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Mapping Of Qtls Associated With Frost Tolerance In Olive (Olea Europaea L.), Öznur Çeti̇n, Nurengi̇n Mete, Handan Ölmez, Hati̇ce Gülen Feb 2025

Mapping Of Qtls Associated With Frost Tolerance In Olive (Olea Europaea L.), Öznur Çeti̇n, Nurengi̇n Mete, Handan Ölmez, Hati̇ce Gülen

Turkish Journal of Agriculture and Forestry

The olive (Olea europaea L.) is widely distributed due to its high adaptability to different environmental conditions. However,in recent years, sudden extreme temperature decreases and frost damage have caused significant yield and quality losses in some regions.This situation has led to the development of varieties with high frost tolerance, suitable for regions where cold damage may occur.It takes many years to develop varieties using classical breeding methods in olives. Therefore, early selection should be made usingbiotechnological methods. Markers about any trait provide a great advantage, especially in plant species with a very long juvenile sterilityperiod, as they allow for a …


The Role Of Brassinosteroids In Plant Physiological And Molecular Responses To Counter Salt Stress And Ensure Food Security: A Review And Future Perspectives, Muhammad Umair Hassan, Huang Guoqin, Muhammad Nawaz, Adnan Noor Shah, Tahir Abbas Khan, Muhammad Inzamam Ul Haq, Mehmood Ali Noor, Zhou Ping, Liu Qin, Yasser S. Mostafa, Saad A. Alamri, Melekber Sülüşoğlu Durul, Mehmet Ramazan Bozhüyük, Mohamed Hashem Feb 2025

The Role Of Brassinosteroids In Plant Physiological And Molecular Responses To Counter Salt Stress And Ensure Food Security: A Review And Future Perspectives, Muhammad Umair Hassan, Huang Guoqin, Muhammad Nawaz, Adnan Noor Shah, Tahir Abbas Khan, Muhammad Inzamam Ul Haq, Mehmood Ali Noor, Zhou Ping, Liu Qin, Yasser S. Mostafa, Saad A. Alamri, Melekber Sülüşoğlu Durul, Mehmet Ramazan Bozhüyük, Mohamed Hashem

Turkish Journal of Agriculture and Forestry

Excessive salinity poses serious threats to crop productivity and global food security. Salt stress reduces crop growth and final productivity by inducing ionic, osmotic, and oxidative damage. Applying plant growth hormones is thought to be an efficient method of reducing the negative effects of salinity. Brassinosteroids (BRs) are plant hormones that have demonstrated appreciable effects against different abiotic stresses. BRs can mitigate the deleterious impacts of salt stress by improving water and nutrient uptake, membrane stability, antioxidant activities, and osmolyte synthesis while maintaining the hormonal balance. Furthermore, BRs can also improve the metabolic and molecular responses of plants to help …


Chemical Composition And Larvicidal Toxicity Of Ricinus Communis L. (Euphorbiaceae) Extracts Against Larvae Of Thaumetopoea Pityocampa (Denis & Schiffermüller, 1775) (Lepidoptera: Notodontidae), Memi̇ş Kesdek, Şaban Kordali, Selçuk Küçükaydin Feb 2025

Chemical Composition And Larvicidal Toxicity Of Ricinus Communis L. (Euphorbiaceae) Extracts Against Larvae Of Thaumetopoea Pityocampa (Denis & Schiffermüller, 1775) (Lepidoptera: Notodontidae), Memi̇ş Kesdek, Şaban Kordali, Selçuk Küçükaydin

Turkish Journal of Agriculture and Forestry

In this study, the toxicities of extracts obtained from the seeds and leaves of castor bean (Ricinus communis L.) (Euphorbiaceae) plant against five larval stages of the pine processionary moth (PPM) (Thaumetopoea pityocampa (Denis & Schiffermüller, 1775) (Lepidoptera: Notodontidae)) were investigated under laboratory conditions. Petroleum ether, acetone, and methanol extracts were prepared at various concentrations (0.25, 0.5, and 1 mg/mL) and sprayed on each larval stage. Each test was performed with three replications and two repetitions. Sterile water + ethanol was used as a negative control and the commercial chemical Kormilin 25 WP (25% diflubenzuron) was used as a positive …


Cover And Contents Feb 2025

Cover And Contents

Turkish Journal of Agriculture and Forestry

No abstract provided.


