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Full-Text Articles in Life Sciences

A Middle Bronze Age Burial Cave At Tur‘An, Lilly Gershuny, Emanuel Eisenberg Jan 2025

A Middle Bronze Age Burial Cave At Tur‘An, Lilly Gershuny, Emanuel Eisenberg

'Atiqot

The burial cave, carved into limestone, consists of a square, vertical shaft and an elliptical room. The cave’s contents, which included pottery vessels, carnelian beads, a bronze toggle pin and a stone pommel, were scattered on a fill on the floor. Six adult individuals and one child were identified. The bones of sheep and cattle, which served as food offerings, were found as well. The pottery included bowls, a storage jar, a large krater with loop feet, jugs, dipper and piriform juglets, and a unique Tell el-Yahudiyeh juglet with a zoomorphic protome. The cave is a typical Early Bronze Age …


Biodiversity And Cold Tolerance Of Dung Beetles In Cattle Pastures And Forested Habitats In Northeast Arkansas, Becca Lynn Lett Jan 2025

Biodiversity And Cold Tolerance Of Dung Beetles In Cattle Pastures And Forested Habitats In Northeast Arkansas, Becca Lynn Lett

Student Theses and Dissertations

Dung beetles play vital ecological roles, including dung removal and pest reduction. They rely on environmental temperature for activity, and forest habitats typically provide more favorable temperatures. This study occurred in Northeast Arkansas and compared dung beetle diversity in forests and pastures, finding greater diversity in forests. In addition, this study looked at abundance in one pasture 15 years apart and found that abundance remained stable over 15 years, while overall diversity increased. Thermal limit assays on three Onthophagus species provided insights into temperature tolerances. These findings offer valuable information on dung beetle abundance and diversity in the region and …


Timber Harvesting Was The Most Important Factor Driving Changes In Vegetation Composition, As Compared To Climate And Fire Regime Shifts, In The Mixedwood Temperate Forests Of Temiscamingue Since Ad 1830, Daniela Robles, Yan Boulanger, Jesus Pascual, Victor Danneyrolles, Yves Bergeron, Igor Drobyshev Jan 2025

Timber Harvesting Was The Most Important Factor Driving Changes In Vegetation Composition, As Compared To Climate And Fire Regime Shifts, In The Mixedwood Temperate Forests Of Temiscamingue Since Ad 1830, Daniela Robles, Yan Boulanger, Jesus Pascual, Victor Danneyrolles, Yves Bergeron, Igor Drobyshev

Aspen Bibliography

Context The vegetation composition of northeastern North American forests has significantly changed since pre-settlement times, with a marked reduction in conifer-dominated stands, taxonomic and functional diversity. These changes have been attributed to fire regime shifts, logging, and climate change.

Methods In this study, we disentangled the individual effects of these drivers on the forest composition in southwestern Quebec from 1830 to 2000 by conducting retrospective modelling using the LANDIS-II forest landscape model. The model was run based on pre-settlement forest composition and fire history reconstructions, historical timber harvest records, and climate reanalysis data. We compared counterfactual scenarios excluding individual factors …


Behavioral Ecology And Physiology Of Spotted Turtles (Clemmys Guttata) In A Fragmented And Polluted Landscape, Jessica Rojas Lindberg Jan 2025

Behavioral Ecology And Physiology Of Spotted Turtles (Clemmys Guttata) In A Fragmented And Polluted Landscape, Jessica Rojas Lindberg

Master's Theses

Turtles are one of the most threatened groups of animals across the globe. This is especially true for freshwater turtles that rely on multiple habitats to fulfill their life history requirements. Wetlands are a crucial habitat type for many freshwater turtle species, and this ecosystem has been susceptible to conversion, fragmentation, and pollution. In turn, these hazards to wetland habitats threaten already declining freshwater turtle populations. The spotted turtle (Clemmys guttata) is a species of freshwater turtle that is particularly at-risk due to life history traits as well as habitat fragmentation and pollution. This study aims to investigate the effects …


Plasmodium Berghei Subpellicular Microtubule Protein-1 (Pbspm-1) Is A Microtubule Stabilizing Protein That Affects Schizont Development, Manuel Joseph Widuch Jan 2025

Plasmodium Berghei Subpellicular Microtubule Protein-1 (Pbspm-1) Is A Microtubule Stabilizing Protein That Affects Schizont Development, Manuel Joseph Widuch

