Biology Commons^™

Psilostachyin B As Potential Immune Checkpoint Inhibitor Targeting Ctla-4 And Pd-L1 In The Development Of Cancer Immunotherapy: A Computational Investigation, Moh Dliyauddin, Nabila Shafa Yumna Salsabila, Noviana Dwi Lestari, Sapti Puspitarini, Mansur Ibrahim, Sri Rahayu, Muhammad Sasmito Djati, Muhaimin Rifa’I

Karbala International Journal of Modern Science

Immunotherapy is a promising treatment approach by targeting immune checkpoints such as CTLA-4 and PD-L1 to overcome cancer progression. The utilization of Curcuma longa and Phyllanthus niruri as potential immune checkpoint inhibitors offers an alternative cancer therapy. Computational analyses including molecular docking and molecular dynamics with validation using Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA), Dynamic Cross-Correlation Matrix (DCCM), and Principal Component Analysis (PCA), were performed in this study. Results show that Psilostachyin B is the most promising inhibitor candidate against CTLA-4 and PD-L1, with binding affinity values of -6.9 and -6.8 kcal/mol, respectively. Molecular dynamics simulation results indicated that Psilostachyin B …

Investigating Molecular Mechanisms Of Meiosis And Mitosis In Cryptosporidium Parvum, Abigail Kimball

Arts & Sciences Graduate Student Theses and Dissertations

The apicomplexan parasite Cryptosporidium parvum (Cp) is a major global contributor to infectious diarrhea in children and poses a serious threat to immunocompromised adults. This dissertation investigates Cp's unique life cycle, which alternates between sexual and asexual reproduction to achieve three critical objectives: producing oocysts capable of transmission, enhancing genetic variation through recombination, and generating sufficient progeny for survival. Sexual reproduction is essential for forming infectious oocysts that facilitate disease transmission. Yet, the process of meiosis in Cp has been historically understudied due to limitations of traditional in vitro culture methods. The newly developed air-liquid interface (ALI) culture system supports …

Characterization Of Dna Background On Duct Tape Stored In Domestic Environments, Elaan A. Lukasiewicz

Student Theses

With lower detection limits for forensic DNA analysis, it is important to have a better understanding of background DNA levels unrelated to the crime to facilitate accurate data interpretation. Duct tape is used in crimes, e.g. to bind victims and seal drug packaging, and may be tested for DNA. To determine DNA background levels, twelve volunteers were recruited to donate a used roll of duct tape from their home. The duct tape was divided into three areas: inside, outside, and sides of the roll, and swabbed for DNA. The average concentration of DNA was determined for the inside (0.0723 ng/µL …

Role Of Staphylococcus Aureus And Streptococcus Pyogenes Biofilms On The Alternation Of Cellular Immunity In Pediat-Ric Tonsillitis Patients, Shayma Ali Hussein, Taban Kamal Rasheed

Karbala International Journal of Modern Science

This study examines the effect of Staphylococcus aureus and Streptococcus pyogenes biofilms on cellular hematological parameters and distribution and phenotyping of cellular immunity in mucosal tissue of tonsils. Thirty healthy controls and fifty pediatric tonsillitis patients participated in the research. Thirty isolated S. aureus and S. pyogenes were tested for biofilm-forming capability (BFC). Hematological parameters were assessed before tonsillectomy, and 9 tonsil samples were evaluated using hematoxylin and eosin stain to investigate the histopathological alterations. Immunohistochemistry (IHC) staining was carried out for detecting dendritic cells (CD1a), neutrophils (CD15), macrophages (CD68), helper T cells (CD4), and cytotoxic T cells (CD8). Hematological …

Neurophysiology And Endocrine Responses To Hunger And Satiety Mechanisms: The Brain-Gut Crosstalk, Nour Shakir Rezaieg, Muthanna M. Awad

Karbala International Journal of Modern Science

Background: Obesity is a main public health problem which substantially increases the risk of many diseases. The complex neural circuitry controls energy homeostasis and food consumption by the incorporation of hormonal and neural signals. Circulating hormones, in specific the gut hormones, have been found to be very important in appetite regulation. These hormones transfer energy situation signs to the brain throughout three principle paths: the circulation system, activation of the vagus nerve, and direct modification of main brain regions such as the hypothalamus and brainstem. The control of food eating is not exclusively dependent on the homeostatic processes, rather it …

