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Articles 1 - 30 of 5816

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Release Of Bound Steroid From The Androgen And Estrogen Receptors Is Induced By Ddt And Its Analogs, Matthew D. Rosales, Tahyra Soto, Jacqueline I. Goodship, Ahyssa R. Cruz, Isaac A. Rodriguez, Ventura Cuba Flores, Amanda Chavez, Monica P. Solis, Esmeralda Lopez, Frank B. Dean, Evangelia Kotsikorou Nov 2026

Release Of Bound Steroid From The Androgen And Estrogen Receptors Is Induced By Ddt And Its Analogs, Matthew D. Rosales, Tahyra Soto, Jacqueline I. Goodship, Ahyssa R. Cruz, Isaac A. Rodriguez, Ventura Cuba Flores, Amanda Chavez, Monica P. Solis, Esmeralda Lopez, Frank B. Dean, Evangelia Kotsikorou

School of Integrative Biological & Chemical Sciences Faculty Publications

The pesticide p,p'-DDT (DDT) and its analogs (p,p'-DDD, o,p'-DDD, and p,p'-DDE) inhibit the binding of dihydrotestosterone (DHT) to the androgen receptor (AR) and estradiol (E2) to the estrogen receptor (ERα) ligand-binding domains (LBDs), as previously reported. In this study, we introduce assays to measure the release of receptor-bound steroids. These compounds induced the release of DHT from the AR LBD and E2 from the ERα LBD. These findings suggest that DDT and its analogs may interact with a surface site on the LBD, thereby allosterically disrupting steroid binding. One potential site is binding function 3 (BF3). To explore this possibility, …

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The Β2Αb Loop Determines Nad(P) Cofactor Specificity And Kinetics In Trypanosomal D-3-Hydroxybutyrate Dehydrogenases, Hideharu Hashimoto, Ian H. Mawn, William Escobar-Arrillaga, Linh Nguyen, Laura A. Madigan, Gina Antuono, Tatiana Rossy, Jorna Sojati, Anna Mienko, Erik W. Debler, Jennifer B. Palenchar Oct 2026

The Β2Αb Loop Determines Nad(P) Cofactor Specificity And Kinetics In Trypanosomal D-3-Hydroxybutyrate Dehydrogenases, Hideharu Hashimoto, Ian H. Mawn, William Escobar-Arrillaga, Linh Nguyen, Laura A. Madigan, Gina Antuono, Tatiana Rossy, Jorna Sojati, Anna Mienko, Erik W. Debler, Jennifer B. Palenchar

Department of Biochemistry and Molecular Biology Faculty Papers

Bacterial d-3-hydroxybutyrate dehydrogenases (HBDHs) catalyze the conversion between d-3-hydroxybutyrate and acetoacetate with NAD as the cofactor but not with NAD 2'-phosphate (NADP). However, HBDHs of the early-branched eukaryotic genus Trypanosoma utilize both NAD and NADP (T. brucei) or exclusively NADP (T. cruzi). Here we reveal that NADP specificity of T. cruzi HBDH arises from stabilization of the flexible β2αB loop by the 2'-phosphate interaction. Stabilization of this loop by a nearby C64Y mutation enables T. cruzi HBDH to use NAD in addition to NADP; thus, the Cys/Tyr residue is critical for determining cofactor specificity in trypanosomal HBDHs, suggesting that most …

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Molecular And Structural Basis For Replication Initiation And Strand Separation By Human Mitochondrial Dna Polymerase Γ, Viktoriia Sokolova, Gina Buchel, S. Strock, Ashok R. Nayak, Dmitry Temiakov Sep 2026

Molecular And Structural Basis For Replication Initiation And Strand Separation By Human Mitochondrial Dna Polymerase Γ, Viktoriia Sokolova, Gina Buchel, S. Strock, Ashok R. Nayak, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

Defects in human mitochondrial DNA (mtDNA) replication can lead to somatic mutations associated with a range of devastating mitochondrial diseases. However, the molecular mechanisms governing the earliest steps of mtDNA replication and their fidelity remain poorly understood. Here, we found that DNA polymerase gamma (Polγ) forms stable complexes with RNA-DNA primer-template substrates, exhibiting greater stability and lower misincorporation than on DNA-primed substrates. Structural analysis revealed that Polγ interacts with the 2'-OH groups of ribose within the first four nucleotides of the primer, explaining the stability of complexes that utilize RNA primers. Although Polγ requires TWINKLE to extend RNA primers, its …

