Alexander Lemenze

Alexander Lemenze

Genomics and microbiology backround- but really enjoy making computers talk back

Posts by Collection

portfolio

publications

Keeping it together: absence of genetic variation and DNA incorporation by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus during predation

Published in Research in Microbiology, 2018

Recommended citation: Gupta S, Lemenze A, Donnelly RJ, Connell ND, Kadouri DE. Res Microbiol. Keeping it together: absence of genetic variation and DNA incorporation by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus during predation. https://www.ncbi.nlm.nih.gov/pubmed/29751066

Transcriptomic studies provide insights into the tumor suppressive role of miR-146a-5p in non-small cell lung cancer (NSCLC) cells

Published in RNA Biology, 2019

Recommended citation: Iacona JR, Monteleone NJ, Lemenze AD, Cornett AL, Lutz CS. Transcriptomic studies provide insights into the tumor suppressive role of miR-146a-5p in non-small cell lung cancer (NSCLC) cells. RNA Biol. 2019 Dec;16(12):1721-1732. doi: 10.1080/15476286.2019.1657351. Epub 2019 Aug 23. https://www.ncbi.nlm.nih.gov/pubmed/31425002

Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of Mycobacterium tuberculosis.

Published in ACS Infectious Disease, 2019

Recommended citation: Wang X, Perryman AL, Li SG, Paget SD, Stratton TP, Lemenze A, Olson AJ, Ekins S, Kumar P, Freundlich JS. Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of Mycobacterium tuberculosis. ACS Infect Dis. 2019 Dec 13;5(12):2148-2163. doi: 10.1021/acsinfecdis.9b00295. Epub 2019 Nov 5 https://www.ncbi.nlm.nih.gov/pubmed/31625383

Differences in the soil microbial community and carbon use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica

Published in Restoration Ecology, 2019

Recommended citation: Eaton, W.D., McGee, K.M., Donnelly, R.H., Lemenze, A., Karas, O., & Hajibabaei, M. (2019). Differences in the soil microbial community and carbon‐use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica. https://onlinelibrary.wiley.com/doi/abs/10.1111/rec.12978

Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell

Published in PLoS Pathogens, 2020

Recommended citation: Inclan-Rico J.M., Hernandez C.M., Henry E.K., Federman H.G., Sy C.B., Ponessa J.J., Lemenze A.D., Joseph N., Soteropoulos P., Beaulieu A.M., Yap G.S., & Siracusa M.C. Trichinella spiralis-induced mastocytosis and erythropoiesis are simultaneously supported by a bipotent mast cell/erythrocyte precursor cell. PLoS Pathog. 2020;16(5):e1008579. Published 2020 May 18. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259795/

Hypoxia Induces Trophoblast Migration and Invasion Gene Pathways a Subset of which are Reduced in Preeclampsia CVS

Published in Fertility and Sterility, 2020

Recommended citation: Perlman BE, Merriam A, Lemenze AD, Begum S, Zhao Q, Shawber CJ, Douglas NC. Hypoxia Induces Trophoblast Migration and Invasion Gene Pathways a Subset of which are Reduced in Preeclampsia CVS. Fertility and Sterility. 2020;114(3):E339-E340. Published 2020 Sept 01. https://www.fertstert.org/article/S0015-0282(20)31771-4/fulltext

Dysregulation of Wnt Canonical Signaling Portends Pre-Transplant Immune Dysfunction and Post-Transplant Morbidity and Mortality in Liver Transplant Recipients

Published in Transplantation and Tissue Engineering, 2020

Recommended citation: Panayotova G, Lemenze AD, Minze LJ, Aware N, Nguyen CT, Graviss EA, Ghobrial M, Guarrera JV, Lunsford KE. HDysregulation of Wnt Canonical Signaling Portends Pre-Transplant Immune Dysfunction and Post-Transplant Morbidity and Mortality in Liver Transplant Recipients. Transplantation and Tissue Engineering. 2020;231(34):E221. Published 2020 Oct 01. https://www.journalacs.org/article/S1072-7515(20)31918-9/fulltext