Identification And Functional Characterization Of The Icse1 Gene From Ilex Cornuta, Xiaoxi Zhang, Li Zhu, Weiwei Zhang, Feng Xu, Jiabao Ye, Yongling Liao Feb 2025

Identification And Functional Characterization Of The Icse1 Gene From Ilex Cornuta, Xiaoxi Zhang, Li Zhu, Weiwei Zhang, Feng Xu, Jiabao Ye, Yongling Liao

Turkish Journal of Agriculture and Forestry

Ilex cornuta (I. cornuta) is a traditional Chinese medicine that is rich in various secondary metabolites with pharmacological activities, among which triterpenoid saponins are one of the main active components. Squalene epoxidase (SE) is a key regulatory enzyme in the biosynthesis of triterpenoids. In this study, we isolated a squalene epoxidase (IcSE1) from I. cornuta and analyzed its molecular characteristics and functions. The results indicated that the total length of the IcSE1 sequence was 1942 bp, which includes a 1638 bp open reading frame (ORF) that encodes 545 amino acids. The theoretical isoelectric point (pI) and molecular weight of the …


Otolaryngology Practitioner Attitudes Toward Human Papillomavirus Vaccination In Academic Otolaryngology Clinics, Dante J. Merlino, Katelyn S. Rourk, George B. Sankar, Adam J. Luginbuhl, Brian J. Boyce, Michelle M. Chen, Eric M. Dowling, Michael C. Topf, Raymond L. Chai, Karthik Rajasekaran, Eric J. Moore, Daniel L. Price, George Saieed, Kathryn M. Van Abel Feb 2025

Otolaryngology Practitioner Attitudes Toward Human Papillomavirus Vaccination In Academic Otolaryngology Clinics, Dante J. Merlino, Katelyn S. Rourk, George B. Sankar, Adam J. Luginbuhl, Brian J. Boyce, Michelle M. Chen, Eric M. Dowling, Michael C. Topf, Raymond L. Chai, Karthik Rajasekaran, Eric J. Moore, Daniel L. Price, George Saieed, Kathryn M. Van Abel

Department of Otolaryngology - Head and Neck Surgery Faculty Papers

Despite the existence of a highly effective and safe vaccine against human papillomavirus (HPV) infection, vaccination rates remain low. The most prevalent HPV-associated malignancy in the United States is oropharyngeal cancer, but otolaryngology practitioners do not offer the HPV vaccine, and their feelings around offering HPV vaccination have not been evaluated. A 43-question survey, including a twelve-question knowledge quiz, was sent to otolaryngology practitioners at seven academic institutions. Twelve questions comprised a knowledge quiz testing practitioner understanding of HPV, while the remainder of the questions evaluated comfort with and likelihood of recommending vaccination. Of the 442 practitioners who were sent …


Safe Passage To Social And Academic Support: First Year Stem Identity And Belonging Interventions For Under-Resourced Students, Benjamin Haywood, John Kaup, John Wheeler Feb 2025

Safe Passage To Social And Academic Support: First Year Stem Identity And Belonging Interventions For Under-Resourced Students, Benjamin Haywood, John Kaup, John Wheeler

Open Access Fund Publications

Institutions of higher education continue to grapple with the challenges associated with increasing access to STEM learning and STEM majors for resource-limited students. Longstanding differences among well and under-resourced student groups with respect to STEM course enrollment, STEM major retention and persistence, and research opportunities persist despite decades of research on interventions. This article reports on outcomes of a cohort-based, multi-pronged S-STEM scholarship program at a small liberal arts institution for Pell-eligible first-year students that focuses on reducing college transition anxiety; building peer and mentor networks in STEM; providing gateway science course cohort learning; and layering multiple levels of advising …


Exploring Genetic Diversity: The Inheritance Of Protein And Mineral Contents In Dwarf Common Beans, Ercan Ceyhan, Ayşegül Korkmaz, Amjad Ali̇, Serdar Karadaş, Mustafa Harmankaya, Duran Şi̇mşek, Tolga Karaköy Feb 2025

Exploring Genetic Diversity: The Inheritance Of Protein And Mineral Contents In Dwarf Common Beans, Ercan Ceyhan, Ayşegül Korkmaz, Amjad Ali̇, Serdar Karadaş, Mustafa Harmankaya, Duran Şi̇mşek, Tolga Karaköy

Turkish Journal of Agriculture and Forestry

Beans are a vital plant-based protein, containing essential minerals that are necessary for human health. Their protein and mineral compositions vary due to factors including cultivar or variety, growth conditions, and processing methods. Global deficiencies in protein and minerals necessitate fortification, supplementation, and dietary diversification. The present study focuses on common bean (Phaseolus vulgaris) cultivars, aiming to understand their genetic variation and inheritance of protein and mineral contents. Five dwarf common bean cultivars (Lida, Beyzade, Ribera, Albeni, and Garrafol) were used in a full-diallel hybridization method and the experiment was conducted in Konya, Türkiye. The diallel analysis assessed both general …