A Novel Chaotic Dna-Based Image Cryptosystem Leveraging Euclidean Division, Dynamic Josephus Traversal, And Reservoir Computing, Ahmed Kareem Shibeeb, Salah Albermany, Sadiq A. Mehdi

Karbala International Journal of Modern Science

This study presents a new chaotic DNA-based image cryptosystem that combines Euclidean division, dynamic Josephus traversal (DJT), and reservoir computing to address the weaknesses of current methods. Old chaotic DNA cryptosystems usually have problems such as using the same keys for different messages, simple DNA processes, and being vulnerable to attacks where the attacker can choose the input or try many options. The cryptosystem in this study uses a 7D hyperchaotic system that starts with keys created from SHA-512 hashes to produce changing keystreams based on the plaintext, making it very strong against such attacks. The proposed cryptosystem uses a …

Bridging Prairie Restoration And Regenerative Agriculture With Compost Tea, April Hersey

2025 Symposium

Inland Pacific Northwest prairie is an endangered ecosystem that has been reduced by conversion to agriculture. There is growing interest in the role of soil microorganisms in prairie ecosystems, which may be crucial for restoration of the plant community through interspecies interactions within the soil near plant roots. One method for improving soil microorganism community composition is compost tea: enriched liquid compost extract. Compost tea is used in regenerative agriculture to improve crop yields and protect against pathogens, ostensibly through the activity of the added compost microbes. While research has supported compost tea application in regenerative agriculture, it has not …

Life Of Moo Deng, The Internet Sensation Pygmy Hippopotamus: An Overview Of The Biology And Conservation Breeding Program In Thailand, Ampika Thongphakdee, Atthapon Nundee, Umaporn Maikeaw, Narongwit Chodchoy, Chainarong Punkong, Kaywalee Chatdarong

The Thai Journal of Veterinary Medicine

The hippopotamus, commonly known as the hippo, is classified into two extant species: the common hippopotamus (Hippopotamus amphibius) and the pygmy hippopotamus (Choeropsis liberiensis). Pygmy hippos are fascinating creatures native to the forests and swamps of West Africa. Their survival is increasingly threatened by habitat loss resulting from agricultural expansion and urban development. As the population declines, zoological institutions play a crucial role in conservation by acting as genetic reservoirs and promoting public awareness of wildlife and environmental protection. “Moo Deng”, a pygmy hippo, whose name in Thai has gained international recognition, represents a notable success …

Human Contributions To Global Soundscapes Are Less Predictable Than The Acoustic Rhythms Of Wildlife, Panu Somervuo, Tomas Roslin, Brian L. Fisher, Bess Hardwick, Deirdre Kerdraon, Dimby Raharinjanahary, Eric Tsiriniaina Rajoelison, Patrik Lauha, Lukas Griem, Petteri Lehikoinen, Pekka Niittynen, Esko Piirainen, Markus Lumme, Ville-Matti Riihikoski, Orlando Acevedo-Charry, Solny A. Adalsteinsson, Maaz Ahmad, Sandra Alcobia, Jón Aldará, Tad Dallas

Faculty Publications

Across the world, human (anthropophonic) sounds add to sounds of biological (biophonic) and geophysical (geophonic) origin, with human contributions including both speech and technophony (sounds of technological devices). To characterize society’s contribution to the global soundscapes, we used passive acoustic recorders at 139 sites across 6 continents, sampling both urban green spaces and nearby pristine sites continuously for 3 years in a paired design. Recordings were characterized by bird species richness and by 14 complementary acoustic indices. By relating each index to seasonal, diurnal, climatic and anthropogenic factors, we show here that latitude, time of day and day of year …

Complete Genome Sequence Of Staphylococcus Haemolyticus Umb6531b, Isolated From A Perineal Swab, Alex Kula, Olive Kolar, Karolina Gilewicz, Zainab Qureshi, Anmol Singh, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

Staphylococcus haemolyticus UMB6531B was isolated from a perineal swab of a female with overactive bladder symptoms and sequenced to better characterize opportunistic pathogens of the female urogenital tract. Here, we present the complete genome sequence, which includes the chromosome as well as two complete plasmid sequences.