Master's Theses

In eukaryotes, microtubules (MTs) are regulated by microtubule-associated proteins (MAP), only a few of which have been characterized in the malaria parasite to date. Here we present the functional characterization of STOP axonemal protein 1 (SAXO1) of the rodent parasite Plasmodium berghei. The protein exhibits high sequence and organizational conservation to the subpellicular microtubule protein 1 (SPM1) of the apicomplexan parasite Toxoplasma gondii and SAXO1 of Trypanosoma brucei. SAXO1 proteins are conserved in most eukaryotes where they form a protein family. We refer to this protein as PbSPM1. It is a 38 kD protein that is organized into an N-terminal …


A Climatically Significant Abiotic Mechanism Driving Carbon Loss And Nitrogen Limitation In Peat Bogs, Alexandra B. Cory, Rachel M. Wilson, M. Elizabeth Holmes, William J. Riley, Yueh Fen Li, Malak M. Tfaily, Sarah C. Bagby, Darya Anderson, Robert M. Jones, Gareth Trubl, Nicole Irwin-Raab, Sky Dominguez, Moira Hough, Virginia I. Rich, Matthew B. Sullivan, Maria F. Fahnestock, Suzanne B. Hodgkins, Ruth K. Varner, Michael Ibba, Regis Ferriere, Ahmed Zayed, Patrick M. Crill, Jessica G. Ernakovich, Jeffrey P. Chanton Jan 2025

A Climatically Significant Abiotic Mechanism Driving Carbon Loss And Nitrogen Limitation In Peat Bogs, Alexandra B. Cory, Rachel M. Wilson, M. Elizabeth Holmes, William J. Riley, Yueh Fen Li, Malak M. Tfaily, Sarah C. Bagby, Darya Anderson, Robert M. Jones, Gareth Trubl, Nicole Irwin-Raab, Sky Dominguez, Moira Hough, Virginia I. Rich, Matthew B. Sullivan, Maria F. Fahnestock, Suzanne B. Hodgkins, Ruth K. Varner, Michael Ibba, Regis Ferriere, Ahmed Zayed, Patrick M. Crill, Jessica G. Ernakovich, Jeffrey P. Chanton

Michigan Tech Publications

Sphagnum-dominated bogs are climatically impactful systems that exhibit two puzzling characteristics: CO2:CH4 ratios are greater than those predicted by electron balance models and C decomposition rates are enigmatically slow. We hypothesized that Maillard reactions partially explain both phenomena by increasing apparent CO2 production via eliminative decarboxylation and sequestering bioavailable nitrogen (N). We tested this hypothesis using incubations of sterilized Maillard reactants, and live and sterilized bog peat. Consistent with our hypotheses, CO2 production in the sterilized peat was equivalent to 8–13% of CO2 production in unsterilized peat, and the increased formation of aromatic N compounds decreased N-availability. Numerous sterility assessments …


Fast 3d Printing Of Fine, Continuous, And Soft Fibers Via Embedded Solvent Exchange, Wonsik Eom, Mohammad Tanver Hossain, Vidush Parasramka, Jeongmin Kim, Ryan W. Y. Siu, Kate A. Sanders, Dakota Piorkowski, Andrew Lowe, Hyun Gi Koh, Michael F. L. De Volder, Douglas S. Fudge, Randy H. Ewoldt, Sameh H. Tawfick Jan 2025

Fast 3d Printing Of Fine, Continuous, And Soft Fibers Via Embedded Solvent Exchange, Wonsik Eom, Mohammad Tanver Hossain, Vidush Parasramka, Jeongmin Kim, Ryan W. Y. Siu, Kate A. Sanders, Dakota Piorkowski, Andrew Lowe, Hyun Gi Koh, Michael F. L. De Volder, Douglas S. Fudge, Randy H. Ewoldt, Sameh H. Tawfick

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nature uses fibrous structures for sensing and structural functions as observed in hairs, whiskers, stereocilia, spider silks, and hagfish slime thread skeins. Here, we demonstrate multi-nozzle printing of 3D hair arrays having freeform trajectories at a very high rate, with fiber diameters as fine as 1.5 µm, continuous lengths reaching tens of centimeters, and a wide range of materials with elastic moduli from 5 MPa to 3500 MPa. This is achieved via 3D printing by rapid solvent exchange in high yield stress micro granular gel, leading to radial solidification of the extruded polymer filament at a rate of 2.33 μm/s. …


Scaling Arctic Landscape And Permafrost Features Improves Active Layer Depth Modeling, Wouter Hantson, Daryl Yang, Shawn P. Serbin, Joshua B. Fisher, Daniel J. Hayes Jan 2025