Enhancing Salt Tolerance And Yield Potential In Cotton: Insights From Physiological Responses, Genetic Variability, And Heterosis, Muhammad Mubashar Zafar, Abdul Razzaq, Zunaira Anwar, Aqsa Ijaz, Muhammad Zahid, Muhammad Shahid Iqbal, Ghulam Farid, Mahmoud F. Seleiman, Rana Qammar Uz Zaman, Abdur Rauf, Xuefei Jiang Feb 2025

Enhancing Salt Tolerance And Yield Potential In Cotton: Insights From Physiological Responses, Genetic Variability, And Heterosis, Muhammad Mubashar Zafar, Abdul Razzaq, Zunaira Anwar, Aqsa Ijaz, Muhammad Zahid, Muhammad Shahid Iqbal, Ghulam Farid, Mahmoud F. Seleiman, Rana Qammar Uz Zaman, Abdur Rauf, Xuefei Jiang

Turkish Journal of Agriculture and Forestry

Soil salinity is a growing global concern, necessitating the development of salt-tolerant cotton cultivars to enhance the utilization of salt-affected soils and boost crop productivity. Salt tolerance is regulated by a complex interplay of genetic and physiological factors involving multiple genes. To investigate the genetic basis of salt stress tolerance, eight parental genotypes (four lines and four testers) and their 16 hybrid combinations were evaluated under normal and salt stress conditions (15 dS m⁻¹). Data were collected on various traits including the plant height (PH), number of bolls per plant (NBP), boll weight (BW), lint percentage (LP), seed cotton yield …


Nutritional And Microbiological Properties Of Cheese With Dried Elderberry And Red Grape Pomace, Andreea Dodan, Romina Alina Marc, Crina Carmen Mureşan, Carmen Rodica Pop, Delia Michiu, Miuța Rafila Filip, Roxana Nicoleta Rațu, Florina Stoica, Ioana Cristina Crivei, Alina Narcisa Postolache, Melinda Kovacs, Rodica Maria Sima, Mircea Valentin Muntean Feb 2025

Nutritional And Microbiological Properties Of Cheese With Dried Elderberry And Red Grape Pomace, Andreea Dodan, Romina Alina Marc, Crina Carmen Mureşan, Carmen Rodica Pop, Delia Michiu, Miuța Rafila Filip, Roxana Nicoleta Rațu, Florina Stoica, Ioana Cristina Crivei, Alina Narcisa Postolache, Melinda Kovacs, Rodica Maria Sima, Mircea Valentin Muntean

Turkish Journal of Agriculture and Forestry

This study aimed to explore the use of grape byproducts such as red grape pomace and elderberry, in the form of bioactive powders to obtain three-month old cheese assortments. Grape pomace powder (GPP) and elderberry fruit powder (EFP) contain antioxidant components such as phenols, anthocyanins and flavonoids, and compounds characterized by high bioactivity. This study investigated not only the potential of incorporating different percentages (1%, 2%, and 3%) of GPP and EFP in cheese, to increase its nutritional value, but also the changes that occur during the 2 months of ripening. The results indicated that the incorporation of GPP and …


Transcriptome And Metabolome Analysis Of Low-Temperature Storage On Fruit Quality Deterioration Of Mangoes, Hanqing Cong, Ting Huo, Xinran Huang, Yeyuan Chen, Yibo Bai, Haiyan Luo, Xiaona Fu, Rongxiang Wang, Mahmoud F. Seleiman, Tanweer Ahmad, Pingyin Guan, Mohsin Bashir, Muhammad Asif, Fei Qiao Feb 2025

Transcriptome And Metabolome Analysis Of Low-Temperature Storage On Fruit Quality Deterioration Of Mangoes, Hanqing Cong, Ting Huo, Xinran Huang, Yeyuan Chen, Yibo Bai, Haiyan Luo, Xiaona Fu, Rongxiang Wang, Mahmoud F. Seleiman, Tanweer Ahmad, Pingyin Guan, Mohsin Bashir, Muhammad Asif, Fei Qiao

Turkish Journal of Agriculture and Forestry

Mango, a typical respiratory climacteric fruit, is susceptible to a short shelf life and quality deterioration during postharvest ripening. Although low temperature can prolong the storage time significantly, its effects on fruit quality have yet to be elucidated. Through a combination of transcriptome and metabolome analyses, this study aimed to elucidate the effects of low-temperature storage on the biosynthesis of volatile organic compounds (VOCs), flavonoids, sucrose, and the degradation of organic acids in mango. Carbohydrate-related metabolism maintained high activity when stored at 13 °C by upregulating the expression of certain gene members in the neutral invertase (NI), sucrose phosphate synthase …


