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Evaluating Greenhouse Gas Emissions And Climate Mitigation Goals Of The Global Food And Beverage Sector, Megan Reavis, Jenny Ahlen, Joe Rudek, Kusum Naithani

Biological Sciences Faculty Publications and Presentations

The dramatic increase in greenhouse gas (GHG) emissions by humans over the past century and a half has created an urgency for monitoring, reporting, and verifying GHG emissions as a first step toward mitigating the effects of climate change. Fifteen percent of global GHG emissions come from agriculture, and companies in the food and beverage industry are starting to set climate goals. We examined the GHG emissions reporting practices and climate goals of the top 100 global food and beverage companies (as ranked by Food Engineering) and determined whether their goals are aligned with the science of keeping climate warming …

Massively Parallel Assessment Of The Functional Effects Of De Novo Autism Spectrum Disorder Patient-Derived Genetic Variants In 3’ Untranslated Regions, Tomas Lagunas Jr

Arts & Sciences Graduate Student Theses and Dissertations

Human genetic studies have identified a large number of patient-derived de novo variants in presumptive regulatory regions of the genome that pose a challenge for interpretation of their effects since the impact of regulatory variants is highly dependent on the cellular context. In particular, current investigations have made significant investments in sequencing the genomes of autism spectrum disorder (ASD) families as a diagnostic method and to further understand the genetic architecture of this complex neurodevelopmental disease. These studies have revealed an enrichment of mutations in the untranslated regions (UTRs) of genes, which are noncoding regulatory regions, in ASD genomes. Assessment …

Cell-Type Specific Expression Of Apolipoprotein E By Astrocytes And Microglia: Implications For The Development Of Amyloid-Β Pathology In Alzheimer Disease, Thomas Mahan

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer disease (AD) is characterized by two main pathological hallmarks, extracellular amyloid plaques primarily comprised of the amyloid-β (Aβ) peptide, and intracellular neurofibrillary tangles mainly comprised of the tau protein. Although the pathologies underlying AD were first described over one hundred years ago, researchers today are still trying to understand how the development of Aβ pathology is regulated in the hopes of developing more effective treatments. Advances in genetics over the last several decades have allowed for several genetic risk factors to be identified that increase or decrease ones likelihood for developing (AD). Of these genetic risk factors, the strongest …

The Role Of Endoplasmic Reticulum Modifications In Protein Export In Plasmodium Falciparum, Alexander Polino

Arts & Sciences Graduate Student Theses and Dissertations

Following invasion of a host red blood cell (RBC), the malaria parasite Plasmodium falciparum undertakes a program of dramatic host cell renovation. The parasite exports hundreds of effectors into the RBC, altering its shape and rigidity, increasing its permeability to nutrients, and constituting an intracellular transport network that traffics adhesins to the RBC surface. These adhesins mediate binding of the parasitized RBC to the host vascular endothelium, allowing the parasite to avoid destruction in the spleen, but contributing to the pathogenesis of cerebral malaria. Most of these exported effectors bear a pentameric amino acid sequence that marks them for protein …

Introduction To Epigenetics, Yevgeniy Grigoryev

Open Educational Resources

Syllabus for Bio481 Introduction to Epigenetics

Secretogranin Iii Stringently Regulates Pathological But Not Physiological Angiogenesis In Oxygen-Induced Retinopathy, Chang Dai, Prabuddha Waduge, Liyang Ji, Chengchi Huang, Ye He, Hong Tian, Elizabeth Zuniga-Sanchez, Amit Bhatt, Iok-Hou Pang, Guanfang Su, Keith A Webster, Wei Li

Faculty, Staff and Students Publications

Conventional angiogenic factors, such as vascular endothelial growth factor (VEGF), regulate both pathological and physiological angiogenesis indiscriminately, and their inhibitors may elicit adverse side effects. Secretogranin III (Scg3) was recently reported to be a diabetes-restricted VEGF-independent angiogenic factor, but the disease selectivity of Scg3 in retinopathy of prematurity (ROP), a retinal disease in preterm infants with concurrent pathological and physiological angiogenesis, was not defined. Here, using oxygen-induced retinopathy (OIR) mice, a surrogate model of ROP, we quantified an exclusive binding of Scg3 to diseased versus healthy developing neovessels that contrasted sharply with the ubiquitous binding of VEGF. Functional immunohistochemistry visualized …

Mutations In Hcfc1 And Ronin Result In An Inborn Error Of Cobalamin Metabolism And Ribosomopathy, Tiffany Chern, Annita Achilleos, Xuefei Tong, Matthew C Hill, Alexander B Saltzman, Lucas C Reineke, Arindam Chaudhury, Swapan K Dasgupta, Yushi Redhead, David Watkins, Joel R Neilson, Perumal Thiagarajan, Jeremy B A Green, Anna Malovannaya, James F Martin, David S Rosenblatt, Ross A Poché

