Biochemistry, Biophysics, and Structural Biology Commons^™

Bitumen Aging—Laboratory Simulation Methods Used In Practice And Selected Directions Of Research On New Methods, Paweł Czajkowski, Andrzej Przyjazny, Grzegorz Boczkaj

Natural Sciences Publications

Changes in the properties of bitumen binders that occur as a result of aging have a huge impact on the durability of products produced from them. In particular, asphalt pavements, which constitute the most common use of petroleum bitumen, are susceptible to damage resulting from the increasing stiffness of the bitumen during its life cycle. Increased stiffness of asphalt pavements reduces the pavement resistance to low-temperature cracks and fatigue cracks, ultimately leading to the loss of their functional properties and the need for road repair. The rate of changes in bitumen properties is influenced by many factors, the most important …

Comparison Of Serum Albu-Min Levels In The Breast Milk Of Breastfeeding Infants Aged 1-3 Months And 4-6 Months, Ninik Mudjihartini

Indonesian Journal of Medical Chemistry and Bioinformatics

Abstract: Background: Serum albumin is the most abundant plasma protein in the blood, contributing to maintaining colloid osmotic pressure and binding substances that are poorly soluble in plasma so that they can be distributed throughout the body. Serum albumin levels in breast milk can vary, influenced by various factors such as the lactation phase (age of the baby), number of parities, age and body mass index (BMI) of the mother. This study aims to determine the comparison of serum albumin levels in breast milk of mothers who breastfeed infants aged 1-3 months and 4-6 months and to find the relationship …

Change And Stasis Of Distinct Sediment Microbiomes Across Port Everglades Inlet (Pei) And The Adjacent Coral Reefs, Lauren E. Krausfeldt, Jose V. Lopez, Catherine Bilodeau, Hyo Won Lee, Shelby L. Casali

Biology Faculty Articles

Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S …

Functional Impact Of A Cancer-Related Variant In Human Δ1‑Pyrroline-5-Carboxylate Reductase 1, Oseeyi I. Daudu, Kaylen R. Meeks, Lu Zhang, Javier Seravalli, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Pyrroline-5-carboxylate reductase (PYCR) is a proline biosynthetic enzyme that catalyzes the NAD(P)H-dependent reduction of Δ¹-pyrroline-5-carboxylate (P5C) to proline. Humans have three PYCR isoforms, with PYCR1 often upregulated in different types of cancers. Here, we studied the biochemical and structural properties of the Thr171Met variant of PYCR1, which is found in patients with malignant melanoma and lung adenocarcinoma. Although PYCR1 is strongly associated with cancer progression, characterization of a PYCR1 variant in cancer patients has not yet been reported. Thr171 is conserved in all three PYCR isozymes and is located near the P5C substrate binding site. We found that …

A Bioengineered Probiotic For The Oral Delivery Of A Peptide Kv13 Channel Blocker To Treat Rheumatoid Arthritis, Yuqing Wang, Duolong Zhu, Laura C Ortiz-Velez, Jacob L Perry, Michael W Pennington, Joseph M Hyser, Robert A Britton, Christine Beeton

Faculty, Staff and Students Publications

New therapeutics that combine efficacy with limited side effects and can be delivered noninvasively are needed to adequately treat patients with rheumatoid arthritis (RA) and other autoimmune diseases. Kv1.3 channel-expressing CCR7− effector memory T (TEM) lymphocytes are significant players in the pathogenesis of multiple autoimmune diseases, and blocking Kv1.3 reduces disease severity in rat models of RA and patients with plaque psoriasis. However, peptide therapeutics require repeated injections, reducing patient compliance. We used a bioengineered Lactobacillus reuteri as an oral delivery method of a Kv1.3 blocker for immunomodulation in rat models of atopic dermatitis and RA. This study demonstrates a …

Rbp Image Database: A Resource For The Systematic Characterization Of The Subcellular Distribution Properties Of Human Rna Binding Proteins, Louis Philip Benoit Bouvrette, Xiaofeng Wang, Jonathan Boulais, Jian Kong, Easin Uddin Syed, Steven M Blue, Lijun Zhan, Sara Olson, Rebecca Stanton, Xintao Wei, Brian Yee, Eric L Van Nostrand, Xiang-Dong Fu, Christopher B Burge, Brenton R Graveley, Gene W Yeo, Eric Lécuyer