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Three-Dimensional Chromatin Architecture Is Rapidly Restored After Dna Replication, Tyler K. Fenstermaker, Svetlana Petruk, Alexander Mazo Sep 2026

Three-Dimensional Chromatin Architecture Is Rapidly Restored After Dna Replication, Tyler K. Fenstermaker, Svetlana Petruk, Alexander Mazo

Department of Biochemistry and Molecular Biology Faculty Papers

Studies of post-replicative chromatin exclusively focus on the kinetics of protein binding after DNA replication to understand maintenance of transcriptional programs. Here we investigated both chromatin-bound factors and the three-dimensional architecture of the post-replicative genome in human cells. We found that transcription factors and chromatin looping proteins rapidly associate with nascent DNA. We discovered that the architectural factors, CTCF and YY1, bind to their target sequences immediately following DNA replication, and that chromatin loops from 39 to 425 kb re-form within 10 min of DNA replication. This suggests that the 3D structure of chromatin is at most briefly disrupted by …

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Cultivating Collaboration In Biomolviz: Key Attributes For Building A Stem Educator Community Of Practice, Pamela S. Mertz, Charmita Burch, Roderico Acevedo, Josh T. Beckham, Didem Vardar-Ulu, Kristin M. Fox, Lauren A. Genova, Rachel M. Mitton-Fry, Swati Agrawal, Daniel R. Dries, Kristen Procko Sep 2026

Cultivating Collaboration In Biomolviz: Key Attributes For Building A Stem Educator Community Of Practice, Pamela S. Mertz, Charmita Burch, Roderico Acevedo, Josh T. Beckham, Didem Vardar-Ulu, Kristin M. Fox, Lauren A. Genova, Rachel M. Mitton-Fry, Swati Agrawal, Daniel R. Dries, Kristen Procko

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

BioMolViz is an educational community of practice (CoP) focused on creating resources to improve biomolecular visual literacy instruction and assessment. The community of life science instructors developed in three phases, beginning with a small Core Team that emerged from a conference session and established the domain of interest for the CoP. In-person workshops, supported by short-term funding, drove the initial expansion of the community and the development of shared activities in Phase 2. This CoP was sustained through intentional choices about how members interact, collaborate, and share work. As the community matured in Phase 3, it was supported by longer-term …

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Waste Streams From Next Generation Molten Salt Reactors: The Challenge Of Creating An Insoluble Ceramic For Chloride Salt Waste, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye Sep 2026

Waste Streams From Next Generation Molten Salt Reactors: The Challenge Of Creating An Insoluble Ceramic For Chloride Salt Waste, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Molten salt reactors (MSRs) design development is of interest to many research groups and companies. Waste management for MSRs is one of the most important issues that needs to be resolved due to its impact on environmental safety, primarily via the dissolution of radionuclides in water. Furthermore, the waste treatment strategy will have a significant influence on the operating cost of MSRs, which is why a reliable process for the immobilization, transportation, storage and disposal of MSR waste must be addressed. This work presents a new approach for the immobilization of chloride salts from molten salt reactors in stable oxyhalide …

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Characterization Of Mettl3/14-Mediated M6a Modification In Human Transcriptome Using Nanopore Direct Rna Sequencing, Emily Kurtyan, Andrew J. Stein, Kelly J. Abdalla, Zhangerjiao Yuan, Miten Jain, Fadia Ibrahim Sep 2026

Characterization Of Mettl3/14-Mediated M6a Modification In Human Transcriptome Using Nanopore Direct Rna Sequencing, Emily Kurtyan, Andrew J. Stein, Kelly J. Abdalla, Zhangerjiao Yuan, Miten Jain, Fadia Ibrahim

Department of Biochemistry and Molecular Biology Faculty Papers

Post-transcriptional RNA modifications modulate diverse aspects of RNA metabolism. N6-methyladenosine (m6A), one of the most abundant internal RNA modifications, is deposited by the core methyltransferase complex, METTL3 and METTL14. Oxford Nanopore Technologies (ONT) platform permits direct, single RNA molecule sequencing while preserving native modifications. However, without rigorous benchmarking, the accuracy and reproducibility of modification detection remain uncertain. Here, we leveraged ONT to comprehensively profile bona fide m6A modifications in cellular RNAs at single-nucleotide resolution by integrating two direct RNA sequencing chemistries (RNA002 and RNA004) with the m6Anet and Dorado modification-detection models. We independently depleted METTL3 and METTL14 in human cells …

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Instruction Guide, Mark C. Hall Aug 2026

Instruction Guide, Mark C. Hall

Analytical Biochemistry: A Practical Handbook for Undergraduates

The instruction guide provides useful information for setting up and running the lab activities each week and assessing student preparation, performance, and comprehension.