Understanding The Role Of Thermal Stress In Modulating Growth, Yield, And Quality Attributes Of Tomato At Two Locations, Muhammad Uzair, Rabia Kalsoom, Kotb A. Attia, Irfan Ali, Tanveer Hussain, Asmaa M. Abushady, Haider Ali, Sajid Fiaz, Saima Jameel, Muhammad Usman Hameed, Rashid Iqbal, Muhammad Ramzan Khan Feb 2025

Understanding The Role Of Thermal Stress In Modulating Growth, Yield, And Quality Attributes Of Tomato At Two Locations, Muhammad Uzair, Rabia Kalsoom, Kotb A. Attia, Irfan Ali, Tanveer Hussain, Asmaa M. Abushady, Haider Ali, Sajid Fiaz, Saima Jameel, Muhammad Usman Hameed, Rashid Iqbal, Muhammad Ramzan Khan

Turkish Journal of Agriculture and Forestry

Tomato is a well-recognized and extensively cultivated crop on a global scale. However, the development of tomato varieties is hindered by adverse environments, limited genetic diversity, and low rates of seed setting. In this study, we evaluated 21 genotypes at two different locations in Pakistan. We analyzed morphological traits including vine length, days to 50% flowering, days to fruit setting initiation, number of clusters per plant (NCP), and number of flowers per cluster (NFC); yield-related traits such as fruit setting percentage per cluster, fruit setting percentage per plant, number of marketable fruits per plant (NMFP), marketable fruit yield per plant …


Agronomic Performance Of Fenugreek Genotypes Grown Under Various Sowing And Nitrogen Rates In A Highland Environment, Furkan Çoban, Hakan Özer Feb 2025

Agronomic Performance Of Fenugreek Genotypes Grown Under Various Sowing And Nitrogen Rates In A Highland Environment, Furkan Çoban, Hakan Özer

Turkish Journal of Agriculture and Forestry

Fenugreek is an important medicinal plant used in food, medicine, and other industries. In recent years, there has been increased interest in the fenugreek plant, with increased support given for fenugreek in Türkiye. However, there is a need for sound recommendations on agronomic practices such as variety selection, plant density, and fertilization due to local differences in the climate and soil structure. This research was conducted to determine the yield and some agricultural characteristics of two fenugreek genotypes (Turkish and Iranian) grown under different nitrogen (N) (0, 20, 40, 60, and 80 kg ha–1) and sowing (20, 40, and 60 …


Thrombocytopenia In Sepsis, Alireza Setarehaseman, Robert W. Maitta Feb 2025

Thrombocytopenia In Sepsis, Alireza Setarehaseman, Robert W. Maitta

Faculty Scholarship

Platelets, traditionally known for their role in hemostasis, have emerged as key players in immune response and inflammation. Sepsis, a life-threatening condition characterized by systemic inflammation, often presents with thrombocytopenia, which at times, can be significant. Platelets contribute to the inflammatory response by interacting with leukocytes, endothelial cells, and the innate immune system. However, excessive platelet activation and consumption can lead to thrombocytopenia and exacerbate the severity of sepsis. Understanding the multifaceted roles of platelets in sepsis is crucial for developing effective therapeutic strategies. Targeting platelet-mediated inflammatory responses and promoting platelet production may offer potential avenues for improving outcomes in …


The Experience Of Genetic Testing Among Latinas With Brca1/2 Mutation, Lisania Milli Feb 2025

The Experience Of Genetic Testing Among Latinas With Brca1/2 Mutation, Lisania Milli

Seton Hall University Dissertations and Theses (ETDs)

Healthy women with BRCA1 (BReast CAncer gene 1) or BRCA2 (BReast CAncer gene 2), (henceforth, BRCA1/2 mutation) without a diagnosis of breast or ovarian cancer (unaffected), have up to 80% increased lifetime risk of developing breast cancer, and up to 40% increased lifetime risk of ovarian cancer. Genetic counseling and testing based upon family history is essential to diagnose genetic mutations increasing one’s risk for certain cancers. Latinas have the second highest prevalence of BRCA1/2 mutations after Ashkenazi Jewish women, and cancer is now the leading cause of death among Latinos, surpassing cardiovascular disease. However, no qualitative study has been …