Scaling Arctic Landscape And Permafrost Features Improves Active Layer Depth Modeling, Wouter Hantson, Daryl Yang, Shawn P. Serbin, Joshua B. Fisher, Daniel J. Hayes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Tundra ecosystems in the Arctic store up to 40% of global below-ground organic carbon but are exposed to the fastest climate warming on Earth. However, accurately monitoring landscape changes in the Arctic is challenging due to the complex interactions among permafrost, micro-topography, climate, vegetation, and disturbance. This complexity results in high spatiotemporal variability in permafrost distribution and active layer depth (ALD). Moreover, these key tundra processes interact at different scales, and an observational mismatch can limit our understanding of intrinsic connections and dynamics between above and below-ground processes. Consequently, this could limit our ability to model and anticipate how ALD …


A Novel Case Of Glial Transdifferentiation In Renal Medullary Carcinoma Brain Metastasis, Maria A Gubbiotti, Ian E Mccutcheon, Priya Rao, Giannicola Genovese, Linghua Wang, Vladislav Putintsev, Danil Stupichev, Kirill Kriukov, Suren Davitavyan, Basim Salem, Alexander Sarachakov, Dmitry Lebedev, Michael Hensley, Alexander Bagaev, Francesca Paradiso, Vladimir Kushnarev, Gleb Khegai, Nizar M Tannir, Pavlos Msaouel Jan 2025

A Novel Case Of Glial Transdifferentiation In Renal Medullary Carcinoma Brain Metastasis, Maria A Gubbiotti, Ian E Mccutcheon, Priya Rao, Giannicola Genovese, Linghua Wang, Vladislav Putintsev, Danil Stupichev, Kirill Kriukov, Suren Davitavyan, Basim Salem, Alexander Sarachakov, Dmitry Lebedev, Michael Hensley, Alexander Bagaev, Francesca Paradiso, Vladimir Kushnarev, Gleb Khegai, Nizar M Tannir, Pavlos Msaouel

Faculty, Staff and Student Publications

Renal medullary carcinoma is a rare undifferentiated tumor of the kidney associated with sickle cell trait and characterized by INI1 (SMARCB1) loss. Although metastasis to lungs, lymph nodes, and bone is commonly reported, distant spread to the central nervous system almost never occurs. Here we present an unusual case of a patient with renal medullary carcinoma with metastasis to the brain following treatment which included tazemetostat, an EZH2 inhibitor. The metastatic brain lesion harbored morphologic, immunohistochemical, and methylation profile supportive of a primary CNS phenotype with loss of the trimethylated lysine 27 residue of histone 3 while maintaining INI1 loss …


A Dual Role Of Cohesin In Dna Dsb Repair, Michael Fedkenheuer, Yafang Shang, Seolkyoung Jung, Kevin Fedkenheuer, Solji Park, Robin Sebastian, Dali Zong, Hua Tan, Sushil Kumar Jaiswal, Haiqing Fu, Anthony Cruz, Supriya V Vartak, Jan Wisniewski, Vittorio Sartorelli, John J O'Shea, Laura Elnitski, Andre Nussenzweig, Mirit I Aladjem, Fei-Long Meng, Rafael Casellas Jan 2025

A Dual Role Of Cohesin In Dna Dsb Repair, Michael Fedkenheuer, Yafang Shang, Seolkyoung Jung, Kevin Fedkenheuer, Solji Park, Robin Sebastian, Dali Zong, Hua Tan, Sushil Kumar Jaiswal, Haiqing Fu, Anthony Cruz, Supriya V Vartak, Jan Wisniewski, Vittorio Sartorelli, John J O'Shea, Laura Elnitski, Andre Nussenzweig, Mirit I Aladjem, Fei-Long Meng, Rafael Casellas

Faculty, Staff and Student Publications

Cells undergo tens of thousands of DNA-damaging events each day. Defects in repairing double-stranded breaks (DSBs) can lead to genomic instability, contributing to cancer, genetic disorders, immunological diseases, and developmental defects. Cohesin, a multi-subunit protein complex, plays a crucial role in both chromosome organization and DNA repair by creating architectural loops through chromatin extrusion. However, the mechanisms by which cohesin regulates these distinct processes are not fully understood. In this study, we identify two separate roles for cohesin in DNA repair within mammalian cells. First, cohesin serves as an intrinsic architectural factor that normally prevents interactions between damaged chromatin. Second, …


