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228 results on '"Lorenzi, Hernan"'

2. From TgO/GABA-AT, GABA, and T-263 Mutant to Conception of Toxoplasma

Author

Lykins, Joseph, Moschitto, Matthew J., Zhou, Ying, Filippova, Ekaterina V., Le, Hoang V., Tomita, Tadakimi, Fox, Barbara A., Bzik, David J., Su, Chunlei, Rajagopala, Seesandra V., Flores, Kristin, Spano, Furio, Woods, Stuart, Roberts, Craig W., Hua, Cong, El Bissati, Kamal, Wheeler, Kelsey M., Dovgin, Sarah, Muench, Stephen P., McPhillie, Martin, Fishwick, Colin W.G., Anderson, Wayne F., Lee, Patricia J., Hickman, Mark, Weiss, Louis M., Dubey, Jitender P., Lorenzi, Hernan A., Silverman, Richard B., and McLeod, Rima L.

Published
2024
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6. Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species.

Author

Hockens, Clio, Lorenzi, Hernan, Wang, Tricia T., Lei, Elissa P., and Rosin, Leah F.

Subjects
*CHROMOSOME segregation, *INDIANMEAL moth, *SILKWORMS, *SPINDLE apparatus, *SPERMATOGENESIS, *MICROTUBULES, *CHROMOSOMES, *SPERMATOZOA, *SLEEP spindles
Abstract

Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events such as homolog pairing and chromosome segregation are not fully understood in many species. Here, we employ Oligopaint DNA FISH to investigate mechanisms of meiotic homolog pairing and chromosome segregation in the holocentric pantry moth, Plodia interpunctella, and compare our findings to new and previous studies in the silkworm moth, Bombyx mori, which diverged from P. interpunctella over 100 million years ago. We find that pairing in both Bombyx and Plodia spermatogenesis is initiated at gene-rich chromosome ends. Additionally, both species form rod shaped cruciform-like bivalents at metaphase I. However, unlike the telomere-oriented chromosome segregation mechanism observed in Bombyx, Plodia can orient bivalents in multiple different ways at metaphase I. Surprisingly, in both species we find that kinetochores consistently assemble at non-telomeric loci toward the centers of chromosomes regardless of where chromosome centers are located in the bivalent. Additionally, sister kinetochores do not seem to be paired in these species. Instead, four distinct kinetochores are easily observed at metaphase I. Despite this, we find clear end-on microtubule attachments and not lateral microtubule attachments connecting these separated kinetochores to the meiotic spindle. These findings challenge the classical view of segregation where paired, poleward-facing kinetochores are required for accurate homolog separation in meiosis I. Our studies here highlight the importance of exploring fundamental processes in non-model systems, as employing novel organisms can lead to the discovery of novel biology. Author summary: In order for genetic information to be accurately passed on from one generation to the next, maternal and paternal chromosome copies (homologs) must be separated from each other when making egg and sperm cells in a process called meiosis. To facilitate this equal division, homologous partners pair up from end to end, undergo an exchange of genetic information, and then large protein complexes called kinetochores are formed to enable chromosome segregation. Here, we investigate how homologs pair and how kinetochores form during the formation of sperm in two different moth species: Bombyx mori (the silkworm moth) and Plodia interpunctella (the pantry moth). Using a combination of microscopy approaches, we observe that homologs seem to pair via interactions at chromosome ends. Conversely, we found that kinetochores form at chromosome centers, away from chromosome ends. This is true even when chromosomes are folded into different configurations. These central kinetochores are functional and able to recruit microtubules, the structures that physically pull chromosomes apart for segregation. How chromosome centers are specified to be kinetochore-recruitment sites in meiosis, and what causes the formation of different chromosome folding configurations, are areas of future study. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes.

