella Gulyas, Renata Knop, Csaba Szabo, Levente Czegledi, Adam Z. Lendvai","doi":"10.1101/2023.11.14.567012","DOIUrl":"https://doi.org/10.1101/2023.11.14.567012","url":null,"abstract":"Resources are needed for growth, reproduction and survival, and organisms must trade-off limited resources among competing processes. Nutritional availability in organisms is sensed and monitored by nutrient-sensing pathways that can trigger physiological changes or alter gene expression. Previous studies have proposed that one such signalling pathway, the mechanistic target of rapamycin (mTOR), underpins a form of adaptive plasticity when individuals encounter constraints in their energy budget. Despite the fundamental importance of this process in evolutionary biology, how nutritional limitation is regulated through the expression of genes governing this pathway and its consequential effects on fitness remains understudied, particularly in birds. We used dietary restriction to simulate resource depletion and examined its effects on body mass, reproduction and gene expression in Japanese quails (Coturnix japonica). Quails were subjected to ad libitum (ADL) feeding or 20%, 30%, and 40% restriction levels for two weeks. All restricted groups exhibited reduced body mass, whereas reductions in the number and mass of eggs were observed only under more severe restrictions. Dietary restriction led to decreased expression of mTOR and insulin-like growth factor 1 (IGF1), whereas the ribosomal protein S6 kinase 1 (RPS6K1) and autophagy-related genes (ATG9A and ATG5) were upregulated. The pattern in which mTOR respond to restriction was similar to what has been seen in body mass. Regardless of the treatment, proportionally higher reproductive investment was associated with individual variation in mTOR expression. These findings reveal the connection between dietary intake and the expression of mTOR and related genes in this pathway.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"46 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991743","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 : 2023-11-14DOI: 10.1101/2023.11.14.567047
Hannah R Assour, Tia-Lynn Ashman, Martin M Turcotte
Premise: Polyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their animal associates. Yet, knowledge of whether ploidy affects plant-herbivore dynamics is scarce. Here, we test whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether ploidy impacts plant and herbivore performance, and whether these interactions depend on plant genetic background. Methods: Using multiple pairs of independently synthesized neotetraploid greater duckweed (Spirodela polyrhiza) and their diploid progenitors, we evaluated the effect of neopolyploidy on duckweed's interaction with the water-lily aphid (Rhopalosiphum nymphaeae). Using two-way choice experiments, we first evaluated feeding preference by the herbivore. We then evaluated the consequences of ploidy on aphid and plant performance by measuring population growth over multiple generations. Key Results: Aphids preferred neopolyploids over diploids when the plants were provided at equal abundances but not when they were provided at equal surface area, indicating the role of plant size in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was highly dependent on the genetic lineage of the plant. Lastly, the impact of herbivory on neopolyploids vs. diploid duckweed varied greatly with genetic lineage, but overall, neopolyploids appeared to be generally less tolerant than diploids. Conclusions: We conclude that polyploidization can impact the preference and performance of herbivores on their plant hosts, whereas plant performance depends on complex interactions between herbivory, ploidy, and genetic lineage. These results have significant implications for the establishment and persistence of plants and herbivores in nature.
