Explanipedia

Protocol for in vivo two-photon calcium imaging of the Drosophila brain Open

Yue Tian, Rays H. Y. Jiang, Fang Guo · 2025

Faecalibaculum rodentium Alleviates Ionizing Radiation‐Induced Damage in Mice by Improving Intestinal Integrity and Hematopoiesis via Its Metabolite Butyrate Open

Hanyong Zhu, Hui Guo, Na Sun, Rui Xiao, Binbin Ji , et al. · 2025

The gut microbiota is key to mitigating ionizing radiation (IR)–induced injuries; however, the specific species involved in and the molecular mechanisms remain elusive. Mitochondrial dynamics affect gut microbiota diversity. To identify th…

Spatial Transcriptomics Reveals Distinct Architectures but Shared Vulnerabilities in Primary and Metastatic Liver Tumors Open

Swamy R. Adapa, Sahanama Porshe, Divya Priyanka Talada, Timothy M. Nywening, Margaret Lavinia Anderson , et al. · 2025

Background: Primary hepatocellular carcinoma (HCC) and liver metastases differ in origin, progression, and therapeutic response, yet a direct high-resolution spatial comparison of their tumor microenvironments (TMEs) within the liver has n…

Ancient Origins and Global Diversity of Plague: Genomic Evidence for Deep Eurasian Reservoirs and Recurrent Emergence Open

Subhajeet Dutta, Aditya Upadhyay, Swamy R. Adapa, Gregory O’Corry-Crowe, Sucheta Tripathy , et al. · 2025

Yersinia pestis, the causative agent of plague, has triggered multiple pandemics throughout human history, yet its long-term evolutionary patterns and reservoir dynamics remain poorly understood. Here, we present a global phylogenomic anal…

Genetic Evidence of Yersinia pestis from the First Pandemic Open

Swamy R. Adapa, Karen D. Hendrix, Aditya Upadhyay, Subhajeet Dutta, Andrea Vianello , et al. · 2025

Background/Objectives: The Plague of Justinian marked the beginning of the First Pandemic (541–750 CE), yet no genomic evidence of Yersinia pestis has previously been recovered from the Eastern Mediterranean, where the outbreak was first r…

GCN5 Is a Master Regulator of Gene Expression in the Malaria Parasite Plasmodium falciparum Open

Amuza Byaruhanga Lucky, Ahmad Rushdi Shakri, Xiaoying Liang, Hui Min, X. Li , et al. · 2025

GCN5-containing SAGA complex is evolutionarily conserved across yeast, plants, and humans and acts as a general transcription coactivator in the genome-wide regulation of genes. In Plasmodium falciparum, PfGCN5 forms a divergent complex, a…

Design and experimental research on intelligent harvesting device for citrus fruits Open

Rays H. Y. Jiang, Cheng Wei, Yong Fan, WU Shu-qin, Wu Xie · 2025

Aiming at the problems of low efficiency and high labor intensity in traditional manual picking of citrus fruits, a set of intelligent picking devices integrating a five-degree-of-freedom mechanical arm, a shear gripper, and an omnidirecti…

Cohesin ring gates are specialized for meiotic cell division Open

Yuanyuan Liu, Bohan Liu, Ruirui Zhang, Zixuan Zhu, Li Zhao , et al. · 2024

Cohesin is a ring complex closed with structural maintenance of chromosome 1 (SMC-1), SMC-3, and a kleisin subunit, mediating sister chromatid cohesion in mitosis and meiosis. Kleisin N- and C-terminal domains interact with SMC-3 and SMC-1…

Harnessing Porphyrin Accumulation in Liver Cancer: Combining Genomic Data and Drug Targeting Open

Swamy R. Adapa, Pravin Meshram, Abdus Sami, Rays H. Y. Jiang · 2024

The liver, a pivotal organ in human metabolism, serves as a primary site for heme biosynthesis, alongside bone marrow. Maintaining precise control over heme production is paramount in healthy livers to meet high metabolic demands while ave…

Uncovering Porphyrin Accumulation in the Tumor Microenvironment Open

Swamy R. Adapa, Abdus Sami, Pravin U. Meshram, Glória C. Ferreira, Rays H. Y. Jiang · 2024

Heme, an iron-containing tetrapyrrole, is essential in almost all organisms. Heme biosynthesis needs to be precisely regulated particularly given the potential cytotoxicity of protoporphyrin IX, the intermediate preceding heme formation. H…

Targeting Host Metabolic Niche to Kill Malaria Parasites Open

Rays H. Y. Jiang, Faiza Amber Siddiqui, Swamy R. Adapa, Liwang Cui · 2024

Malaria remains a global health challenge, exacerbated by artemisinin resistance. Inspired by our recent study targeting aberrant cancer heme metabolism, we propose a novel "bait-and-kill" strategy, focusing on the unique metabolic vulnera…

Unraveling the first world pandemic in an ancient cosmopolitan city with archaeological and genetic evidence Open

Rays H. Y. Jiang, Swamy R. Adapa, Karen D. Hendrix, Aditya Upadhyay, Subhajeet Dutta , et al. · 2024

The first world pandemic (541-767 CE) was investigated using archaeological, proteomic, genetic, and genomic technologies. Focusing on a mass burial site in Jerash, present-day Jordan, we generated evidence of a pandemic for the first time…

Autochthonous Plasmodium vivax Infections, Florida, USA, 2023 Open

Azhar Muneer, Swamy R. Adapa, Suzane Silbert, Kelly Scanlan, Harold Vore , et al. · 2024