Author

Lorenzi, Hernan, Khan, Asis, Behnke, Michael S, Namasivayam, Sivaranjani, Swapna, Lakshmipuram S, Hadjithomas, Michalis, Karamycheva, Svetlana, Pinney, Deborah, Brunk, Brian P, Ajioka, James W, Ajzenberg, Daniel, Boothroyd, John C, Boyle, Jon P, Dardé, Marie L, Diaz-Miranda, Maria A, Dubey, Jitender P, Fritz, Heather M, Gennari, Solange M, Gregory, Brian D, Kim, Kami, Saeij, Jeroen PJ, Su, Chunlei, White, Michael W, Zhu, Xing-Quan, Howe, Daniel K, Rosenthal, Benjamin M, Grigg, Michael E, Parkinson, John, Liu, Liang, Kissinger, Jessica C, Roos, David S, and Sibley, L David

Subjects
Toxoplasma, Protozoan Proteins, DNA, Protozoan, RNA, Messenger, Phylogeny, Virulence, Gene Expression Regulation, Conserved Sequence, Synteny, Polymorphism, Single Nucleotide, Genome, Protozoan, DNA, Protozoan, Genome, Polymorphism, Single Nucleotide, RNA, Messenger
Abstract

Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are significantly enriched in tandemly clustered secretory pathogenesis determinants. The shared inheritance of these conserved haploblocks, which show a different ancestry than the genome as a whole, may thus influence transmission, host range and pathogenicity.

Published
2016

12. Author Correction: New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections

Author

McPhillie, Martin, Zhou, Ying, El Bissati, Kamal, Dubey, Jitender, Lorenzi, Hernan, Capper, Michael, Lukens, Amanda K., Hickman, Mark, Muench, Stephen, Verma, Shiv Kumar, Weber, Christopher R., Wheeler, Kelsey, Gordon, James, Sanders, Justin, Moulton, Hong, Wang, Kai, Kim, Taek-Kyun, He, Yuqing, Santos, Tatiana, Woods, Stuart, Lee, Patty, Donkin, David, Kim, Eric, Fraczek, Laura, Lykins, Joseph, Esaa, Farida, Alibana-Clouser, Fatima, Dovgin, Sarah, Weiss, Louis, Brasseur, Gael, Wirth, Dyann, Kent, Michael, Hood, Leroy, Meunieur, Brigitte, Roberts, Craig W., Hasnain, S. Samar, Antonyuk, Svetlana V., Fishwick, Colin, and McLeod, Rima

Published
2020
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18. Publisher Correction: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer

Author

Ngô, Huân M., Zhou, Ying, Lorenzi, Hernan, Wang, Kai, Kim, Taek-Kyun, Zhou, Yong, El Bissati, Kamal, Mui, Ernest, Fraczek, Laura, Rajagopala, Seesandra V., Roberts, Craig W., Henriquez, Fiona L., Montpetit, Alexandre, Blackwell, Jenefer M., Jamieson, Sarra E., Wheeler, Kelsey, Begeman, Ian J., Naranjo-Galvis, Carlos, Alliey-Rodriguez, Ney, Davis, Roderick G., Soroceanu, Liliana, Cobbs, Charles, Steindler, Dennis A., Boyer, Kenneth, Noble, A. Gwendolyn, Swisher, Charles N., Heydemann, Peter T., Rabiah, Peter, Withers, Shawn, Soteropoulos, Patricia, Hood, Leroy, and McLeod, Rima

Published
2019
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19. Chemokine positioning determines mutually exclusive roles for their receptors in extravasation of pathogenic human T cells

Author

Parween, Farhat, primary, Singh, Satya P., additional, Zhang, Hongwei H, additional, Kathuria, Nausheen, additional, Otaizo-Carrasquero, Francisco A., additional, Shamsaddini, Amirhossein, additional, Gardina, Paul J., additional, Ganesan, Sundar, additional, Kabat, Juraj, additional, Lorenzi, Hernan A., additional, Myers, Timothy G., additional, and Farber, Joshua M., additional

Published
2023
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21. Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer

Author

Ngô, Huân M., Zhou, Ying, Lorenzi, Hernan, Wang, Kai, Kim, Taek-Kyun, Zhou, Yong, El Bissati, Kamal, Mui, Ernest, Fraczek, Laura, Rajagopala, Seesandra V., Roberts, Craig W., Henriquez, Fiona L., Montpetit, Alexandre, Blackwell, Jenefer M., Jamieson, Sarra E., Wheeler, Kelsey, Begeman, Ian J., Naranjo-Galvis, Carlos, Alliey-Rodriguez, Ney, Davis, Roderick G., Soroceanu, Liliana, Cobbs, Charles, Steindler, Dennis A., Boyer, Kenneth, Noble, A. Gwendolyn, Swisher, Charles N., Heydemann, Peter T., Rabiah, Peter, Withers, Shawn, Soteropoulos, Patricia, Hood, Leroy, and McLeod, Rima

Published
2017
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22. Protein nanovaccine confers robust immunity against Toxoplasma

Author

El Bissati, Kamal, Zhou, Ying, Paulillo, Sara Maria, Raman, Senthil Kumar, Karch, Christopher P., Roberts, Craig W., Lanar, David E., Reed, Steve, Fox, Chris, Carter, Darrick, Alexander, Jeff, Sette, Alessandro, Sidney, John, Lorenzi, Hernan, Begeman, Ian J., Burkhard, Peter, and McLeod, Rima

Published
2017
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23. New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections

Author

McPhillie, Martin, Zhou, Ying, El Bissati, Kamal, Dubey, Jitender, Lorenzi, Hernan, Capper, Michael, Lukens, Amanda K, Hickman, Mark, Muench, Stephen, Verma, Shiv Kumar, Weber, Christopher R., Wheeler, Kelsey, Gordon, James, Sanders, Justin, Moulton, Hong, Wang, Kai, Kim, Taek-Kyun, He, Yuqing, Santos, Tatiana, Woods, Stuart, Lee, Patty, Donkin, David, Kim, Eric, Fraczek, Laura, Lykins, Joseph, Esaa, Farida, Alibana-Clouser, Fatima, Dovgin, Sarah, Weiss, Louis, Brasseur, Gael, Wirth, Dyann, Kent, Michael, Hood, Leroy, Meunieur, Brigitte, Roberts, Craig W., Hasnain, S. Samar, Antonyuk, Svetlana V., Fishwick, Colin, and McLeod, Rima

Published
2016
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24. The Role of microRNAs in the Infection by T. gondii in Humans

Author

de Faria Junior, Geraldo Magela, primary, Murata, Fernando Henrique Antunes, additional, Lorenzi, Hernan Alejandro, additional, Castro, Bruno Bello Pede, additional, Assoni, Letícia Carolina Paraboli, additional, Ayo, Christiane Maria, additional, Brandão, Cinara Cássia, additional, and de Mattos, Luiz Carlos, additional

Published
2021
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25. High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii

Author

Massachusetts Institute of Technology. Department of Biology, Whitehead Institute for Biomedical Research, Markus, Benedikt M, Waldman, Benjamin S, Lorenzi, Hernan A, Lourido, Sebastian, Massachusetts Institute of Technology. Department of Biology, Whitehead Institute for Biomedical Research, Markus, Benedikt M, Waldman, Benjamin S, Lorenzi, Hernan A, and Lourido, Sebastian

