Digital Commons Network^™

Structural Biology Of Mcr-1-Mediated Resistance To Polymyxin Antibiotics, Isabel Cristina Materon, Timothy Palzkill

Faculty, Staff and Students Publications

Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and …

Co-Targeting Bcl-Xl And Bcl-2 By Protac 753b Eliminates Leukemia Cells And Enhances Efficacy Of Chemotherapy By Targeting Senescent Cells, Yannan Jia, Lina Han, Cassandra L Ramage, Zhe Wang, Connie C Weng, Lei Yang, Simona Colla, Helen Ma, Weiguo Zhang, Michael Andreeff, Naval Daver, Nitin Jain, Naveen Pemmaraju, Kapil Bhalla, Satu Mustjoki, Peiyi Zhang, Guangrong Zheng, Daohong Zhou, Qi Zhang, Marina Konopleva

Faculty, Staff and Student Publications

BCL-XL and BCL-2 are key anti-apoptotic proteins and validated cancer targets. 753B is a novel BCL-XL/BCL-2 proteolysis targeting chimera (PROTAC) that targets both BCL-XL and BCL-2 to the von Hippel-Lindau (VHL) E3 ligase, leading to BCLX L/BCL-2 ubiquitination and degradation selectively in cells expressing VHL. Because platelets lack VHL expression, 753B spares on-target platelet toxicity caused by the first-generation dual BCL-XL/BCL-2 inhibitor navitoclax (ABT-263). Here, we report pre-clinical single-agent activity of 753B against different leukemia subsets. 753B effectively reduced cell viability and induced dose-dependent degradation of BCL-XL and BCL-2 in a subset of hematopoietic cell lines, acute myeloid leukemia (AML) …

Rational Design For The Recombinant Expression Of The Receptor Binding Domain Of Sars-Cov-2 Spike Glycoprotein, Luis Mario Rodriguez, Mario Alberto Rodriguez, Hugo A. Barrera-Saldaña, Rocio Marisol Martinez, Daniela Rodriguez

Research Symposium

Background: COVID-19 represents a significant threat to global human health. SARS-CoV-2, the etiologic viral agent, needs to be under-covered at the structural biology level to facilitate the rational design of diagnostic tests and vaccine candidates. SARS-CoV-2 Receptor Binding Domain of Spike protein (RBD-S) acts as the key to open the gate, to enter the cells during infection. Thus, it is a stronger candidate for designing effective antigens for vaccines and diagnostics. Here, we relied on the viral DNA codifying to RBD-S to use synthetic biology for optimizing the recombinant expression of this (rRBD-S) as a proof of concept of rational …

Increasing Temperatures Can Pose An Opportunity To Recover Endemic And Endangered Oriental Sweetgum Tree (Liquidambar Orientalis Mill.) From Extinction, Okan Ürker, Nurbahar Usta Baykal, Eren Ada

Turkish Journal of Botany

Evidence suggests that past climatic oscillations caused many species to drastically change their distribution range and had significant impacts on their survival capabilities. There is significant evidence suggesting that today's changing climate threatens many species to face a rapid extinction period in the coming decades and centuries. Understanding the changing range patterns provides significant input on biodiversity and conservation biology studies. However, warming climatic conditions may also present an opportunity for some species to expand their habitats?particularly those adapted to warmer environments. In this study, we asked how near-future climate change will affect the distribution range of the oriental sweetgum …

Icvd Polymer Thin Film Bio-Interface-Performance For Fibroblasts, Cancer-Cells, And Viruses Connected To Their Functional Groups And In Silico Studies, Torge Hartig, Asmaa T. Mohamed, Nasra F. Abdel Fattah, Aydin Gülses, Tim Tjardts, Esther Afiba Kangah, Kwing Pak Gabriel Chan, Salih Salih Veziroglu, Yahya Acil, Oral Cenk Aktas, Jörg Jörg Wiltfang, Samah A. Loutfy, Thomas Strunskus, Franz Faupel, Amal Amin, Stefan Schröder