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Crystal Structure Of New Polar Rare Earth Borates Na2.62Ln2.12(Bo3)3 (Ln = Pr, Nd, Sm) Containing Isolated Bo3 Groups, Alevtina A. Maksimova, Mark D. Smith, Hans Conrad Zur Loye Aug 2026

Crystal Structure Of New Polar Rare Earth Borates Na2.62Ln2.12(Bo3)3 (Ln = Pr, Nd, Sm) Containing Isolated Bo3 Groups, Alevtina A. Maksimova, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Three new rare earth borates, Na2.62Ln2.12(BO3)3 (Ln = Pr, Nd, Sm), were synthesized via a high-temperature solution reaction using a BaCO3–H3BO3–NaF flux and structurally characterized by single-crystal X-ray diffraction analysis. The compounds crystallize in the orthorhombic space group Amm2 with lattice parameters a = 5.0985(10) Å, b = 11.180(2) Å, c = 7.1483(14) Å, and a unit cell volume of 407.48(14) Å3 (Z = 2) for Na2.62Pr2.12(BO3)3, a = 5.0983(10) Å, b = 11.181(2) Å, c = 7.1491(14) Å, and a unit cell volume of 407.51(14) Å3 (Z = 2) for Na2.62Nd2.12(BO3)3, and a = 5.08630(10) Å, b …

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Single Crystal Growth Of The Orthoborate Nabalu(Bo3)2 And Optical Investigation Of Eu3+ And Tb3+ Doped Nabalu(Bo3)2, Alevtina A. Maksimova, Mark D. Smith, Lakshani W. Masachchi, Hans Conrad Zur Loye Aug 2026

Single Crystal Growth Of The Orthoborate Nabalu(Bo3)2 And Optical Investigation Of Eu3+ And Tb3+ Doped Nabalu(Bo3)2, Alevtina A. Maksimova, Mark D. Smith, Lakshani W. Masachchi, Hans Conrad Zur Loye

Faculty Publications

Sodium barium lutetium borate NaBaLu(BO3)2 crystals were synthesized using a high-temperature solution method. The crystal structure of this layered orthoborate is described and corresponds to that of an extensive orthoborates family, NaBaR(BO3)2 (R = Sc, Y, Yb, Tb – Lu). NaBaLu(BO3)2 was doped by Eu3+ and Tb3+ to explore its performance as a host material and to investigate the luminescent properties of the Eu3+ and Tb3+ doped materials. The emission spectra of the NaBaLu(BO3)2:Ln (Ln = Eu, Tb) crystals are presented. The most …

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Biomolecular Corona Of Extracellular Vesicles: Report On Isev Workshop, Lucia Paolini, Selene Tassoni, Khuloud T. Al-Jamal, Xavier Banquy, Tamás Beke-Somfai, Paolo Bergese, Fanni Annamária Boros, Massimo Bottini, Ben Boyd, Sara Busatto, Benedetta Bussolati, Ester Canepa, Valentina Castagnola, Aled Clayton, Kenneth Dawson, Samir El-Andaloussi, András Försönits, Orazio Fortunato, Roberto Frigerio, Martina Gabrielli, Cristina Grange, Michele Guescini, Yuya Hayashi, Jonas Klejs Hemmingsen, Seungmin Kim, Ilyes Kinga, Heikki Kyykallio, Metka Lenassi, Luize Goncalves Lima, Mỹ G. Mahoney, Camille Menaceur Vandenbroucke, Andreas Möller, Angelo Musicò, Inge Nelissen, Lucas Fabrício Bahia Nogueira, Christa Nöhammer, Pietro Parisse, Charles Ramassamy, Kelly Cristine Santos Roballo, Anna Salvati, María Sancho-Albero, Ganesh Shelke, Paniz Shirmast, Tasvilla Sonallya, Imola Csilla Szigyártó, Monique A. J. Van Eijndhoven, Tapani Viitala, Shan Wang, Yan Yan, Andrea Zendrini, Edit Buzás, Annalisa Radeghieri Aug 2026