Faculty, Staff and Students Publications

RNA binding proteins (RBPs) are central regulators of gene expression implicated in all facets of RNA metabolism. As such, they play key roles in cellular physiology and disease etiology. Since different steps of post-transcriptional gene expression tend to occur in specific regions of the cell, including nuclear or cytoplasmic locations, defining the subcellular distribution properties of RBPs is an important step in assessing their potential functions. Here, we present the RBP Image Database, a resource that details the subcellular localization features of 301 RBPs in the human HepG2 and HeLa cell lines, based on the results of systematic immuno-fluorescence studies …

Dual Ionic Liquid-Functionalized Cellulosic Materials: Thermal, Mechanical And Conductive Properties, Elizabeth Mcgrew, Kevin M. Miller Phd

Posters-at-the-Capitol

Cellulose, an inexpensive and renewable biomacromolecule, represents an intriguing synthetic foundation for new materials with task-specific properties. Here, we wish to report a synthetic route for functionalizing cellulose with a side chain containing two ionic liquid functional groups using azide-alkyne ‘click’ cyclization strategy, followed by quaternization of the two resulting heterocycles (1,2,3-triazole and imidazole). Through this functionalization strategy, the resulting cellulosic materials exhibited significant softening, with several glass transition (T_g) values observed below room temperature, indicating the amorphous nature of the materials, with the T_g dependent on both the length of the side chain and the …

Cellular Zinc Deficiency Impairs Heme Biosynthesis In Developing Erythroid Progenitors, Juyoung Kim, Jaekwon Lee, Moon-Suhn Ryu

Department of Biochemistry: Faculty Publications

Anemia is the most prevalent nutrition-related disorder worldwide. Zinc is an essential trace element for various biological processes in the body, and zinc deficiency has been associated with anemia in humans. However, the molecular mechanisms by which zinc availability alters red blood cell development remain uncertain. The present study identifies the essentiality of zinc during erythroid development, particularly for normal heme biosynthesis. G1E-ER4 mouse cells were used as an in vitro model of terminal erythroid differentiation, which featured elevated cellular zinc content by development. Restriction of zinc import compromised the rate of heme and -globin production and, thus, the hemoglobinization …

Progress Towards The Total Synthesis Of Frondosin D Lab Report, Admirabilis Kalolella

CISLA Senior Integrative Projects

No abstract provided.

A Low-Fat/Sucrose Diet Rich In Complex Carbohydrates Reverses High-Fat/Sucrose Diet-Induced Corneal Dysregulation, Prince K Akowuah, Carolina Lema, Rolando E Rumbaut, Alan R Burns

Faculty, Staff and Students Publications

High-fat/sucrose diet feeding in mice causes loss of corneal nerve function and impairs corneal wound healing. While changing to a diet with a low fat/sugar composition and enrichments in complex carbohydrates mitigates the reduction in nerve function, it remains to be determined if it has an effect on corneal wound healing. In this study, 6-week-old C57BL/6 male mice were fed either a normal diet or a high-fat/sucrose diet for 20 weeks. A third group (diet reversal) was placed on a high-fat/sucrose diet for 10 weeks followed by a normal diet for an additional 10 weeks. A central corneal epithelial abrasion …

Characterization Of Cl-Par-4: Wt Vs. Mutant, Samjhana Pandey, Krishna K. Raut, Andrea M. Clark, Antoine Baudin, Lamya Djemri, David S. Libich, Steven M. Pascal

The Graduate School Posters

Intrinsically disordered proteins (IDPs) play important roles in regulation of cell signaling pathways as well as cellular processes. Dysregulation of these proteins is associated with several human diseases. Prostate apoptosis response-4 (Par-4), a proapoptotic tumor suppressor protein, is categorized as an intrinsically disordered protein and downregulation of this protein has been reported in myriad of cancers including glioma, breast cancers, and prostate cancers. The caspase-cleaved fragment of Par-4 (cl-Par-4) plays an active role in tumor suppression by inhibiting several cell survival pathways.