Faculty, Staff and Students Publications

Combined methylmalonic acidemia and homocystinuria (cblC) is the most common inborn error of intracellular cobalamin metabolism and due to mutations in Methylmalonic Aciduria type C and Homocystinuria (MMACHC). Recently, mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) were shown to result in cellular phenocopies of cblC. Since HCFC1/RONIN jointly regulate MMACHC, patients with mutations in these factors suffer from reduced MMACHC expression and exhibit a cblC-like disease. However, additional de-regulated genes and the resulting pathophysiology is unknown. Therefore, we have generated mouse models of this disease. In addition to exhibiting loss of Mmachc, metabolic perturbations, and developmental defects previously …

Evolutionary Analyses Of Visual Opsin Genes In Frogs And Toads: Diversity, Duplication, And Positive Selection, Ryan K. Schott, Leah Perez, Matthew Kwiatkowski, Vance Imhoff, Jennifer M. Gumm

Faculty Publications

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found …

Rapid Response: Cat-Scan Machine And 3d Printers Vital In Covid-19, Laura Meader

Colby Magazine

Colby’s Assistant Professor of Biology Josh Martin is using his expertise and sophisticated scientific equipment to create face shields, respirator masks, and air filter cartridges for local first responders and hospitals in need of equipment that is crucial to treating patients with COVID-19.

Plant Canopy May Promote Seed Dispersal By Wind, Xuanping Qin, Wei Liang, Zhimin Liu, Minghu Liu, Carol C. Baskin, Jerry M. Baskin, Zhiming Xin, Zhigang Wang, Quanlai Zhou

Biology Faculty Publications

Seed dispersal has received much research attention. The plant canopy can intercept diaspores, but the effect of the plant canopy (the aboveground portion of a plant consisting of branches and leaves) on dispersal distance has not been explored empirically. To determine the effect of plant canopy on seed dispersal distance, a comparison of diaspores falling through open air and through plant canopy was made in a wind tunnel using three wind speeds and diaspores with various traits. Compared with diaspores falling through open air, the dispersal distance of diaspores falling through plant canopy was decreased or increased, depending on wind …

The Epiphytic Diatom Community Of An Invasive Macroalga, Starry Stonewort (Charales: Nitellopsis Obtusa) And Its Native Relative, Chara Contraria (Charales) From Two Drowned River Mouth Lakes, Kelsey Inman-Carter

Student Summer Scholars Manuscripts

Epiphytic diatoms are essential primary producers in aquatic environments, but the relationship between them and their hosts is not well understood. The purpose of this project is to understand the specificity of a macroalgal host-epiphytic diatom relationship in Pentwater and Muskegon Lakes, and compare the epiphytic diatom communities of the invasive Nitellopsis obtusa to its close native relative, Chara contraria, using a metabarcoding approach. To these ends, host samples were collected monthly from July to September in 2020 (90 samples) and in June 2021 (55 samples). DNA was extracted from each sample and the plastid RUBISCO (rbcL) barcoding region of …

Associations Between Resources And Practices Of Ild Centers And Outcomes In Patients With Idiopathic Pulmonary Fibrosis: Data From The Ipf-Pro Registry, Joao A De Andrade, Tejaswini Kulkarni, Megan L Neely, Anne S Hellkamp, Amy Hajari Case, Daniel A Culver, Kalpalatha Guntupalli, Shaun Bender, Craig S Conoscenti, Laurie D Snyder, Ipf-Pro Registry Investigators

Faculty, Staff and Students Publications

BACKGROUND: Performance benchmarks for the management of idiopathic pulmonary fibrosis (IPF) have not been established. We used data from the IPF-PRO Registry, an observational registry of patients with IPF managed at sites across the US, to examine associations between the characteristics of the enrolling sites and patient outcomes.