Monocyte-derived alveolar macrophages mediate resistance to migrating helminths through depletion of arginine availability

Published in bioRxiv, 2020

Recommended citation: Fei Chen, Darine W. El Naccache, John Ponessa, Alexander Lemenze, Vanessa Espinosa, Wenhui Wu, Katherine Lothstein, Linhua Jin, Amariliz Rivera, Mark Siracusa, William C. Gause. Monocyte-derived alveolar macrophages mediate resistance to migrating helminths through depletion of arginine availability. bioRxiv 2020.10.02.322388; doi: https://doi.org/10.1101/2020.10.02.322388 https://www.biorxiv.org/content/10.1101/2020.10.02.322388v1

Danish and British dementia ITM2b/BRI2 mutations reduce BRI2 protein stability and impair glutamatergic synaptic transmission

Published in Journal of Biological Chemistry, 2020

Recommended citation: Yin T, Yao W, Lemenze AD, D'Adamio L. Danish and British dementia ITM2b/BRI2 mutations reduce BRI2 protein stability and impair glutamatergic synaptic transmission. J Biol Chem. 2020 Nov 10:jbc.RA120.015679. doi: 10.1074/jbc.RA120.015679 https://www.jbc.org/content/early/2020/11/10/jbc.RA120.015679.long

Influence of Two Important Leguminous Trees on Their Soil Microbiomes and Nitrogen Cycle Activities in a Primary and Recovering Secondary Forest in the Northern Zone of Costa Rica

Published in Soil Systems, 2020

Recommended citation: Eaton, W.D.; McGee, K.M.; Hoke, E.; Lemenze, A.; Hajibabaei, M. Influence of Two Important Leguminous Trees on Their Soil Microbiomes and Nitrogen Cycle Activities in a Primary and Recovering Secondary Forest in the Northern Zone of Costa Rica. Soil Syst. 2020, 4, 65. https://www.mdpi.com/2571-8789/4/4/65

Type 1 Interferon–Activated STAT4 Regulation of Follicular Helper T Cell–Dependent Cytokine and Immunoglobulin Production in Lupus

Published in Arthritis and Rheumatology, 2021

Recommended citation: Dong X, Antao OQ, Song W, Sanchez GM, Zembrzuski K, Koumpouras F, Lemenze A, Craft J, Weinstein JS. Type I Interferon-Activated STAT4 Regulation of Follicular Helper T Cell-Dependent Cytokine and Immunoglobulin Production in Lupus. Arthritis Rheumatol. 2021 Mar;73(3):478-489. doi: 10.1002/art.41532. Epub 2021 Jan 29. PMID: 33512094; PMCID: PMC7914134. https://onlinelibrary.wiley.com/doi/10.1002/art.41532

The impacts of a logging road on the soil microbial communities, and carbon and nitrogen components in a Northern Zone Costa Rican forest

Published in Applied Soil Ecology, 2021

Recommended citation: Eaton WD, McGee KM, Donnelly R, Lemenze A, Larimer M, Hajibabaei M. The impacts of a logging road on the soil microbial communities, and carbon and nitrogen components in a Northern Zone Costa Rican forest. Applied Soil Ecology, Volume 164, 2021, 103937, ISSN 0929-1393, https://doi.org/10.1016/j.apsoil.2021.103937. https://www.sciencedirect.com/science/article/pii/S0929139321000585

Development of Tbet- and CD11c-Expressing B Cells in a Viral Infection Requires T Follicular Helper Cells Outside of Germinal Centers