Here, we employed site-directed mutagenesis to introduce a point mutation in the cl-Par-4 wildtype (WT) to generate the …

Using Nspefs To Sensitize Mrsa To Vancomycin Treatment, Areej Malik, Alexandra E. Chittams-Miles, Claudia Muratori, Erin B. Purcell

The Graduate School Posters

Staphylococcus aureus (S. aureus) is a biofilm-forming pathogen. S. aureus treatment is marked by the development of antibiotic resistance. The public health impact has increased since the emergence of methicillin-resistant S. aureus (MRSA), which has started to show intermediate resistance to vancomycin in MRSA. Nano-second pulse electric fields (nsPEFs) are low-energy and high-power electric pulses, which have been suggested to sensitize pathogens to antibiotics by creating transient pores in the cell membrane. Our combinatorial treatment includes nsPEF pre-treatment and vancomycin post-treatment of MRSA cells. Our results show that MRSA log phase cells had the highest susceptibility to vancomycin. …

Par-4: An Attractive Target For Cancer Therapy, Krishna K. Raut, Antoine Baudin, David S. Libich, Lijun Liu, Scott Lovell, Steven M. Pascal

College of Sciences Posters

Lack of early diagnosis, cancer recurrence, metastasis, and adverse side effects are some of the major problems in the treatment of cancers. Par-4, a tumor suppressor protein, is an attractive target for cancer therapy as it selectively kills cancer cells. Cl-Par-4 is the active fragment of Par-4 that enters the nucleus and selectively induces apoptosis in cancer cells. It has also been reported that Par-4 increases the susceptibility of cancer cells to chemotherapy and reverses cancer recurrence. Further, Par-4 has been shown to play a dual role: inhibition of EMT (Epithelial-mesenchymal transition) as well as assistance in the reverse process, …

Quantification Of Nuclear Dynamics During Epithelial Remodeling, Noah De Leeuw

Electronic Theses and Dissertations

The morphogenesis of developing tissues is contingent on an extensive array of rearrangements in cellular shape, position and identity at large and small scales. One commonly used process to reshape tissues is the cell intercalation-driven elongation of a tissue in a common axis, in which rows of epithelial cells undergo oriented intercalation in a directional fashion. In most models of intercalation, cells are treated as homogeneous objects directed in their shape changes by cortical forces localized along cell-cell interfaces or tricellular junctions. However, less attention has been paid to how inhomogeneities in mechanical resistance of their own internal structures affects …

Mechanistic Insights Into Mftr-Dependent Regulation Of The Redox Cofactor Mycofactocin, Aigera Mendauletova

Electronic Theses and Dissertations

Organic redox cofactors are essential for life. While classic flavins and nicotinamides are widely distributed across all domains of life, nature has also evolved niche cofactors in subsets of life domains. For example, in Actinobacteria, coenzyme F420 is commonly used in place of flavin mononucleotide in enzymes associated with carbon fixation and oxidation of secondary alcohols. The importance of niche cofactors has long been recognized however, detailed understanding about their biosynthesis and physiological uses has been lagging. One class of niche cofactors is derived from ribosomally synthesized and posttranslationally modified peptides (RiPPs). To achieve their mature form, the genetically …

Incorporating Culinary Medicine Into A First Year Science Course, Elizabeth Merz, Sarah Bultje, Luke Witvliet, Amy Wilstermann, Kumar Sinniah

Summer Research

• Culinary medicine uses an evidence-based approach to translate nutrition research into practical use in order to bring medicine and cooking together 1
• Medical schools are bringing in culinary medicine programs so that prehealth students can relate to their patients in the clinical setting when sharing necessary dietary changes
• Obesity is one of the leading risk factors for early death – From 1990 to 2017, globally, deaths due to obesity has increased by 78%2
• By introducing culinary medicine at the undergraduate level into a first year course, we hope to track the students in the course throughout their four years at …

Tagtools: New Toolkit Analyzing High Resolution Biologging Data In R, Yuqian Wang, Oghenesuvwe Ogedegbe, Stacy L. De Ruiter

Summer Research

Bio-logging studies with high-resolution movement-sensors offer opportunities to observe animal behavior in unprecedented detail, but analysis of the resulting data is often complex, and there is a need for freely available, easy-to-use, flexible, welldocumented software tools to facilitate analysis and interpretation. We introduce a new open-source tool kit for processing data from tags with highresolution movement sensors.

Examples of Tags: DTAG, CATS, Acousonde, DailyDiary, etc.

