The Experts below are selected from a list of 75 Experts worldwide ranked by ideXlab platform
Joseph D Jakowski - One of the best experts on this subject based on the ideXlab platform.
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The chance identification of unusual-appearing bacteria in bronchoalveolar lavage fluid.
Acta cytologica, 2012Co-Authors: Matthew L Hearp, Joseph D JakowskiAbstract:A well-known indication for the cytologic examination of bronchoalveolar lavage (BAL) fluid is the identification of infectious organisms. However, an important distinction must be made as to whether the organisms seen represent a true opportunistic lower respiratory tract infection or a non-pathologic contamination. We describe herein the case of a 13-month-old male infant who presented with persistent chest congestion and tracheobronchitis and who underwent BAL as part of his clinical work-up. On cytological examination of the BAL fluid, the Romanowsky-stained cytospin slides contained numerous squamous epithelial cells with some showing rare striated rod-like structures on their surfaces. The peculiar structures also had rounded ends and were very large when compared to adjacent known bacterial cocci. We have determined that the striated rod-like structures in the infant's BAL fluid were indeed bacteria, Simonsiella sp. Simonsiella has reportedly been found in up to 32% of oral swabs in normal humans and it is considered a commensal and non-pathogenic organism. The characteristically large size, the association with normal oral-derived squamous cells and the striated appearance is diagnostic and will hopefully eliminate any possibility of confusion with a truly pathogenic organism. Copyright © 2012 S. Karger AG, Basel.
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The chance identification of unusual-appearing bacteria in bronchoalveolar lavage fluid.
Acta cytologica, 2012Co-Authors: Matthew L Hearp, Joseph D JakowskiAbstract:Background: A well-known indication for the cytologic examination of bronchoalveolar lavage (BAL) fluid is the identification of infectious organisms. However, an important distinction must be made as to whether the organisms seen represent a true opportunistic lower respiratory tract infection or a non-pathologic contamination. Case: We describe herein the case of a 13-month-old male infant who presented with persistent chest congestion and tracheobronchitis and who underwent BAL as part of his clinical work-up. On cytological examination of the BAL fluid, the Romanowsky-stained cytospin slides contained numerous squamous epithelial cells with some showing rare striated rod-like structures on their surfaces. The peculiar structures also had rounded ends and were very large when compared to adjacent known bacterial cocci. Conclusion: We have determined that the striated rod-like structures in the infant’s BAL fluid were indeed bacteria, Simonsiella sp. Simonsiella has reportedly been found in up to 32% of oral swabs in normal humans and it is considered a commensal and non-pathogenic organism. The characteristically large size, the association with normal oral-derived squamous cells and the striated appearance is diagnostic and will hopefully eliminate any possibility of confusion with a truly pathogenic organism.
Andrew N. Miller - One of the best experts on this subject based on the ideXlab platform.
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Studies in genera similar to Torula: Bahusaganda, Bahusandhika, Pseudotorula, and Simmonsiella gen. nov
IMA Fungus, 2016Co-Authors: J. Leland Crane, Andrew N. MillerAbstract:A generic key is presented to delimit Torula from seven hyphomycete genera whose type species were at one time included in the genus or whose conidium ontogeny and conidium development appear similar or superficially similar to that of Torula herbarum , the type of the genus. In Bahusaganda , two new species are described (B. elliseverhartii and B. simmonsii spp. nov.) and three new combinations made (B. ambrosiae, B. elaeodes , and B. heteromorpha combs. nov.). In Bahusandhika , one new species (B. hughesii sp. nov.) is introduced, and two new combinations made (B. rhombica and B. terrestris combs. nov.), along with emendations in the circumscription of B. caligans and B. intercalaris. Latorua is considered synonymous with Bahusandhika . In Pseudotorula , one new combination is made (P. sundara comb. nov.), and one emendation proposed (P. helica) . The transfer of Dwayabeeja sundara , the type species of the genus, to Pseudotorula will require a new generic name to be introduced for D. aethiopica and D. cubensis . The new generic name Simmonsiella is established for Torula ndjilensis. Bahusandhika compacta is shown to be synonymous with Torula verrucospora .
Xin Daniel Gao - One of the best experts on this subject based on the ideXlab platform.