Comparative Transcriptomics Reveals A Mixed Basal, Club, And Hillock Epithelial Cell Identity In Castration-Resistant Prostate Cancer, Samuel P Pitzen, Amber N Rudenick, Yinjie Qiu, Weijie Zhang, Sarah A Munro, Braedan M Mccluskey, Colleen Forster, Hannah E Bergom, Atef Ali, Ella Boytim, John T Lafin, Simon Linder, Mazlina Ismail, Wout Devlies, Conner J Sessions, Frank Claessens, Steven Joniau, Gerhardt Attard, Wilbert Zwart, Peter S Nelson, Eva Corey, Yuzhuo Wang, Joshua M Lang, Himisha Beltran, Douglas Strand, Emmanuel S Antonarakis, Justin Hwang, Paari Murugan, R Stephanie Huang, Scott M Dehm Feb 2025

Comparative Transcriptomics Reveals A Mixed Basal, Club, And Hillock Epithelial Cell Identity In Castration-Resistant Prostate Cancer, Samuel P Pitzen, Amber N Rudenick, Yinjie Qiu, Weijie Zhang, Sarah A Munro, Braedan M Mccluskey, Colleen Forster, Hannah E Bergom, Atef Ali, Ella Boytim, John T Lafin, Simon Linder, Mazlina Ismail, Wout Devlies, Conner J Sessions, Frank Claessens, Steven Joniau, Gerhardt Attard, Wilbert Zwart, Peter S Nelson, Eva Corey, Yuzhuo Wang, Joshua M Lang, Himisha Beltran, Douglas Strand, Emmanuel S Antonarakis, Justin Hwang, Paari Murugan, R Stephanie Huang, Scott M Dehm

Faculty, Staff and Student Publications

Inhibiting the androgen receptor (AR) is effective for treatment of advanced prostate cancers because of their AR-dependent luminal epithelial cell identity. Tumors progress during therapy to castration-resistant prostate cancer (CRPC) by restoring AR signaling and maintaining luminal identity or by converting through lineage plasticity to a neuroendocrine (NE) identity or double-negative CRPC (DNPC) lacking luminal or NE identities. Here, we show that DNPC cells express genes defining basal, club, and hillock epithelial cells from benign prostate. We identified KLF5 as a regulator of genes defining this mixed basal, club, and hillock cell identity in DNPC models. KLF5-mediated upregulation of


Spartan Daily, February 11, 2025, San Jose State University, School Of Journalism And Mass Communications Feb 2025

Spartan Daily, February 11, 2025, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2025

Volume 164, Issue 8


Nprl2 Gene Therapy Induces Effective Antitumor Immunity In Kras/Stk11 Mutant Anti-Pd1 Resistant Metastatic Non-Small Cell Lung Cancer (Nsclc) In A Humanized Mouse Model, Ismail M Meraz, Mourad Majidi, Renduo Song, Feng Meng, Lihui Gao, Qi Wang, Jing Wang, Elizabeth J Shpall, Jack A Roth Feb 2025

Nprl2 Gene Therapy Induces Effective Antitumor Immunity In Kras/Stk11 Mutant Anti-Pd1 Resistant Metastatic Non-Small Cell Lung Cancer (Nsclc) In A Humanized Mouse Model, Ismail M Meraz, Mourad Majidi, Renduo Song, Feng Meng, Lihui Gao, Qi Wang, Jing Wang, Elizabeth J Shpall, Jack A Roth

Faculty, Staff and Student Publications

Expression of NPRL2/TUSC4, a tumor-suppressor gene, is reduced in many cancers including NSCLC. Restoration of NPRL2 induces DNA damage, apoptosis, and cell-cycle arrest. We investigated NPRL2 antitumor immune responses in aPD1R/KRAS/STK11mt NSCLC in humanized-mice. Humanized-mice were generated by transplanting fresh human cord blood-derived CD34 stem cells into sub-lethally irradiated NSG mice. Lung-metastases were developed from KRAS/STK11mt/aPD1R A549 cells and treated with NPRL2 w/wo pembrolizumab. NPRL2-treatment reduced lung metastases significantly, whereas pembrolizumab was ineffective. Antitumor effect was greater in humanized than non-humanized-mice. NPRL2 + pembrolizumab was not synergistic in KRAS/STK11mt/aPD1R tumors but was …


Engineered Immunomodulatory Extracellular Vesicles From Epithelial Cells With The Capacity For Stimulation Of Innate And Adaptive Immunity In Cancer And Autoimmunity, Xin Luo, Fernanda G Kugeratski, Dara P Dowlatshahi, Hikaru Sugimoto, Kent A Arian, Yibo Fan, Li Huang, Danielle Wills, Sergio Lilla, Kelly Hodge, Sara R Zanivan, Valerie S Lebleu, Kathleen M Mcandrews, Raghu Kalluri Feb 2025