Biomolecular Corona Of Extracellular Vesicles: Report On Isev Workshop, Lucia Paolini, Selene Tassoni, Khuloud T. Al-Jamal, Xavier Banquy, Tamás Beke-Somfai, Paolo Bergese, Fanni Annamária Boros, Massimo Bottini, Ben Boyd, Sara Busatto, Benedetta Bussolati, Ester Canepa, Valentina Castagnola, Aled Clayton, Kenneth Dawson, Samir El-Andaloussi, András Försönits, Orazio Fortunato, Roberto Frigerio, Martina Gabrielli, Cristina Grange, Michele Guescini, Yuya Hayashi, Jonas Klejs Hemmingsen, Seungmin Kim, Ilyes Kinga, Heikki Kyykallio, Metka Lenassi, Luize Goncalves Lima, Mỹ G. Mahoney, Camille Menaceur Vandenbroucke, Andreas Möller, Angelo Musicò, Inge Nelissen, Lucas Fabrício Bahia Nogueira, Christa Nöhammer, Pietro Parisse, Charles Ramassamy, Kelly Cristine Santos Roballo, Anna Salvati, María Sancho-Albero, Ganesh Shelke, Paniz Shirmast, Tasvilla Sonallya, Imola Csilla Szigyártó, Monique A. J. Van Eijndhoven, Tapani Viitala, Shan Wang, Yan Yan, Andrea Zendrini, Edit Buzás, Annalisa Radeghieri

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

The concept of the "biomolecular corona" (BC) was first introduced to describe the spontaneous absorption of molecules, mainly proteins, onto the surface of synthetic nanoparticles upon exposure to biological fluids. More recently, the same term has been used to describe biomolecules that dynamically interact with the surface of extracellular vesicles (EVs) during their biogenesis, secretion, or upon exposure to intracellular or extracellular milieus, including biological fluids. The EV biomolecular corona is a key determinant of EV identity, shaping their cellular uptake, biodistribution, and functional outcomes in both physiological and pathological contexts. EVs, in contrast to synthetic nanoparticles, introduce distinct challenges …

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Machine Learning Integrated Designing And Screening Of 8-Hydroxyquinoline Based Metallo-Beta-Lactamase Inhibitors, Anthony M. Baudino, Kari Stone Jul 2026

Machine Learning Integrated Designing And Screening Of 8-Hydroxyquinoline Based Metallo-Beta-Lactamase Inhibitors, Anthony M. Baudino, Kari Stone

Chemistry Department Faculty Articles

The rapid emergence of metallo-b-lactamase-mediated antibiotic resistance has created an urgent need for new inhibitor discovery strategies. In this work, a machine-learning-guided workflow was developed to generate and prioritize potential inhibitors targeting NDM-1. A SMILES-based variational autoencoder was first pretrained on a broad molecular dataset to learn general chemical syntax and latent molecular representations. The model was then fine-tuned on an 8-hydroxyquinoline-enriched dataset to bias molecular generation toward zinc-binding chemical space relevant to metallo-β-lactamase inhibition. Generated compounds were processed through structural filtering and docking-based evaluation to create training data for downstream predictive modeling. Molecular fingerprints and physicochemical descriptors were then …

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Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li Jul 2026

Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li

UConn Library Presentations

Many first-year students enter college unprepared to fully engage with scientific literature and academic library resources. Drawing on experiences from academic librarians working with STEM students, this session explores common gaps in science research skills, including navigating databases, identifying scholarly sources, and understanding the structure of scientific literature. Participants will be introduced to practical strategies and classroom-ready activities to better prepare students for college-level research. Discussion questions: What science research skills do students struggle with most when entering college? How can high school instruction better support these skills? Where can librarians and educators collaborate to support student success?