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Potent Cas9 Inhibition in Bacterial and Human Cells by AcrIIC4 and AcrIIC5 Anti-CRISPR Proteins.
mBio, 2018Co-Authors: Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E. Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin Daniel GaoAbstract:In their natural settings, CRISPR-Cas systems play crucial roles in bacterial and archaeal adaptive immunity to protect against phages and other mobile genetic elements, and they are also widely used as genome engineering technologies. Previously we discovered bacteriophage-encoded Cas9-specific anti-CRISPR (Acr) proteins that serve as countermeasures against host bacterial immunity by inactivating their CRISPR-Cas systems (A. Pawluk, N. Amrani, Y. Zhang, B. Garcia, et al., Cell 167:1829-1838.e9, 2016, https://doi.org/10.1016/j.cell.2016.11.017). We hypothesized that the evolutionary advantages conferred by anti-CRISPRs would drive the widespread occurrence of these proteins in nature (K. L. Maxwell, Mol Cell 68:8-14, 2017, https://doi.org/10.1016/j.molcel.2017.09.002; A. Pawluk, A. R. Davidson, and K. L. Maxwell, Nat Rev Microbiol 16:12-17, 2018, https://doi.org/10.1038/nrmicro.2017.120; E. J. Sontheimer and A. R. Davidson, Curr Opin Microbiol 37:120-127, 2017, https://doi.org/10.1016/j.mib.2017.06.003). We have identified new anti-CRISPRs using the same bioinformatic approach that successfully identified previous Acr proteins (A. Pawluk, N. Amrani, Y. Zhang, B. Garcia, et al., Cell 167:1829-1838.e9, 2016, https://doi.org/10.1016/j.cell.2016.11.017) against Neisseria meningitidis Cas9 (NmeCas9). In this work, we report two novel anti-CRISPR families in strains of Haemophilus parainfluenzae and Simonsiella muelleri, both of which harbor type II-C CRISPR-Cas systems (A. Mir, A. Edraki, J. Lee, and E. J. Sontheimer, ACS Chem Biol 13:357-365, 2018, https://doi.org/10.1021/acschembio.7b00855). We characterize the type II-C Cas9 orthologs from H. parainfluenzae and S. muelleri, show that the newly identified Acrs are able to inhibit these systems, and define important features of their inhibitory mechanisms. The S. muelleri Acr is the most potent NmeCas9 inhibitor identified to date. Although inhibition of NmeCas9 by anti-CRISPRs from H. parainfluenzae and S. muelleri reveals cross-species inhibitory activity, more distantly related type II-C Cas9s are not inhibited by these proteins. The specificities of anti-CRISPRs and divergent Cas9s appear to reflect coevolution of their strategies to combat or evade each other. Finally, we validate these new anti-CRISPR proteins as potent off-switches for Cas9 genome engineering applications.IMPORTANCE As one of their countermeasures against CRISPR-Cas immunity, bacteriophages have evolved natural inhibitors known as anti-CRISPR (Acr) proteins. Despite the existence of such examples for type II CRISPR-Cas systems, we currently know relatively little about the breadth of Cas9 inhibitors, and most of their direct Cas9 targets are uncharacterized. In this work we identify two new type II-C anti-CRISPRs and their cognate Cas9 orthologs, validate their functionality in vitro and in bacteria, define their inhibitory spectrum against a panel of Cas9 orthologs, demonstrate that they act before Cas9 DNA binding, and document their utility as off-switches for Cas9-based tools in mammalian applications. The discovery of diverse anti-CRISPRs, the mechanistic analysis of their cognate Cas9s, and the definition of Acr inhibitory mechanisms afford deeper insight into the interplay between Cas9 orthologs and their inhibitors and provide greater scope for exploiting Acrs for CRISPR-based genome engineering.
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Potent Cas9 inhibition in bacterial and human cells by new anti-CRISPR protein families
2018Co-Authors: Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E. Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin Daniel GaoAbstract:CRISPR-Cas systems are widely used for genome engineering technologies, and in their natural setting, they play crucial roles in bacterial and archaeal adaptive immunity, protecting against phages and other mobile genetic elements. Previously we discovered bacteriophage-encoded Cas9-specific anti-CRISPR (Acr) proteins that serve as countermeasures against host bacterial immunity by inactivating their CRISPR-Cas systems. We hypothesized that the evolutionary advantages conferred by anti-CRISPRs would drive the widespread occurrence of these proteins in nature. We have identified new anti-CRISPRs using the bioinformatic approach that successfully identified previous Acr proteins against Neisseria meningitidis Cas9 (NmeCas9). In this work we report two novel anti-CRISPR families in strains of Haemophilus parainfluenzae and Simonsiella muelleri , both of which harbor type II-C CRISPR-Cas systems. We characterize the type II-C Cas9 orthologs from H. parainfluenzae and S. muelleri , show that the newly identified Acrs are able to inhibit these systems, and define important features of their inhibitory mechanisms. The S. muelleri Acr is the most potent NmeCas9 inhibitor identified to date. Although inhibition of NmeCas9 by anti-CRISPRs from H. parainfluenzae and S. muelleri reveals cross-species inhibitory activity, more distantly related type II-C Cas9s are not inhibited by these proteins. The specificities of anti-CRISPRs and divergent Cas9s appear to reflect co-evolution of their strategies to combat or evade each other. Finally, we validate these new anti-CRISPR proteins as potent off-switches for Cas9 genome engineering applications.
