Life Sciences Commons^™

Indoor Airborne Microbiome And Endotoxin: Meteorological Events And Occupant Characteristics Are Important Determinants, Hesham Amin, Tina Šantl-Temkiv, Christine Cramer, Kai Finster, Francisco Gomez Real, Thorarinn Gislason, Mathias Holm, Christer Janson, Nils Oskar Jögi, Rain Jogi, Andrei Malinovschi, Ian P G Marshall, Lars Modig, Dan Norbäck, Rajesh Shigdel, Torben Sigsgaard, Cecilie Svanes, Hulda Thorarinsdottir, Inge M Wouters, Vivi Schlünssen, Randi J Bertelsen

Faculty, Staff and Student Publications

Airborne bacteria and endotoxin may affect asthma and allergies. However, there is limited understanding of the environmental determinants that influence them. This study investigated the airborne microbiomes in the homes of 1038 participants from five cities in Northern Europe: Aarhus, Bergen, Reykjavik, Tartu, and Uppsala. Airborne dust particles were sampled with electrostatic dust fall collectors (EDCs) from the participants’ bedrooms. The dust washed from the EDCs’ clothes was used to extract DNA and endotoxin. The DNA extracts were used for quantitative polymerase chain (qPCR) measurement and 16S rRNA gene sequencing, while endotoxin was measured using the kinetic chromogenic limulus amoebocyte …

Enigma Chek2gether Project: A Comprehensive Study Identifies Functionally Impaired Chek2 Germline Missense Variants Associated With Increased Breast Cancer Risk, Lenka Stolarova, Petra Kleiblova, Petra Zemankova, Barbora Stastna, Marketa Janatova, Jana Soukupova, Maria Isabel Achatz, Christine Ambrosone, Paraskevi Apostolou, Banu K Arun, Paul Auer, Mollie Barnard, Birgitte Bertelsen, Biobank Japan, Marinus J Blok, Nicholas Boddicker, Joan Brunet, Elizabeth S Burnside, Mariarosaria Calvello, Ian Campbell, Sock Hoai Chan, Fei Chen, Jian Bang Chiang, Anna Coppa, Laura Cortesi, Ana Crujeiras-González, Consortium Czecanca, Kim De Leeneer, Robin De Putter, Allison Depersia, Lisa Devereux, Susan Domchek, Anna Efremidis, Christoph Engel, Corinna Ernst, D Gareth R Evans, Lidia Feliubadaló, Florentia Fostira, Olivia Fuentes-Ríos, Encarna B Gómez-García, Sara González, Christopher Haiman, Thomas Van Overeem Hansen, Jan Hauke, James Hodge, Chunling Hu, Hongyan Huang, Nur Diana Binte Ishak, Yusuke Iwasaki, Irene Konstantopoulou, Peter Kraft, James Lacey, Conxi Lázaro, Na Li, Weng Khong Lim, Sara Lindstrom, Adriana Lori, Elana Martinez, Alexandra Martins, Koichi Matsuda, Giuseppe Matullo, Simone Mcinerny, Kyriaki Michailidou, Marco Montagna, Alvaro N A Monteiro, Luigi Mori, Katherine Nathanson, Susan L Neuhausen, Heli Nevanlinna, Janet E Olson, Julie Palmer, Barbara Pasini, Alpa Patel, Maria Piane, Bruce Poppe, Paolo Radice, Alessandra Renieri, Nicoletta Resta, Marcy E Richardson, Toon Rosseel, Kathryn J Ruddy, Marta Santamariña, Elizabeth Santana Dos Santos, Lauren Teras, Amanda E Toland, Amy Trentham-Dietz, Celine M Vachon, Alexander E Volk, Nana Weber-Lassalle, Jeffrey N Weitzel, Lisa Wiesmuller, Stacey Winham, Siddhartha Yadav, Drakoulis Yannoukakos, Song Yao, Valentina Zampiga, Magnus Zethoven, Ze Wen Zhang, Tomas Zima, Amanda B Spurdle, Ana Vega, Maria Rossing, Jesús Del Valle, Arcangela De Nicolo, Eric Hahnen, Kathleen B M Claes, Joanne Ngeow, Yukihide Momozawa, Paul A James, Fergus J Couch, Libor Macurek, Zdenek Kleibl

Faculty, Staff and Student Publications

PURPOSE: Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT).