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Analysis Of The Atypical Temperature Dependence And Conformational Changes During Turnover Of A Lactobacillus Chlorogenic Acid Esterase, Nathaniel Carl, Yianni Tsigaris, Dan Ji, Nora K. Anpree, Kellie K. Omori, Cedric P. Owens Jul 2026

Analysis Of The Atypical Temperature Dependence And Conformational Changes During Turnover Of A Lactobacillus Chlorogenic Acid Esterase, Nathaniel Carl, Yianni Tsigaris, Dan Ji, Nora K. Anpree, Kellie K. Omori, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Many bacterial chlorogenic acid esterases (ChlEs) exhibit atypical temperature behavior, featuring activities that barely change with temperature and activity maxima that fall below the thermal denaturation point. This work focuses on a ChlE from Lactobacillus helveticus (Lh–ChlE), which has a flat temperature dependence. First, it was determined that conformational changes during Lh–ChlE turnover are not rate-limiting and that the overall rate depends on the chemical step at all temperatures. Next, Lh–ChlE’s temperature dependence was investigated using a conformational equilibrium model that assumes the existence of a temperature-dependent equilibrium between an active and an inactive conformation and an activation heat capacity …

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Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas Jul 2026

Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas

Funded Research Records

No abstract provided.

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Mechanistic Determination Of Host Environmental Impacts On Shigella Virulence, Nicholas E. Dickenson Jul 2026

Mechanistic Determination Of Host Environmental Impacts On Shigella Virulence, Nicholas E. Dickenson

Funded Research Records

No abstract provided.

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Decoding The Allosteric Grammar Of Protein Kinases: A Dual-Stream Framework Integrating Protein Language Models And Energy Landscape Frustration Analysis, Will Gatlin, Max Ludwick, Lucas Turano, Brandon Foley, Kamila Riedlova, Vít Škrhák, Marian Novotný, David Hoksza, Gennady M. Verkhivker Jul 2026

Decoding The Allosteric Grammar Of Protein Kinases: A Dual-Stream Framework Integrating Protein Language Models And Energy Landscape Frustration Analysis, Will Gatlin, Max Ludwick, Lucas Turano, Brandon Foley, Kamila Riedlova, Vít Škrhák, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The spatial and energetic encoding of allosteric regulatory sites remains a major challenge in structural biology, frequently representing a “blind spot” for sequence-based artificial intelligence (AI) models. We present a protein language model (PLM)-guided approach complemented by the energy landscape frustration analysis as a dual-stream framework to investigate the relationship between AI prediction of binding sites and biophysical organization of regulatory pockets across the human kinome. By probing a fine-tuned residue-level PLM classifier across 453 kinase structures, a clear performance gap is discovered between highly predictable orthosteric pockets (Types I, I.5, and II) and poorly resolved distal allosteric sites (Type …

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Upar-Guided Dendrimer Gel Nanoparticles Reprogram Inflammation To Stabilize Atherosclerotic Plaques, Hsin Yin Chuang, Huari Kou, Yue-Wern Huang, Hu Yang Jul 2026

Upar-Guided Dendrimer Gel Nanoparticles Reprogram Inflammation To Stabilize Atherosclerotic Plaques, Hsin Yin Chuang, Huari Kou, Yue-Wern Huang, Hu Yang

Biological Sciences Faculty Research & Creative Works

Atherosclerosis is characterized by lipid deposition, chronic inflammation, and apoptosis within the arterial wall, leading to plaque progression and instability. Current lipid-lowering therapies fail to fully address residual cardiovascular risk driven by local inflammation and cell death. Here, we report the development of uPA-functionalized, rapamycin-encapsulated dendrimer nanoparticles (G5PM-uPA/RA) that preferentially accumulate in urokinase plasminogen activator receptor (uPAR)-enriched atherosclerotic plaque, including macrophage- and apoptosis-rich lesion microenvironments. G5PM-uPA/RA was constructed by cross-linking reaction-enabled flash nanoprecipitation in a custom-made multi-inlet vortex mixer, followed by thiol-maleimide conjugation of uPA for uPAR-guided targeting. The nanoparticles demonstrated uniform morphology, favorable stability, and efficient rapamycin loading. In …

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Biophysical Insights Into A Cryptic Ligand Site In The Hydrophobic Core Of Human Pcna, Alexis N. Dispensa, Sharon N, Greenwood, Jason Yang, Daniel E. Logatto, James Fusco, E. Railey White, Roderic G. Eckenhoff, Zhiwei Liu, Brian P. Weiser Jul 2026

Biophysical Insights Into A Cryptic Ligand Site In The Hydrophobic Core Of Human Pcna, Alexis N. Dispensa, Sharon N, Greenwood, Jason Yang, Daniel E. Logatto, James Fusco, E. Railey White, Roderic G. Eckenhoff, Zhiwei Liu, Brian P. Weiser