Acknowledgment Note Jan 2025

Acknowledgment Note

Mansoura Engineering Journal

Acknowledgement


The Clinical Utility Of A Next-Generation Sequencing-Based Approach To Detecting Circulating Hpv Dna In Patients With Advanced Anal Cancer, Deepak Bhamidipati, Jay R Johnson, Kangyu Lin, Helene Pelicano, Cathy Eng, Robert A Wolff, Michael F Frumovitz, Ignacio I Wistuba, Dzifa Y Duose, Saradhi Mallampati, Rajyalakshmi Luthra, Van K Morris Jan 2025

The Clinical Utility Of A Next-Generation Sequencing-Based Approach To Detecting Circulating Hpv Dna In Patients With Advanced Anal Cancer, Deepak Bhamidipati, Jay R Johnson, Kangyu Lin, Helene Pelicano, Cathy Eng, Robert A Wolff, Michael F Frumovitz, Ignacio I Wistuba, Dzifa Y Duose, Saradhi Mallampati, Rajyalakshmi Luthra, Van K Morris

Faculty, Staff and Student Publications

Background: To extend the practicality of liquid biopsy beyond the historical HPV circulating tumor DNA (ctDNA) assays, we evaluated the clinical relevance of a novel next-generation sequencing HPV ctDNA assay in patients with locally advanced and metastatic squamous cell cancer of the anal canal (mSCCA).

Methods: ctDNA isolated from the plasma of patients with mSCCA was sequenced using a 1.4 Mb hybrid-capture target-enrichment panel covering the whole genome sequences of all 193 HPV types. The HPV type, copy number (CN), and integration sites were determined using a bioinformatic pipeline.

Results: A total of 77 plasma samples from 28 patients with …


Computational Investigation Of The Unveils Nsd2 Inhibition Potential Of Berberis Vulgaris, Sambucus Nigra, And Morus Alba Through Virtual Screening, Molecular Docking, Md Simulation, And Dft Analyses, Supriyo Saha, Vanshita Gupta, Ahad Hossain, Prinsa Prinsa, Jannatul Ferdous, Kiran Bharat Lokhande, Vikash Jakhmola, Sarkar M. A. Kawsar Jan 2025

Computational Investigation Of The Unveils Nsd2 Inhibition Potential Of Berberis Vulgaris, Sambucus Nigra, And Morus Alba Through Virtual Screening, Molecular Docking, Md Simulation, And Dft Analyses, Supriyo Saha, Vanshita Gupta, Ahad Hossain, Prinsa Prinsa, Jannatul Ferdous, Kiran Bharat Lokhande, Vikash Jakhmola, Sarkar M. A. Kawsar

Karbala International Journal of Modern Science

Nuclear receptor binding set domain protein 2 (NSD2) plays a key role in chromatin regulation and is associated with different cancers and other developmental problems. Berries are rich in major secondary metabolites with anticancer properties. Here, we virtually screened 145 berry phytochemicals as putative NSD2 inhibitors via structure-based virtual screening, molecular docking, MD simulations, and DFT and ADMET analyses. Among them, α-carotene had the maximum docking score of -9.9 kcal/mol, followed by sulfuretin and β-amyrin. MD simulation analysis revealed that the dynamic behavior of the ligand‒NSD2 complexes was within the limit, indicating no significant changes in the structural integrity of …


Antimicrobial Effect Of Herbs Extracted With Ethanol Compared To Ampicillin, Brianna Neilan, Laura Rowe Jan 2025

Antimicrobial Effect Of Herbs Extracted With Ethanol Compared To Ampicillin, Brianna Neilan, Laura Rowe

Posters-at-the-Capitol

Antibiotics are commonly used to treat bacterial infections within the medical field, however there are growing concerns of antibiotic resistance. Before the introduction of antibiotics herbs were commonly used to treat infections, and herbal medicine is still used in many communities and cultures. Bacteria’s increasing resistance to traditional antibiotics has caused herbal medicines to become a significant research topic recently. Methods of herbal medicine preparation include preparing teas using hot water, and tinctures that soak herbs in alcohol for several weeks. Previous research has shown significant antimicrobial effects of some herbs when soaked in water and other liquids. The aim …


The Effects Of Improper Waste Disposal On Marine Life: Why Does It Matter And How Can We Prevent It?, Abbey Ward, Ashlee Davis Jan 2025

The Effects Of Improper Waste Disposal On Marine Life: Why Does It Matter And How Can We Prevent It?, Abbey Ward, Ashlee Davis

