Biology Commons^™

Harnessing The Neon Data Revolution To Advance Open Environmental Science With A Diverse And Data-Capable Community, R. Chelsea Nagy, Jennifer K. Balch, Erin K. Bissell, Megan E. Cattau, Nancy F. Glenn, Benjamin S. Halpern, Nayani Ilangakoon, Brian Johnson, Maxwell B. Joseph, Sergio Marconi, Catherine O'Riordan, Sydne Record

Biology Faculty Research and Scholarship

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks …

Addressing Bias In Faculty Retention, Sparkle L. Malone, Sydne Record

Biology Faculty Research and Scholarship

The field of ecology in the United States is not fully harnessing the diverse perspectives of the American population. Two major limitations to advancing diversity and inclusion include insufficient awareness of biased attitudes and the lack of large-scale faculty engagement in diversity and inclusion programs. Academic institutions must recognize and value individuals that participate in diversity and inclusion programs. Valuing this work will motivate all ecologists to accept the responsibility for these efforts and not simply assume that the few minorities in their field can do this work.

Modular Organization Of Engulfment Receptors And Proximal Signaling Networks: Avenues To Reprogram Phagocytosis, Emily A. Britt, Vanessa Gitau, Amara Saha, Adam Williamson

Biology Faculty Research and Scholarship

Transmembrane protein engulfment receptors expressed on the surface of phagocytes engage ligands on apoptotic cells and debris to initiate a sequence of events culminating in material internalization and immunologically beneficial outcomes. Engulfment receptors are modular, comprised of functionally independent extracellular ligation domains and cytosolic signaling motifs. Cognate kinases, adaptors, and phosphatases regulate engulfment by controlling the degree of receptor activation in phagocyte plasma membranes, thus acting as receptor-proximal signaling modules. Here, we review recent efforts to reprogram phagocytes using modular synthetic receptors composed of antibody-based extracellular domains fused to engulfment receptor signaling domains. To aid the development of new phagocyte …

Modular Organization Of Engulfment Receptors And Proximal Signaling Networks: Avenues To Reprogram Phagocytosis, Emily A. Britt, Vanessa Gitau, Amara Saha, Adam Williamson

Biology Faculty Research and Scholarship

Transmembrane protein engulfment receptors expressed on the surface of phagocytes engage ligands on apoptotic cells and debris to initiate a sequence of events culminating in material internalization and immunologically beneficial outcomes. Engulfment receptors are modular, comprised of functionally independent extracellular ligation domains and cytosolic signaling motifs. Cognate kinases, adaptors, and phosphatases regulate engulfment by controlling the degree of receptor activation in phagocyte plasma membranes, thus acting as receptor-proximal signaling modules. Here, we review recent efforts to reprogram phagocytes using modular synthetic receptors composed of antibody-based extracellular domains fused to engulfment receptor signaling domains. To aid the development of new phagocyte …

Viropana (Vna) 5, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 5

• ID – vna 5
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 391

Viropana (Vna) 1, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 1

• ID – vna 1

• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens

• Base pairs – 492

Optimized Microbial Recombinant Production Of Hiv-1 Anti-Envelope Antibody Fragments With Applications To Single Particle Tracking Of Virus Assembly, Merissa Michelle Bruns

Electronic Theses and Dissertations

In my findings, I have established a set series of protocols to recombinantly produce, purify and apply various fluorescent probes in vitro for the fluorescent labeling and study of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) protein during HIV viral assembly. There remains insufficient knowledge about the molecular dynamics and interactions of HIV-1 Env protein with its counterpart, Gag, on the inner host cell surface during assembly of a mature virus particle. There also remains an insufficient amount of data for the understanding and clarification of the mechanism of action of a known host cell HIV-1 restriction factor, …

Propranolol Sensitizes Vascular Sarcoma Cells To Doxorubicin By Altering Lysosomal Drug Sequestration And Drug Efflux, Jhuma Saha, Jong Hyuk Kim, Clarissa N. Amaya, Caleb M. Witcher, Ali Khammanivong, Derek M. Korpela, David R. Brown, Josephine Taylor, Brad A. Bryan, Erin B. Dickerson