Published in Immunity, 2021

Recommended citation: Song, Wenzhi and Antao, Olivia Q. and Condiff, Emily and Sanchez, Gina M. and Chernova, Irene and Zembrzuski, Krzysztof and Steach, Holly and Rubtsova, Kira and Lemenze, Alexander and Laidlaw, Brian J. and Craft, Joseph and Weinstein, Jason, Development of Tbet- and CD11c-Expressing B Cells in a Viral Infection Requires T Follicular Helper Cells Outside of Germinal Centers. Available at SSRN: https://ssrn.com/abstract=3825161 or http://dx.doi.org/10.2139/ssrn.3825161 https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3825161

A Frame-Shift for IGF-1R in Breast Cancer and Metastasis

Published in Journal of the Endocrine Society, 2021

Recommended citation: Alison E Obr, PhD, Alexander Lemenze, PhD, Krystopher Maingrette, MS, Virginia Ciliento, PhD, Yun-juan Chang, PhD, Joseph J Bulatowicz, MS, Teresa L Wood, PhD, A Frame-Shift for IGF-1R in Breast Cancer and Metastasis, Journal of the Endocrine Society, Volume 5, Issue Supplement_1, April-May 2021, Pages A1009–A1010, https://doi.org/10.1210/jendso/bvab048.2065 https://academic.oup.com/jes/article/5/Supplement_1/A1009/6239954

γδ intraepithelial lymphocytes facilitate pathological epithelial cell shedding via CD103-mediated granzyme release.

Published in Gastroenterology, 2021

Recommended citation: Hu MD, Golovchenko NB, Burns GL, Nair PM, Kelly TJ 4th, Agos J, Irani MZ, Soh WS, Zeglinski MR, Lemenze A, Bonder EM, Sandrock I, Prinz I, Granville DJ, Keely S, Watson AJM, Edelblum KL. γδ Intraepithelial Lymphocytes Facilitate Pathological Epithelial Cell Shedding Via CD103-Mediated Granzyme Release. Gastroenterology. 2021 Dec 1:S0016-5085(21)03804-X. doi: 10.1053/j.gastro.2021.11.028. Epub ahead of print. PMID: 34861219. https://www.gastrojournal.org/article/S0016-5085(21)03804-X/fulltext

Helminth resistance is mediated by differential activation of recruited monocyte-derived alveolar macrophages and arginine depletion

Published in Cell Reports, 2022

Recommended citation: Fei Chen, Darine W. El-Naccache, John J. Ponessa, Alexander Lemenze, Vanessa Espinosa, Wenhui Wu, Katherine Lothstein, Linhua Jin, Olivia Antao, Jason S. Weinstein, Payal Damani-Yokota, Kamal Khanna, Peter J. Murray, Amariliz Rivera, Mark C. Siracusa, William C. Gause, Helminth resistance is mediated by differential activation of recruited monocyte-derived alveolar macrophages and arginine depletion, Cell Reports, Volume 38, Issue 2, 2022, 110215, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2021.110215. https://www.sciencedirect.com/science/article/pii/S2211124721017198

Gut Microbial Shifts Indicate Melanoma Presence and Bacterial Interactions in a Murine Model

Published in Diagnostics, 2022

Recommended citation: Rossi M, Aspromonte SM, Kohlhapp FJ, Newman JH, Lemenze A, Pepe RJ, DeFina SM, Herzog NL, Donnelly R, Kuzel TM, Reiser J, Guevara-Patino JA, Zloza A. Gut Microbial Shifts Indicate Melanoma Presence and Bacterial Interactions in a Murine Model. Diagnostics. 2022; 12(4):958. https://doi.org/10.3390/diagnostics12040958 https://www.mdpi.com/2075-4418/12/4/958

A transmissible γδ intraepithelial lymphocyte hyperproliferative phenotype is associated with the intestinal microbiota and confers protection against acute infection