Nanotechnology Research Centre

Thin polymer coatings are used to improve the interface between biological species and functional materials. Their interaction is significantly influenced by the functional groups and roughness of the polymer film and prediction of the interaction is thus of great interest. However, for conventional polymer films, this cannot be examined independently because of the interplay of defects, residual solvent molecules, roughness, and functional groups. Solvent-free polymer films prepared by initiated chemical vapor deposition (iCVD) exhibit conformal, defect-free characteristics and enable precise tailoring of the functional groups. This facilitates to isolate the contribution of functional groups on the bio-interface performance. Consequently, in …

Simultaneous 3d Construction And Imaging Of Plant Cells Using Plasmonic Nanoprobe-Assisted Multimodal Nonlinear Optical Microscopy, Kun Liu, Yutian Lei, Dawei Li

Department of Civil and Environmental Engineering: Faculty Publications

Nonlinear optical (NLO) imaging has emerged as a promising plant cell imaging technique due to its large optical penetration, inherent 3D spatial resolution, and reduced photodamage; exogenous nanoprobes are usually needed for nonsignal target cell analysis. Here, we report in vivo, simultaneous 3D labeling and imaging of potato cell structures using plasmonic nanoprobe-assisted multimodal NLO microscopy. Experimental results show that the complete cell structure can be imaged via the combination of second-harmonic generation (SHG) and two-photon luminescence (TPL) when noble metal silver or gold ions are added. In contrast, without the noble metal ion solution, no NLO signals from the …

Simultaneous 3d Construction And Imaging Of Plant Cells Using Plasmonic Nanoprobe-Assisted Multimodal Nonlinear Optical Microscopy, Kun Liu, Yutian Lei, Dawei Li

Department of Civil and Environmental Engineering: Faculty Publications

Nonlinear optical (NLO) imaging has emerged as a promising plant cell imaging technique due to its large optical penetration, inherent 3D spatial resolution, and reduced photodamage; exogenous nanoprobes are usually needed for nonsignal target cell analysis. Here, we report in vivo, simultaneous 3D labeling and imaging of potato cell structures using plasmonic nanoprobe-assisted multimodal NLO microscopy. Experimental results show that the complete cell structure can be imaged via the combination of second-harmonic generation (SHG) and two-photon luminescence (TPL) when noble metal silver or gold ions are added. In contrast, without the noble metal ion solution, no NLO signals from the …

Instructors At A Crossroad: Perceptions Of Collaboration And Support Intersect With Intentions To Implement A Cure, Justin Berl

Dissertations and Theses

An ongoing crisis of student drop-off from undergraduate science, technology, engineering and mathematics (STEM) education has led to a sustained call over the last 15+ years for the increased implementation of updated practices in undergraduate STEM education. Though over the past few decades many researchers have developed and analyzed the efficacy of various evidence-based teaching practices (EBTPs) designed to improve the state of undergraduate STEM education throughout the country, the rate at which these EBTPs are implemented in undergraduate STEM classrooms remains low.

In order to better understand the specific factors that affect individual instructors' efforts to implement EBTPs, we …

Evolutionary Action-Machine Learning Model Identifies Candidate Genes Associated With Early-Onset Coronary Artery Disease, Dillon Shapiro, Kwanghyuk Lee, Jennifer Asmussen, Thomas Bourquard, Olivier Lichtarge

Faculty, Staff and Students Publications

Background Coronary artery disease is a primary cause of death around the world, with both genetic and environmental risk factors. Although genome-wide association studies have linked >100 unique loci to its genetic basis, these only explain a fraction of disease heritability. Methods and Results To find additional gene drivers of coronary artery disease, we applied machine learning to quantitative evolutionary information on the impact of coding variants in whole exomes from the Myocardial Infarction Genetics Consortium. Using ensemble-based supervised learning, the Evolutionary Action-Machine Learning framework ranked each gene's ability to classify case and control samples and identified 79 significant associations. …