Str Analysis Performance Comparison For Two Capillary Electrophoresis Instruments: The Seqstudio And The 3500 Genetic Analyzers, Yana Leichyk

Student Theses

This study compares the performance of two capillary electrophoresis instruments—the SeqStudio™ Genetic Analyzer and the 3500™ Genetic Analyzer—for forensic short tandem repeat (STR) analysis. Using the GlobalFiler STR kit and certified reference material (SRM 2391d), five key performance metrics were evaluated: sizing precision, signal reproducibility, detection sensitivity, mixture resolution, and overload tolerance. STR profiles were generated from single-source and mixture samples with DNA inputs ranging from 500 pg to 15.6 pg. Both instruments met the < 0.15 bp sizing precision requirement for forensic casework. Signal reproducibility tests showed that the SeqStudio often produced higher average RFU values, but with greater variability, while the 3500 demonstrated more stable signal performance across days and samples. Mixture detection was effective on both platforms up to 1:10 ratios. Dropout of minor alleles began to appear at 1:20 ratios, especially in green and yellow dye channels, on both instruments. Sensitivity studies confirmed full profile recovery down to 62.5 pg, with increasing allelic and locus dropout at lower inputs. Enhanced injection voltage (1.5 kV) did not improve low-template performance. In overload testing (1–5 ng input), the 3500 maintained a consistent signal output, while the SeqStudio exhibited signal suppression at 5 ng, likely due to internal normalization. The SeqStudio exhibited better spectral overlap compensation, with fewer occurrences of spectral bleed-through artifacts. These findings support the use of both platforms in forensic casework, while emphasizing the importance of platform-specific calibration and analytical threshold settings for optimal performance.

Complete Genome Sequence Of Vaginal Swab Isolate Enterococcus Faecalis Umb6935b, Including Two Complete Plasmids, Olive Kolar, Helen Appleberry, Alan J. Wolfe, Alex Kula, Catherine Putonti

Biology: Faculty Publications and Other Works

Enterococcus faecalis has been identified as a member of the vaginal community of healthy females, in addition to its association with vaginitis and urinary tract infections. Here we present the hybrid assembly of an E. faecalis strain, UMB6935B, isolated from a vaginal swab from a female with overactive bladder symptoms.

Emergent Collective Reproduction Via Evolving Neuronal Flocks, Nam H. Le, Michael Levin, Richard A. Watson, Josh Bongard, Christopher L. Buckley

Northeast Journal of Complex Systems (NEJCS)

This study advances the understanding of evolutionary transitions in individuality (ETIs) through a novel artificial life framework, VitaNova, which integrates self-organization and natural selection to simulate the emergence of complex, reproductive groups. By dynamically modeling individual agents within an environment shaped by predators and spatial constraints, VitaNova reveals mechanisms by which simple agents evolve into cohesive units exhibiting collective reproduction. The findings highlight the synergy between self-organized behaviors and adaptive evolutionary strategies as fundamental drivers of ETIs. This approach deepens our understanding of higher-order biological individuality and offers a new empirical pathway for investigating ETIs, extending current theoretical frameworks.

Positive And Negative Parity States Of 226-236th Isotopes, Ali A. Mezban, Falih H. Al-Khudair

Karbala International Journal of Modern Science

The level scheme of the ^226-236Th nuclei is analyzed using the Interacting Boson Model (IBM-1). The ground state band (g. s.-band), beta band (β-band), gamma band (γ-band) have been described in the sd model space. To calculate the negative parity energy levels, the model space is extended to sdf by adding the f-boson (L=3). A sequence of states in energy bands up to 3.5 MeV has been obtained. The decay of negative states below 1 MeV built on an octupole vibration modes is investigated. The transition probabilities in-band and inter-band are calculated using the wave function of the …