Faculty Publications

Angiosarcoma is a rare cancer of blood vessel–forming cells with a high patient mortality and few treatment options. Although chemotherapy often produces initial clinical responses, outcomes remain poor, largely due to the development of drug resistance. We previously identified a subset of doxorubicin-resistant cells in human angiosarcoma and canine hemangiosarcoma cell lines that exhibit high lysosomal accumulation of doxorubicin. Hydrophobic, weak base chemotherapeutics, like doxorubicin, are known to sequester within lysosomes, promoting resistance by limiting drug accessibility to cellular targets. Drug synergy between the beta adrenergic receptor (β-AR) antagonist, propranolol, and multiple chemotherapeutics has been documented in vitro, and …

Analysis Of Methods To Measure Heart Rate In Mytilus Edulis, Kristin Pinho

Student Research Poster Presentations 2021

Non-invasive research will be performed to limit the additional stress from equipment and focus on the harmful effects that polluted run-off water has on mussels’ heart rates. The chemical that will be introduced to the laboratory environment will be weed killer. This research will simulate how water pollution affects different aquatic species and how that ultimately leads to environmental changes, while evaluating the most effective methods to conduct this research.

Metagenome Sequencing To Explore Phylogenomics Of Terrestrial Cyanobacteria, Ryan D. Ward, Jason E. Stajich, Jeffrey R. Johansen, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, Tbk Reddy, Chirs Daum, Alex Copeland, Ima Chen, Natalia N. Ivanova, Nikos C. Kyrpides, Nicole Shapiro, Emiley A. Eloe-Fadrosh, Nicole Pietrasiak

2021 Faculty Bibliography

Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology relates to aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cultures. These data will support phylogenomic studies of evolutionary relationships and gene content among these unique algae and their aquatic relatives.

Trichotorquatus Gen. Nov. - A New Genus Of Soil Cyanobacteria Discovered From American Drylands, Nicole Pietrasiak, Sharon Reeve, Karina Osorio-Santos, David A. Lipson, Jeffrey R. Johansen

2021 Faculty Bibliography

Cyanobacteria are crucial ecosystem components in dryland soils. Advances in describing a–level taxonomy are needed to understand what drives their abundance and distribution. We describe Trichotorquatus gen. nov. (Oculatellaceae, Synechococcales, Cyanobacteria) based on four new species isolated from dryland soils including the coastal sage scrub near San Diego, California (USA), the Mojave and Colorado Deserts with sites at Joshua Tree National Park and Mojave National Preserve, California (USA), and the Atacama Desert (Chile). The genus is morphologically characterized by having thin trichomes (<4.5 lm wide), cells both shorter and longer than wide, rarely occurring single and double false branching, necridia appearing singly or in rows, and sheaths with a distinctive collar-like fraying and widening mid-filament, the feature for which the genus is named. The genus is morphologically nearly identical with Leptolyngbya sensu stricto but is phylogenetically quite distant from that genus. It is consequently a cryptic genus that will likely be differentiated in future studies based on 16S rRNA sequence data. The type species, T. maritimus sp. nov. is morphologically distinct from the other three species, T. coquimbo sp. nov., T. andrei sp. nov. and T. ladouxae sp. nov. However, these latter three species are morphologically very close and are considered by the authors to be cryptic species. All species are separated phylogenetically based on sequence of the 16S-23S ITS region. Three distinct ribosomal operons were recovered from the genus, lending difficulty to recognizing further diversity in this morphologically cryptic genus.

Bntir: An Online Transcriptome Platform For Exploring Rna‐Seq Libraries For Oil Crop Brassica Napus, Dongxu Liu, Liangqian Yu, Lulu Wei, Pugang Yu, Jing Wang, Hu Zhao, Yuting Zhang, Shuntai Zhang, Zhiquan Yang, Guanqun Chen, Xuan Yao, Yanjun Yang, Yongming Zhou, Xuemin Wang, Shaoping Lu, Cheng Dai, Qing-Yong Yang, Liang Guo

Biology Department Faculty Works

No abstract provided.