Posters-at-the-Capitol

Improperly disposed of waste, specifically plastic, can end up in the ocean and negatively impact marine life, and in turn, negatively impact human health. Marine life, such as turtles, have faced serious health consequences and even death from entanglement in abandoned fishing gear and consuming plastics. Larger plastic particles can break down into smaller particles known as microplastics which can harbor harmful substances (such as Bisphenol A and persistent organic pollutants) and can cause several negative health effects when consumed by marine life such as loss of nutrition, starvation, and death. Microplastics have been found in 75% of commercial fish. …


Research Progress And Clinical Translation Potential Of Coronary Atherosclerosis Diagnostic Markers From A Genomic Perspective, Hanxiang Liu, Yuchen Zhang, Yueyan Zhao, Yuzhen Li, Xiaofeng Zhang, Lingyu Bao, Rongkai Yan, Yixin Yang, Huixian Zhou, Jinming Zhang, Siyuan Song Jan 2025

Research Progress And Clinical Translation Potential Of Coronary Atherosclerosis Diagnostic Markers From A Genomic Perspective, Hanxiang Liu, Yuchen Zhang, Yueyan Zhao, Yuzhen Li, Xiaofeng Zhang, Lingyu Bao, Rongkai Yan, Yixin Yang, Huixian Zhou, Jinming Zhang, Siyuan Song

Children’s Nutrition Research Center Staff Publications

Objective: Coronary atherosclerosis (CAD) is characterized by arterial intima lipid deposition, chronic inflammation, and fibrous tissue proliferation, leading to arterial wall thickening and lumen narrowing. As the primary cause of coronary heart disease and acute coronary syndrome, CAD significantly impacts global health. Recent genetic studies have demonstrated CAD's polygenic and multifactorial nature, providing molecular insights for early diagnosis and risk assessment. This review analyzes recent advances in CAD-related genetic markers and evaluates their diagnostic potential, focusing on their applications in diagnosis and risk stratification within precision medicine.

Methods: We conducted a systematic review of CAD genomic studies from PubMed and …


Automatic Genetic Phenotype Normalization From Dysmorphology Physical Examinations: An Overview Of The Biocreative Viii-Task 3 Competition, Sarah F Schmidt, Karen O'Connor, Ekin Soysal, Kirk Roberts, Jiewei Qi, Ling Luo, Zhihao Yang, Hongfei Lin, Hajung Kim, Chanhwi Kim, Jiwoong Sohn, Tim Beck, Marek Rei, Sunkyu Kim, T Ian Simpson, Joram M Posma, Antoine Lain, Mujeen Sung, Jaewoo Kang, Areej Alhassan, Viktor Schlegel, Monira Aloud, Riza Batista-Navarro, Goran Nenadic, Ying-Jia Lin, Zhi-Quan Feng, Hung-Yu Kao, Ian M Campbell, Graciela Gonzalez-Hernandez Jan 2025

Automatic Genetic Phenotype Normalization From Dysmorphology Physical Examinations: An Overview Of The Biocreative Viii-Task 3 Competition, Sarah F Schmidt, Karen O'Connor, Ekin Soysal, Kirk Roberts, Jiewei Qi, Ling Luo, Zhihao Yang, Hongfei Lin, Hajung Kim, Chanhwi Kim, Jiwoong Sohn, Tim Beck, Marek Rei, Sunkyu Kim, T Ian Simpson, Joram M Posma, Antoine Lain, Mujeen Sung, Jaewoo Kang, Areej Alhassan, Viktor Schlegel, Monira Aloud, Riza Batista-Navarro, Goran Nenadic, Ying-Jia Lin, Zhi-Quan Feng, Hung-Yu Kao, Ian M Campbell, Graciela Gonzalez-Hernandez

Faculty, Staff and Student Publications

We present here an overview of the BioCreative VIII Task 3 competition, which called for the development of state-of-the-art approaches to automatic normalization of observations noted by physicians in dysmorphology physical examinations to the Human Phenotype Ontology (HPO). We made available for the task 3136 deidentified and manually annotated observations extracted from electronic health records of 1652 paediatric patients at the Children’s Hospital of Philadelphia. This task is challenging due to the discontinuous, overlapping, and descriptive mentions of the observations corresponding to HPO terms, severely limiting the performance of straightforward strict matching approaches. Ultimately, an effective automated solution to the …


A Pathway From Fragmentation To Interoperability Through Standards-Based Enterprise Architecture To Enhance Patient Safety Jan 2025

A Pathway From Fragmentation To Interoperability Through Standards-Based Enterprise Architecture To Enhance Patient Safety

Faculty, Staff and Student Publications

Creating an ontology is the essential step in natural language processing (NLP). To improve patient safety in this era of generative AI, it is crucial to develop a standards-driven, ontology-based architecture for patient safety that can seamlessly integrate with health systems, thereby facilitating effective detection and monitoring potentially preventable harms in healthcare. This visionary, whole-system approach to patient safety addresses a significant gap in establishing resilient safety systems within the healthcare sector.