Cortical Functional Organization In Early Childhood, Jiaxin Tu

Arts & Sciences Graduate Student Theses and Dissertations

The advent of connectivity-based methods, particularly those utilizing spontaneous BOLD signals, has significantly advanced brain mapping and deepened our understanding of the human brain's functional architecture. While prior research has explored functional organization in early childhood, most studies have focused on coarse, group-level distinctions aligned with adult literature, often within narrow age ranges. This dissertation extends these investigations by examining cortical functional organization in greater detail among healthy infants and toddlers aged 1 to 5 years. Chapter 1 employs spontaneous BOLD signals in sleeping infants and toddlers to derive a group-level functional organization at the resolution of areas and networks. …

Chaperone-Usher Pathway Pili Adhesin Conformations And Inhibitors In Urinary Tract Infections, Edward Lopatto

Arts & Sciences Graduate Student Theses and Dissertations

Antibiotic resistant bacteria are becoming increasingly difficult-to-treat resulting in increased morbidity and mortality, especially for common infections such as urinary tract infections (UTIs). Globally, UTIs afflict over 400 million people a year. Numerous different gram-negative and gram-positive bacterial species cause UTIs, including uropathogenic Escherichia coli (UPEC), Klebsiella pneumoniae, and Acinetobacter baumannii. Many of these bacterial species are listed as pathogens of urgent concern by the Center for Disease Control due to the dangerous rise and prevalence of antibiotic resistance necessitating development of new therapeutic measures. Bacteria utilize adhesin factors, such as chaperone-usher pathway (CUP) pili to gain a foothold in …

Implementing A Sustainability Approach By Converting Plastic Bottle Waste From A Mischievous Substance To A Beneficial Material By Means Of Zero Residue Level Concept, Younus Mohammed Abed, Fatima Allawi, Shahad Mudhafar Ali, Salem Jawad Alhamd, Thekra Atta Ibrahim, Mohammed Nsaif Abbas

Karbala International Journal of Modern Science

Plastic waste represents a serious environmental and health hazard due to its non-biodegradability and toxic leachates. This study investigates the potential conversion of plastic waste into a sustainable raw material for producing a useful substance. This investigation focuses on repurposing PET beverage bottles—a major contributor to microplastic pollution—into high-value activated carbon (AC) for water treatment, aligning with circular economy principles. The chemical preparation method for AC using phosphoric acid as an activating agent was evaluated. Results demonstrated the successful conversion of 68% of plastic waste into AC under the following conditions: pyrolysis temperature of 700°C, pyrolysis time of 7 hours, …

Correction: Turn-On Fluorescent Glucose Transport Bioprobe Enables Wash-Free Real-Time Monitoring Of Glucose Uptake Activity In Live Cells And Small Organisms, Monica S. Hensley, David Hutchings, Abdelrahman Ismail, Micaela Rayne Geborkoff, Thomas Werner, Marina Tanasova

Michigan Tech Publications

Correction for “Turn-on fluorescent glucose transport bioprobe enables wash-free real-time monitoring of glucose uptake activity in live cells and small organisms” by Monica S. Hensley et al., RSC Chem. Biol., 2025, 6, 987–995, https://doi.org/10.1039/D4CB00239C.

The authors regret that two contributors, Micaela Rayne Geborkoff and Professor Dr Thomas Werner, were inadvertently omitted from the original author list of this article. Both individuals made significant contributions to the research reported.

Micaela Rayne Geborkoff was involved in the design, planning, and execution of the Drosophila experiments, specifically in the growth and treatment of fruit fly larvae. Professor Dr Thomas Werner provided …

Robust Embeddings Of Genetics, Anatomy, And State Decoded From A Neuron’S Activity, Aidan Schneider

Arts & Sciences Graduate Student Theses and Dissertations

Neural spike trains are shaped by both extrinsic inputs and intrinsic structural constraints. While prior work has focused on how spike timing encodes externally driven variables, such as stimuli or behavior, this dissertation explores whether principles that organize neural activity in space and time—such as genetic cell type, anatomical location, and arousal state—are also embedded in the spiking output of individual neurons. I hypothesize that these organizing principles are not quenched as irrelevant variability, but rather multiplexed within the neural code itself. To test this, I attempt to decode these principles from the spike trains of neurons recorded in behaving …

Response Of Various Body Parts Of House Flies, Musca Domestica, To Sucrose, Panchalie B. Gunathunga, Merveille Muyizere, Bethia H. King