EXPERIMENTAL DESIGN: We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case-control datasets, including …

Targeting Bcl2 Overcomes Resistance And Augments Response To Aurora Kinase B Inhibition By Azd2811 In Small Cell Lung Cancer, Kavya Ramkumar, Azusa Tanimoto, Carminia M Della Corte, C Allison Stewart, Qi Wang, Li Shen, Robert J Cardnell, Jing Wang, Urszula M Polanska, Courtney Andersen, Jamal Saeh, J Elizabeth Pease, Jon Travers, Giulia Fabbri, Carl M Gay, Jelena Urosevic, Lauren A Byers

Faculty, Staff and Student Publications

PURPOSE: Therapeutic resistance to frontline therapy develops rapidly in small cell lung cancer (SCLC). Treatment options are also limited by the lack of targetable driver mutations. Therefore, there is an unmet need for developing better therapeutic strategies and biomarkers of response. Aurora kinase B (AURKB) inhibition exploits an inherent genomic vulnerability in SCLC and is a promising therapeutic approach. Here, we identify biomarkers of response and develop rational combinations with AURKB inhibition to improve treatment efficacy.

EXPERIMENTAL DESIGN: Selective AURKB inhibitor AZD2811 was profiled in a large panel of SCLC cell lines (n = 57) and patient-derived xenograft (PDX) models. …

Safe Food Through Better Labelling: A Robust Method For The Rapid Determination Of Caprine And Bovine Milk Allergens, Joost L. D. Nelis, Amanda L. Dawson, Utpal Bose, Alisha Anderson, Michelle L. Colgrave, James A. Broadbent

Research outputs 2022 to 2026

Accidental milk cross-contamination is one of the most common causes for costly food recalls. Yet, quantifying trace-levels of allergen is time-consuming and current methods are not adapted for routine analyses making quality control for trace-level allergen content impractical. This perpetuates voluntary “may-contain” statements that are unhelpful for people suffering from food allergies. Here, we developed a rapid LC-MS method enabling milk allergen quantification by comparing all tryptic-peptides of major milk allergens. The bovine-specific αS-2 casein peptide and allergen-epitope NAVPITPTLNR provided excellent performance in sensitivity (LOD 1 mg.kg ^{− 1}; LOQ 2 mg.kg ^{− 1}) across various dairy products, …

Euscorpius Sulfur Sp. N. (Scorpiones: Euscorpiidae), A New Cave Scorpion From Albania And Northwestern Greece, František Kovařík, Marek Audy, Serban M. Sarbu, Victor Fet

Euscorpius

A new species of cave scorpion, Euscorpius sulfur sp. n. (Scorpiones: Euscorpiidae) from Albania and northwestern Greece is described, fully complemented with color photographs of both live and preserved specimens, as well as their habitats.

Potential Clean-Label Astringency Maskers For Acidic Whey Protein Beverages, Jozxelle Tongson Gao