Mechanism Of Dna Damage Checkpoint (Ddc)- Mediated Repression Of Histone Mrnas And Role Of Acetyl-Coa In Histone Transcription, Madhura Bhagwat

Theses and Dissertations

My dissertation contains two projects. The first project is focused on the mechanism of DNA damage checkpoint (DDC)- mediated repression of histone mRNAs. The second project deals with the role of acetyl-CoA in histone transcription. Proliferating cells coordinate histone and DNA synthesis to maintain correct stoichiometric amounts for chromatin assembly. Histone mRNA levels must be repressed when DNA replication is inhibited to prevent toxicity and genome instability due to free non-chromatinized histone proteins. In the first project we show that, unlike in mammalian cells, DNA replication stress does not trigger decay of histone mRNAs in the yeast Saccharomyces cerevisiae. However, …

Rna Splicing In Neuron Physiology And Neurodegenerative Diseases, Md Faruk Hossain

Theses and Dissertations

Gene expression is regulated at multiple levels, including transcription, RNA editing, pre-mRNA splicing, mRNA export, translation, and posttranslational modifications. Alternative splicing is a process by which exons can be included or excluded, giving rise to multiple mRNA isoforms from the same transcript. Alternative splicing is an important mechanism in developmental, tissue- and cell-specific control of gene expression, and it is key for expanding proteomic diversity and complexity from a limited number of genes. Moreover, more than 95% of multiexon genes undergo alternative splicing in humans, and about half of all disease-causing point mutations in humans affect pre-mRNA splicing, including neurological …

Characterizing Ferroptosis Pathways In In Vitro Motor Neuron Models, Alejandra Martinez

Theses and Dissertations

Ferroptosis is a non-apoptotic regulated form of cell death driven by the toxic accumulation of lipid peroxides and the presence of iron. The mechanism by which ferroptosis operates requires further investigation; here I will discuss the findings regarding the role of ferroptosis in different cellular models as well as the genes that may be involved with either promoting or hindering the ferroptotic pathway. NSC-34 is a hybrid cell line of neuroblastoma and primary spinal cord cells that can be differentiated into a motor neuron-like state allowing the characterization of ferroptosis in two distinct cellular conditions. Additionally, iNIL cells are a …

The Ion Channel Trpm7 Regulates Zinc Depletion-Induced Mdmx Degradation, Herui Wang

Theses and Dissertations

Zinc deficiency has been linked to human diseases including cancer. p53, a zinc-containing transcription factor, is the most frequently mutated tumor suppressor protein in human cancer. MDM2 and MDMX are zinc- containing proteins and crucial negative regulators of p53, which have been found to be amplified or overexpressed in various cancers. To investigate the effects of zinc depletion on the p53 signaling pathway, we have used ion chelators TPEN and bispicen as well as zinc-deficient medium to treat cells. We report here that zinc depletion results in MDMX degradation in a ubiquitination-independent and 20S proteasome-dependent manner. Restoration of zinc recovers …

Alpha-Synuclein Multimerization Is Dependent On Structural Characteristics Of Repeated Ktkegv Regions, Benjamin Ira Rosen

Theses and Dissertations

Parkinson’s disease (PD) is the most common movement disorder and is characterized by neuronal loss and the presence of Lewy bodies in dopaminergic neurons of the substantia nigra pars compacta. PD is a chronic, progressive, and irreversible neurodegenerative disorder associated with the selective loss of dopaminergic neurons. Initially described in an Ayurvedic medical treatise and Galen’s writings, and later by James Parkinson in 1817, the most common symptoms of PD are resting tremors, abnormal posture and gait, and muscle rigidity. Approximately 1 million people are living with PD in the United States and worldwide estimates are between 7 and 10 …

Microrna Regulation And Cellular Proteostasis In Parkinson's Disease, Alberim Kurtishi

Theses and Dissertations

Parkinson’s disease (PD) is a chronic and progressive neurodegenerative disorder predominately affecting the aging population. It is the second most common neurodegenerative disorder after Alzheimer’s disease (AD) affecting over 1 million individuals in the US alone. Recent studies have tried to understand the exact nature in which healthy neurons transition to a degenerative state in PD. There are a multitude of combinatory factors that can lead to the development of PD including environmental factors, genetic factors, and aging. The majority of PD cases are sporadic in nature, however familial cases account for 5-10% of total PD cases world-wide. The hallmark …

Evolution And Flower Shape From The Hawaiian Lobelioids To The Campanulaceae, Jingjing Tong

Theses and Dissertations

Campanulaceae, with roughly 2,400 species, is divided into five subfamilies, in part, by differences in their floral orientation and symmetry, with broad transitions between radial and bilateral floral symmetry. The Hawaiian lobelioids in the Campanulaceae is the largest endemic clade of Hawaiian angiosperms, and they have long been viewed as one of the most spectacular examples of an adaptive radiation in plants. In the first part of our study, we focus on Clermontia, which is one of the largest genera of Hawaiian lobelioids, employing variable low-copy nuclear gene sequences to determine their phylogenetic relationships. We use intron regions from four …