Faculty Articles, Papers, and Other Scholarship

Insects use multiple body parts, not just their mouth, to taste. Whether a particular body part has a taste function can be determined by examining the morphology or electrophysiological response of its sensilla (sense organs) or by its behavioral response. The present study investigated taste response of each of the three pairs of tarsi, tibiae, femurs, as well as the antennae and wings, in house flies, Musca domestica L. (Diptera: Muscidae). This was done by measuring the proboscis extension response (PER), and in the case of the wings, also the grooming behavior. PER is a visible precursor to consumption. The …

Genetic Gain And Loss In The Evolution Of Amniote T Cell Receptor And Immunoglobulin Genes, Jordan M. Sampson

Biology ETDs

The immune system of most jawed vertebrates consists of three major cell types: αβ T cells, γδ T cells, and B cells. Every species evaluated contains the loci that encode the highly conserved αβ T cells, however, γδ T cells are less conserved and have been lost in squamate reptiles. The loci that encode the B cell receptor have also varied across evolution. Seven immunoglobulin (Ig) heavy chain isotypes have been identified in amniotes: IgM, IgD, IgY, IgG, IgE, IgO, and IgA. Some are found in most species (IgM and IgD) and others only in specific lineages (IgY or IgG). …

Vibrio Cholerae Endemic To The Lower Rio Grande Delta Segregate Into Urban And Rural Phylotypes, Daniele Provenzano, Jeffrey W. Turner, Jorge Duran-Gonzalez, David A. Laughlin, David Silva, Viviana Trevino, Miguel F. Gonzales, Boris Ermolinsky, Stefan Pukatzki

School of Integrative Biological & Chemical Sciences Faculty Publications

The lifestyle of Vibrio cholerae is primarily environmental, yet a chance encounter with a human host can lead to cholera, a potentially lethal form of diarrhea. Strains belonging to O1 and O139 serogroups have pandemic potential, but the contribution of non-O1/non-O139 serovars towards the genesis of cholera remains unclear. Endemic V. cholerae lineages were investigated given several historical accounts describing cholera epidemics and sporadic, contemporary cholera-like outbreaks along the lower Rio Grande Delta (LRGD). Seven isolates were recovered from an urban segment of the Rio Grande and six from a rural segment where the river empties into the Gulf of …

​​Site Fidelity Is Associated With The Social Experience Of Forked Fungus Beetles (Bolitotherus Cornutus), Joo Yeon Kim , '22, C. W. Wood, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Consistently returning to or remaining within a specific location, a behavior known as site fidelity, is a useful metric for quantifying animal space use. When multiple individuals display similar site fidelity patterns, they are likely to interact, shaping the degree and quality of their social interactions. However, the link between the expression of site fidelity behavior and an individual’s social experience has not been thoroughly investigated. In this study we examined (1) how intrinsic individual properties (body size and sex) predicted variation in site fidelity and (2) whether site fidelity was linked to the social experience of individuals in wild …

Activation Of Toll-Like Receptor 2 Promotes The Expression Of Inflammatory Mediators And Cell Proliferation Of Human Polycystic Kidney Disease Cells, Yang Zhang, Matthew Plansinis, Sophia Peak, Elisabeth Weber, Aiping Wei, Yu Xu, Madelyn Ross, Abigail Leagjeld, Darren P. Wallace, Yan Zhang

Michigan Tech Publications

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the progressive enlargement of fluid-filled cysts, leading to a decline in renal function. Toll-like receptors (TLR)-2 and TLR4 are pattern recognition receptors and components of the innate immune response. We found that mRNA levels for TLR2 and TLR4, an adaptor protein MyD88, and the transcription factor NF-κB were elevated in the kidneys of ADPKD patients and PKD mice. There was decreased expression of IκBα, an inhibitory protein sequestering NF-κB in the cytosol, and increased NF-κB nuclear translocation in human ADPKD kidneys compared with normal human kidneys (NHK). Pam3CSK4, a synthetic TLR2 …

Un(Der)Explored Links Between Plant Diversity And Particulate And Mineral-Associated Organic Matter In Soil, Šárka Angst, Gerrit Angst, Kevin E. Mueller, Markus Lange, Nico Eisenhauer