Congenital Rickets, Melissa Intriago Jan 2025

Congenital Rickets, Melissa Intriago

Mako: NSU Undergraduate Student Journal

No abstract provided.


One Heart, One Vessel: Unraveling The Mystery Of Truncus Arteriosus, Claudette C. Artiles Jan 2025

One Heart, One Vessel: Unraveling The Mystery Of Truncus Arteriosus, Claudette C. Artiles

Mako: NSU Undergraduate Student Journal

No abstract provided.


What’S New In Esophageal Atresia Treatment?, Alexandra N. Jimenez Gonzalez Jan 2025

What’S New In Esophageal Atresia Treatment?, Alexandra N. Jimenez Gonzalez

Mako: NSU Undergraduate Student Journal

No abstract provided.


Retracted: Conserved Domains In Promoters Of Differentially Expressed Genes: How To Find Them And What Can They Tell Us?, Emalynn E. Tobias Jan 2025

Retracted: Conserved Domains In Promoters Of Differentially Expressed Genes: How To Find Them And What Can They Tell Us?, Emalynn E. Tobias

Mako: NSU Undergraduate Student Journal

THIS ARTICLE HAS BEEN RETRACTED DUE TO THE FOLLOWING REASON: inadvertent errors in several citations.

The complex process of regulating gene expression involves a large number of cis- and trans-acting components. The cis elements also referred to as cis regulatory elements (CREs) are highly conserved across species, and are often referred to as conserved domains mainly located in the promoters of genes. The trans acting sequences such as enhancers, moderators and insulators are also crucial in the regulation of gene expression. With an increased influx of genomic and transcriptomic data, study of differentially expressed genes (DEGs) is highly effective in …


How Did Covid-19 Impact Physiology Research Globally? – Lessons Learned And Future Recommendations, Jeet Patel, Santanu De Jan 2025

How Did Covid-19 Impact Physiology Research Globally? – Lessons Learned And Future Recommendations, Jeet Patel, Santanu De

Mako: NSU Undergraduate Student Journal

The Coronavirus Infectious Disease 2019 (COVID-19) pandemic caused massive changes in the medical field across the globe. As the whole world moved from in-person to remote activities, students found themselves in a predicament where they were compelled towards schooling and work online from home. This would mean that all projects, research, tests, and meetings were conducted over Zoom or other online meeting platforms. Laboratories were shut down or only a limited number of people were allowed to enter to conduct the necessary research. This paper discusses how the COVID-19 pandemic affected research process and experiments within various aspects of the …


Discerning The Role Of Microtubule Acetylation During Hiv-1 Infection, Drew Michael Lichon Jan 2025

Discerning The Role Of Microtubule Acetylation During Hiv-1 Infection, Drew Michael Lichon

Dissertations

The host-pathogen interactions underlying Human Immunodeficiency Virus type 1 (HIV-1) infection are complex and involve the exploitation of host cellular machinery. This thesis investigates the roles of dynein adaptors, microtubule acetylation, and TRIM69-mediated restriction in HIV-1 infection. Through a series of detailed experiments, we explore how HIV-1 utilizes multiple dynein adaptors, such as BICDR1 and Hook3, for intracellular transport, and reveal that these adaptors are critical for efficient viral trafficking. Conversely, the knockdown of Ninein surprisingly enhances HIV-1 infectivity, suggesting a nuanced regulatory role for this adaptor in viral transport. Further, this thesis challenges the prevailing paradigm that microtubule acetylation …


Investigating The Role Of The Nsp15 Amino-Terminal Domain In Nsp15 Function, Viral Replication, And Pathogenesis, Monika Evdokimova Jan 2025

Investigating The Role Of The Nsp15 Amino-Terminal Domain In Nsp15 Function, Viral Replication, And Pathogenesis, Monika Evdokimova