Integrating Glycolysis, Citric Acid Cycle, Pentose Phosphate Pathway, And Fatty Acid Beta‑Oxidation Into A Single Computational Model, Sylwester M. Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Beata J. Wysocki, Paul H. Davis, Tadeusz A. Wysocki

Department of Electrical and Computer Engineering: Faculty Publications

The metabolic network of a living cell is highly intricate and involves complex interactions between various pathways. In this study, we propose a computational model that integrates glycolysis, the pentose phosphate pathway (PPP), the fatty acids beta-oxidation, and the tricarboxylic acid cycle (TCA cycle) using queueing theory. The model utilizes literature data on metabolite concentrations and enzyme kinetic constants to calculate the probabilities of individual reactions occurring on a microscopic scale, which can be viewed as the reaction rates on a macroscopic scale. However, it should be noted that the model has some limitations, including not accounting for all the …

Hhp 529.01: Advanced Physiology Of Exercise I, Charles L. Dumke

University of Montana Course Syllabi, 2021-2025

No abstract provided.

Evaluation Of A Wave Powered Water Pump Performance By Ocean Field Testing And Wec-Sim Modeling, Chelsea Kimball

Master's Theses and Capstones

A rising demand for macroalgae (or seaweed) has led researchers to seek out methods of increasing macroalgae aquaculture yields. Macroalgae is a food product, and may be used in biofuel, animal feed, and fertilizer. Applying upwelling technology to macroalgae aquaculture has been shown to increase biomass yield. A wave-powered upwelling device (or water pump) generates cold, nutrient-rich water flow to the surface of an aquaculture operation. A wave pump device developed at University of New Hampshire was refurbished and outfitted with instrumentation to determine its performance. Testing in the laboratory on both the device and instrumentation was conducted to prepare …

Inhibition Of The Interaction Between Hippo/Yap And Akt Signaling With Ursolic Acid And 3’3-Diindolylmethane Suppresses Esophageal Cancer Tumorigenesis, Ruo Yu Meng, Cong Shan Li, Dan Hu, Soon-Gu Kwon, Hua Jin, Ok Hee Chai, Ju-Seog Lee, Soo Mi Kim

Faculty, Staff and Student Publications

Hippo/YAP signaling hinders cancer progression. Inactivation of this pathway contributes to the development of esophageal cancer by activation of Akt. However, the possible interaction between Akt and Hippo/YAP pathways in esophageal cancer progression is unclear. In this study, we found that ursolic acid (UA) plus 3'3-diindolylmethane (DIM) efficiently suppressed the oncogenic Akt/Gsk-3β signaling pathway while activating the Hippo tumor suppressor pathway in esophageal cancer cells. Moreover, the addition of the Akt inhibitor LY294002 and the PI3K inhibitor 3-methyladenine enhanced the inhibitory effects of UA plus DIM on Akt pathway activation and further stimulated the Hippo pathway, including the suppression of …

Paradoxes Of Cellular Sumoylation Regulation: A Role Of Biomolecular Condensates?, Xiaodong Cheng, Wenli Yang, Wei Lin, Fang Mei

Faculty, Staff and Student Publications

Protein SUMOylation is a major post-translational modification essential for maintaining cellular homeostasis. SUMOylation has long been associated with stress responses as a diverse array of cellular stress signals are known to trigger rapid alternations in global protein SUMOylation. In addition, while there are large families of ubiquitination enzymes, all small ubiquitin-like modifiers (SUMOs) are conjugated by a set of enzymatic machinery comprising one heterodimeric SUMO-activating enzyme, a single SUMO-conjugating enzyme, and a small number of SUMO protein ligases and SUMO-specific proteases. How a few SUMOylation enzymes specifically modify thousands of functional targets in response to diverse cellular stresses remains an …

Characterization Of The Conformational Binding Of N-Methyl Mesoporphyrin Ix With Dna Model Telomeric G-Quadruplex Forming Sequences, Jessica Desamero