Theses and Dissertations

Whey Protein Ready-to-Drink (RTD) beverages are popular nutritional products due to their high protein content, complete amino acid profile, convenience, and flavor. However, astringency imparted by whey protein at low pH (pH <4.5) can significantly reduce consumer liking. Astringency is a complex problem, so it may require a multi-faceted solution. Samples were created through Response Surface Methodology (RSM), utilizing parameters determined through literature review and preliminary testing. There is evidence that sucrose may help to reduce astringency in wine. Various natural sweeteners like stevia, monk fruit extract, and sweet proteins: thaumatin and brazzein were evaluated to observe if they may reduce the astringency in acidic whey protein RTD beverages. Samples were assessed by trained quantitative descriptive analysis (QDA), consumer acceptance, and focus group panels. Formulas were instrumentally measured for pH, brix, zeta potential, and particle size. pH and brix were useful measures for monitoring processing consistency, but neither related to level of astringency of samples. Zeta potential instrumental data coincided with results of previous studies finding that a decrease in zeta potential within the range of pH 3-5 correlated with less astringency with whey protein isolates. Particle size relation to astringency is dependent on the zeta potential. A large particle size measurement does not lead to higher astringency if the molecules do not interact due to electrostatic repulsion. Analytical measurements of the samples were statistically compared for differences that may relate to less astringent beverages. The QDA panel determined the combination of 0.20% thaumatin and 0.22% stevia rebaudioside M to most reduce astringency, however this did not correlate with higher acceptability as its acceptability remained as a neither like nor dislike rating. Consumers evaluated thaumatin, brazzein, and monk fruit to be clean-label ingredients after learning about their natural sources and flavor functionalities. More research about thaumatin, monk fruit, and especially brazzein is needed to find the ideal usage levels in AWB formulation. Brazzein was least preferred according to the focus group panel, who felt it did not reduce astringency. Future research could evaluate whether a higher concentration would be more effective. These findings aim to help sensorially improve acidic whey protein beverage formulations and provide the dairy beverage industry insight on creating and marketing more clean-label products.

Self-Supervised Pretraining And Transfer Learning On Fmri Data With Transformers, Sean Paulsen

Dartmouth College Ph.D Dissertations

Transfer learning is a machine learning technique founded on the idea that knowledge acquired by a model during “pretraining” on a source task can be transferred to the learning of a target task. Successful transfer learning can result in improved performance, faster convergence, and reduced demand for data. This technique is particularly desirable for the task of brain decoding in the domain of functional magnetic resonance imaging (fMRI), wherein even the most modern machine learning methods can struggle to decode labelled features of brain images. This challenge is due to the highly complex underlying signal, physical and neurological differences between …

Exploring The Role Of Salt-Tolerant Halomonas Inoculant In Altering Plant Gene Expression To Improve Salt Tolerance In Alfalfa., Ashley Kay Miller

Theses and Dissertations

Soil salinity is an increasing problem facing agriculture in many parts of the world. Climate change and irrigation practices have led to decreased yields of large areas of farmland due to increased salt levels in the soil. Irrigation introduces salts to the soil that with time accumulate and threaten crop yield. In arid climates like Utah, the practice of irrigation is especially threatening to salt-sensitive crops including alfalfa (Medicago sativa). Plants that have tolerance to salt are needed to feed livestock and the world's population. One approach to address this problem is to introduce genes encoding salt tolerance into the …

Black Experiences With Community Gardening In Southeast Louisiana, Kiarah Craft

LSU Master's Theses

Community gardens have been rising in popularity over the past few years (Mayers, 2023). In response to the COVID-19 pandemic, many people across the United States have decided that it is crucial to grow their own food and develop sustainability within their community. Historically, Black communities have been underserved and ignored, especially in relation to food security and community safety (White, 2019, Penniman, 2018). The purpose of this study was to collect information about the effects of community-based gardening programs on Black people in Southeast Louisiana. Additionally, the researcher would like to gain knowledge regarding the reasons that Black people …

Function Of Deubiquitinase Mysm1 In Attenuation Of Dna Damage Responses, Brendan Mathias

Arts & Sciences Graduate Student Theses and Dissertations

MYSM1 deficiency has been identified in patients with B cell lymphopenia, hypogammaglobulinemia, primary immune deficiency and bone marrow failure. MYSM1 is a known deubiquitinase that acts on histone H2A to promote gene expression. MYSM1 also functions in cellular responses to DNA injury and patients with loss of MYSM1 have increased sensitivity to DNA damaging agents. The specific role and function of MYSM1 in DNA damage responses has yet to be determined. Here, I have shown that MYSM1 does not mediate generation or repair of DSBs, but rather acts to attenuate and terminate DNA damage signaling after repair. Loss of MYSM1 …