Dissertations

Identifying conserved mechanisms used by viruses to delay host innate responses can reveal potential targets for antiviral therapeutics. Here, we investigated coronavirus nonstructural protein 15 (nsp15), which encodes a highly conserved endoribonuclease (EndoU). EndoU functions as an immune antagonist by limiting the accumulation of viral replication intermediates that would otherwise be sensed by the host. Despite being a promising antiviral target, it has been difficult to develop small molecule inhibitors that target the EndoU active site. We generated nsp15 mutants of SARS-CoV-2 and mouse coronavirus MHV-A59 and identified conserved residues within the amino-terminal domain that are required for EndoU activity. …


Effects Of Aging On Diurnal Transcriptome Change In The Mouse Corpus Callosum, Hidehiro Ishikawa, Tomonori Hoshino, Gen Hamanaka, Emiri T. Mandeville, Shuzhen Guo, Shintaro Kimura, Norito Fukuda, Wenlu Li, Akihiro Shindo, Sava Sakadzic, Mary E. Harrington, Eng H. Lo, Ken Arai Jan 2025

Effects Of Aging On Diurnal Transcriptome Change In The Mouse Corpus Callosum, Hidehiro Ishikawa, Tomonori Hoshino, Gen Hamanaka, Emiri T. Mandeville, Shuzhen Guo, Shintaro Kimura, Norito Fukuda, Wenlu Li, Akihiro Shindo, Sava Sakadzic, Mary E. Harrington, Eng H. Lo, Ken Arai

Neuroscience: Faculty Publications

The corpus callosum, a major white matter region central to cognitive function, is vulnerable to aging. Using zeitgeber time (ZT) aligned with environmental light/dark cycles, we investigated temporal gene expression patterns in the corpus callosum of young (5-month-old) and aged (24-month-old) mice using RNA-seq. Comparative analysis revealed more differentially expressed genes across ZT pairs in young mice than aged mice. In addition, complement pathway genes, including C4b, C3, C1qa, C1qb, and C1qc, were consistently upregulated in aged mice regardless of ZT. Furthermore, genes such as Etnppl, Tinagl1, Hspa12b, Ppp1r3c, Thbd, Pla2g3, and Tsc22d3 exhibited ZT-dependent rhythmicity in young mice, but …


Corn And Soybean Responses To Phosphorus And Potassium Application Timings And Methods And Fertilizer Sources, Abrar Bin Wahid Jan 2025

Corn And Soybean Responses To Phosphorus And Potassium Application Timings And Methods And Fertilizer Sources, Abrar Bin Wahid

LSU Master's Theses

This research was driven by concerns over phosphorus (P) and potassium (K) losses from fall-applied fertilizers and the increasing marketing popularity of liquid-P and K fertilizers over traditional granular-dry forms. We evaluated corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] yield and tissue nutrient concentration responses to fertilizer-P and K application timings, methods, and sources across 9-13 site-years on silt-loam soils in Louisiana from 2020-2024. For timing and method study, five treatments were evaluated: a no fertilizer-P and/or K check, fall broadcast followed by rehipping the seedbed, spring broadcast without rehipping, spring broadcast with rehipping, and spring top-of-bed …


Pooled Safety Analysis And Management Of Sotorasib-Related Adverse Events In Kras G12c-Mutated Advanced Non-Small Cell Lung Cancer, Ferdinandos Skoulidis, Bob T Li, Maximilian Hochmair, Ramaswamy Govindan, Mark Vincent, Noemi Reguart Aransay, Nicolas Girard, Frank Griesinger, Makoto Nishio, Simon Häfliger, Colin Lindsay, Niels Reinmuth, Astrid Paulus, Pavlos Papakotoulas, Sang-We Kim, Carlos Gil Ferreira, Giulia Pasello, Michael Duruisseaux, Spyridon Gennatas, Anastasios Dimou, Bhakti Mehta, William Kormany, Chidozie Nduka, Brooke E Sylvester, Christine Ardito-Abraham, Yang Wang, Adrianus Johannes De Langen Jan 2025

Pooled Safety Analysis And Management Of Sotorasib-Related Adverse Events In Kras G12c-Mutated Advanced Non-Small Cell Lung Cancer, Ferdinandos Skoulidis, Bob T Li, Maximilian Hochmair, Ramaswamy Govindan, Mark Vincent, Noemi Reguart Aransay, Nicolas Girard, Frank Griesinger, Makoto Nishio, Simon Häfliger, Colin Lindsay, Niels Reinmuth, Astrid Paulus, Pavlos Papakotoulas, Sang-We Kim, Carlos Gil Ferreira, Giulia Pasello, Michael Duruisseaux, Spyridon Gennatas, Anastasios Dimou, Bhakti Mehta, William Kormany, Chidozie Nduka, Brooke E Sylvester, Christine Ardito-Abraham, Yang Wang, Adrianus Johannes De Langen

Faculty, Staff and Student Publications

Introduction: We describe the safety of sotorasib monotherapy in patients with KRAS G12C-mutated advanced non-small cell lung cancer (NSCLC) and discuss practical recommendations for managing key risks.