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Potent Cas9 Inhibition in Bacterial and Human Cells by AcrIIC4 and AcrIIC5 Anti-CRISPR Proteins
American Society for Microbiology, 2018Co-Authors: Jooyoung Lee, Aamir Mir, Alireza Edraki, Bianca Garcia, Nadia Amrani, Hannah E. Lou, Ildar Gainetdinov, April Pawluk, Raed Ibraheim, Xin Daniel GaoAbstract:As one of their countermeasures against CRISPR-Cas immunity, bacteriophages have evolved natural inhibitors known as anti-CRISPR (Acr) proteins. Despite the existence of such examples for type II CRISPR-Cas systems, we currently know relatively little about the breadth of Cas9 inhibitors, and most of their direct Cas9 targets are uncharacterized. In this work we identify two new type II-C anti-CRISPRs and their cognate Cas9 orthologs, validate their functionality in vitro and in bacteria, define their inhibitory spectrum against a panel of Cas9 orthologs, demonstrate that they act before Cas9 DNA binding, and document their utility as off-switches for Cas9-based tools in mammalian applications. The discovery of diverse anti-CRISPRs, the mechanistic analysis of their cognate Cas9s, and the definition of Acr inhibitory mechanisms afford deeper insight into the interplay between Cas9 orthologs and their inhibitors and provide greater scope for exploiting Acrs for CRISPR-based genome engineering.In their natural settings, CRISPR-Cas systems play crucial roles in bacterial and archaeal adaptive immunity to protect against phages and other mobile genetic elements, and they are also widely used as genome engineering technologies. Previously we discovered bacteriophage-encoded Cas9-specific anti-CRISPR (Acr) proteins that serve as countermeasures against host bacterial immunity by inactivating their CRISPR-Cas systems (A. Pawluk, N. Amrani, Y. Zhang, B. Garcia, et al., Cell 167:1829–1838.e9, 2016, https://doi.org/10.1016/j.cell.2016.11.017). We hypothesized that the evolutionary advantages conferred by anti-CRISPRs would drive the widespread occurrence of these proteins in nature (K. L. Maxwell, Mol Cell 68:8–14, 2017, https://doi.org/10.1016/j.molcel.2017.09.002; A. Pawluk, A. R. Davidson, and K. L. Maxwell, Nat Rev Microbiol 16:12–17, 2018, https://doi.org/10.1038/nrmicro.2017.120; E. J. Sontheimer and A. R. Davidson, Curr Opin Microbiol 37:120–127, 2017, https://doi.org/10.1016/j.mib.2017.06.003). We have identified new anti-CRISPRs using the same bioinformatic approach that successfully identified previous Acr proteins (A. Pawluk, N. Amrani, Y. Zhang, B. Garcia, et al., Cell 167:1829–1838.e9, 2016, https://doi.org/10.1016/j.cell.2016.11.017) against Neisseria meningitidis Cas9 (NmeCas9). In this work, we report two novel anti-CRISPR families in strains of Haemophilus parainfluenzae and Simonsiella muelleri, both of which harbor type II-C CRISPR-Cas systems (A. Mir, A. Edraki, J. Lee, and E. J. Sontheimer, ACS Chem Biol 13:357–365, 2018, https://doi.org/10.1021/acschembio.7b00855). We characterize the type II-C Cas9 orthologs from H. parainfluenzae and S. muelleri, show that the newly identified Acrs are able to inhibit these systems, and define important features of their inhibitory mechanisms. The S. muelleri Acr is the most potent NmeCas9 inhibitor identified to date. Although inhibition of NmeCas9 by anti-CRISPRs from H. parainfluenzae and S. muelleri reveals cross-species inhibitory activity, more distantly related type II-C Cas9s are not inhibited by these proteins. The specificities of anti-CRISPRs and divergent Cas9s appear to reflect coevolution of their strategies to combat or evade each other. Finally, we validate these new anti-CRISPR proteins as potent off-switches for Cas9 genome engineering applications
Matthew L Hearp - One of the best experts on this subject based on the ideXlab platform.