{"title":"Neopolyploidy-induced changes in the giant duckweed (Spirodela polyrhiza) alter herbivore preference, performance, and plant population performance","authors":"Hannah R Assour, Tia-Lynn Ashman, Martin M Turcotte","doi":"10.1101/2023.11.14.567047","DOIUrl":"https://doi.org/10.1101/2023.11.14.567047","url":null,"abstract":"Premise: Polyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their animal associates. Yet, knowledge of whether ploidy affects plant-herbivore dynamics is scarce. Here, we test whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether ploidy impacts plant and herbivore performance, and whether these interactions depend on plant genetic background. Methods: Using multiple pairs of independently synthesized neotetraploid greater duckweed (Spirodela polyrhiza) and their diploid progenitors, we evaluated the effect of neopolyploidy on duckweed's interaction with the water-lily aphid (Rhopalosiphum nymphaeae). Using two-way choice experiments, we first evaluated feeding preference by the herbivore. We then evaluated the consequences of ploidy on aphid and plant performance by measuring population growth over multiple generations. Key Results: Aphids preferred neopolyploids over diploids when the plants were provided at equal abundances but not when they were provided at equal surface area, indicating the role of plant size in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was highly dependent on the genetic lineage of the plant. Lastly, the impact of herbivory on neopolyploids vs. diploid duckweed varied greatly with genetic lineage, but overall, neopolyploids appeared to be generally less tolerant than diploids. Conclusions: We conclude that polyploidization can impact the preference and performance of herbivores on their plant hosts, whereas plant performance depends on complex interactions between herbivory, ploidy, and genetic lineage. These results have significant implications for the establishment and persistence of plants and herbivores in nature.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"46 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991901","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 : 2023-11-14DOI: 10.1101/2023.11.13.566949
Shota Morikawa, Callum Verdonk, Evan John, Leon Lenzo, Nicolau Sbaraini, Chala J Turo, Hang Li, David Jiang, Yit-Heng Chooi, Kar-Chun Tan
The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion of the P. nodorum VeA ortholog, PnVeA , resulted in growth abnormalities including pigmentation, abolished asexual sporulation and highly reduced virulence on wheat. Comparative RNA-Seq and RT-PCR analyses revealed that the deletion of PnVeA also decoupled the expression of major necrotrophic effector genes. In addition, the deletion of PnVeA resulted in an up-regulation of four predicted secondary metabolite (SM) gene clusters. Using liquid-chromatography mass-spectrometry, it was observed that one of the SM gene clusters led to an accumulation of the mycotoxin alternariol. PnVeA is essential for asexual sporulation, full virulence, secondary metabolism and necrotrophic effector regulation.
{"title":"The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen<i>Parastagonospora nodorum</i>","authors":"Shota Morikawa, Callum Verdonk, Evan John, Leon Lenzo, Nicolau Sbaraini, Chala J Turo, Hang Li, David Jiang, Yit-Heng Chooi, Kar-Chun Tan","doi":"10.1101/2023.11.13.566949","DOIUrl":"https://doi.org/10.1101/2023.11.13.566949","url":null,"abstract":"The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion of the P. nodorum VeA ortholog, PnVeA , resulted in growth abnormalities including pigmentation, abolished asexual sporulation and highly reduced virulence on wheat. Comparative RNA-Seq and RT-PCR analyses revealed that the deletion of PnVeA also decoupled the expression of major necrotrophic effector genes. In addition, the deletion of PnVeA resulted in an up-regulation of four predicted secondary metabolite (SM) gene clusters. Using liquid-chromatography mass-spectrometry, it was observed that one of the SM gene clusters led to an accumulation of the mycotoxin alternariol. PnVeA is essential for asexual sporulation, full virulence, secondary metabolism and necrotrophic effector regulation.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"48 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992195","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 : 2023-11-14DOI: 10.1101/2023.11.11.566685
Isabella Burda, Chun-Biu Li, Frances K Clark, Adrienne HK Roeder
Organ sizes and shapes are highly reproducible, or robust, within a species and individuals. Arabidopsis thaliana sepals, which are the leaf-like organs that enclose flower buds, have consistent size and shape, which indicates robust development. Counterintuitively, variability in cell growth rate over time and between cells facilitates robust development because cumulative cell growth averages to a uniform rate. Here we investigate how sepal morphogenesis is robust to changes in cell division but not robust to changes in cell growth variability. We live image and quantitatively compare the development of sepals with increased or decreased cell division rate (lgo mutant and LGO overexpression, respectively), a mutant with altered cell growth variability (ftsh4), and double mutants combining these. We find that robustness is preserved when cell division rate changes because there is no change in the spatial pattern of growth. Meanwhile when robustness is lost in ftsh4 mutants, cell growth accumulates unevenly, and cells have disorganized growth directions. Thus, we demonstrate in vivo that both cell growth rate and direction average in robust development, preserving robustness despite changes in cell division.