Green Team - Ecological Restoration Of Plaster Creek, Jia Luchs, Caleb Mathai, Rachel Warners, David Warners, Deanna Geelhoed

Student Papers and Reports

Plaster Creek, though its watershed is home to many potential stewards in Grand Rapids, is the most polluted creek in West Michigan. The Green Team, a branch of Plaster Creek Stewards, is a group of students that work during the summer with a focus on research, education, and working directly to restore Plaster Creek. The team works toward this goal through urban green infrastructure, utilizing native plants to manage stormwater. Two Calvin students, Caleb Mathai and Jia Luchs, one high school intern, Ben Zwart, and twelve high school students living in the Plaster Creek watershed were hired by PCS this …

Synthetic Pathways For Potential Platinum 1,10-Phenanthroline Compounds, Jacob Young

Mahurin Honors College Capstone Experience/Thesis Projects

There are extremely important uses for platinum when it comes to the treatment of cancers and dementias. One potential therapeutic combines platinum with a structure known as phenanthroline. This platinum phenanthroline structure is normally extremely water-insoluble, rendering it difficult to study and use in biological systems. The Williams’ Biochemistry Laboratory endeavored to find a simpler synthetic pathway for a water-soluble phenanthroline product. While unsuccessful in identifying a product as of yet, many synthetic pathways have been ruled out, and more hypothetical pathways are being formulated for testing.

Among the strategies analyzed are varying solvent, reagents, apparatus, methodology, and temperature in …

Phylogenetic Placement Of Seven Strains Of Synechococcales (Cyanobacteria) Isolated From Desert Soils In Zion National Park., Kevin Houk

Senior Honors Projects

Seven strains of cyanobacteria of the order Synechococcales were isolated from the sandstone derived soil of Zion National Park. These strains were analyzed using 16S rRNA and 16S-23S phylogenetic analysis, percent dissimilarity of the ITS sequence, morphology, and the similarity of the 16S rRNA sequence. One strain was placed within the genus Plectolyngbya, but the Bayesian inference and 16S rRNA similarity analysis support the conclusion that Plectolyngbya should not considered a valid genus, and that it should be integrated into the taxonomically prioritized Leptolybya. Two of the strains were found to be similar to Phormidesmus morphologically, but the …

Gypsum-Exclusive Plants Accumulate More Leaf S Than Non-Exclusive Species Both In And Off Gypsum, Andreu Cera, Gabriel Montserrat-Martí, Juan Pedro Ferrio, Rebecca E. Drenovsky, Sara Palacio

2021 Faculty Bibliography

Gypsum-exclusive species (gypsophiles), are restricted to gypseous soils in natural environments. However, it is unclear why gypsophiles display greater affinity to gyspeous soils than other soils. These plants are edaphic endemics, growing in alkaline soils with high Ca and S. Gypsophiles tend to show higher foliar Ca and S, lower K and, sometimes, higher Mg than non-exclusive gypsum species, named gypsovags. Our aim was to test if the unique leaf elemental signature of gypsophiles could be the result of special nutritional requirements linked to their specificity to gypseous soils. These nutritional requirements could hamper the completion of their life cycle …

Repeatability Of Foraging Behavior Following A Simulated Predation Attempt Depends On Color Morph, Sex, And Foraging Metric In Red-Backed Salamanders (Plethodon Cinereus), Brian P. Waldron*, Marissa C. Ganzfried*, Cari-Ann M. Hickerson, Carl D. Anthony

2021 Faculty Bibliography

Behavioral repeatability greatly affects the capacity of an individual to respond to varying environments. When multiple behaviors within individuals are repeatable and correlated across time or across contexts, it is termed a behavioral syndrome. However, not all behaviors exhibit the same level of repeatability, and relatively few studies have examined repeatability in amphibians. We examined the repeatability of foraging behavior in the Eastern Red-backed salamander (Plethodon cinereus), a color-polymorphic terrestrial salamander, following a simulated predation attempt. We tested several hypotheses: (1) Simulated predation would negatively affect foraging, increasing latency to feed and decreasing the number of prey items eaten in …

New Piperidine Alkaloids From Fire Ants Are Not Sequestered By The Green And Black Poison Frog ( Dendrobates Auratus ), Ian Davison, Ralph Saporito, Lisa M. Shulte, Kyle Summers