Methods: Incidence rates of treatment-related adverse events (TRAEs) were pooled from 4 clinical trials: CodeBreaK 100 (NCT03600883), CodeBreaK 101 (NCT04185883), CodeBreaK 105 (NCT04380753), and CodeBreaK 200 (NCT04303780) and graded according to CTCAE v5.0. Adverse events were deemed sotorasib-related per investigator causality assessment.

Results: In the pooled population (n = 549), TRAEs were reported in 388 (70.7%) patients (grade 1: 124 [22.6%]; grade 2: 117 [21.3%]; …


Utilizing Patient-Derived Xenografts To Model Precision Oncology For Biliary Tract Cancer, Timothy P Diperi, Kurt W Evans, Stephen Scott, Xiaofeng Zheng, Kaushik Varadarajan, Michael Kahle, Ching-Wei Tzeng, Thuy Vu, Sunhee Kim, Fei Su, Maria Gabriela Raso, Yasmeen Rizvi, Ming Zhao, Huamin Wang, Sunyoung S Lee, Timothy A Yap, Jordi Rodon, Milind Javle, Funda Meric-Bernstam Jan 2025

Utilizing Patient-Derived Xenografts To Model Precision Oncology For Biliary Tract Cancer, Timothy P Diperi, Kurt W Evans, Stephen Scott, Xiaofeng Zheng, Kaushik Varadarajan, Michael Kahle, Ching-Wei Tzeng, Thuy Vu, Sunhee Kim, Fei Su, Maria Gabriela Raso, Yasmeen Rizvi, Ming Zhao, Huamin Wang, Sunyoung S Lee, Timothy A Yap, Jordi Rodon, Milind Javle, Funda Meric-Bernstam

Faculty, Staff and Student Publications

Purpose: Biliary tract cancers, which are rare and aggressive malignancies, are rich in clinically actionable molecular alterations. A major challenge in the field is the paucity of clinically relevant biliary tract cancer models that recapitulate the diverse molecular profiles of these tumors. The purpose of this study was to curate a collection of patient-derived xenograft (PDX) models that reflect the spectrum of genomic alterations present in biliary tract cancers to create a resource for modeling precision oncology.

Experimental design: PDXs were derived from biliary tract cancer samples collected from surgical resections or metastatic biopsies. Alterations present in the PDXs were …


Clinical And Molecular Characteristics Of Patients With Brain Metastasis Secondary To Pancreatic Ductal Adenocarcinoma, Mahmoud Yousef, Mark W Hurd, Abdelrahman Yousef, Ethan B Ludmir, Ashwathy B Pillai, Eugene J Koay, Ching-Wei Tzeng, Rebecca Snyder, Matthew H G Katz, Huamin Wang, Michael J Overman, Anirban Maitra, Shubham Pant, Brandon G Smaglo, Robert A Wolff, James Yao, John P Shen, Dan Zhao Jan 2025

Clinical And Molecular Characteristics Of Patients With Brain Metastasis Secondary To Pancreatic Ductal Adenocarcinoma, Mahmoud Yousef, Mark W Hurd, Abdelrahman Yousef, Ethan B Ludmir, Ashwathy B Pillai, Eugene J Koay, Ching-Wei Tzeng, Rebecca Snyder, Matthew H G Katz, Huamin Wang, Michael J Overman, Anirban Maitra, Shubham Pant, Brandon G Smaglo, Robert A Wolff, James Yao, John P Shen, Dan Zhao

Faculty, Staff and Student Publications

Background: The prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) is poor. Secondary brain metastasis (Br-M) occurs in less than 1% of patients. Clinical characteristics and molecular alterations have not been characterized in this rare patients' subset.

Materials and methods: The Foundry software platform was used to retrospectively query electronic health records for patients with Br-M secondary to PDAC from 2005 to 2023; clinical, molecular, and overall survival (OS) data were analyzed.

Results: Br-M was diagnosed in 44 patients with PDAC. Median follow-up was 78 months; median OS from initial PDAC diagnosis was 47 months. Median duration from PDAC diagnosis …