Engineered Immunomodulatory Extracellular Vesicles From Epithelial Cells With The Capacity For Stimulation Of Innate And Adaptive Immunity In Cancer And Autoimmunity, Xin Luo, Fernanda G Kugeratski, Dara P Dowlatshahi, Hikaru Sugimoto, Kent A Arian, Yibo Fan, Li Huang, Danielle Wills, Sergio Lilla, Kelly Hodge, Sara R Zanivan, Valerie S Lebleu, Kathleen M Mcandrews, Raghu Kalluri

Faculty, Staff and Student Publications

Extracellular vesicles (EVs) are generated by all cells. Systemic administration of allogenic EVs derived from epithelial and mesenchymal cells have been shown to be safe, despite carrying an array of functional molecules, including thousands of proteins. To address whether epithelial cells derived EVs can be modified to acquire the capacity to induce immune response, we engineered 293T EVs to harbor the immunomodulatory molecules CD80, OX40L and PD-L1. We demonstrated abundant levels of these proteins on the engineered cells and EVs. Functionally, the engineered EVs efficiently elicited positive and negative co-stimulation of human and murine T cells. In the setting of …


Complete Genome Sequence Of A Penicillin-Resistant Fusobacterium Necrophorum Subsp Funduliforme Isolate From A Tonsillitis Patient, Bibek G C, Anders Jensen, Chenggang Wu Feb 2025

Complete Genome Sequence Of A Penicillin-Resistant Fusobacterium Necrophorum Subsp Funduliforme Isolate From A Tonsillitis Patient, Bibek G C, Anders Jensen, Chenggang Wu

Faculty, Staff and Student Publications

We report the complete genome sequence of a penicillin-resistant Fusobacterium necrophorum subsp. funduliforme isolate, AJ79, from a tonsillitis patient. The AJ79 genome consists of a chromosome (2,440,359 bp) and plasmid (9,887 bp), providing insights into the genetic basis of penicillin resistance in F. necrophorum and its implications for treating tonsillitis.


Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker Feb 2025

Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The rapid evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural and energetic analysis of SARS-CoV-2 spike receptor-binding domain (RBD) complexes with neutralizing antibodies from four distinct groups (A–D), including group A LY-CoV016, group B AZD8895 and REGN10933, group C LY-CoV555, and group D antibodies AZD1061, REGN10987, and LY-CoV1404. Using coarse-grained simplified simulation models, rapid energy-based mutational scanning, and rigorous MM-GBSA binding free energy calculations, we elucidated the molecular mechanisms of antibody binding and escape mechanisms, identified key …


Intensive Lifestyle Intervention, Cardiac Biomarkers, And Cardiovascular Outcomes In Diabetes: Look Ahead Cardiac Biomarker Ancillary Study, Kershaw V Patel, Zainali Chunawala, Subodh Verma, Matthew W Segar, Katelyn R Garcia, Chiadi E Ndumele, Thomas J Wang, James L Januzzi, Antoni Bayes-Genis, Javed Butler, Carolyn S P Lam, Christie M Ballantyne, James A De Lemos, Alain G Bertoni, Mark Espeland, Ambarish Pandey Feb 2025

Intensive Lifestyle Intervention, Cardiac Biomarkers, And Cardiovascular Outcomes In Diabetes: Look Ahead Cardiac Biomarker Ancillary Study, Kershaw V Patel, Zainali Chunawala, Subodh Verma, Matthew W Segar, Katelyn R Garcia, Chiadi E Ndumele, Thomas J Wang, James L Januzzi, Antoni Bayes-Genis, Javed Butler, Carolyn S P Lam, Christie M Ballantyne, James A De Lemos, Alain G Bertoni, Mark Espeland, Ambarish Pandey

Faculty, Staff and Students Publications

Background: N-terminal pro-B-type natriuretic peptide (NT-proBNP) and high-sensitivity cardiac troponin T (hs-cTnT) are associated with cardiovascular outcomes and are recommended for measurement in type 2 diabetes (T2D). However, the effects of an intensive lifestyle intervention (ILI) targeting weight loss on cardiac biomarkers and the prognostic association of changes in these biomarkers with risk of adverse cardiovascular outcomes in T2D are not well-established.

Objectives: This study sought to evaluate the effects of an ILI on cardiac biomarkers and the association of changes in cardiac biomarkers with risk of cardiovascular outcomes in T2D.

Methods: Participants of the Look AHEAD (Action for Health …


Restore The Shore: A Guide To Lakeshore Revegetation In The Great Basin, Jes V. Braun, Rae Robinson, Annie L. Henry, Karin M. Kettenring Feb 2025

Restore The Shore: A Guide To Lakeshore Revegetation In The Great Basin, Jes V. Braun, Rae Robinson, Annie L. Henry, Karin M. Kettenring

All Current Publications

Lakeshore vegetation supports many valuable aspects of lake ecosystems: foraging areas for birds, rearing grounds for fish, nutrient cycling, carbon storage, and aesthetic, cultural, and spiritual values. Yet, the vegetation of many lakeshores has been lost or heavily impacted by humans. What can be done to restore lakeshore vegetation to ensure that lakes remain healthy for future generations? In this guide, we summarize best practices for lakeshore revegetation (i.e., the process of actively reintroducing vegetation, usually native species, to a restoration site through seeding and planting) in the Great Basin.


A Genome-Wide Association Study To Detect Candidate Genes Controlling Iron And Manganese Accumulation In Walnut (Juglans Regia L.), Özge Doğanay, Erdal Orman, Bülent Yağmur, Muhammed Bahatti̇n Tanyolaç, Duygu Ateş Feb 2025

A Genome-Wide Association Study To Detect Candidate Genes Controlling Iron And Manganese Accumulation In Walnut (Juglans Regia L.), Özge Doğanay, Erdal Orman, Bülent Yağmur, Muhammed Bahatti̇n Tanyolaç, Duygu Ateş

Turkish Journal of Agriculture and Forestry

The walnut is one of the important low-glycemic sources of vegetable protein that benefit human health. Iron (Fe) and Manganese (Mn) are two of the walnut’s important nutritional components. This study aimed to identify single-nucleotide polymorphism (SNP) markers associated with the concentrations of Mn and Fe in walnut kernels and the genetic variation in these concentrations. The population was evaluated for two different years using 154 walnut genotypes and genotyping was performed with 16,473 SNP markers. A genome-wide association study was performed on 154 genotypes. A total of five and 15 SNPs were identified in different walnut genotypes, which were …


Phytochemical Analysis And In Vitro And In Vivo Pharmacological Activities Of Cordia Myxa Extracts, Tatheer Fatima, Mirza Imran Shahzad, Adnan Noor Shah, Zhang Yi, Bushra Gillani, Iqra Hussain, Adina Gillani, Zeli̇ha Çi̇ftçi̇, Marcello Locatelli, Ashraf Atef Hatamleh, Munirah Abdullah Al-Dosary Feb 2025

Phytochemical Analysis And In Vitro And In Vivo Pharmacological Activities Of Cordia Myxa Extracts, Tatheer Fatima, Mirza Imran Shahzad, Adnan Noor Shah, Zhang Yi, Bushra Gillani, Iqra Hussain, Adina Gillani, Zeli̇ha Çi̇ftçi̇, Marcello Locatelli, Ashraf Atef Hatamleh, Munirah Abdullah Al-Dosary

Turkish Journal of Agriculture and Forestry

Cordia myxa is found in tropical regions of Pakistan, where it is commonly known as lasura. This study aimed to assess the preliminary results of phytochemical analysis and the pharmacological activities of C. myxa. After pulverizing the fresh plant, extracts were prepared using different solvents, including aqueous, methanol, ethanol, dichloromethane, ethyl acetate, and n-hexane extracts. These extracts were examined for total phenolic contents using standard biochemical tests and high performance liquid chromatography with a photodiode array. In further evaluations, antioxidant, antibacterial, antiviral, hen’s egg test on chorioallantoic membrane (HETCAM) assay, antipyretic, antiinflammatory, and antidiabetic activities were monitored. Using ferric reducing …


Bioactive Content And Antioxidant Capacity Of Some Plants And Fruits Grown In Türkiye, Gülay Özkan, Fatma Betül Sakarya, Bayram Yurt, Elwira Sieniawska, Yakup Yapar, Esra Çapanoğlu Güven Feb 2025

Bioactive Content And Antioxidant Capacity Of Some Plants And Fruits Grown In Türkiye, Gülay Özkan, Fatma Betül Sakarya, Bayram Yurt, Elwira Sieniawska, Yakup Yapar, Esra Çapanoğlu Güven

Turkish Journal of Agriculture and Forestry

Recently, some edible plants and fruits have undergone extensive research to identify potential health effects arising from their valuable nutritional and bioactive properties. The present study aims to investigate the phenolic compounds of nine edible plants and fruits throughout the gastrointestinal digestion model by comparing their total content and antioxidant activity. Of the species studied, Eremurus spectabilis and Gundelia tournefortii had the lowest total phenolic content, whereas Prunus armeniaca showed the highest value of 1026 ± 164 mg GAE/100 g. Except for Prunus armeniaca , the total phenolic contents of all samples were increased following gastric digestion, while the total …