Department of Anesthesiology Faculty Papers

Proteins contain small pockets that form due to imperfections in residue packing or the rotational and conformational movement of amino acids. In this work, we used the fluorescent probe 1-aminoanthracene (AMA) to detect a small ligand pocket in the hydrophobic core of human proliferating cell nuclear antigen (PCNA), which is a critical protein for DNA replication and repair. Fluorescence measurements of AMA reported that the core of PCNA had a dielectric constant (ε) of 4, which was very apolar and similar to cyclohexane (ε = 2). Protein mutagenesis, photoaffinity labeling, and molecular dynamics simulations localized the binding site for AMA …

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Investigation Into Molecular Bases Of Pregnancy-Associated Malaria, Nicole Pozo Jul 2026

Investigation Into Molecular Bases Of Pregnancy-Associated Malaria, Nicole Pozo

Biochemistry and Molecular Biology

Plasmodium falciparum causes the most severe and deadly form of malaria and remains a major global health problem, especially in sub-Saharan Africa (Milner, 2018). The parasite infects and multiplies inside red blood cells, leading to fever, anemia, organ damage, and death if untreated (Milner, 2018; Song et al., 2022). It is especially dangerous because it avoids the immune system by changing surface proteins called Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), which are encoded by more than 60 var genes. By switching between these genes, the parasite hides from immune detection and creates repeated waves of infection (Deitsch & Dzikowski, …

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Personalizable Metabolic Models To Enable Immune Characterization And Drug Discovery, Joshua Loecker Jul 2026

Personalizable Metabolic Models To Enable Immune Characterization And Drug Discovery, Joshua Loecker

Department of Biochemistry: Dissertations, Theses, and Student Research

Cellular metabolism is reshaped by disease and physiological state, and genome-scale metabolic networks (GSMNs) offer a systematic way to interrogate this biology and identify therapeutic targets. Building a GSMN from expression data, however, requires a sequence of stages including read processing, normalization and gene-activity classification, multi-omic integration, model reconstruction, simulation, and biological interpretation. These are typically handled by disconnected tools spanning multiple programming languages, file formats, and databases. The resulting reliance on heterogeneous interfaces and manual steps threatens reproducibility. This work develops an ecosystem of computational tools that carry an analysis from raw sequencing reads to mechanistic biological interpretation. First, …

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Rna G-Quadruplexes Function As A Tunable Switch Of Fus Phase Separation, Jenny L. Carey, Miyuki Hayashi, Emily A. Welebob, Laura R. Ganser, Huan Wang, Kerry Buckhaults, Jacquelyn A. Depierro, Zheng Shi, James Shorter, Sua Myong, Aaron R. Haeusler, Lin Guo Jun 2026

Rna G-Quadruplexes Function As A Tunable Switch Of Fus Phase Separation, Jenny L. Carey, Miyuki Hayashi, Emily A. Welebob, Laura R. Ganser, Huan Wang, Kerry Buckhaults, Jacquelyn A. Depierro, Zheng Shi, James Shorter, Sua Myong, Aaron R. Haeusler, Lin Guo

Department of Biochemistry and Molecular Biology Faculty Papers

Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) to support essential cellular functions, but aberrant phase transitions promote toxic aggregation in neurodegenerative disease. Short RNA oligonucleotides can reverse this behavior, yet the structural determinants that govern RNA activity remain poorly defined. Here, we identify RNA G-quadruplexes (rG4s) as tunable structural motifs that potently modulate FUS LLPS. rG4 activity depends on its concentration and is modulated by rG4 length and stability: increasing repeat number switches rG4s from inhibitor to nucleator of FUS assembly, whereas chemical modifications that stabilize rG4 enhance inhibitory function and render these activities resilient to ionic perturbation. …

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Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Brian C. Benicewicz, Huina Lin Jun 2026

Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Brian C. Benicewicz, Huina Lin

Faculty Publications

Proton exchange membrane (PEM) fuel cells are promising for clean and efficient energy conversion across diverse applications. High-temperature PEM fuel cells (HT-PEMFCs) using phosphoric acid (PA)-doped polybenzimidazole (PBI) can operate up to 200°C, but at lower temperatures, water-induced PA loss often leads to performance degradation and reduced durability. In this work, we present a new class of main-chain ion-pair PBI membranes by integrating the imidazolium-biphosphate ion-pair units directly into the PBI backbone. This design results in membranes with high acid content, stronger acid-polymer interactions and stabilized acid retention. In single-cell tests, the Im+-PBI15-3 wt.% exhibits peak power densities of 0.79 …