Abstract

© Copyright © 2021 Markus, Waldman, Lorenzi and Lourido. Toxoplasma gondii is a common parasite of humans and animals, causing life-threatening disease in the immunocompromized, fetal abnormalities when contracted during gestation, and recurrent ocular lesions in some patients. Central to the prevalence and pathogenicity of this protozoan is its ability to adapt to a broad range of environments, and to differentiate between acute and chronic stages. These processes are underpinned by a major rewiring of gene expression, yet the mechanisms that regulate transcription in this parasite are only partially characterized. Deciphering these mechanisms requires a precise and comprehensive map of transcription start sites (TSSs); however, Toxoplasma TSSs have remained incompletely defined. To address this challenge, we used 5′-end RNA sequencing to genomically assess transcription initiation in both acute and chronic stages of Toxoplasma. Here, we report an in-depth analysis of transcription initiation at promoters, and provide empirically-defined TSSs for 7603 (91%) protein-coding genes, of which only 1840 concur with existing gene models. Comparing data from acute and chronic stages, we identified instances of stage-specific alternative TSSs that putatively generate mRNA isoforms with distinct 5′ termini. Analysis of the nucleotide content and nucleosome occupancy around TSSs allowed us to examine the determinants of TSS choice, and outline features of Toxoplasma promoter architecture. We also found pervasive divergent transcription at Toxoplasma promoters, clustered within the nucleosomes of highly-symmetrical phased arrays, underscoring chromatin contributions to transcription initiation. Corroborating previous observations, we asserted that Toxoplasma 5′ leaders are among the longest of any eukaryote studied thus far, displaying a median length of approximately 800 nucleotides. Further highlighting the utility of a precise TSS map, we pinpointed motifs associated with t

Published
2021

26. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novopiRNA-precursor formation in mammals

Author

Konstantinidou, Parthena, Loubalova, Zuzana, Ahrend, Franziska, Friman, Aleksandr, Almeida, Miguel Vasconcelos, Poulet, Axel, Horvat, Filip, Wang, Yuejun, Losert, Wolfgang, Lorenzi, Hernan, Svoboda, Petr, Miska, Eric A., van Wolfswinkel, Josien C., and Haase, Astrid D.

Abstract

PIWI-interacting RNAs (piRNAs) play a crucial role in safeguarding genome integrity by silencing mobile genetic elements. From flies to humans, piRNAs originate from long single-stranded precursors encoded by genomic piRNA clusters. How piRNA clusters form to adapt to genomic invaders and evolve to maintain protection remain key outstanding questions. Here, we generate a roadmap of piRNA clusters across seven species that highlights both similarities and variations. In mammals, we identify transcriptional readthrough as a mechanism to generate piRNAs from transposon insertions (piCs) downstream of genes (DoG). Together with the well-known stress-dependent DoG transcripts, our findings suggest a molecular mechanism for the formation of piRNA clusters in response to retroviral invasion. Finally, we identify a class of dynamic piRNA clusters in humans, underscoring unique features of human germ cell biology. Our results advance the understanding of conserved principles and species-specific variations in piRNA biology and provide tools for future studies.

Published
2024
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27. New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections (vol 6, 29179, 2016)

Author

McPhillie, Martin, Zhou, Ying, El Bissati, Kamal, Dubey, Jitender, Lorenzi, Hernan, Capper, Michael, Lukens, Amanda K, Hickman, Mark, Muench, Stephen, Verma, Shiv Kumar, Weber, Christopher R, Wheeler, Kelsey, Gordon, James, Sanders, Justin, Moulton, Hong, Wang, Kai, Kim, Taek-Kyun, He, Yuqing, Santos, Tatiana, Woods, Stuart, Lee, Patty, Donkin, David, Kim, Eric, Fraczek, Laura, Lykins, Joseph, Esaa, Farida, Alibana-Clouser, Fatima, Dovgin, Sarah, Weiss, Louis, Brasseur, Gael, Wirth, Dyann, Kent, Michael, Hood, Leroy, Meunieur, Brigitte, Roberts, Craig W, Hasnain, S Samar, Antonyuk, Svetlana V, Fishwick, Colin, and McLeod, Rima