An Assessment Of Cattle Traffic On, And Seed Dispersion Patterns Of, Sclerocactus Wrightiae, David D. Lariviere

Theses and Dissertations

Cattle grazing has been a historic use of rangelands in Utah since Pioneer settlement in the mid 1800's. Wright fishhook cactus is a small globose cactus endemic to an area of 280,000 ha in south-central Utah and was listed as endangered in October of 1979, by the U.S. Fish and Wildlife Service (USFWS). By 2010, concerns were expressed that soil compaction in proximity to the cactus posed a threat to this species, though there was no empirical data to support such concern. In order to assess the impact of cattle traffic on Wright fishhook cactus, we used an imprint device …

Using De Novo Transcriptomes To Decipher The Relationships In Cutthroat Trout Subspecies (Oncorhynchus Clarkii), Andrea Leena Kokkonen

Theses and Dissertations

Cutthroat trout (Oncorhynchus clarkii) is a salmonid native to Western North America. For almost 200 years, the taxonomy of these species has fluctuated as ichthyologists and fisheries managers alike have tried to understand the diversity seen within these fishes. In the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological observations, Pleistocene events, and modern geographic ranges. These designations were instrumental in preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, and mtDNA) have largely replicated Behnke's phylogenies. However, these studies have revealed that some of these relationships are consistently …

Evapotranspiration In Urban And Agricultural Systems With Interacting Irrigation And Nitrogen Fertilizer Treatments, Samantha R. Shumate

Theses and Dissertations

Nitrogen (N) fertilizer and irrigation are important inputs for all managed plant species, especially in arid and semi-arid climates. The interaction between N management and irrigation can lead to more sustainable practices. This is true for both agricultural and urban environments. Precision nutrient management has been widely adopted by producers in recent decades, and water conservation has become an important goal for turfgrass managers. In urban systems, our goal was to evaluate Kentucky bluegrass (Poa pratensis L.) to determine response to three N fertilizer rates and three irrigation rates in all possible combinations. The main and interacting treatment effects were …

Using Μct Scans To Create 3d Skull Puzzles As Open-Access Pedagogical Tools For Anatomy And Comparative Osteology Classes., Alexis Slack

Honors Thesis

As access to affordable 3D printing technologies increases, the use of Computed Tomography (CT) technologies is well positioned to contribute to the advancement of pedagogical experiences through the creation of physical models for teaching. Such complementary efforts may enhance broader impacts by simultaneously boosting the education system with a unique hands-on experience for students and providing an alternative to expensive osteological and other artificial models. Two 3D printed skull puzzles were created to aid in teaching human and vertebrate anatomy, and comparative osteology courses. After segmenting all the bones from each respective skull, the individual skeletal elements were 3D printed, …

Loss Of Syncrip Unleashes Apobec-Driven Mutagenesis, Tumor Heterogeneity, And Ar-Targeted Therapy Resistance In Prostate Cancer, Xiaoling Li, Yunguan Wang, Su Deng, Guanghui Zhu, Choushi Wang, Nickolas A Johnson, Zeda Zhang, Carla Rodriguez Tirado, Yaru Xu, Lauren A Metang, Julisa Gonzalez, Atreyi Mukherji, Jianfeng Ye, Yuqiu Yang, Wei Peng, Yitao Tang, Mia Hofstad, Zhiqun Xie, Heewon Yoon, Liping Chen, Xihui Liu, Sujun Chen, Hong Zhu, Douglas Strand, Han Liang, Ganesh Raj, Housheng Hansen He, Joshua T Mendell, Bo Li, Tao Wang, Ping Mu