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Structure-Based Discovery Of Malate Dehydrogenase Inhibitors With Efficacy Against C. Parvum Oocysts, Ankita Bharatbhai Kheni Jun 2026

Structure-Based Discovery Of Malate Dehydrogenase Inhibitors With Efficacy Against C. Parvum Oocysts, Ankita Bharatbhai Kheni

Biochemistry and Molecular Biology

Cryptosporidium parvum, the etiological agent of Cryptosporidiosis (diarrheal illness) represents a significant global health burden, particularly affecting immunodeficient and pediatric populations. Since the parasite has a highly reduced mitochondrion and relies on glycolysis, enzymes such as C. parvum malate dehydrogenase (CpMDH), which are believed to be indispensable for parasite viability due to their pivotal roles in NAD⁺ regeneration and redox balance, remain largely unexplored as therapeutic targets. The present study employed a multifaceted experimental and computational strategy to evaluate the inhibitory activity of two lead-like and drug-like small molecules, referred to as compound 1.8 and compound 1.5, against the cofactor …

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High Mobility Group Motif Proteins’ Role In Fibrosis, Inflammation, And Vascular Injury In Systemic Sclerosis, Fabian A. Mendoza, Sonsoles Piera-Velazquez, Sergio A. Jimenez Jun 2026

High Mobility Group Motif Proteins’ Role In Fibrosis, Inflammation, And Vascular Injury In Systemic Sclerosis, Fabian A. Mendoza, Sonsoles Piera-Velazquez, Sergio A. Jimenez

Jefferson Institute of Molecular Medicine Papers and Presentations

Systemic Sclerosis (SSc) is an idiopathic systemic autoimmune disease characterized by progressive cutaneous and systemic fibrosis, severe vasculopathy, and multiple humoral and cellular immunological alterations. The pathogenesis of SSc is highly complex and remains incompletely elucidated. The fibrotic process is a crucial component of SSc and is responsible for organ failure and high mortality. Although an increasing understanding of the fibrotic process has enabled the clinical development of antifibrotic therapeutic agents, these agents have limited clinical efficacy. Recently, the potential role of a group of transcription factors containing a High Mobility Group (HMG) motif, in the development and pathological manifestations …

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Terrestrial Abiotic Synthesis Of Simple Precursor Molecules Starting From Two Approaches: The Universality Of Carbon Reduction, Eloi Camprubi, Ben K.D. Pearce, Martina Preiner Jun 2026

Terrestrial Abiotic Synthesis Of Simple Precursor Molecules Starting From Two Approaches: The Universality Of Carbon Reduction, Eloi Camprubi, Ben K.D. Pearce, Martina Preiner

School of Integrative Biological & Chemical Sciences Faculty Publications

To address the chemistry responsible for life’s emergence, we examine the simple chemicals accessible on early Earth and the processes that could have transformed them. We focus on carbon reduction as a process central to the direct precursors of life. Two main approaches for the emergence of life’s building blocks and their associated functions are discussed. One approach investigates chemical routes for forming life’s building blocks via processes that worked differently from those of extant life, referred to as “unrestricted” prebiotic chemistries. The other approach establishes a direct mechanistic connection between prebiotic building blocks and extant biochemistry, referred to as …

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Chromatin Insulators Homie And Nhomie Can Interact With Distant Copies Either Together Or Separately, With Distinct Outcomes For Enhancer-Promoter Interactions, Miki Fujioka, Wenfan Ke, Paul Schedl, James B. Jaynes Jun 2026

Chromatin Insulators Homie And Nhomie Can Interact With Distant Copies Either Together Or Separately, With Distinct Outcomes For Enhancer-Promoter Interactions, Miki Fujioka, Wenfan Ke, Paul Schedl, James B. Jaynes

Department of Biochemistry and Molecular Biology Faculty Papers

Chromatin insulators, a.k.a. boundary elements, separate regions of the chromosome with distinct chromatin characteristics, including distinct histone modifications. This activity affects gene expression by allowing chromatin domains to be stably regulated and maintained. Insulators also block enhancer-promoter interactions and, somewhat paradoxically, facilitate other interactions, particularly when they stitch together distant regions of the chromosome by pairing with specific partners. Here we explore how long-range interactions facilitated by insulator pairing are affected by the presence of two potentially competing partners. Our results show that when two partners are present, they can reduce each other's effects on distant gene expression, suggesting that …