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The chance identification of unusual-appearing bacteria in bronchoalveolar lavage fluid.
Acta cytologica, 2012Co-Authors: Matthew L Hearp, Joseph D JakowskiAbstract:A well-known indication for the cytologic examination of bronchoalveolar lavage (BAL) fluid is the identification of infectious organisms. However, an important distinction must be made as to whether the organisms seen represent a true opportunistic lower respiratory tract infection or a non-pathologic contamination. We describe herein the case of a 13-month-old male infant who presented with persistent chest congestion and tracheobronchitis and who underwent BAL as part of his clinical work-up. On cytological examination of the BAL fluid, the Romanowsky-stained cytospin slides contained numerous squamous epithelial cells with some showing rare striated rod-like structures on their surfaces. The peculiar structures also had rounded ends and were very large when compared to adjacent known bacterial cocci. We have determined that the striated rod-like structures in the infant's BAL fluid were indeed bacteria, Simonsiella sp. Simonsiella has reportedly been found in up to 32% of oral swabs in normal humans and it is considered a commensal and non-pathogenic organism. The characteristically large size, the association with normal oral-derived squamous cells and the striated appearance is diagnostic and will hopefully eliminate any possibility of confusion with a truly pathogenic organism. Copyright © 2012 S. Karger AG, Basel.
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The chance identification of unusual-appearing bacteria in bronchoalveolar lavage fluid.
Acta cytologica, 2012Co-Authors: Matthew L Hearp, Joseph D JakowskiAbstract:Background: A well-known indication for the cytologic examination of bronchoalveolar lavage (BAL) fluid is the identification of infectious organisms. However, an important distinction must be made as to whether the organisms seen represent a true opportunistic lower respiratory tract infection or a non-pathologic contamination. Case: We describe herein the case of a 13-month-old male infant who presented with persistent chest congestion and tracheobronchitis and who underwent BAL as part of his clinical work-up. On cytological examination of the BAL fluid, the Romanowsky-stained cytospin slides contained numerous squamous epithelial cells with some showing rare striated rod-like structures on their surfaces. The peculiar structures also had rounded ends and were very large when compared to adjacent known bacterial cocci. Conclusion: We have determined that the striated rod-like structures in the infant’s BAL fluid were indeed bacteria, Simonsiella sp. Simonsiella has reportedly been found in up to 32% of oral swabs in normal humans and it is considered a commensal and non-pathogenic organism. The characteristically large size, the association with normal oral-derived squamous cells and the striated appearance is diagnostic and will hopefully eliminate any possibility of confusion with a truly pathogenic organism.
J. Leland Crane - One of the best experts on this subject based on the ideXlab platform.
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Studies in genera similar to Torula: Bahusaganda, Bahusandhika, Pseudotorula, and Simmonsiella gen. nov
IMA Fungus, 2016Co-Authors: J. Leland Crane, Andrew N. MillerAbstract:A generic key is presented to delimit Torula from seven hyphomycete genera whose type species were at one time included in the genus or whose conidium ontogeny and conidium development appear similar or superficially similar to that of Torula herbarum , the type of the genus. In Bahusaganda , two new species are described (B. elliseverhartii and B. simmonsii spp. nov.) and three new combinations made (B. ambrosiae, B. elaeodes , and B. heteromorpha combs. nov.). In Bahusandhika , one new species (B. hughesii sp. nov.) is introduced, and two new combinations made (B. rhombica and B. terrestris combs. nov.), along with emendations in the circumscription of B. caligans and B. intercalaris. Latorua is considered synonymous with Bahusandhika . In Pseudotorula , one new combination is made (P. sundara comb. nov.), and one emendation proposed (P. helica) . The transfer of Dwayabeeja sundara , the type species of the genus, to Pseudotorula will require a new generic name to be introduced for D. aethiopica and D. cubensis . The new generic name Simmonsiella is established for Torula ndjilensis. Bahusandhika compacta is shown to be synonymous with Torula verrucospora .