Published in Mucosal Immunology, 2022

Recommended citation: Jia L, Wu G, Alonso S, Zhao C, Lemenze A, Lam YY, Zhao L, Edelblum KL. A transmissible γδ intraepithelial lymphocyte hyperproliferative phenotype is associated with the intestinal microbiota and confers protection against acute infection. Mucosal Immunol. 2022 May 19. doi: 10.1038/s41385-022-00522-x. PMID: 35589986. https://pubmed.ncbi.nlm.nih.gov/35589986/

Rickettsia Aglow: A Fluorescence Assay and Machine Learning Model to Identify Inhibitors of Intracellular Infection

Published in ACS Infectious Diseases, 2022

Recommended citation: Lemenze A, Mittal N, Perryman A, Daher S, Ekins S, Occi J, Ahn Y, Wang X, Russo R, Patel J, Daugherty R, Wood D, Connell N, Freundlich J. Rickettsia Aglow: A Fluorescence Assay and Machine Learning Model to Identify Inhibitors of Intracellular Infection. ACS Infectious Diseases. 2022; https://doi.org/10.1021/acsinfecdis.2c00014 https://pubs.acs.org/doi/10.1021/acsinfecdis.2c00014?ref=pdf

Adenosine metabolized from extracellular ATP promotes type 2 immunity through triggering A2BAR signaling in intestinal epithelial cells

Published in Cell Reports, 2022

Recommended citation: El-Naccache D, Chen F, Palma M, Lemenze A, Fischer M, Wu W, Mishra P, Eltzschig H, Robson S, Virgilio F, Yap G, Edelblum K, Hasko G, Gause W. Adenosine metabolized from extracellular ATP promotes type 2 immunity through triggering A2BAR signaling in intestinal epithelial cells. Cell Reports. 2022; https://doi.org/10.1016/j.celrep.2022.111150 https://www.cell.com/cell-reports/fulltext/S2211-1247(22)00959-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124722009597%3Fshowall%3Dtrue

Monocytes maintain central nervous system homeostasis following helminth-induced inflammation

Published in Proceedings of the National Academy of Sciences, 2022

Recommended citation: Peng J, Sy CB, Ponessa JJ, Lemenze AD, Hernandez CM, Inclan-Rico JM, Siracusa MC (2022). Monocytes maintain central nervous system homeostasis following helminth-induced inflammation. Proceedings of the National Academy of Sciences, 119(37), e2201645119. doi:10.1073/pnas.2201645119 https://www.pnas.org/doi/10.1073/pnas.2201645119

STAT4 increases the phenotypic and functional heterogeneity of intestinal tissue-resident memory T cells

Published in Mucosal Immunology, 2023

Recommended citation: Helen Y. Fung, Angie M. Espinal, Matthew Teryek, Alexander D. Lemenze, Tessa Bergsbaken, STAT4 increases the phenotypic and functional heterogeneity of intestinal tissue-resident memory T cells, Mucosal Immunology, 2023. ISSN 1933-0219 https://doi.org/10.1016/j.mucimm.2023.03.002. https://www.sciencedirect.com/science/article/pii/S1933021923000168

Mesenchymal Stem Cell Secretome Alters Gene Expression and Upregulates Motility of Human Endometrial Stromal Cells

Published in Reproduction, 2023

Recommended citation: Zhao Q, Larios K, Naaldijk Y, Sherman L, Chemerinski A, Okereke K, Rameshwar P, Lemenze A, Douglas NC, Morelli SS. Mesenchymal Stem Cell Secretome Alters Gene Expression and Upregulates Motility of Human Endometrial Stromal Cells. Reproduction. 2023 May 1:REP-22-0485. doi: 10.1530/REP-22-0485. PMID: 37252830. https://pubmed.ncbi.nlm.nih.gov/37252830/

Endometrial Adhesion G Protein-Coupled Receptors are differentially expressed across the menstrual cycle and early mouse pregnancy