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Detection And Evaluation Of Hazardous Mercury Contamination In Various Biological Samples, Krish Italiya Jun 2026

Detection And Evaluation Of Hazardous Mercury Contamination In Various Biological Samples, Krish Italiya

Biochemistry and Molecular Biology

Mercury is a toxic environmental pollutant that threatens ecosystems and human health. This study investigates mercury contamination in Lactuca sativa (lettuce) and selected fish species, including tuna and salmon, focusing on plant responses and the limitations of X-ray fluorescence (XRF) analysis. In a controlled experiment, lettuce plants were exposed to mercury to evaluate uptake and toxicity, and XRF spectroscopy was used for quick, non-destructive elemental analysis. Results confirmed mercury accumulation in lettuce, along with visible stress symptoms such as leaf yellowing, purple pigmentation, and tissue damage. Mercury was not detected in tuna and salmon samples, likely due to concentrations below …

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Hydroxamate Formation In The Lipopeptide Containing Siderophore Taiwachelin, Aaron J. Gringer, Kernen P. Agwaza, Isabel Da Fonseca, Pablo Sobrado Jun 2026

Hydroxamate Formation In The Lipopeptide Containing Siderophore Taiwachelin, Aaron J. Gringer, Kernen P. Agwaza, Isabel Da Fonseca, Pablo Sobrado

Chemistry Faculty Research & Creative Works

Cupriavidus taiwanensis is a nitrogen-fixing bacterium found in root nodules of the invasive tropical weed Mimosa pudica . C. taiwanensis has been shown to grow in environments contaminated with heavy metals such as Pb, Cu, and Cd. Taiwachelin, a recently identified siderophore produced by C. taiwanensis , is an iron chelator that contains a hydroxamate functional group for metal binding. In its biosynthesis, a flavin-dependent N-monooxygenase (NMO) was predicted to hydroxylate l -ornithine, leading to formation of the metal binding hydroxamate moiety. Here, we report the cloning, expression, and biochemical characterization of this enzyme, herein referred to as CtNMO. CtNMO …

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Structure Of Ergosteryl-Aspartate Synthase Reveals How An Entrapped Trna Is Used Like A Prosthetic Swinging Arm In The Synthesis Of Aminoacylated Sterols, Hanako Murayama, Nathaniel Yakobov, Nassira Mahmoudi, Sasha Legrosdidier, Nicolas Fournier, Solène Zuttion, Kanata Matsumoto, Michihiro Nishimura, Jingwei Ji, Bruno Senger, Laurence Huck, Howard Gamper, Yoshiaki Kise, Ralph Kleiner, Mathieu Frechin, Ya-Ming Hou, Hubert Becker, Yuzuru Itoh, Frédéric Fischer, Osamu Nureki May 2026

Structure Of Ergosteryl-Aspartate Synthase Reveals How An Entrapped Trna Is Used Like A Prosthetic Swinging Arm In The Synthesis Of Aminoacylated Sterols, Hanako Murayama, Nathaniel Yakobov, Nassira Mahmoudi, Sasha Legrosdidier, Nicolas Fournier, Solène Zuttion, Kanata Matsumoto, Michihiro Nishimura, Jingwei Ji, Bruno Senger, Laurence Huck, Howard Gamper, Yoshiaki Kise, Ralph Kleiner, Mathieu Frechin, Ya-Ming Hou, Hubert Becker, Yuzuru Itoh, Frédéric Fischer, Osamu Nureki

Department of Biochemistry and Molecular Biology Faculty Papers

Ergosteryl-3β-O-L-aspartate synthase (ErdS) catalyzes tRNA-dependent aspartylation of ergosterol, a lipid essential for fungal cell membrane integrity. However, the functional significance of ergosteryl-aspartate and the molecular mechanisms underlying its synthesis remain unclear. Here, we show that ErdS localization is highly dynamic and that Erg-Asp is required for proper hyphal growth, sporulation, and spore germination, and likely influences stress tolerance. The cryo-electron microscopy structure of ErdS revealed an unprecedented sterol-binding pocket. In addition, the structures in complex with a non-hydrolyzable Asp-N-tRNAAsp show a tRNA-guided intramolecular aminoacyl transfer mechanism between two functional domains of the enzyme. The CCA end of tRNAAsp undergoes a …

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