METHODS: An online survey was used to collect information on the resources, operations, and self-assessment practices of IPF-PRO Registry sites that enrolled ≥ 10 patients. Site variability in 1-year event rates of clinically relevant outcomes, including death, death or lung transplant, and hospitalization, was assessed. Models were adjusted for differences in patient …

Seasonal Changes In Mitochondrial Bioenergetics And Physiological Performance Of The Bluegill Sunfish, Lepomis Macrochirus, From A Shallow, Midwest River., Derick I. Lamptey, Ryan W. Sparks, Rolando Monte De Oca, Robert Skolik, Michael Menze, Eloy Martinez

Faculty and Staff Scholarship

As global temperature shifts due to anthropogenic impacts, the frequency and magnitude of extreme temperatures in shallow aquatic ecosystems are expected to increase. Previous studies performed on fish under fluctuating temperature regimes have reported increased physiological stresses, compared to stable thermal conditions, leading to morphological, behavioral and biochemical adaptations. Moreover, many studies have reported the effects of warmer temperatures on numerous aquatic species, but seasonal temperature changes experienced in aquatic systems are understudied. We surveyed changes in the bioenergetic machinery of a native fish population ( Lepomis macrochirus) in the temperate zone of North America and observed season-dependent thresholds in …

Chronic Background Radiation Correlates With Sperm Swimming Endurance In Bank Voles From Chernobyl, Kati Kivisaari, Sara Calhim, Zbyszek Boratyríski, Timothy Mousseau, Anders P. Møller, Tapio Mappes

Faculty Publications

Sperm quantity and quality are key features explaining intra- and interspecific variation in male reproductive success. Spermatogenesis is sensitive to ionizing radiation and laboratory studies investigating acute effects of ionizing radiation have indeed found negative effects of radiation on sperm quantity and quality. In nature, levels of natural background radiation vary dramatically, and chronic effects of low-level background radiation exposure on spermatogenesis are poorly understood. The Chernobyl region offers a unique research opportunity for investigating effects of chronic low-level ionizing radiation on reproductive properties of wild organisms. We captured male bank voles (Myodes glareolus) from 24 locations in the Chernobyl …

Aav5 Delivery Of Crispr-Cas9 Supports Effective Genome Editing In Mouse Lung Airway, Shun-Qing Liang, Christopher J Walkey, Alexa E Martinez, Qin Su, Mary E Dickinson, Dan Wang, William R Lagor, Jason D Heaney, Guangping Gao, Wen Xue

Faculty, Staff and Students Publications

Genome editing in the lung has the potential to provide long-term expression of therapeutic protein to treat lung genetic diseases. Yet efficient delivery of CRISPR to the lung remains a challenge. The NIH Somatic Cell Genome Editing (SCGE) Consortium is developing safe and effective methods for genome editing in disease tissues. Methods developed by consortium members are independently validated by the SCGE small animal testing center to establish rigor and reproducibility. We have developed and validated a dual adeno-associated virus (AAV) CRISPR platform that supports effective editing of a lox-stop-lox-Tomato reporter in mouse lung airway. After intratracheal injection of the …

Data From: Glucose Tolerance Of Iguanas Is Affected By High Sugar Diets In The Lab And Supplemental Feeding By Ecotourists In The Wild, Susannah S. French

Browse all Datasets

Physiological responses to both natural and anthropogenic perturbations involve changes in glucose use and metabolism to enable animals to respond to challenges. The responses are at least partially mediated via the glucocorticoids, and the proper functioning of these systems are critical to animal health. Prolonged high-sugar diets in humans can compromise physiological functions and lead to a range of diseases including diabetes. Such outcomes are less common in natural, non-human systems, likely because of evolutionarily based balances between sugar intake and the ability to process it. Due to both landscape changes and human feeding of wildlife, the introduction of unnatural …

Impact Of Edds Dosage On Lead Phytoextraction In Contaminated Urban Residential Soils, Zhiming Zhang, Dibyendu Sarkar, Virinder Sidhu, Manas Warke, Rupali Datta

Michigan Tech Publications, Part 1

Lead (Pb) contamination in soils of residential properties due to peeling and chipping of Pb-based paint can cause human health problems. Phytoextraction is a green technology that has the potential to remediate soil Pb. The efficiency of phytoextraction is dependent on the geochemical forms of Pb in soil. A biodegradable chelating agent, ethylenediaminedisuccinic acid (EDDS), was previously shown to enhance Pb removal by facilitating phytoextraction. In this study, EDDS was tested at various concentrations for its potential in mobilizing Pb in urban residential soils in Jersey City, New Jersey, and San Antonio, Texas. Results show that the concentrations of plant-available …

Autophagosomes Fuse To Phagosomes And Facilitate The Degradation Of Apoptotic Cells In Caenorhabditis Elegans, Omar Peña-Ramos, Lucia Chiao, Xianghua Liu, Xiaomeng Yu, Tianyou Yao, Henry He, Zheng Zhou

