scholarly journals Citrus Stubborn Disease: Current Insights on an Enigmatic Problem Prevailing in Citrus Orchards

2022 ◽  
Vol 10 (1) ◽  
pp. 183
Author(s):  
Tourya Sagouti ◽  
Zineb Belabess ◽  
Naima Rhallabi ◽  
Essaid Ait Barka ◽  
Abdessalem Tahiri ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Primary Source ◽  
Poor Quality ◽  
Disease Spread ◽  
Spiroplasma Citri ◽  
A Genome ◽  
A Cell ◽  
Citrus Orchards ◽  
A Minor ◽  
Citrus Stubborn Disease

Citrus stubborn was initially observed in California in 1915 and was later proven as a graft-transmissible disease in 1942. In the field, diseased citrus trees have compressed and stunted appearances, and yield poor-quality fruits with little market value. The disease is caused by Spiroplasma citri, a phloem-restricted pathogenic mollicute, which belongs to the Spiroplasmataceae family (Mollicutes). S. citri has the largest genome of any Mollicutes investigated, with a genome size of roughly 1780 Kbp. It is a helical, motile mollicute that lacks a cell wall and peptidoglycan. Several quick and sensitive molecular-based and immuno-enzymatic pathogen detection technologies are available. Infected weeds are the primary source of transmission to citrus, with only a minor percentage of transmission from infected citrus to citrus. Several phloem-feeding leafhopper species (Cicadellidae, Hemiptera) support the natural spread of S. citri in a persistent, propagative manner. S. citri-free buds are used in new orchard plantings and bud certification, and indexing initiatives have been launched. Further, a quarantine system for newly introduced types has been implemented to limit citrus stubborn disease (CSD). The present state of knowledge about CSD around the world is summarized in this overview, where recent advances in S. citri detection, characterization, control and eradication were highlighted to prevent or limit disease spread through the adoption of best practices.

scholarly journals New Perspectives on the Epidemiology of Citrus Stubborn Disease in California Orchards

2010 ◽  
Vol 11 (1) ◽  
pp. 37
Author(s):  
Alexandre F. S. Mello ◽  
Raymond K. Yokomi ◽  
Ulrich Melcher ◽  
Jianchi Chen ◽  
Edwin Civerolo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fruit Quality ◽  
Pathogen Detection ◽  
Disease Incidence ◽  
Sampling Technique ◽  
The United States ◽  
Citrus Industry ◽  
Spiroplasma Citri ◽  
Specific Pcr ◽  
Citrus Stubborn Disease

Although citrus stubborn disease (CSD), caused by the phloem resident mollicute Spiroplasma citri, is a significant threat to California citrus industry, our knowledge of its epidemiology is mostly anecdotal. We optimized multiple pathogen-detection protocols, measured disease incidence in two plots of commercial California groves, assessed pathogen impact on fruit quality and yield, and evaluated genetic diversity among S. citri isolates. Fruit columellas and receptacles were more suitable than leaves or bark for bacterial cultivation. Using cultivation and S. citri-specific PCR for detection, the incidence of CSD in two orchards, respectively, ranged from 46 to 85% and 1 to 4%, depending on the sampling technique. Yield and quality of fruits produced by trees that were mildly or severely CSD-symptomatic were compared to those of S. citri-free trees in one California orchard in 2006 and 2007. These infected trees had reduced fruit quality and up to 32% lower yield relative to S. citri-free trees. Using RAPD markers to compare 35 S. citri isolates collected 20 years ago from the United States and Mediterranean region with 34 isolates recently collected from California, significant genetic diversity was identified but was not correlated with the time or location of collection. Our findings suggest that CSD incidence in the commercial groves evaluated could be as high as 85% and its impact on yield and fruit quality are significant. Accepted for publication 1 March 2010. Published 26 May 2010.