Dissertations, Theses, and Capstone Projects

DNA G-quadruplexes are alternative secondary structures formed from guanine rich DNA sequences. G-quadruplexes are found most abundantly at the ends of chromosomes called telomeres, where they can ultimately prevent further tumor growth and progression. Thus, quadruplex interactive agents, or ligands that can bind to and stabilize DNA G-quadruplex structures, are of high interest for their potential chemotherapeutic abilities. One quadruplex interactive agent is the porphyrin N-methyl mesoporphyrin IX (NMM), which has high binding selectivity for quadruplex structures. While the NMM-quadruplex complex in crystallized form has been greatly studied, this complex in solution form is not as well studied. Through circular …

Development Of Chemical Probes For Two Pro-Metastatic Enzymes: Cysteine Cathepsins And Nek2 Kinase, Ashif I. Bhuiyan

Dissertations, Theses, and Capstone Projects

Proteases, specifically cysteine proteases, are crucial for the survival and growth of living organisms. They hydrolyze proteins and use different mechanisms to function. Cysteine proteases are classified into three types: papain, caspase, and picornaviridae. The papain class, with 11 cysteine cathepsins, regulates essential physiological functions, and abnormal expression is linked to various diseases. Our research aims to develop small molecules that inhibit cathepsins B and L to develop probes for functional proteomics.

The centrosome is critical for proper cell division and is regulated by multiple kinases, including Nek2. Nek2 is highly concentrated at the centrosome in vertebrates and plays a …

Separation Of Zr From Complex Matrices For Isotope Harvesting Applications, Jake A. Bence

Dissertations, Theses, and Capstone Projects

Zr isotopes have various applications in nuclear science, such as ⁸⁶Zr and ⁸⁹Zr in nuclear medicine, ⁸⁸Zr as a diagnostic isotope relevant to stockpile stewardship, and the fission product ⁹⁵Zr useful as an s-process branch nucleus for study in astrophysics. To access these isotopes of interest, dedicated production methods and subsequent processing chemistry are required. Direct production routes can be technically challenging and difficult to obtain enough activity to meet demand. The processing chemistry of Zr isotopes is tedious due to the tendency for Zr to hydrolyze in solution without highly acidic conditions or a strong …

Celebrating Leeuwenhoek’S Life 300 Years Later, Alan L. Gillen

Faculty Publications and Presentations

Antony van Leeuwenhoek entered eternity 300 years ago (August 26, 1723). He made hundreds of discoveries with his simple microscope. Perhaps his most notable discovery was of bacteria and its many shapes. He found great joy in God [http://answersingenesis.org/god/] ’s smallest creatures. I believe that his curiosity about the world, fueled by his belief in biblical creation [http://answersingenesis.org/creation/] , led to his discovery of bacteria. In a similar manner, his curiosity of blood led to his discovery of red corpuscles and capillaries. He remained a curious man until the last days of his life 300 years …

2019 Great Day Program, State University Of New York At Geneseo

GREAT Day Programs

SUNY Geneseo’s Thirteenth Annual GREAT Day.

Morphometric Analysis And Biochemical Estimation Of Wild Shrimps (Family: Penaeidae) Found In Coastal Waters Of Pakistan, Noor Us Saher, Syeda Hadiqa Noor

Journal of Bioresource Management

The world recognition of Seafood nutritional value for human consumption remain consistent throughout the time. Different informations and aspects have been studied and considered and generated various data sets but limited informations found about the biochemical concentration of various fishery species caught in the Pakistan. Therefore, the recent study design to evaluate the proximate levels of components in the edible component (flesh) of commercial shrimp species were studied. Four shrimp species; Fenneropenaeus indicus, Metapenaeopsis stridulans, Metapenaeus stebbingi, and Parapenaeopsis stylifera were selected for the assessment of proximate composition. The selected shrimp species were collected from the fishery catch of Korangi …

Utility Of Body And Otolith Morphometry To Discriminate Cryptic Juveniles Of Two Sympatric Red Snappers (Perciformes: Lutjanidae), Miwa Takahashi, Corey B. Wakefield, Stephen J. Newman, Kyle B. Hillcoat, Benjamin J. Saunders, Euan S. Harvey