Dna Damage Response Activates The Electron Transport Chain And Oxidative Metabolism By Two Parallel Mechanisms, Shreya Nagar

Theses and Dissertations

The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. Major part of DDR is coordinated by DNA damage checkpoint (DDC). In addition to DDC, eukaryotic cells also have DNA replication checkpoint (DRC) that is distinct from the DDC and specifically signals slowly progressing or arrested replication forks. DDR involves stalling or arrest of the cell cycle, initiation of DNA repair, and altered regulation of transcription, translation, and the ubiquitin-proteasome system. DDR also triggers transcription shut-off of histone genes. One of the key outcomes of DDC/DRC activation is the increased synthesis of the deoxyribonucleoside triphosphates (dNTPs), …

Chemical Disinfection In Rural Ecuador, Lachlan Beebe, Chad Tatko, Julie Wildschut

Summer Research

The Clean Water Institute, in conjunction with Calvin University seeks to address issues with water availability in developing countries, particularly as it relates to quality of the water. The research done this summer was to investigate the potential implementations of improvements for clean water in rural Ecuador. These improvements manifested themselves in two distinct initiatives: The first initiative was to investigate the implementation of a passive chlorinator in a small Ecuadorean community. This involved literature review to decide a chlorinator to pursue, followed by extensive testing to validate the efficacy of the chlorinator under a variety of conditions. The second …

Temperature Effects On Conductivity Of Phospholipid Bilayers, Dylan Mount, Sebastian Grabill, Loren Haarsma

Summer Research

Phospholipids molecules contain a fatty acid tail and a head made of a phosphate group (Fig.1) and serve as the building blocks of cellular membranes. The tails are hydrophobic, meaning they are weakly attracted to water, while the head group is hydrophilic, which is strongly attracted to water. Lipids in water will spontaneously form into bilayers with the tails towards the center (Fig.2) and the heads pointing towards the water on either side. This is how the lipid bilayers are formed to separate a cell's interior from exterior. Biological cells contain mixtures of many lipids and other molecules. In our …

Molecular Regulation Of The Salicylic Acid Hormone Pathway In Plants Under Changing Environmental Conditions, Christina A. M. Rossi, Eric J. R. Marchetta, Jong Hum Kim, Christian Castroverde

Biology Faculty Publications

Salicylic acid (SA) is a central plant hormone mediating immunity, growth, and development. Recently, studies have highlighted the sensitivity of the SA pathway to changing climatic factors and the plant microbiome. Here we summarize organizing principles and themes in the regulation of SA biosynthesis, signaling, and metabolism by changing abiotic/biotic environments, focusing on molecular nodes governing SA pathway vulnerability or resilience. We especially highlight advances in the thermosensitive mechanisms underpinning SA-mediated immunity, including differential regulation of key transcription factors (e.g., CAMTAs, CBP60g, SARD1, bHLH059), selective protein–protein interactions of the SA receptor NPR1, and dynamic phase separation of the recently identified …

Developing Red Fluorescent Zn2+ Sensors And Characterizing Zn2+ Homeostasis In Mucolipidosis Type Iv Disease, Anna M. Dischler

Electronic Theses and Dissertations

Zinc (Zn²⁺) is a divalent, redox-inert metal that plays a vital role in many cellular processes either by acting as a catalytic cofactor or a labile signaling molecule in the cytoplasm. Cytosolic Zn²⁺ levels are tightly regulated to stay within a narrow window of concentrations, but fluctuations in Zn²⁺ signals have been detected in a variety of cells. We developed a genetically encoded, single red fluorescent protein (RFP) based Zn²⁺ sensor, RZnP1, that can be used alongside green-wavelength sensors for the simultaneous detection of different signaling molecules within the same cells or among different subcellular …

Alterations In C:N Ratio To Understand Plant Metabolic Pathways In Response To Pressure From Goat Grazing In The Invasive Species: Rhamnus Cathartica, Vivian Marchan

Ignite the Spark Outstanding Undergraduate Research and Scholarship

The high fecundity and high germination rates of Rhamus cathartica serves the species to out-compete regional plant native species. Its high abundance in deciduous forest ecosystems forces species that are unable to utilize R. cathartica as a food source to migrate to areas of lower density, further contributing to the decline in regional biodiversity. Bare soil conditions left as the result of the high concentration of Nitrogen in senesced leaves and leaf litter, cause further amplification of the migration of non-plant species to areas of lower R. cathartica density. Nitrogen is essential to primary and secondary metabolism, thus minimizing the …

Post-Translational Modification Of Proteins Via Ambient Air Pollutants And Endogenous Reactive Species, Rachel Lauren Davey