Faculty, Staff and Students Publications

Autophagosomes are double-membrane intracellular vesicles that degrade protein aggregates, intracellular organelles, and other cellular components. During the development of the nematode Caenorhabditis elegans, many somatic and germ cells undergo apoptosis. These cells are engulfed and degraded by their neighboring cells. We discovered a novel role of autophagosomes in facilitating the degradation of apoptotic cells using a real-time imaging technique. Specifically, the double-membrane autophagosomes in engulfing cells are recruited to the surfaces of phagosomes containing apoptotic cells and subsequently fuse to phagosomes, allowing the inner vesicle to enter the phagosomal lumen. Mutants defective in the production of autophagosomes display significant …

Clinical Performance Of The Xpert® Ct/Ng Test For Detection Of Chlamydia Trachomatis And Neisseria Gonorrhoeae: A Multicenter Evaluation In Chinese Urban Hospitals, Fred C. Tenover, Yan Han, Mei-Qin Shi, Qing-Ping Jiang, Wen-Jing Le, Xiao-Lin Qin, Han-Zhen Xiong, He-Ping Zheng, Yi-Wei Tang, Yue-Ping Yin

Biology Faculty Publications

Background: We aimed to evaluate the clinical performance of the GeneXpert® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.

Methods: This study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.

Results: In this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were …

Analysis Of Lactobacillus Spp Isolates From Human Urinary Bladder, Tatyana Sysoeva

Summer Community of Scholars (RCEU and HCR) Project Proposals

No abstract provided.

Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page

Theses and Dissertations

The need for an internal control to govern engineered strain survival is becoming apparent when considering the biosafety and ethics within biotechnological research. Using understudied regulatory elements known as RNA thermometers (RNATs) that can modulate protein translation based on temperature changes and a Type II restriction modification system, we posit the creation of a synthetic temperature-activated epigenetic biocontainment system, termed the ‘sentinel switch’. We have mined a wide variety of bacteria from Yersinia pestis to Synechocystis sp. looking for novel RNATs. A complementary synthetic biology approach based on library generation and screening of chimeric RNATs (ChRNATs) was also conducted. RNATs …

Phage Hunters: The Discovery Of Two Novel Bacteriophages That Infect Gordonia Rubripertincta, Sarah Ballarin, Neel Balusa, Melissa Bell, Samia Caballero, Joshua Chan, Maria Farez, Ashley J. Guillen-Tapia, Nashrah Pierre-Louis, Victoria Polishuk, Bhavya Soni, Julie Torruellas Garcia, Katie E. Crump

Sea-Phages

Antibiotic resistance is a global healthcare concern because it poses a threat to effectively treating bacterial infections and the need for alternative therapeutics are urgently required. Phage therapy, which uses viruses to treat bacterial infections, is a promising alternative to conventional antibiotics. Phages have also been widely used in the food industry to prevent microbial growth on certain foods and are currently being explored as a method for bioremediation of oil spills and wastewater treatment. Although phages are ubiquitous in nature, many have yet to be discovered. Through the SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) program …

Transcriptomic Profiling Of Mice Brain Under Bex3 Regulation, Zhimin Xu, Noor Bahadar, Yingxin Zhang, Shuang Tan, Zhongze Wang, Bingyi Ren, Shitao Liu, Huanyan Dai, Yaowu Zheng, Bing Han

Turkish Journal of Biology

BEX family genes are expressed in various tissues and play significant roles in neuronal development. A mouse model of Bex3 gene knock-out was generated in this study, using the CRISPR-Cas9 system. Transcriptomic analysis of the brain was performed to identify genes and pathways under Bex3 regulation. Essential biological functions under the control of Bex3 related to brain development were identified. Ninety-five genes were differentially expressed under Bex3-/- regulation, with 53 down and 42 up. Among down-regulated genes, LOC102633156 is a member of zf-C2H2, Xlr3a is an X-linked lymphocyte regulated gene, LOC101056144 is a hippocampal related gene, 2210418O10Rik and Fam205a3 are …

Noncoding Rnas In Apoptosis: Identification And Function, Özge Tüncel, Merve Kara, Bi̇lge Yaylak, İpek Erdoğan, Bünyami̇n Akgül

Turkish Journal of Biology

Apoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein-coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes …

Modeling Of C-Terminal Tail Of Human Sting And Its Interaction With Tank-Binding Kinase 1, Rahaf Ata Ouda Al-Masri, Hajara Audu-Bida, Şebnem Eşsi̇z

Turkish Journal of Biology

Stimulator of interferon genes (STING) plays a significant role in a cell's intracellular defense against pathogens or self-DNA by inducing inflammation or apoptosis through a pathway known as cGAS-cGAMP-STING. STING uses one of its domains, the C-terminal tail (CTT) to recruit the members of the pathway. However, the structure of this domain has not been solved experimentally. STING conformation is open and more flexible when inactive. When STING gets activated by cGAMP, its conformation changes to a closed state covered by 4 beta-sheets over the binding site. This conformational change leads to its binding to Tank-binding kinase 1 (TBK1). TBK1 …