Fisheries Research Articles

The sympatric red snappers, Lutjanus erythropterus and Lutjanus malabaricus, are highly valued by commercial and recreational fishers along the tropical northern coasts of Australia and throughout their distribution. Studies on the life history and ecology of these congeners are confounded by difficulties in distinguishing the cryptic juveniles of each species (i.e., < 200 mm total length). This study aimed to validate a robust and cost-effective method to discriminate these juveniles using body and/or otolith morphometric data in a multivariate analysis. Juvenile samples were collected from the northwest (n = 71) and northeast (n = 19) coasts of Australia, and species identification was confirmed using DNA barcoding. The most parsimonious multivariate models achieved accurate species prediction rates of 98.8%, which consisted of just three body variables (dorsal fin length, the distance from the snout to the anterior edge of the eye, and either jaw length or distance from the snout to the preoperculum). The high level of discrimination for these cryptic juveniles highlights the robustness of this morphometric approach. The slightly lower rate of discrimination using otolith morphology (84.9%) was associated with greater regional variation in L. malabaricus between the northwest and northeast coasts. Slight variations in otolith shape are typically used to determine stock structure, which highlights the potential need to collect samples over a broader area of a species geographic range when using an otolith morphometric discrimination model. The method outlined in this study could be applied to distinguish other cryptic congeneric fish species, including from archived otolith collections. Moreover, this method has the potential to be utilized in assessing species compositions using body measurements from in situ stereo-video.

An Odontometric Biodistance Analysis Of The Rong And The A'Chik, Mary Ashley Stough

Anthropology

Little is known about the population history and genetic affinities of many of the tribal groups of northeastern India, including the Rong and the A'chik. Previous linguistic and genetic studies have suggested that these non-Hindu tribal groups may be descendants of East Asian immigrants. Due to the linguistic and genetic research, cultural differences between the groups, and geographic barriers it was hypothesized that members of these two tribal groups share a population history different from that of ethnic groups of other regions of the subcontinent. This study employs tooth size allocation analysis to test hypotheses concerning the origins of the …

Trophic Pathways And Their Relationship To Growth In Nearshore Consumers Across The Northern Gulf Of Alaska, Katherine M. Corliss

Marine Biology

Highly productive nearshore ecosystems in cold-temperate regions, such as the Northern Gulf of Alaska (NGOA), are supported by macroalgae and phytoplankton at the base of their food webs. Biomass of these primary producers varies seasonally, suggesting that longer-term environmental change could also shift biomass and/or range of basal producers. Our goal was to determine how proportional contributions of organic matter from macroalgae and phytoplankton to the diet of nearshore consumer species in the NGOA vary in space and time, and if these differences affect consumer growth. We used carbon and nitrogen stable isotope analysis to investigate diet sourcing of filter-feeding …

A Review Of Sapodilla Beneficial Use, Production Status, And Propagation Technique, Rahmat Budiarto, Syahvan Rifqi Dwinanda, Hansel Arie Pakpahan, Mega Komala, Yusti

Jurnal Kultivasi

Manilkara zapota, commonly known as sapodilla, is one of tropical fruits, originating from Central and South America that is still less popular in Indonesia, as compared to banana, citrus, mango, etc. To gain its popularity, it is crucial to review beneficial uses, existing production status and propagation techniques of sapodilla. In general, sapodilla is used for either table fresh fruit. Additionally, it contains various bioactivities in its fruit, stem, and leaves, such as antioxidant, antimicrobe, and antitumor activity; thus, become very potential for pharmaceutical purposes. The existing production data of sapodilla determine the West Java Province as the biggest production …

Dna Methylation Networks Underlying Mammalian Traits, Amin Haghani

Department of Animal Science: Faculty Publications

INTRODUCTION: Comparative epigenomics is an emerging field that combines epigenetic signatures with phylogenetic relationships to elucidate species characteristics such as maximum life span. For this study, we generated cytosine DNA methylation (DNAm) profiles (n = 15,456) from 348mammalian species using amethylation array platform that targets highly conserved cytosines.