Electronic Theses and Dissertations

Proteins can react with reactive oxygen species (ROS) and reactive nitrogen species (RNS) to form post-translational modifications (PTMs), which can affect protein structure and function. The formation of 3-nitrotyrosine (NTyr) and dityrosine (DiTyr) upon reaction of proteins with ROS/RNS are two common PTMs studied due to their stability and irreversibility, as well as their ability to enhance the allergenicity of pollen allergens upon formation. Many common techniques used to study the formation of these PTMs can reliably detect the PTMs but can only provide semi-quantitative information due to many assumptions and limitations. In Chapter 2 we present an analysis of …

Identifying The Role Of Phospholipase D1 And Phosphatidic Acid In Exocytosis, Broderick L. Bills

Electronic Theses and Dissertations

Exocytosis is an essential process for intercellular communication in eukaryotic cells. This process involves significant changes in membrane curvature, and lipids and curvature-sensing proteins can assist these processes. One protein in particular, phospholipase D1 (PLD1), and its product, the lipid phosphatidic acid (PA), are involved in multiple exocytic processes. However, PLD1 and PA’s role in this process has remained unclear. In this work, PLD1 and the production of PA were visualized during exocytosis, and PA localization to regions of membrane curvature was established. Together, these results support the hypothesis that PLD1 production of PA stabilizes negative curvature during membrane fusion. …

Investigating The Binding Of G-Quadruplex Dna To Lispro And Bovine Insulin, Sarah E. Bultje, Luke D. Witvliet, Kumar Sinniah

Summer Research

Type 1 Diabetes (T1D) is a disease characterized by the inability to produce insulin. Susceptibility to T1D is complex, involving both genetic and environmental factors. o One of the genetic components involved in insulin gene expression, and suspected T1D susceptibility, is the insulin-linked polymorphic region (ILPR). The ILPR element is located on chromosome 11p15 in the proximal promoter region, 363 base pairs upstream from the gene transcription site. o Other researchers (using fluorescence spectroscopy) and we (using ITC) have demonstrated that insulin binds to G-Quadruplex DNA with µM affinity. Since the DNA sequences in the ILPR form G-Quadruplexes and are …

Interferon Gamma Signaling In Ovarian Cancer Cells, Bijaya Gaire

Theses and Dissertations

Interferon gamma (IFNγ) is a pleiotropic cytokine that can have, depending on the cellular and molecular context, both anti-tumor and pro-tumorigenic functions. IFNγ expression can be induced in cancer cells in response to radiation therapy or immune checkpoint blockade used in cancer treatment. We have previously shown that IFNγ induces expression of the Bcl3 proto-oncogene in ovarian cancer (OC) cells, resulting in their increased proliferation and migration, but the mechanisms are unknown. Here, I demonstrate that the IFNγ-induced Bcl3 expression is dependent on JAK1 and STAT1 signaling, and on p65 NFkB. Furthermore, my data show that the IFNγ-induced Bcl3 expression …

Comparing Insect Biodiversity Between Curb-Cut Rain Gardens And Residential Lawns, Dave Warners, Naomi Dykstra, Julia Klooster

Summer Research

Global insect biodiversity is at a major decline. The drop in population can largely be attributed to a loss of natural habitat through conversion into urban and agricultural land. Insects are important parts of food webs and many play an important role in pollination, control of weeds, control of agricultural pests, and the decomposition of wood and leaves.

Role Of Integrins In Hiv Infection Of Resting Cd4+ T Cells Stimulated By Intestinal Endothelial Cells, Anding Shen, Sarah Logan, Tim Kim, Zihan Zhang

Summer Research

Eradicating HIV remains a formidable challenge due to the persistence of latent reservoirs within resting CD4+ T cells. Intestinal endothelial cells (IECs) have been shown to promote HIV infection and latent reservoir formation in resting CD4+ T cells. Our research investigates the role of integrins and their ligands, specifically ICAM, VCAM, and MAdCAM, in resting T cells and their impact on productive and latent HIV infection. Findings reveal that VCAM stimulation was the most effective in promoting productive HIV infection. MAdCAM and ICAM had minimal effect. Cytokine IL-6 consistently displayed synergy with all CAMs, amplifying effects on productive HIV infection. …

Selective Reduction Of Nitriles In The Presence Of Aromatic Nitro Groups, Esther Seoha Yoo, Dr. Michael Barbachyn

Summer Research

• Identify reliable aprotic reaction conditions for selective reduction of a nitrile in the presence of a nitro group. •
• Examine a range of nitrobenzonitriles and nitrophenyl acetonitriles to determine the scope of the methodology.