Faculty, Staff and Student Publications

Tumor mutational burden and heterogeneity has been suggested to fuel resistance to many targeted therapies. The cytosine deaminase APOBEC proteins have been implicated in the mutational signatures of more than 70% of human cancers. However, the mechanism underlying how cancer cells hijack the APOBEC mediated mutagenesis machinery to promote tumor heterogeneity, and thereby foster therapy resistance remains unclear. We identify SYNCRIP as an endogenous molecular brake which suppresses APOBEC-driven mutagenesis in prostate cancer (PCa). Overactivated APOBEC3B, in SYNCRIP-deficient PCa cells, is a key mutator, representing the molecular source of driver mutations in some frequently mutated genes in PCa, including FOXA1, …

Bacteroides Uniformis-Induced Perturbations In Colonic Microbiota And Bile Acid Levels Inhibit Th17 Differentiation And Ameliorate Colitis Developments, Yiting Yan, Yu Lei, Ying Qu, Zhen Fan, Ting Zhang, Yangbin Xu, Qian Du, Daniel Brugger, Yulin Chen, Ke Zhang, Enping Zhang

Faculty, Staff and Student Publications

Inflammatory bowel disease (IBD) is associated with gut dysbiosis and can lead to colitis-associated malignancies. Bacteroides uniformis (Bu) regulates animal intestinal homeostasis; however, the mechanism by which it alleviates colitis in mice remains unknown. We investigated the effects of B. uniformis JCM5828 and its metabolites on female C57BL/6J mice with dextran sulfate sodium salt (DSS) induced colitis. Treatment with Bu considerably alleviated colitis progression and restored the mechanical and immune barrier protein expression. Additionally, Bu increased the abundance of the symbiotic bacteria Bifidobacterium and Lactobacillus vaginalis while decreasing that of pathogenic Escherichia-Shigella, and modulated intestinal bile acid metabolism. Bu largely …

Evolution Of Immune And Stromal Cell States And Ecotypes During Gastric Adenocarcinoma Progression, Ruiping Wang, Shumei Song, Jiangjiang Qin, Katsuhiro Yoshimura, Fuduan Peng, Yanshuo Chu, Yuan Li, Yibo Fan, Jiankang Jin, Minghao Dang, Enyu Dai, Guangsheng Pei, Guangchun Han, Dapeng Hao, Yating Li, Deyali Chatterjee, Kazuto Harada, Melissa Pool Pizzi, Ailing W Scott, Ghia Tatlonghari, Xinmiao Yan, Zhiyuan Xu, Can Hu, Shaowei Mo, Namita Shanbhag, Yang Lu, Matheus Sewastjanow-Silva, Ahmed Adel Fouad Abdelhakeem, Guang Peng, Samir M Hanash, George A Calin, Cassian Yee, Pawel Mazur, Autumn N Marsden, Andrew Futreal, Zhenning Wang, Xiangdong Cheng, Jaffer A Ajani, Linghua Wang

Faculty, Staff and Student Publications

Understanding tumor microenvironment (TME) reprogramming in gastric adenocarcinoma (GAC) progression may uncover novel therapeutic targets. Here, we performed single-cell profiling of precancerous lesions, localized and metastatic GACs, identifying alterations in TME cell states and compositions as GAC progresses. Abundant IgA+ plasma cells exist in the premalignant microenvironment, whereas immunosuppressive myeloid and stromal subsets dominate late-stage GACs. We identified six TME ecotypes (EC1–6). EC1 is exclusive to blood, while EC4, EC5, and EC2 are highly enriched in uninvolved tissues, premalignant lesions, and metastases, respectively. EC3 and EC6, two distinct ecotypes in primary GACs, associate with histopathological and genomic characteristics, and prognosis. …

Immunological Monitoring In Hepatitis C Virus Controlled Human Infection Model, Naglaa H Shoukry, Andrea L Cox, Christopher M Walker

Faculty, Staff and Student Publications

Controlled human infection model trials for hepatitis C virus represent an important opportunity to identify correlates of protective immunity against a well-characterized inoculum of hepatitis C virus and how such responses are modified by vaccination. In this article, we discuss the approach to immunological monitoring during such trials, including a set of recommendations for optimal sampling schedule and preferred immunological assays to examine the different arms of the immune response. We recommend that this approach be adapted to different trial designs. Finally, we discuss how these studies can provide surrogate predictors of the success of candidate vaccines.