Published
2020

30. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease

Author

Sayed, Najib M. El-, Myler, Peter J., Bartholomeu, Daniela C., Nilsson, Daniel, Aggarwal, Gautam, Tran, Anh-Nhi, Ghedin, Elodie, Worthey, Elizabeth A., Delcher, Arthur L., Blandin, Gaelle, Westenberger, Scott J., Caler, Elisabet, Cerqueira, Gustavo C., Branche, Carole, Haas, Brian, Anupama, Atashi, Arner, Erik, Aslund, Lena, Attipoe, Philip, Bontempi, Esteban, Bringaud, Frederic, Burton, Peter, Cadag, Eithon, Campbell, David A., Carrington, Mark, Crabtree, Jonathan, Darban, Hamid, da Silveira, Jose Franco, de Jong, Pieter, Edwards, Kimberly, Englund, Paul T., Fazelina, Gholam, Feldblyum, Tamara, Ferella, Marcela, Frasch, Alberto Carlos, Gull, Keith, Horn, David, Hou, Lihua, Huang, Yiting, Kindlund, Ellen, Klingbeil, Michele, Kluge, Sindy, Koo, Hean, Lacerda, Daniela, Levin, Mariano J., Lorenzi, Hernan, Louie, Tin, Machado, Carlos Renato, McCulloch, Richard, McKenna, Alan, Mizuno, Yumi, Mottram, Jeremy C., Nelson, Siri, Ochaya, Stephen, Osoegawa, Kazutoyo, Pai, Grace, Parsons, Marilyn, Pentony, Martin, Pettersson, Ulf, Pop, Mihai, Ramirez, Jose Luis, Rinta, Joel, Robertson, Laura, Salzberg, Steven L., Sanchez, Daniel O., Seyler, Amber, Sharma, Reuben, Shetty, Jyoti, Simpson, Anjana J., Sisk, Ellen, Tammi, Martti T., Tarleton, Rick, Teixeira, Santuza, Van Aken, Susan, Vogt, Christy, Ward, Pauline N., Wickstead, Bill, Wortman, Jennifer, White, Owen, Fraser, Claire M., Stuart, Kenneth D., and Andersson, Bjorn

Subjects
Trypanosoma cruzi -- Genetic aspects, Science and technology
Abstract

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention., Trypanosoma cruzi causes Chagas disease in humans. Acute infection can be lethal, but the disease usually evolves into a chronic stage, accompanied in 25 to 30% of cases by severe [...]

Published
2005

32. Potent Tetrahydroquinolone Eliminates Apicomplexan Parasites

Author

McPhillie, Martin J., primary, Zhou, Ying, additional, Hickman, Mark R., additional, Gordon, James A., additional, Weber, Christopher R., additional, Li, Qigui, additional, Lee, Patty J., additional, Amporndanai, Kangsa, additional, Johnson, Rachel M., additional, Darby, Heather, additional, Woods, Stuart, additional, Li, Zhu-hong, additional, Priestley, Richard S., additional, Ristroph, Kurt D., additional, Biering, Scott B., additional, El Bissati, Kamal, additional, Hwang, Seungmin, additional, Hakim, Farida Esaa, additional, Dovgin, Sarah M., additional, Lykins, Joseph D., additional, Roberts, Lucy, additional, Hargrave, Kerrie, additional, Cong, Hua, additional, Sinai, Anthony P., additional, Muench, Stephen P., additional, Dubey, Jitender P., additional, Prud'homme, Robert K., additional, Lorenzi, Hernan A., additional, Biagini, Giancarlo A., additional, Moreno, Silvia N., additional, Roberts, Craig W., additional, Antonyuk, Svetlana V., additional, Fishwick, Colin W. G., additional, and McLeod, Rima, additional

Published
2020
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35. Pathema: a clade-specific bioinformatics resource center for pathogen research

Author

Brinkac, Lauren M., Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Caler, Elisabet, Dodson, Robert J., Durkin, A. Scott, Harkins, Derek M., Lorenzi, Hernan, Madupu, Ramana, Sebastian, Yinong, Shrivastava, Susmita, Thiagarajan, Mathangi, Orvis, Joshua, Sundaram, Jaideep P., Crabtree, Jonathon, Galens, Kevin, Zhao, Yongmei, Inman, Jason M., Montgomery, Robert, Schobel, Seth, Galinsky, Kevin, Tanenbaum, David M., Resnick, Adam, Zafar, Nikhat, White, Owen, and Sutton, Granger