Ubiquitin Specific Protease 7 Maintains Pluripotency Of Mouse Embryonic Stem Cells Through Stabilization Of Ss-Catenin, Taha Bartu Hayal

Turkish Journal of Biology

Embryonic stem cells (ESCs), which are derived from the undifferentiated inner cell mass of the embryo, can differentiate every cell type of the body regarding their pluripotency. Therefore, human or mouse ESCs can be used as an unlimited cell source for numerous researches or therapeutical approaches. However, pluripotency maintenance of ESCs during in vitro culture is challenging because of their endless differentiation capacity. In the current study, the effect of USP7 on pluripotency maintenance of mouse ESCs (mESCs) has been investigated with the help of cell viability assay, morphological analysis, alkaline phosphatase (ALP) staining, qPCR analysis, and Western Blotting. 600 …

P110Α Activity At The M-To-G1 Transition Is Critical For Cellular Proliferation And Reentry Into The Cell Cycle, Onur Çi̇zmeci̇oğlu

Turkish Journal of Biology

Phosphoinositide 3-kinase (PI3K) signaling pathway is essential for normal physiology and is impaired in diseases such as premalignant hyperproliferative disorders, primary immunodeficiency, metabolic disorders, and cancer. Although the core PI3K pathway components are known today, a long-standing gap in our knowledge of PI3K signaling concerns how distinct PI3K isoforms and their activity patterns contribute to the functional consequences of pathway upregulation. In order to address this issue, we devised a molecular genetic cell model, which allowed temporal regulation of the indispensable PI3K isoform, p110α in distinct stages of the cell cycle. We found that late M and early G1 …

Cytoplasmically Localized Trna-Derived Fragments Inhibit Translationin Drosophila S2 Cells, Syed Muhammad Hamid, Bünyami̇n Akgül

Turkish Journal of Biology

Transfer ribonucleic acids (tRNAs) serve not only as amino acid carriers during translation but also as a template for the biogenesis of short fragments that can regulate gene expression. Despite recent progress in the function of tRNA-derived fragments (tRFs), their intracellular localization, protein partners, and role in regulating translation are not well understood. We used synthetic tRFs to investigate their localization and function in Drosophila S2 cells. Under our experimental setting, all synthetic tRFs tested were localized at distinct sites within the cytoplasm in a similar manner in Drosophila S2 cells. Cytoplasmically-localized tRFs were positioned in close proximity to GW182 …

Sirna-Mediated Stathmin1 Silencing Inhibits Proliferation Of Prostate Carcinoma Cell Line, Asude Aksoy, Safi̇ye Selcen Vi̇cdanli, Ebru Önalan, Ahmet Tektemur, Gökhan Artaş, Asuman Orhan Varoğlu, Mustafa Koç

Turkish Journal of Biology

Stathmin1 (STMN1) has been proposed as a possible prognostic marker and a potential therapeutic target for some cancers. We aimed to analyze the changes in autophagy, invasion, apoptosis-related genes in prostate cancer (PCa) cell line (PC-3), after small interfering RNA (siRNA)-mediated STMN1 silencing, and also the relationships of STMN1 expression, clinicopathological parameters, and survival (OS) in PCa cases. The STMN1 expressions were analyzed, immunohistochemically, in formalin-fixed paraffin-embedded 75 PCa and 15 benign prostatic hypertrophy (BPH) tissues. The correlation between the levels of expression STMN1, clinicopathological features, and OS was determined in PCa cases. The siRNA-mediated STMN1 incubated PC-3 cells were …

Transcriptome Sequencing Reveals Circrna Expression Profile In Parkinson's Disease-Like Mice After Aerobic Exercise, Tianlun Fan, Xiating Li, Chuan Fu, Lichun Sun

Turkish Journal of Biology

Parkinson's disease (PD) is a common complex neurodegenerative disease, and aerobic exercise (EX) has potential to improve motor dysfunction. This study aimed to explore whether EX acts on PD in mice mode. Mice were administered 1-methyl-4-phenyl- 1,2,3,6-tetrahydropyridine (MPTP) and subjected to a 4-week physical exercise regimen (EX-PD group) and underwent RNA-Seq. Here, MPTP caused PD, which was characterized by neuron shrinkage and behavioral deficits, whereas EX improved PD by rescuing neuronal survival and motor function in mice. Moreover, circRNA expression profiles identified a total of 142 differentially expressed circRNAs (DEcircRNAs) between PD and EX-PD group. These DEcircRNAs were mainly involved …