During May-July 2023, a cluster of 7 patients at local hospitals in Florida, USA, received a diagnosis of Plasmodium vivax malaria. Whole-genome sequencing of the organism from 4 patients and phylogenetic analysis with worldwide representa…

Correction: Porphyrin overdrive rewires cancer cell metabolism Open

Swamy R. Adapa, Gregory A. Hunter, Narmin E. Amin, Christopher Marinescu, Andrew Borsky , et al. · 2024

Cancer cells exhibit a metabolic phenotype termed “porphyrin overdrive,” characterized by dysregulated heme metabolic pathways for intermediate accumulation. This rewiring is cancer-essential and cancer-specific. Targeting this vulnerabili…

The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum Open

Hui Min, Xiaoying Liang, Chengqi Wang, Junling Qin, Rachasak Boonhok , et al. · 2024

Where Does the Heme Go? Unraveling Heme and Porphyrin Metabolism in Healthy and Oncogenic Human Livers Open

Swamy R. Adapa, Pravin U. Meshram, Abudas Sami, Rays H. Y. Jiang · 2024

The liver, a pivotal organ in human metabolism, serves as a primary site for heme biosynthesis, critical for detoxification and drug metabolism. Maintaining precise control over heme production is paramount in healthy livers to meet high m…

Porphyrin overdrive rewires cancer cell metabolism Open

Swamy R. Adapa, Gregory A. Hunter, Narmin E. Amin, Christopher Marinescu, Andrew Borsky , et al. · 2024

All cancer cells reprogram metabolism to support aberrant growth. Here, we report that cancer cells employ and depend on imbalanced and dynamic heme metabolic pathways, to accumulate heme intermediates, that is, porphyrins. We coined this …

Uncovering porphyrin accumulation in the tumor microenvironment Open

Swamy R. Adapa, Abdus Sami, Pravin U. Meshram, Glória C. Ferreira, Rays H. Y. Jiang · 2024

Heme, an iron-containing tetrapyrrole, is essential in almost all organisms. Heme biosynthesis needs to be exquisitely regulated particularly given the potential cytotoxicity of protoporphyrin IX, the intermediate preceding heme formation.…

Unraveling the first world pandemic in an ancient cosmopolitan city with archaeological and genetic evidence Open

Rays H. Y. Jiang, Swamy R. Adapa, Karen D. Hendrix, Aditya Upadhyay, Subhajeet Dutta , et al. · 2024

The first world pandemic (541–767 CE) was investigated using archaeological, proteomic, genetic, and genomic technologies. Focusing on a mass burial site in Jerash, present-day Jordan, we generated evidence of a pandemic for the first time…

MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites Open

Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang , et al. · 2023

Bacterial sepsis triggers stronger transcriptomic immune responses in larger primates Open

Ryan McMinds, Rays H. Y. Jiang, Swamy R. Adapa, Emily Cornelius Ruhs, Rachel A. Munds , et al. · 2023

Empirical data relating body mass to immune defense against infections remain limited. Although the Metabolic Theory of Ecology predicts that larger organisms would have weaker immune responses, recent studies have suggested that the oppos…

A type II protein arginine methyltransferase regulates merozoite invasion in Plasmodium falciparum Open

Amuza Byaruhanga Lucky, Chengqi Wang, Min Liu, Xiaoying Liang, Hui Min , et al. · 2023

Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins Open

Camilla Valente Pires, Jenna Oberstaller, Chengqi Wang, Debora Casandra, Min Zhang , et al. · 2023

Malaria control is seriously threatened by the emergence and spread of Plasmodium falciparum resistance to the leading antimalarial, artemisinin. The potent killing activity of artemisinin results from oxidative damage unleashed by free he…

Characterization of the dual role of Plasmodium falciparum DNA methyltransferase in regulating transcription and translation Open

Amuza Byaruhanga Lucky, Chengqi Wang, Xiaolian Li, Anongruk Chim-Ong, Swamy R. Adapa , et al. · 2023

DNA modifications are critical in fine-tuning the biological processes in model organisms. However, the presence of cytosine methylation (5mC) and the function of the putative DNA methyltransferase, PfDNMT2, in the human malaria pathogen, …

Additional file 1 of MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites Open

Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang , et al. · 2023

Additional file 1: Table S1. MalariaSED model configuration.

MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites Open

Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller, Min Zhang , et al. · 2022

Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework…

A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile Open

M. Sacco, Shaohui Wang, Swamy R. Adapa, Xiujun Zhang, Eric M. Lewandowski , et al. · 2022

Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-bas…

Porphyrin overdrive rewires pan-cancer cell metabolism Open

Swamy R. Adapa, Gregory A. Hunter, Narmin E. Amin, Christopher Marinescu, Andrew Borsky , et al. · 2022

Porphyrin overdrive rewires pan-cancer cell metabolism All cancer cells reprogram metabolism to support aberrant growth. Here, we report that cancer cells employ and depend on imbalanced and dynamic heme metabolic pathways for their oncoge…

A unique class of Zn2+-binding PBPs underlies cephalosporin resistance and sporogenesis of Clostridioides difficile Open

M. Sacco, Shaohui Wang, Swamy R. Adapa, Xiujun Zhang, Maura V. Gongora , et al. · 2022

β-Lactam antibiotics, particularly cephalosporins, are major risk factors for C. difficile infection (CDI), the most common hospital acquired infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBP…

Probing the distinct chemosensitivity of Plasmodium vivax liver stage parasites and demonstration of 8-aminoquinoline radical cure activity in vitro Open

Steven P. Maher, Amélie Vantaux, Victor Chaumeau, Adeline C. Y. Chua, Caitlin Cooper , et al. · 2021

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