Published in Fertility and Sterility, 2023

Recommended citation: N. Kalkota, A Lemenze, A Babwah, N Douglas, Endometrial Adhesion G Protein-Coupled Receptors are differentially expressed across the menstrual cycle and early mouse pregnancy, Fertility and Sterility, 2023. https://doi.org/10.1016/j.fertnstert.2023.05.113 https://www.fertstert.org/article/S0015-0282(23)00484-3/fulltext

Interferon ɛ restricts Zika virus infection in the female reproductive tract

Published in PNAS Nexus, 2023

Recommended citation: Xu C, Wang A, Ebraham L, Sullivan L, Tasker C, Pizutelli V, Couret J, Hernandez C, Kolli P, Deb PQ, Fritzky L, Subbian S, Gao N, Lo Y, Salvatore M, Rivera A, Lemenze A, Fitzgerald-Bocarsly P, Tyagi S, Lu W, Beaulieu A, Chang TL. Interferon ɛ restricts Zika virus infection in the female reproductive tract. PNAS Nexus. 2023 Oct 25;2(11):pgad350. doi: 10.1093/pnasnexus/pgad350. PMID: 37954158; PMCID: PMC10639110. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10639110/

Genetic identification of potential nodulating bacteria and nodule-associated bacteria (NAB) within root nodules of Inga punctata trees in a Costa Rican Cloud Forest

Published in Europe PMC, 2023

Recommended citation: Eaton W, Hamilton D, Chen W, Lemenze A, Soteropoulos PP. Genetic identification of potential nodulating bacteria and nodule-associated bacteria (NAB) within root nodules of Inga punctata trees in a Costa Rican Cloud Forest. Research Square; 2023. DOI: 10.21203/rs.3.rs-3767521/v1. https://europepmc.org/article/ppr/ppr776791

Natural regeneration or tree planting in a tropical forest-to-pasture damaged area: which is more efficacious for soil ecosystem recovery?

Published in Restoration Ecology, 2024

Recommended citation: Eaton, W.D., Hamilton, D.A., Lemenze, A. and Soteropoulos, P. (2024), Natural regeneration or tree planting in a tropical forest-to-pasture damaged area: which is more efficacious for soil ecosystem recovery?. Restor Ecol e14127. https://doi.org/10.1111/rec.14127 https://onlinelibrary.wiley.com/doi/10.1111/rec.14127

The impact of ovarian stimulation on the human endometrial microenvironment

Published in Human Reproduction, 2024

Recommended citation: Anat Chemerinski, May Shen, Nuriban Valero-Pacheco, Qingshi Zhao, Trystn Murphy, Lea George, Alex Lemenze, Lauren Sherman, Debra Heller, Xiaowei Chen, Tracy Wu, Peter G McGovern, Sara S Morelli, Ripla Arora, Aimee M Beaulieu, Nataki C Douglas, The impact of ovarian stimulation on the human endometrial microenvironment, Human Reproduction, 2024;, deae048, https://doi.org/10.1093/humrep/deae048 https://academic.oup.com/humrep/advance-article-abstract/doi/10.1093/humrep/deae048/7632816?redirectedFrom=fulltext

Use of high throughput DNA analysis to characterize the nodule-associated bacterial community from four ages of Inga punctata trees in a Costa Rican cloud forest

Published in AIMS Microbiology, 2024

Recommended citation: William D. Eaton, Debra A. Hamilton, Wen Chen, Alexander Lemenze, Patricia Soteropoulos. Use of high throughput DNA analysis to characterize the nodule-associated bacterial community from four ages of Inga punctata trees in a Costa Rican cloud forest[J]. AIMS Microbiology, 2024, 10(3): 572-595. doi: 10.3934/microbiol.2024027 https://www.aimspress.com/article/doi/10.3934/microbiol.2024027