Published
2010
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36. Comparative genomics of the neglected human malaria parasite Plasmodium vivax

Author

Carlton, Jane M., Adams, John H., Silva, Joana C., Bidwell, Shelby L., Lorenzi, Hernan, Caler, Elisabet, Crabtree, Jonathan, Angiuoli, Samuel V., Merino, Emilio F., Amedeo, Paolo, Cheng, Qin, Coulson, Richard M. R., Crabb, Brendan S., del Portillo, Hernando A., Essien, Kobby, Feldblyum, Tamara V., Fernandez-Becerra, Carmen, Gilson, Paul R., Gueye, Amy H., Guo, Xiang, Kang'a, Simon, Kooij, Taco W. A., Korsinczky, Michael, Meyer, Esmeralda V.-S., Nene, Vish, Paulsen, Ian, White, Owen, Ralph, Stuart A., Ren, Qinghu, Sargeant, Tobias J., Salzberg, Steven L., Stoeckert, Christian J., Sullivan, Steven A., Yamamoto, Marcio M., Hoffman, Stephen L., Wortman, Jennifer R., Gardner, Malcolm J., Galinski, Mary R., Barnwell, John W., and Fraser-Liggett, Claire M.

Published
2008
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37. The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease

Author

El-Sayed, Najib M., Myler, Peter J., Bartholomeu, Daniella C., Nilsson, Daniel, Aggarwal, Gautam, Tran, Anh-Nhi, Ghedin, Elodie, Worthey, Elizabeth A., Delcher, Arthur L., Blandin, Gaëlle, Westenberger, Scott J., Caler, Elisabet, Cerqueira, Gustavo C., Branche, Carole, Haas, Brian, Anupama, Atashi, Arner, Erik, Åslund, Lena, Attipoe, Philip, Bontempi, Esteban, Bringaud, Frédéric, Burton, Peter, Cadag, Eithon, Campbell, David A., Carrington, Mark, Crabtree, Jonathan, Darban, Hamid, da Silveira, Jose Franco, de Jong, Pieter, Edwards, Kimberly, Englund, Paul T., Fazelina, Gholam, Feldblyum, Tamara, Ferella, Marcela, Frasch, Alberto Carlos, Gull, Keith, Horn, David, Hou, Lihua, Huang, Yiting, Kindlund, Ellen, Klingbeil, Michele, Kluge, Sindy, Koo, Hean, Lacerda, Daniela, Levin, Mariano J., Lorenzi, Hernan, Louie, Tin, Machado, Carlos Renato, McCulloch, Richard, McKenna, Alan, Mizuno, Yumi, Mottram, Jeremy C., Nelson, Siri, Ochaya, Stephen, Osoegawa, Kazutoyo, Pai, Grace, Parsons, Marilyn, Pentony, Martin, Pettersson, Ulf, Pop, Mihai, Ramirez, Jose Luis, Rinta, Joel, Robertson, Laura, Salzberg, Steven L., Sanchez, Daniel O., Seyler, Amber, Sharma, Reuben, Shetty, Jyoti, Simpson, Anjana J., Sisk, Ellen, Tammi, Martti T., Tarleton, Rick, Teixeira, Santuza, Van Aken, Susan, Vogt, Christy, Ward, Pauline N., Wickstead, Bill, Wortman, Jennifer, White, Owen, Fraser, Claire M., Stuart, Kenneth D., and Andersson, Björn

Published
2005

38. Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth.