RATIONALE: Nature has evolved mammalian species of greatly differing life spans. To resolve the relationship ofDNAmwith maximum life span and phylogeny, we performed a largescale cross-species unsupervised analysis. Comparative studies in many species enables the identification of epigenetic correlates of maximum life span and other traits.

RESULTS: We …

Design, Synthesis, And Characterization Of Peptide Amphiphile Biomaterials, Huihua Xing

Theses & Dissertations

Self-assembled peptide amphiphiles (PAs) have gained significant attention in recent years due to their ability to form various supramolecular nanostructures with unique physical and chemical properties. These amphiphilic molecules consist of a hydrophobic tail and a peptide domain, allowing for the formation of nanoscale assemblies in aqueous environments. The PA supramolecular structures have a wide range of potential applications, including drug delivery, tissue engineering, and regenerative medicine.

By manipulating the driving forces (e.g., hydrophobic interactions, hydrogen bonds, and electrostatic interactions) involved in the self-assembly, researchers can tune the self- assembly properties (size, shape, stability, and surface character) and, consequently, the …

Ten Tips Taylored For Successful Talks With Landowners In Ranching And Range Management Landscapes, Taylor J. Linder, Susan N. Ellis-Felege, Christopher J. Felege

Biology Faculty Publications

Privately owned lands offer substantial land area that have the potential to contribute greatly to wildlife conservation. However, it is dubious for private landowners to engage in such programs that have not readily accepted their input. Given the future directions of wildlife conservation and needing to heavily integrate private lands into habitat objectives to meet wildlife population standards, it will be of growing importance to consider the needs and wants of private landowners to meet production goals and simultaneously wildlife habitat goals (and not the other way around). We recognize the important methodological research that has built foundations for current …

Biosentinel: Mission Summary And Lessons Learned From The First Deep Space Biology Cubesat Mission, Matthew Napoli, Cheryle Kong, Jeffrey Homan, Jesse Fusco, Robert Nakamura, Mike Padgen, Shang Wu, Philip Shih, Mohammad Hejase, Sergio R. Santa Maria, Josh Benton, Dennis Heher, Terry Stevenson, Andres Dono Perez, Jose Alvarellos

Small Satellite Conference

Launched on Artemis I, BioSentinel carries a biology experiment into deep space for the first time in 50 years. A 6U CubeSat form factor was utilized for the spacecraft, which included technologies newly developed or adapted for operations beyond Earth orbit. The spacecraft carries onboard budding yeast, Saccharomyces cerevisiae, as an analog to human cells to test the biological response to deep space radiation. This was the maiden deep-space voyage for many of the subsystems, and the first time to evaluate their performance in flight operation.

Flying a CubeSat beyond LEO comes with unique challenges with respect to trajectory …

Biology Of The Sineguelas Leaf Beetle, Podontia Quatuordecimpunctata (L.) (Chrysomelidae: Galerucinae: Alticini), On Spondias Purpurea L. (Anacardiaceae) In The Philippines, Orlando A. Calcetas, Charles L. Staines, Caroline Simmrita Chaboo, Rachel Ann A. Anabo, Monalisa O. Recuenco

Insecta Mundi

Spondias purpurea L. (Anacardiaceae), native to the Neotropical region, is cultivated in the Phil­ippines for the edible fruits and the tree is economically significant. The adventive leaf beetle, Podontia quatuordecimpunctata (L.) (Chrysomelidae: Galerucinae: Alticini), has become a major defoliating pest of the tree in the country. The Philippines government has initiated study of the pest, now locally called the sineguelas leaf beetle (SLB). This paper reports the results of a one-year field study on the biology of SLB on S. purpurea (red sineguelas), in Batangas City, Philippines. The SLB eggs hatch in 5–7 days. The larval period is 14–16 …

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …