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Evidence That Aquaporin 11 (Aqp11) In The Spiny Dogfish (Squalus Acanthias) May Represent A Pseudogene, Christopher P. Cutler, Meghan Canicatti, Esosa Omoregie 2024 Georgia Southern University

Evidence That Aquaporin 11 (Aqp11) In The Spiny Dogfish (Squalus Acanthias) May Represent A Pseudogene, Christopher P. Cutler, Meghan Canicatti, Esosa Omoregie

Department of Biology Faculty Publications

Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish (Squalus acanthias) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These primers yielded some faint bands from gill cDNA that were sequenced. Blast searches with the sequences showed they were not AQP11. An elasmobranch AQP11 nucleotide sequence alignment was produced to identify conserved regions to make further degenerate primers. One primer pair produced a short 148 bp fragment showing particularly strong amplification in gill and intestine. It was sequenced and represented a piece of the …


Predicting The Identities Of Su(Met-2) And Met-3 In Neurospora Crassa By Genome Resequencing, Kevin McCluskey, Daren Brown, Erin Bredeweg, Scott E. Baker 2024 Fungal Genetics Stock Center, Kansas State University, Manhattan KS

Predicting The Identities Of Su(Met-2) And Met-3 In Neurospora Crassa By Genome Resequencing, Kevin Mccluskey, Daren Brown, Erin Bredeweg, Scott E. Baker

Fungal Genetics Reports

A significant number of classical genetic Neurospora crassa biochemical mutants remain anonymous, unassociated with a physical genome locus. By utilizing short read next-generation sequencing methods, it is possible to sequence the genomes of mutant strains rapidly and economically for the purpose of identifying genes associated with mutant phenotypes. We have taken this approach to connect genes and mutations to “methionineless” phenotypes in N. crassa.


Comparative Animal Mucomics, Antonio R. Cerullo 2024 The Graduate Center, City University of New York

Comparative Animal Mucomics, Antonio R. Cerullo

Dissertations, Theses, and Capstone Projects

Mucus is one of Nature’s most abundant and versatile biomaterials. These secretions are present in all animals, from the lowly garden snail to the great blue whale, and fulfill a multitude of functions, acting as antimicrobial barriers, moisturizers, adhesive glues, surface lubricants, and mineralizing agents. Despite their importance, very little is known about mucus compositions or properties. The largest challenge precluding the greater understanding of mucus function is its complexity; a single mucus contains complex mixtures of proteins, glycans, and ions that all have important roles in function. Therefore, understanding mucus function necessitates analysis that compares different mucus from one …


College Of Natural Sciences 2023 Year-End Publication, College Of Natural Sciences 2024 South Dakota State University

College Of Natural Sciences 2023 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 3 Department Highlights
Page 4 One Day for State
Page 5 Noble Prize Winner Speaks on Campus
Page 6-7 Faculty Excellence
Page 8-9 Student Excellence
Page 10 Outreach Program
Page 10 Events and Traditions
Page 11 Connections Abroad
Page 12 Student Spotlight
Page 13 Alumni Spotlight
Page 14 First Ever Drone Day
Page 15 Grand Opening of POET Bioproducts Center
Page 16 Work Anniversaries


Comparative Analysis Of A Secondary Metabolite Profile From Roots And Leaves Of Iostephane Heterophylla By Uplc-Ms And Gc-Ms, Diana V. Navarrete-Carriola, Alma D. Paz-González, Lenci K. Vázquez-Jiménez, Erick De Luna-Santillana, María A. Cruz-Hernández, Debasish Bandyopadhyay, Gildardo Rivera 2024 The University of Texas Rio Grande Valley

Comparative Analysis Of A Secondary Metabolite Profile From Roots And Leaves Of Iostephane Heterophylla By Uplc-Ms And Gc-Ms, Diana V. Navarrete-Carriola, Alma D. Paz-González, Lenci K. Vázquez-Jiménez, Erick De Luna-Santillana, María A. Cruz-Hernández, Debasish Bandyopadhyay, Gildardo Rivera

School of Integrative Biological and Chemical Sciences Faculty Publications and Presentations

Iostephane heterophylla is a traditional Mexican medicinal plant and is an important source of secondary metabolites with antimicrobial and cytotoxic activity. The aim of this work was to conduct a comparative analysis of secondary metabolites of different roots and leaf extracts of I. heterophylla from two zones in Mexico using ultraperformance liquid chromatography (UPLC) and gas chromatography (GC) coupled with mass spectrometry (MS). Twelve secondary metabolites from roots were identified in the leaves. Five new molecular weight secondary metabolites not previously reported were found. Six bioactive metabolites were quantified (quercetin ≤0.151 mg/mL in root and ≤0.041 mg/mL in leaf; hesperidin …


An Itpa Enzyme With Improved Substrate Selectivity, Nicholas E. Burgis, Kandise VanWormer, Devin Robbins, Jonathan Smith 2024 Eastern Washington University

An Itpa Enzyme With Improved Substrate Selectivity, Nicholas E. Burgis, Kandise Vanwormer, Devin Robbins, Jonathan Smith

Chemistry and Biochemistry Faculty Publications

Recent clinical data have identified infant patients with lethal ITPA deficiencies. ITPA is known to modulate ITP concentrations in cells and has a critical function in neural development which is not understood. Polymorphism of the ITPA gene affects outcomes for both ribavirin and thiopurine based therapies and nearly one third of the human population is thought to harbor ITPA polymorphism. In a previous site-directed mutagenesis alanine screen of the ITPA substrate selectivity pocket, we identified the ITPA mutant, E22A, as a gain-of function mutant with enhanced ITP hydrolysis activity. Here we report a rational enzyme engineering experiment to investigate the …


Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave 2024 The Graduate Center, City University of New York

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …


Protein-Protein Interactions In Cell Cycle Proteins: An In Silico Investigation Of Two Important Players, Andriele Eichner 2024 The Graduate Center, City University of New York

Protein-Protein Interactions In Cell Cycle Proteins: An In Silico Investigation Of Two Important Players, Andriele Eichner

Dissertations, Theses, and Capstone Projects

The examination of the cell cycle carries significant implications for the biology, health, and overall existence of all living things. These implications span from the development and growth of these organisms to the aging process and cancer, as well as the potential of stem cell therapies to repair diseases and injuries. Numerous proteins of the cell cycle are essential for cellular division and proliferation and are widely conserved over the course of evolution. In this work, we aimed to investigate the molecular processes of protein-protein interactions in cell cycle proteins, centering on two key players: Cdc6 in budding yeast and …


Ksp1 Is An Autophagic Receptor Protein For The Snx4-Assisted Autophagy Of Ssn2/Med13, Sara E Hanley, Stephen D Willis, Steven J Doyle, Randy Strich, Katrina F Cooper 2024 Rowan University

Ksp1 Is An Autophagic Receptor Protein For The Snx4-Assisted Autophagy Of Ssn2/Med13, Sara E Hanley, Stephen D Willis, Steven J Doyle, Randy Strich, Katrina F Cooper

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Ksp1 is a casein II-like kinase whose activity prevents aberrant macroautophagy/autophagy induction in nutrient-rich conditions in yeast. Here, we describe a kinase-independent role of Ksp1 as a novel autophagic receptor protein for Ssn2/Med13, a known cargo of Snx4-assisted autophagy of transcription factors. In this pathway, a subset of conserved transcriptional regulators, Ssn2/Med13, Rim15, and Msn2, are selectively targeted for vacuolar proteolysis following nitrogen starvation, assisted by the sorting nexin heterodimer Snx4-Atg20. Here we show that phagophores also engulf Ksp1 alongside its cargo for vacuolar proteolysis. Ksp1 directly associates with Atg8 following nitrogen starvation at the interface of an Atg8-family interacting …


Studying The Genes And Conditions That Influence Root Development, Tessa Holtkamp, Hannah Ordonez Webb 2024 University of Missouri-St. Louis

Studying The Genes And Conditions That Influence Root Development, Tessa Holtkamp, Hannah Ordonez Webb

Undergraduate Research Symposium

Root development in plants is essential for their survival and understanding how hormones influence their development can explain how plants grow under different circumstances. Researching how Indole-3-butyric acid (IBA), a hormone that induces root production, affects the plant model Arabidopsis thaliana helps explain the hormone's effect in agricultural crop systems. To understand root pathways, we performed assays on mutant lines of Arabidopsis by growing plants on varying concentrations of IBA. For wild-type and mutant lines, phenotyping experiments like branching of roots, lengths of stems, and root length were conducted along with PCR and restriction digest genotyping experiments to compare their …


Investigation Of Alzheimer’S Amyloid-Β Protein Aggregation With A New Fluorescent Dye., Emma Alberty 2024 University of Missouri, St. Louis

Investigation Of Alzheimer’S Amyloid-Β Protein Aggregation With A New Fluorescent Dye., Emma Alberty

Undergraduate Research Symposium

Alzheimer’s Disease (AD) is the most common form of dementia characterized by the impairment of at least two brain functions such as memory loss and judgement. AD is a progressive illness that can last as many as 20 years. AD is largely considered to be caused by the formation of extracellular amyloid plaques and intracellular neurofibrillary tangles. A better understanding of the structure and function of these plaques may lead to clearer understanding of the disease. To analyze amyloid plaques, aggregation assays are often used. During these assays we begin with monomer and place the sample in biological conditions to …


The Role Of The Cdk8 Kinase Module In Maintaining Proteostasis, Stephen Willis 2024 Rowan University

The Role Of The Cdk8 Kinase Module In Maintaining Proteostasis, Stephen Willis

Theses and Dissertations

The underlying etiology of numerous disease states results from perturbations in the maintenance of cellular proteostasis. Carcinogenesis relies on these perturbations to foster uncontrolled cell growth and eventual metastases, while neurodegenerative diseases are a consequence of such perturbations. Control of these processes occurs at numerous molecular levels, commonly starting with transcription. A key transcriptional complex that is involved is the CDK8 Kinase Module (CKM). The CKM is conserved from yeast to man, forming a tetrameric complex consisting of MED12, MED13, CDK8, and CCNC. The CKM has not only been implicated in a variety of cancers but also in a spectrum …


Elastin-Like Polypeptide As A Model To Study Intrinsically Disordered Proteins, Sadegh Majdi 2024 Rowan University

Elastin-Like Polypeptide As A Model To Study Intrinsically Disordered Proteins, Sadegh Majdi

Theses and Dissertations

The elastin-like polypeptide (ELP) is a well-studied structural protein that is easily amenable to amino acid (AA) sequence modifications and has the potential to yield a wide variety of uses in bioengineering and biomedical applications. One unique property of ELP is the inclusion of intrinsically disordered domains (IDP) within the structure that allow for its diversity of physical properties. While it is generally understood that amino acid sequence dictates protein folding arrangements, the contributions of specific amino acid sequences to the intrinsic disorder of ELP has yet to be fully resolved. Therefore, identifying the contributions of specific amino acid sequences …


Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee 2024 Coastal Carolina University

Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee

Journal of the South Carolina Academy of Science

Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen associated with a variety of diseases such as strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. One of the virulence factors released by GAS during an invasive infection is a cytotoxic peptide, streptolysin S (SLS), which inhibits the immune response to necrotizing fasciitis. The streptolysin S associated gene A product, SagA, is modified to produce SLS. Thesag operon includes sagA and the genes required for enzyme-mediated post-translational modifications of SagA and the export of SLS. The sagA gene is contained within the pleiotropic …


Course Portfolio For Biochemistry 1: Structure And Metabolism (Bioc431), Didier Mena 2024 University of Nebraska-Lincoln

Course Portfolio For Biochemistry 1: Structure And Metabolism (Bioc431), Didier Mena

UNL Faculty Course Portfolios

This benchmark portfolio encapsulates a comprehensive exploration aimed at enhancing the educational landscape of the BIOC431 course, a part of the general biochemistry course series (431 and 432). These courses are designed to offer a general introduction to the structure and function of cells in the body, along with their chemical reactions. Specifically, BIOC431 focuses on the structure, function, and metabolism of proteins, lipids, carbohydrates, and other major metabolic pathways. The three primary objectives addressed in this portfolio were the reevaluation of learning objectives, reassessment of assessment methods, and documentation of effective classroom strategies. Through background design, the learning objectives …


Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira Makarova, Eugene V Koonin, Satish Nair, Shunsuke Tagami, Konstantin Severinov, Maria Sokolova 2024 Thomas Jefferson University

Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira Makarova, Eugene V Koonin, Satish Nair, Shunsuke Tagami, Konstantin Severinov, Maria Sokolova

Department of Biochemistry and Molecular Biology Faculty Papers

Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of …


Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira S Makarova, Eugene V Koonin, Satish K Nair, Shunsuke Tagami, Konstantin Severinov, Maria L Sokolova 2024 Skolkovo Institute of Science and Technology, Moscow

Tail-Tape-Fused Virion And Non-Virion Rna Polymerases Of A Thermophilic Virus With An Extremely Long Tail, Anastasiia Chaban, Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov, Leena Putzeys, Maarten Boon, Florian Kabinger, Rob Lavigne, Kira S Makarova, Eugene V Koonin, Satish K Nair, Shunsuke Tagami, Konstantin Severinov, Maria L Sokolova

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of …


Source Data For "Flowering Of Developable 2d Crystal Shapes In Closed, Fluid Membranes", Hao Wan, Geunwoong Jeon, Weiyue Xin, Gregory M. Grason, Maria M. Santore 2024 University of Massachusetts Amherst

Source Data For "Flowering Of Developable 2d Crystal Shapes In Closed, Fluid Membranes", Hao Wan, Geunwoong Jeon, Weiyue Xin, Gregory M. Grason, Maria M. Santore

Data and Datasets

Source data for "Flowering of Developable 2D Crystal Shapes in Closed, Fluid Membranes".


Why Should Early-Career Scientists Publish In Society Journals, Stephen K. Dolan, Lori D. Banks, Wenqi Yu 2024 Clemson University

Why Should Early-Career Scientists Publish In Society Journals, Stephen K. Dolan, Lori D. Banks, Wenqi Yu

Molecular Biosciences Faculty Publications

In this editorial, written by early-career scientists, we advocate for the invaluable role of society journals in our scientific community. By choosing to support these journals as authors, peer reviewers, and as editors, we can reinforce our academic growth and benefit from their re-investment back into the scientific ecosystem. Considering the numerous clear merits of this system for future generations of microbiologists and more broadly, society, we argue that early-career researchers should publish our high-quality research in society journals to shape the future of science and scientific publishing landscape.


C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman 2024 Claremont Colleges

C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman

CMC Senior Theses

Clathromorphum compactum, a species of crustose coralline algae (CCA), is incredibly valuable for the future of high latitude ocean health, both as a comprehensive archive of changing ocean conditions, and ecologically as a foundational species for promoting biodiversity. Previous work establishes C. compactum as an effective climate proxy, and its life history provides several advantages for this use. C. compactum grow in nongeniculate, generally radial formations on hard substrates, over a wide distribution in mid-to-high latitude oceans and at subtidal depth ranges. Indeterminate growth leads to extreme longevity in C. compactum (Halfar et al., 2008), and growth rates are relatively …


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