{"title":"Robust organ size in Arabidopsis is primarily governed by cell growth rather than cell division patterns","authors":"Isabella Burda, Chun-Biu Li, Frances K Clark, Adrienne HK Roeder","doi":"10.1101/2023.11.11.566685","DOIUrl":"https://doi.org/10.1101/2023.11.11.566685","url":null,"abstract":"Organ sizes and shapes are highly reproducible, or robust, within a species and individuals. Arabidopsis thaliana sepals, which are the leaf-like organs that enclose flower buds, have consistent size and shape, which indicates robust development. Counterintuitively, variability in cell growth rate over time and between cells facilitates robust development because cumulative cell growth averages to a uniform rate. Here we investigate how sepal morphogenesis is robust to changes in cell division but not robust to changes in cell growth variability. We live image and quantitatively compare the development of sepals with increased or decreased cell division rate (lgo mutant and LGO overexpression, respectively), a mutant with altered cell growth variability (ftsh4), and double mutants combining these. We find that robustness is preserved when cell division rate changes because there is no change in the spatial pattern of growth. Meanwhile when robustness is lost in ftsh4 mutants, cell growth accumulates unevenly, and cells have disorganized growth directions. Thus, we demonstrate in vivo that both cell growth rate and direction average in robust development, preserving robustness despite changes in cell division.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"44 16","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992317","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 : 2023-11-14DOI: 10.1101/2023.11.14.567013
Katrina Leslie Nicolas Mala, Jan Skalak, Elena Zemlyanskaya, Vladislav Dolgikh, Veronika Jedlickova, Helene Robert-Boisivon, Lenka Havlickova, Klara Panzarova, Martin Trtilek, Ian Bancroft, Jan Hejatko
Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control plant development and adaptive responses. The type-A RESPONSE REGULATORs (RRAs), the downstream members of the MSP cascade and cytokinin primary response genes, are supposed to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, the transcriptional data suggest the involvement of RRAs in stress-related responses as well. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRAs, we identified 5 and 38 novel putative RRAs in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassica oleracea and Brassica rapa. We categorized RRAs based on the kinetics of their cytokinin-mediated upregulation and observed both similarities and specificities in this type of response across Brassicaceae. Using bioinformatic analysis and experimental data demonstrating the cytokinin responsiveness of Arabidopsis-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin-mediated upregulation of RRAs in Brassica rapa and Brassica napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus corroborating the role of cytokinin signaling in the crop adaptive responses.
{"title":"Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses in Brassicaceae","authors":"Katrina Leslie Nicolas Mala, Jan Skalak, Elena Zemlyanskaya, Vladislav Dolgikh, Veronika Jedlickova, Helene Robert-Boisivon, Lenka Havlickova, Klara Panzarova, Martin Trtilek, Ian Bancroft, Jan Hejatko","doi":"10.1101/2023.11.14.567013","DOIUrl":"https://doi.org/10.1101/2023.11.14.567013","url":null,"abstract":"Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control plant development and adaptive responses. The type-A RESPONSE REGULATORs (RRAs), the downstream members of the MSP cascade and cytokinin primary response genes, are supposed to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, the transcriptional data suggest the involvement of RRAs in stress-related responses as well. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRAs, we identified 5 and 38 novel putative RRAs in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassica oleracea and Brassica rapa. We categorized RRAs based on the kinetics of their cytokinin-mediated upregulation and observed both similarities and specificities in this type of response across Brassicaceae. Using bioinformatic analysis and experimental data demonstrating the cytokinin responsiveness of Arabidopsis-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin-mediated upregulation of RRAs in Brassica rapa and Brassica napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus corroborating the role of cytokinin signaling in the crop adaptive responses.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992529","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}
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