Clinical and CSF single-cell profiling of post-COVID-19 cognitive impairment

Published in Cell Reports Medicine, 2024

Recommended citation: Hu WT, Kaluzova M, Dawson A, Sotelo V, Papas J, Lemenze A, Shu C, Jomartin M, Nayyar A, Hussain S. Clinical and CSF single-cell profiling of post-COVID-19 cognitive impairment. Cell Rep Med. 2024 May 21;5(5):101561. doi: 10.1016/j.xcrm.2024.101561. Epub 2024 May 13. PMID: 38744274; PMCID: PMC11148803. https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(24)00253-2

Helminth protein enhances wound healing by inhibiting fibrosis and promoting tissue regeneration

Published in Life Sci Alliance, 2024

Recommended citation: Lothstein KE, Chen F, Mishra P, Smyth DJ, Wu W, Lemenze A, Kumamoto Y, Maizels RM, Gause WC. Helminth protein enhances wound healing by inhibiting fibrosis and promoting tissue regeneration. Life Sci Alliance. 2024 Aug 23;7(11):e202302249. doi: 10.26508/lsa.202302249. PMID: 39179288; PMCID: PMC11342954. https://pubmed.ncbi.nlm.nih.gov/39179288/

Dendritic Cells Pulsed with HAM/TSP Exosomes Sensitize CD4 T Cells to Enhance HTLV-1 Infection, Induce Helper T-Cell Polarization, and Decrease Cytotoxic T-Cell Response

Published in Viruses, 2024

Recommended citation: Joseph, J.; Premeaux, T.A.; Tandon, R.; Murphy, E.L.; Bruhn, R.; Nicot, C.; Herrera, B.B.; Lemenze, A.; Alatrash, R.; Baffour Tonto, P.; et al. Dendritic Cells Pulsed with HAM/TSP Exosomes Sensitize CD4 T Cells to Enhance HTLV-1 Infection, Induce Helper T-Cell Polarization, and Decrease Cytotoxic T-Cell Response. Viruses 2024, 16, 1443. https://doi.org/10.3390/v16091443 https://www.mdpi.com/1999-4915/16/9/1443

NFAT5 governs cellular plasticity-driven resistance to KRAS-targeted therapy in pancreatic cancer

Published in JEM, 2024

Recommended citation: Daiyong Deng, Habeebunnisa Begum, Tong Liu, Jiangyan Zhang, Qiang Zhang, Ting-yu Chu, Hong Li, Alexander Lemenze, Mainul Hoque, Patricia Soteropoulos, Pingping Hou; NFAT5 governs cellular plasticity-driven resistance to KRAS-targeted therapy in pancreatic cancer. J Exp Med 4 November 2024; 221 (11): e20240766. doi: https://doi.org/10.1084/jem.20240766 https://rupress.org/jem/article/221/11/e20240766/277034

Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus

Published in Cell Reports, 2024

Recommended citation: Sanchez GM, Hirsch ES, VanValkenburg A, Mayer DP, Gbedande K, Francis RL, Song W, Antao OQ, Brimmer KE, Lemenze A, Stephens R, Johnson WE, Weinstein JS. Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus. Cell Rep. 2024 Nov 10;43(11):114978. doi: 10.1016/j.celrep.2024.114978. 39527476. https://www.cell.com/cell-reports/fulltext/S2211-1247(24)01329-9

talks

teaching

SSRP Workshop

Summer student research experience workshop, Online hosting, 2020

This was a brief 2 day workshop designed to provide baseline NGS/bioinformatics knowledge to students in the SSRP group. The workshop was presented with initial lectures, followed by an interactive RNA-seq experiment walkthrough.

Bioinformatics of Genomics Course

Full course, Online hosting, 2020

The Bioinformatics of Genomics course is designed to be a fully guided course for baseline genomics analyses. The course will begin with basic introductions to Next Generation Sequencing (NGS), bioinformatics, and compute resources. Next it will delve into language specific training, and lastly review individual NGS analysis workflows. Each section will include at minimum a lecture, but will also have interactive Jupyter Notebooks for applicable code.