Author

Li, Weizhong, Tapiainen, Terhi, Brinkac, Lauren, Lorenzi, Hernan A, Moncera, Kelvin, Tejesvi, Mysore V, Salo, Jarmo, and Nelson, Karen E

Subjects
GUT microbiome, DRUG resistance in microorganisms, INFANTS, ANTIBIOTICS, NEWBORN infants
Abstract

Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P =.03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3–7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants. [ABSTRACT FROM AUTHOR]

Published
2021
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39. Specific Immunologic Countermeasure Protocol for Deep-Space Exploration Missions

Author

Makedonas, George, primary, Mehta, Satish, additional, Choukèr, Alexander, additional, Simpson, Richard J., additional, Marshall, Gailen, additional, Orange, Jordan S., additional, Aunon-Chancellor, Serena, additional, Smith, Scott M., additional, Zwart, Sara R., additional, Stowe, Raymond P., additional, Heer, Martina, additional, Ponomarev, Sergey, additional, Whitmire, Alexandra, additional, Frippiat, Jean P., additional, Douglas, Grace L., additional, Krieger, Stephanie S., additional, Lorenzi, Hernan, additional, Buchheim, Judith-Irina, additional, Ginsburg, Geoffrey S., additional, Ott, C. Mark, additional, Downs, Meghan, additional, Pierson, Duane, additional, Baecker, Natalie, additional, Sams, Clarence, additional, and Crucian, Brian, additional

Published
2019
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40. A Molecular Signature in Blood Reveals a Role for p53 in Regulating Malaria-Induced Inflammation

Author

Tran, Tuan M., primary, Guha, Rajan, additional, Portugal, Silvia, additional, Skinner, Jeff, additional, Ongoiba, Aissata, additional, Bhardwaj, Jyoti, additional, Jones, Marcus, additional, Moebius, Jacqueline, additional, Venepally, Pratap, additional, Doumbo, Safiatou, additional, DeRiso, Elizabeth A., additional, Li, Shanping, additional, Vijayan, Kamalakannan, additional, Anzick, Sarah L., additional, Hart, Geoffrey T., additional, O’Connell, Elise M., additional, Doumbo, Ogobara K., additional, Kaushansky, Alexis, additional, Alter, Galit, additional, Felgner, Phillip L., additional, Lorenzi, Hernan, additional, Kayentao, Kassoum, additional, Traore, Boubacar, additional, Kirkness, Ewen F., additional, and Crompton, Peter D., additional

Published
2019
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42. Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes

Author

Bose, Michael E., primary, Shrivastava, Susmita, additional, He, Jie, additional, Nelson, Martha I., additional, Bera, Jayati, additional, Fedorova, Nadia, additional, Halpin, Rebecca, additional, Town, Christopher D., additional, Lorenzi, Hernan A., additional, Amedeo, Paolo, additional, Gupta, Neha, additional, Noyola, Daniel E., additional, Videla, Cristina, additional, Kok, Tuckweng, additional, Buys, Amelia, additional, Venter, Marietjie, additional, Vabret, Astrid, additional, Cordey, Samuel, additional, and Henrickson, Kelly J., additional

Published
2019
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44. Integrated analysis of microRNA regulation and its interaction with mechanisms of epigenetic regulation in the etiology of systemic lupus erythematosus

Author

Navarro Quiroz, Elkin, primary, Navarro Quiroz, Roberto, additional, Pacheco Lugo, Lisandro, additional, Aroca Martínez, Gustavo, additional, Gómez Escorcia, Lorena, additional, Gonzalez Torres, Henry, additional, Cadena Bonfanti, Andres, additional, Marmolejo, Maria del Carmen, additional, Sanchez, Eduardo, additional, Villarreal Camacho, Jose Luis, additional, Lorenzi, Hernan, additional, Torres, Augusto, additional, Navarro, Kelvin Fernando, additional, Navarro Rodriguez, Pablo, additional, Villa, Joe Luis, additional, and Fernández-Ponce, Cecilia, additional

Published
2019
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47. Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species

Author

Wortman Jennifer, Haas Brian, Thiagarajan Mathangi, Lorenzi Hernan, Hall Neil, and Caler Elisabet