Biological, Geological, and Environmental Faculty Publications

Plant diversity can alter soil carbon stocks, but the effects are difficult to predict due to the multitude of mechanisms involved. We propose that these mechanisms and their outcomes can be better understood by testing how plant diversity affects particulate organic matter (POM) and mineral-associated organic matter (MAOM) depending on whether MAOM storage is "saturated" and the total soil organic matter pool is limited by plant inputs. Such context-dependency of plant-diversity effects on POM, MAOM, and total soil organic matter helps explain inconsistencies in plant-diversity-soil-carbon relationships across studies. Further illumination of this context-dependency is required to better predict consequences of …

Redundant Functions Of Mir156-Targeted Squamosa Promoter Binding Protein-Like Transcription Factors In Promoting Cauline Leaf Identity, Darren Manuela, Liren Du, Qi Zhang, Yifei Liao, Tieqiang Hu, Jim P. Fouracre, Mingli Xu

Faculty Publications

No abstract provided.

Circannual And Kinship Cues Shape Reproduction And Epigenetic Aging In Peromyscus, Kim Tuyen Huynh Dam

Theses and Dissertations

Evolutionary success is defined by the ability of a species to adapt and survive across many generations. This success is not determined by any single attribute but rather includes the entrenched, complex system that could be associated with biological rhythms, reproductive strategies, and regulations of epigenetic and genetic components. By using closed Peromyscus colonies as a model and by coupling mathematical modeling, analyses of breeding records, epigenetic studies, and in vitro and in vivo experiments, this dissertation aims to discover how Peromyscus adjusts to the internal and external pressures to ensure their survival and preserve evolutionary fitness in controlled environments. …

Exploring The Ancestry And Mutational Signatures Of Free-Breeding Dogs From Chernobyl And The Galápagos Islands, Gabriella Jean Spatola

Theses and Dissertations

Two free-breeding dog populations, one in Chernobyl, Ukraine, and the other on the Galápagos Islands, Ecuador, exist on opposite sides of the globe, yet both hold unique scientific potential to further our understanding of free-breeding dog population dynamics and evolutionary processes related to their environments. In the following studies, blood samples from more than 400 individual Chernobyl dogs were collected and their genomes were analyzed alongside over 1500 purebred and 200 global free-breeding dogs, describing genetic relationships and the extent of admixture with purebred migrants. Importantly, the sampled Chernobyl dogs had long-term exposures to ionizing radiation because of the 1986 …

Hybrid Penstemon Flowers: Colors, Pigments, And Detectability & Experimental Teaching: Evaluating The Impact Of Active Learning, Josh Thomas Edward Stevens

Theses and Dissertations

Shifts to different primary pollinators are often accompanied by changes in suites of floral traits. Understanding how and why these floral adaptations evolve is a central goal in evolutionary biology. Within the genus Penstemon, the transition from bee-pollinated to hummingbird-pollinated flowers is a common evolutionary pattern. These pollinator shifts have caused several closely related species to exhibit distinct pollination syndromes. One example of this evolutionary phenomenon can be seen within the sister species P. eatonii (hummingbird-pollinated) and P. laevis (bee-pollinated). These two species form several hybrid zones, in which hybrid individuals exhibit colors resembling both parental species, along with a …

Scientific Note: Garden Loosestrife (Lysimachia Vulgaris, Primulaceae), An Emerging Invasive Plant Species Of Riparian Corridors In The Mid-Atlantic Region, Christopher T. Martine, Amy L. Jewitt, Claire M. Ciafre, Kaitlin G. Henry, Elizabeth H. Williams, Pj Newhart, Melody P. Sain

Faculty Journal Articles

Lysimachia vulgaris (garden loosestrife, Primulaceae) is an herbaceous perennial native to Europe that has been identified as an aggressive invasive species in parts of North America. The status of the species in the Mid-Atlantic region of the US, however, is poorly determined. Using recent field observations (from iNaturalist, iMapInvasives, and EDDMapS records) we here report localized incursions of L. vulgaris in the Susquehanna River Valley of central Pennsylvania, along with notes on its ecology, threats to native plant communities, and broader distribution in the state.