scholarly journals Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Rowena DeJesus ◽  
Francesca Moretti ◽  
Gregory McAllister ◽  
Zuncai Wang ◽  
Phil Bergman ◽  
...  
Keyword(s):  
Adaptor Protein ◽  
Er Stress Response ◽  
Genome Wide ◽  
A Genome ◽  
Crispr Screen ◽  
Selection Step ◽  
A Cell ◽  
Cell Type Specific ◽  
Cellular Pathways ◽  
Mtor Signalling

SQSTM1 is an adaptor protein that integrates multiple cellular signaling pathways and whose expression is tightly regulated at the transcriptional and post-translational level. Here, we describe a forward genetic screening paradigm exploiting CRISPR-mediated genome editing coupled to a cell selection step by FACS to identify regulators of SQSTM1. Through systematic comparison of pooled libraries, we show that CRISPR is superior to RNAi in identifying known SQSTM1 modulators. A genome-wide CRISPR screen exposed MTOR signalling and the entire macroautophagy machinery as key regulators of SQSTM1 and identified several novel modulators including HNRNPM, SLC39A14, SRRD, PGK1 and the ufmylation cascade. We show that ufmylation regulates SQSTM1 by eliciting a cell type-specific ER stress response which induces SQSTM1 expression and results in its accumulation in the cytosol. This study validates pooled CRISPR screening as a powerful method to map the repertoire of cellular pathways that regulate the fate of an individual target protein.

scholarly journals Physiological function of Flo11p domains and the particular role of amyloid core sequences of this adhesin in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Clara Bouyx ◽  
Marion Schiavone ◽  
Marie-Ange Teste ◽  
Etienne Dague ◽  
Nathalie Sieczkowski ◽  
...  
Keyword(s):  
Cell Wall ◽  
Amyloid Β ◽  
Surface Hydrophobicity ◽  
Yeast Cells ◽  
Invasive Growth ◽  
Specific Domain ◽  
A Genome ◽  
A Cell ◽  
Cellular Aggregates

Flocculins are a family of glycosylated proteins that provide yeast cells with several properties such as biofilm formation, flocculation, invasive growth or formation of velum. These proteins are similarly organised with a N-terminal (adhesion) domain, a stalk-like central B-domain with several repeats and a C-terminal sequence carrying a cell wall anchor site. They also contain amyloid β-aggregation-prone sequences whose functional role is still unclear. In this work, we show that Flo11p differs from other flocculins by the presence of unique amyloid-forming sequences, whose the number is critical in the formation of adhesion nanodomains under a physical shear force. Using a genome editing approach to identify the function of domains in Flo11p phenotypes, we show that the formation of cellular aggregates whose density increases with the number of amyloid sequences cannot be attributed to a specific domain of Flo11p. The same is true for plastic adhesion and surface hydrophobicity the intensity of which depends mainly on the abundance of Flo11p on the cell surface. In contrast, the N and C domains of Flo11p are essential for invasive growth in agar, whereas a reduction in the number of repeats of the B domain weakens this phenotype. However, expression of FLO11 alone is not sufficient to trigger this invasion phenotype. Finally, we show that this flocculin contributes to the integrity of the cell wall.

scholarly journals A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Thordis Kristjansdottir ◽  
Elleke F. Bosma ◽  
Filipe Branco dos Santos ◽  
Emre Özdemir ◽  
Markus J. Herrgård ◽  
...  
Keyword(s):  
Experimental Data ◽  
Metabolic Engineering ◽  
Growth Rates ◽  
Lactobacillus Reuteri ◽  
Metabolic Model ◽  
Metabolic Reconstruction ◽  
Cell Factory ◽  
A Genome ◽  
A Cell ◽  
Genome Scale

Abstract Background Lactobacillus reuteri is a heterofermentative Lactic Acid Bacterium (LAB) that is commonly used for food fermentations and probiotic purposes. Due to its robust properties, it is also increasingly considered for use as a cell factory. It produces several industrially important compounds such as 1,3-propanediol and reuterin natively, but for cell factory purposes, developing improved strategies for engineering and fermentation optimization is crucial. Genome-scale metabolic models can be highly beneficial in guiding rational metabolic engineering. Reconstructing a reliable and a quantitatively accurate metabolic model requires extensive manual curation and incorporation of experimental data. Results A genome-scale metabolic model of L. reuteri JCM 1112T was reconstructed and the resulting model, Lreuteri_530, was validated and tested with experimental data. Several knowledge gaps in the metabolism were identified and resolved during this process, including presence/absence of glycolytic genes. Flux distribution between the two glycolytic pathways, the phosphoketolase and Embden–Meyerhof–Parnas pathways, varies considerably between LAB species and strains. As these pathways result in different energy yields, it is important to include strain-specific utilization of these pathways in the model. We determined experimentally that the Embden–Meyerhof–Parnas pathway carried at most 7% of the total glycolytic flux. Predicted growth rates from Lreuteri_530 were in good agreement with experimentally determined values. To further validate the prediction accuracy of Lreuteri_530, the predicted effects of glycerol addition and adhE gene knock-out, which results in impaired ethanol production, were compared to in vivo data. Examination of both growth rates and uptake- and secretion rates of the main metabolites in central metabolism demonstrated that the model was able to accurately predict the experimentally observed effects. Lastly, the potential of L. reuteri as a cell factory was investigated, resulting in a number of general metabolic engineering strategies. Conclusion We have constructed a manually curated genome-scale metabolic model of L. reuteri JCM 1112T that has been experimentally parameterized and validated and can accurately predict metabolic behavior of this important platform cell factory.

Non-Hemolytic Antibody Induced Loss of RBC Antigen during Transfusion of Crossmatch Incompatible Blood.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 557-557 ◽  
Author(s):  
James C. Zimring ◽  
Gregory A. Hair ◽  
Traci E. Chadwick ◽  
Seema S. Deshpande ◽  
Kimberly M. Anderson ◽  
...  
Keyword(s):  
Blood Group ◽  
High Titer ◽  
Surface Protein ◽  
Biological Properties ◽  
Target Antigen ◽  
Blood Group Antigens ◽  
A Cell ◽  
Clinically Significant ◽  
Antigen Loss ◽  
A Minor

Abstract Background: Transfusion of red blood cells (RBC) into patients with anti-donor RBC antibodies (crossmatch incompatible transfusion) can result in antibody mediated hemolysis. Less well appreciated is the ability of anti-RBC antibodies to specifically remove their target antigen from donor RBCs without compromising cell survival. This phenomenon has now been reported for the major clinically significant blood group antigens, including Rh, Kell, Kidd and Duffy. Although this has been described multiple times in humans, no mechanistic elucidation has been accomplished. In an effort to investigate the mechanism of this process, we describe the first animal model of non-hemolytic antibody induced RBC antigen loss. Methods: mHEL mice express the model antigen Hen Egg Lysozyme (HEL) as a cell surface protein on RBC. Since mHEL mice are on a C57BL/6 background, the mHEL antigen represents a single antigenic difference between donor RBC and recipient mice. Immunizing C57BL/6 mice with HEL/CFA results in the generation of high titer IgG anti-HEL responses rendering the mice crossmatch incompatible with mHEL RBC. This system was utilized to study the effects of transfusing mHEL RBC into crossmatch incompatible recipients. Results: Similar to the antibody induced antigen loss observed in humans, transfusion of donor mHEL RBC into crossmatch incompatible mice results in selective loss of HEL antigen from donor RBC without affecting other blood group antigens or reducing the circulatory lifespan of the donor RBC. In addition, recovered RBC that have lost their antigen have normal morphology. This process is antigen specific and occurs in mice that have received passive injections of anti-HEL antisera. A spleen is not required for antigen loss to occur. However, antigen loss does not occur in animals with a targeted deletion of the FcγIII receptor. Although polyclonal anti-HEL antisera consistently causes antigen loss, and IgG1 and IgG2b are the predominant subclasses of anti-HEL IgG in the antisera, no antigen loss is observed in response to purified monoclonal anti-HEL antibodies of the IgG1 and IgG2b subclass. Conclusion: These studies demonstrate that antibody induced antigen loss is a process that involves interaction of RBC, anti-RBC IgG and FcγIII receptors, thus providing mechanistic insight into the phenomenon of antigen loss during incompatible transfusion. The lack of antigen loss in response to monoclonal anti-HEL IgG1 or IgG2b suggests that antigen loss occurs in response to a minor IgG subtype in antisera, depends upon biological properties of the antibody (such as affinity), or that additional serum cofactors are involved.

scholarly journals Acidovorax citrulli Seed Inoculum Load Affects Seedling Transmission and Spread of Bacterial Fruit Blotch of Watermelon Under Greenhouse Conditions

Plant Disease ◽  
2012 ◽  
Vol 96 (5) ◽  
pp. 705-711 ◽  
Author(s):  
B. Dutta ◽  
H. Scherm ◽  
R. D. Gitaitis ◽  
R. R. Walcott
Keyword(s):  
Disease Transmission ◽  
Pathogen Detection ◽  
Primary Source ◽  
Immunomagnetic Separation ◽  
Spatial Spread ◽  
Bacterial Fruit Blotch ◽  
Acidovorax Citrulli ◽  
Seed Health ◽  
Polymerase Chain ◽  
The Relationship

Infested seed are typically the primary source of inoculum for bacterial fruit blotch (BFB) of cucurbits. An inoculum threshold of 1 infested seed per 10,000 seeds is widely used in seed health testing for Acidovorax citrulli. However, the influence of seed inoculum load on BFB seedling transmission has not been elucidated. In this study, watermelon seedlots (128 seeds/lot) containing one seed inoculated with A. citrulli at levels ranging from 1 × 101 to 1 × 107 CFU were used to investigate the effect of seed inoculum load on seedling transmission and spatiotemporal spread of BFB under greenhouse conditions. The relationship between A. citrulli seed inoculum load and frequency of BFB seedling transmission followed a sigmoidal pattern (R2 = 0.986, P = 0.0047). In all, 100 and 96.6% of seedlots containing one seed with 1 × 107 and 1 × 105 CFU of A. citrulli, respectively, transmitted the pathogen to seedlings; in contrast, the proportion of seedlots that yielded BFB-infected seedlings was lower for lots with one seed infested with 1 × 103 (46.6%) and 1 × 101 (16.7%) CFU of A. citrulli. The relationship between A. citrulli seed inoculum load and frequency of pathogen detection in seedlots using immunomagnetic separation combined with a real-time polymerase chain reaction assay also followed a sigmoidal pattern (R2 = 0.997, P = 0.0034). Whereas 100% of samples from seedlots (10,000 seeds/lot) with one seed containing ≥1 × 105 CFU tested positive for A. citrulli, 75% of samples from lots with one seed containing 1 × 103 CFU tested positive for the pathogen, and only 16.7% of samples with one seed containing 10 CFU tested positive. Because disease transmission was observed for lots with just one seed containing 10 A. citrulli CFU, zero tolerance for seedborne A. citrulli is recommended for effective BFB management. The seedling transmission experiments also revealed that temporal spread of BFB in 128-cell seedling trays increased linearly with A. citrulli inoculum load (r2 = 0.976, P = 0.0037). Additionally, the frequency of spatial spread of BFB from an inoculated seedling in the center of a planting tray to adjacent healthy seedlings over one-, two-, or three-cell distances was greater for lots with one seed infested with at least 1 × 105 CFU than for lots with one seed infested at lower inoculum loads (1 × 101 and 1 × 103 CFU/seed).

scholarly journals Replication timing maintains the global epigenetic state in human cells

2019 ◽  
Author(s):  
Kyle N. Klein ◽  
Peiyao A. Zhao ◽  
Xiaowen Lyu ◽  
Daniel A. Bartlett ◽  
Amar Singh ◽  
...  
Keyword(s):  
Embryonic Stem ◽  
Cancer Cell Line ◽  
Replication Timing ◽  
Cell Types ◽  
Control Factor ◽  
Epigenetic State ◽  
Genome Wide ◽  
A Genome ◽  
A Cell ◽  
Early Replication

AbstractDNA is replicated in a defined temporal order termed the replication timing (RT) program. RT is spatially segregated in the nucleus with early/late replication corresponding to Hi-C A/B chromatin compartments, respectively. Early replication is also associated with active histone modifications and transcriptional permissiveness. However, the mechanistic interplay between RT, chromatin state, and genome compartmentalization is largely unknown. Here we report that RT is central to epigenome maintenance and compartmentalization in both human embryonic stem cells (hESCs) and cancer cell line HCT116. Knockout (KO) of the conserved RT control factor RIF1, rather than causing discrete RT switches as previously suspected, lead to dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1’s enrichment in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike all prior RIF1 KO cells, including HCT116, which show localized alterations. Regions that retain RT, which are prevalent in HCT116 but rare in hESCs, consist of large H3K9me3 domains revealing two independent mechanisms of RT regulation that are used to different extents in different cell types. RIF1 KO results in a striking genome wide downregulation of H3K27ac peaks and enrichment of H3K9me3 at large domains that remain late replicating, while H3K27me3 and H3K4me3 are re-distributed genome wide in a cell type specific manner. These histone modification changes coincided with global reorganization of genome compartments, transcription changes and a genome wide strengthening of TAD structures. Inducible degradation of RIF1 revealed that disruption of RT is upstream of genome compartmentalization changes. Our findings demonstrate that disruption of RT leads to widespread epigenetic mis-regulation, supporting previously speculative models in which the timing of chromatin assembly at the replication fork plays a key role in maintaining the global epigenetic state, which in turn drives genome architecture.

scholarly journals A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

2019 ◽  
Author(s):  
Thordis Kristjansdottir ◽  
Elleke F. Bosma ◽  
Filipe Branco dos Santos ◽  
Emre Özdemir ◽  
Markus J. Herrgård ◽  
...  
Keyword(s):  
Experimental Data ◽  
Metabolic Engineering ◽  
Growth Rates ◽  
Lactobacillus Reuteri ◽  
Metabolic Model ◽  
Metabolic Reconstruction ◽  
Cell Factory ◽  
A Genome ◽  
A Cell ◽  
Genome Scale

AbstractBackgroundLactobacillus reuteri is a heterofermentative Lactic Acid Bacterium (LAB) that is commonly used for food fermentations and probiotic purposes. Due to its robust properties, it is also increasingly considered for use as a cell factory. It produces several industrially important compounds such as 1,3-propanediol and reuterin natively, but for cell factory purposes, developing improved strategies for engineering and fermentation optimization is crucial. Genome-scale metabolic models can be highly beneficial in guiding rational metabolic engineering. Reconstructing a reliable and a quantitatively accurate metabolic model requires extensive manual curation and incorporation of experimental data.ResultsA genome-scale metabolic model of L. reuteri JCM 1112T was reconstructed and the resulting model, Lreuteri_530, was validated and tested with experimental data. Several knowledge gaps in the metabolism were identified and resolved during this process, including presence/absence of glycolytic genes. Flux distribution between the two glycolytic pathways, the phosphoketolase and Embden-Meyerhof-Parnas pathways, varies considerably between LAB species and strains. As these pathways result in different energy yields, it is important to include strain-specific utilization of these pathways in the model. We determined experimentally that the Embden-Meyerhof-Parnas pathway carried at most 7% of the total glycolytic flux. Predicted growth rates from Lreuteri_530 were in good agreement with experimentally determined values. To further validate the prediction accuracy of Lreuteri_530, the predicted effects of glycerol addition and adhE gene knock-out, which results in impaired ethanol production, were compared to in vivo data. Examination of both growth rates and uptake- and secretion rates of the main metabolites in central metabolism demonstrated that the model was able to accurately predict the experimentally observed effects. Lastly, the potential of L. reuteri as a cell factory was investigated, resulting in a number of general metabolic engineering strategies.ConclusionWe have constructed a manually curated genome-scale metabolic model of L. reuteri JCM 1112T that has been experimentally parameterized and validated and can accurately predict metabolic behavior of this important platform cell factory.

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