Mbnl Overexpression Rescues Cardiac Phenotypes In A Myotonic Dystrophy Type 1 Heart Mouse Model, Rong-Chi Hu, Yi Zhang, Larissa Nitschke, Sara J Johnson, Ayrea E Hurley, William R Lagor, Zheng Xia, Thomas A Cooper Feb 2025

Mbnl Overexpression Rescues Cardiac Phenotypes In A Myotonic Dystrophy Type 1 Heart Mouse Model, Rong-Chi Hu, Yi Zhang, Larissa Nitschke, Sara J Johnson, Ayrea E Hurley, William R Lagor, Zheng Xia, Thomas A Cooper

Faculty, Staff and Students Publications

Myotonic dystrophy type 1 (DM1) is an autosomal dominant disease caused by a CTG repeat expansion in the dystrophia myotonica protein kinase (DMPK) gene. The expanded CUG repeat RNA (CUGexp RNA) transcribed from the mutant allele sequesters the muscleblind-like (MBNL) family of RNA-binding proteins, causing their loss of function and disrupting regulated pre-mRNA processing. We used a DM1 heart mouse model that inducibly expresses CUGexp RNA to test the contribution of MBNL loss to DM1 cardiac abnormalities and explored MBNL restoration as a potential therapy. AAV9-mediated overexpression of MBNL1 and/or MBNL2 significantly rescued DM1 cardiac phenotypes including conduction delays, contractile …


Author Correction: Orthogonal And Multiplexable Genetic Perturbations With An Engineered Prime Editor And A Diverse Rna Array, Qichen Yuan, Hongzhi Zeng, Tyler C Daniel, Qingzhuo Liu, Yongjie Yang, Emmanuel C Osikpa, Qiaochu Yang, Advaith Peddi, Liliana M Abramson, Boyang Zhang, Yong Xu, Xue Gao Feb 2025

Author Correction: Orthogonal And Multiplexable Genetic Perturbations With An Engineered Prime Editor And A Diverse Rna Array, Qichen Yuan, Hongzhi Zeng, Tyler C Daniel, Qingzhuo Liu, Yongjie Yang, Emmanuel C Osikpa, Qiaochu Yang, Advaith Peddi, Liliana M Abramson, Boyang Zhang, Yong Xu, Xue Gao

Faculty, Staff and Students Publications

Correction to: Nature Communications 10.1038/s41467-024-55134-9, published online 30 December 2024

In the version of the article initially published, there were errors in Fig. 3d, where in the x-axis labels now reading “GPP-shRNA1, GPP-shRNA2, GPP-shRNA3…,” the second and third labels were duplicates of the first. The figure is amended in the HTML and PDF versions of the article.


2024 Physician-Scientist Trainee Diversity Summit Conference Proceedings, Jessica Weng, Cynthia Y Tang, Kyle T Enriquez, Rohini N Guin, Briana Christophers, Yentli E Soto Albrecht, Daniel B Amusin, Deborah D Rupert, Paige Cooper Byas Feb 2025

2024 Physician-Scientist Trainee Diversity Summit Conference Proceedings, Jessica Weng, Cynthia Y Tang, Kyle T Enriquez, Rohini N Guin, Briana Christophers, Yentli E Soto Albrecht, Daniel B Amusin, Deborah D Rupert, Paige Cooper Byas

2020-Current year OA Pubs

The Physician-Scientist Trainee Diversity Summit, hosted by the American Physician Scientists Association and the Burroughs Wellcome Fund, was conceived in 2019 with the mission of developing strategic plans to diversify the physician-scientist community using human-centered design thinking. In June 2024, the second iteration of this conference was held in Raleigh, North Carolina, and brought together a network of scientific and medical organizations to discuss issues of justice, equity, diversity, and inclusion facing physician-scientist trainees. This article summarizes the progress made from the first meeting, the proceedings of the 2024 Summit, and a thematic analysis of the recent meeting, offering tangible …


Overview Of Findings From The North Devon World Surfing Reserve Focus Group, Kizzy Beaumont, Greg Borne Feb 2025

Overview Of Findings From The North Devon World Surfing Reserve Focus Group, Kizzy Beaumont, Greg Borne

School of Biological and Marine Sciences

The North Devon World Surfing Reserve (NDWSR) focus group, held on the 19th June, 2024,brought together members of the Local Stewardship Council and key community representatives to reflect on past achievements, discuss current challenges, and envision future opportunities for the region. The focus group is part of a collaborative research project developed and run by researchers from the University of Plymouth and Falmouth University. Discussions revolved around technological advancements, community engagement, environmental concerns, and the socio-economic impacts of surfing tourism. This interim summary presents a high-level summary of initial findings, emphasising participant perspectives and the implications for future strategies.