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Identification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba genomes, Entamoeba histolytica, Entamoeba dispar, and Entamoeba invadens, we performed comparative sequence analysis to identify and map all class I and class II transposable elements in their sequences. Results Here, we report the identification of two novel Entamoeba-specific repeats: ERE1 and ERE2; ERE1 is spread across the three genomes and associated with different repeats in a species-specific manner, while ERE2 is unique to E. histolytica. We also report the identification of two novel subfamilies of LINE and SINE retrotransposons in E. dispar and provide evidence for how the different LINE and SINE subfamilies evolved in these species. Additionally, we found a putative transposase-coding gene in E. histolytica and E. dispar related to the mariner transposon Hydargos from E. invadens. The distribution of transposable elements in these genomes is markedly skewed with a tendency of forming clusters. More than 70% of the three genomes have a repeat density below their corresponding average value indicating that transposable elements are not evenly distributed. We show that repeats and repeat-clusters are found at syntenic break points between E. histolytica and E. dispar and hence, could work as recombination hot spots promoting genome rearrangements. Conclusion The mapping of all transposable elements found in these parasites shows that repeat coverage is up to three times higher than previously reported. LINE, ERE1 and mariner elements were present in the common ancestor to the three Entamoeba species while ERE2 was likely acquired by E. histolytica after its separation from E. dispar. We demonstrate that E. histolytica and E. dispar share their entire repertoire of LINE and SINE retrotransposons and that Eh_SINE3/Ed_SINE1 originated as a chimeric SINE from Eh/Ed_SINE2 and Eh_SINE1/Ed_SINE3. Our work shows that transposable elements are organized in clusters, frequently found at syntenic break points providing insights into their contribution to chromosome instability and therefore, to genomic variation and speciation in these parasites.

Published
2008
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48. Small molecule inhibition of apicomplexan FtsH1 disrupts plastid biogenesis in human pathogens

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Hari, Sanjay B., Sauer, Robert T., Amberg-Johnson, Katherine, Ganesan, Suresh M., Lorenzi, Hernan A., Niles, Jacquin C., Yeh, Ellen, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Hari, Sanjay B., Sauer, Robert T., Amberg-Johnson, Katherine, Ganesan, Suresh M., Lorenzi, Hernan A., Niles, Jacquin C., and Yeh, Ellen

Abstract

The malaria parasite Plasmodium falciparum and related apicomplexan pathogens contain an essential plastid organelle, the apicoplast, which is a key anti-parasitic target. Derived from secondary endosymbiosis, the apicoplast depends on novel, but largely cryptic, mechanisms for protein/lipid import and organelle inheritance during parasite replication. These critical biogenesis pathways present untapped opportunities to discover new parasite-specific drug targets. We used an innovative screen to identify actinonin as having a novel mechanism-of-action inhibiting apicoplast biogenesis. Resistant mutation, chemical-genetic interaction, and biochemical inhibition demonstrate that the unexpected target of actinonin in P. falciparum and Toxoplasma gondii is FtsH1, a homolog of a bacterial membrane AAA+ metalloprotease. PfFtsH1 is the first novel factor required for apicoplast biogenesis identified in a phenotypic screen. Our findings demonstrate that FtsH1 is a novel and, importantly, druggable antimalarial target. Development of FtsH1 inhibitors will have significant advantages with improved drug kinetics and multistage efficacy against multiple human parasites., National Institutes of Health (U.S.) (Award AI016892), National Institutes of Health (U.S.) (Award F32GM116241)

Published
2018

49. Immune System Dysregulation During Spaceflight: Potential Countermeasures for Deep Space Exploration Missions

Author

Crucian, Brian E., primary, Choukèr, Alexander, additional, Simpson, Richard J., additional, Mehta, Satish, additional, Marshall, Gailen, additional, Smith, Scott M., additional, Zwart, Sara R., additional, Heer, Martina, additional, Ponomarev, Sergey, additional, Whitmire, Alexandra, additional, Frippiat, Jean P., additional, Douglas, Grace L., additional, Lorenzi, Hernan, additional, Buchheim, Judith-Irina, additional, Makedonas, George, additional, Ginsburg, Geoffrey S., additional, Ott, C. Mark, additional, Pierson, Duane L., additional, Krieger, Stephanie S., additional, Baecker, Natalie, additional, and Sams, Clarence, additional

Published
2018
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