2021 Faculty Bibliography

Neotropical poison frogs possess alkaloid-based antipredator defenses which they sequester from a diet of arthropods such as oribatid mites and myrmicine ants. Alkaloid sequestration is still poorly understood and although several studies have examined its uptake, most experiments directly feed alkaloids to the frogs. Here, we examined the alkaloid uptake system in the poison frog species Dendrobates auratus by feeding it an alkaloid-containing prey item, the red imported fire ant Solenopsis invicta (Formicidae, Myrmicinae). Captive bred frogs were either fed live ants or fruit flies dusted with powdered ants for 4 months. Using GC–MS, we confirm that S. invicta contain …

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Total Synthesis Of Decahydroquinoline Poison Frog Alkaloids Ent-Cis-195a And Cis-211a, Takuya Okada, Naizhen Wu, Katsuki Takashima, Jungoh Ishimura, Hiroyuki Morita, Takuya Ito, Takeshi Kodama, Yuhei Yamasaki, Shin-Ichi Akanuma, Yoshiyuki Kubo, Ken-Ichi Hosoya, Hiroshi Tsuneki, Tsutomu Wada, Toshiyasu Sasaoka, Takahiro Shimizu, Hideki Sakai, Linda P. Dwoskin, Syed R. Hussaini, Ralph Saporito, Naoki Toyooka

2021 Faculty Bibliography

The total synthesis of two decahydroquinoline poison frog alkaloids ent-cis-195A and cis-211A were achieved in 16 steps (38% overall yield) and 19 steps (31% overall yield), respectively, starting from known compound 1. Both alkaloids were synthesized from the common key intermediate 11 in a divergent fashion, and the absolute stereochemistry of natural cis-211A was determined to be 2R, 4aR, 5R, 6S, and 8aS. Interestingly, the absolute configuration of the parent decahydroquinoline nuclei of cis-211A was the mirror image of that of cis-195A, although both alkaloids were isolated from the same poison frog species, Oophaga (Dendrobates) pumilio, from Panama.

A New Species Of Cryptic Cyanobacteria Isolated From The Epidermis Of A Bottlenose Dolphin And As A Bioaerosol, Amber O. Brown, Caitlin S. Romanis, Petr Dvorak, Amanda J. Foss, Quincy A. Gibson, Chelsea D. Villaneuva, Wendy N. Durden, Anyssa D. Garvey, Phillip Jenkins, Petr Hasler, Jeffrey R. Johansen, Brett A. Neilan, Dale A. Casamatta

2021 Faculty Bibliography

No abstract provided.

The Crazy Critter Club - Lesson Plans, Caitlin Flynn Copenhaver, Audrey Anderson

Honors Program: Expanded Learning Clubs

This curriculum covers the lesson plans for the 2021 "Cool Critter Club". It is focused on teaching students about animals and the environment, especially at a local level. This club engages students through the use of games, art, and spending time outside.

Assessing Pace-Of-Life: Comparing Metabolism And Behavior In Tarantulas, Haley Vanscoyoc

Master's Theses and Doctoral Dissertations

Pace-of-Life Syndrome (PoLS) links physiology, behavior, and life history to understand how an organism lives and is under-researched in many invertebrate groups. In this study I used five tarantula species to assess if they follow the predictions of PoLS. I compared individual species as well as Old- and New-World lineages and solitary and sub-social species. I predicted that Old- World and sub-social species would have higher resting metabolic rates (RMRs) and activity levels compared to New-World and solitary species. RMRs were measured using an open-flow respirometry system, and a classic open-arena test was used to assess activity level. Spearman’s correlation …

Dung Beetle (Scarabaeinae) Diversity Of The Highest Elevation In West Africa: The Nimba Mountain Range, Jacob Bowen

Mahurin Honors College Capstone Experience/Thesis Projects

The Nimba Mountain Range in Guinea, Ivory Coast, and Liberia is within the Upper Guinean Forests, a critical biodiversity hotspot highly threatened by various human activities. The region is home to many endemic species including the viviparous Nimba toad, Nimba otter-shrew, and the discrete Bossou chimpanzee population. Dung beetles can act as a focal taxon from which extrapolation to the diversity of other taxa and ecosystem health can be made. Elevational trends in dung beetle diversity were investigated on the Nimba Mountain Range and in the nearby Bossou Chimpanzee reserve in Guinea. Dung beetle species diversity surveys aimed to document …