Investigation Of Metabolic And Molecular Pathways That Promote Gastric Parietal Cell Regeneration, Mahliyah Lenore Adkins-Threats

Arts & Sciences Graduate Student Theses and Dissertations

The stomach contains gastric epithelial cells, including acid-pumping parietal cells (PCs), that are constantly renewed throughout life from a multipotent stem cell to maintain a balance between producing and protecting from the acid and enzymes needed to kill pathogens and initiate digestion. Despite this dynamic renewal, disorders of the gastric epithelium occur and are one of the most common etiologies of human diseases ranging from simple heartburn to reflux, peptic ulcers and gastric cancer. PCs are characterized by elaborate plasma membrane foldings and vesicles that house their proton pumps and an abundance of mitochondria needed to power secretion of that …

Investigating Novel Neoantigen Sources For Personalized Cancer Vaccines, Megan Richters

Arts & Sciences Graduate Student Theses and Dissertations

The adaptive immune system has inherent antitumor properties that are capable of inducing tumor-specific cell death. CD8+ and CD4+ T cells, two immune cell types critical to this process, recognize antigens bound by class I and II major histocompatibility complexes on the cell surface, respectively. After antigen recognition, T cells can signal growth arrest and cell death to tumor cells displaying the antigen. Neoantigens, or tumor-specific peptides, are targeted by cancer immunotherapies to induce T cell-mediated degradation. Treatments such as personalized vaccines and immune checkpoint blockade thus provide a unique avenue to selectively recognize and destroy tumor cells while keeping …

Mass Spectrometry-Based Discovery Of Tumor Antigens For Cancer Immunotherapy, Wei Meng

Arts & Sciences Graduate Student Theses and Dissertations

The immune system plays an essential role in cancer evolution and cancer treatment. One of the major mechanisms of immune-mediated tumor rejection is the recognition of tumor antigens by T cells. Upon recognition of tumor antigens, naïve T cells become activated and subsequently infiltrate inside the tumor. Since the early discovery of tumor-specific T cells, many efforts have elucidated the molecular nature of their cognate antigens. It is now established that MHC-I and MHC-II restricted peptides are critical to generate CD8+ and CD4+ antigen-specific T cells that can recognize tumor-derived antigens. Two main categories of these antigens are those originating …

Response Of Four Local Cassava Accessions To Bio-Mulch Application Time, Bayu Suwitono, Muhamad Achmad Chozin, Dwi Guntoro, Suwarto

Jurnal Kultivasi

Cassava (Manihot esculenta Crantz) is widely planted on marginal land with low soil fertility. During the initial growth phase, cassava often loses competition against weeds. Legume cover crops are widely used to increase soil fertility, prevent erosion, and suppress weeds. This study aimed to determine the effect of Arachis pintoi bio-mulch application time on the growth and yield of cassava. This study was conducted using a factorial randomized block design. The first factor was four cassava accessions: Ketan Malang, Genjah Bayam, IR Jonggol, and Mangu. The second factor was six levels of bio-mulch planting time: manual weeding (without bio-mulch applications), …

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 …

Effectiveness Of Modified Nitrogen Fertilizer On Soil Chemical Properties And Rice Plant Growth In The Textile Industrial Area, Rija Sudirja, Santi Rosniawaty, Sri Muji Rahayu, Budy Frasetya Taufik Qurrohman

Jurnal Kultivasi

The imbalance of nutrients and heavy metal contamination is a challenge in increasing plant growth surround the textile industry area. This study aimed to determine the effectiveness of the dosage of Biologically Agent N Organo Mineral Fertilizer (Biomix-N) as a fertilizer and an ameliorant in paddy soil contaminated with textile liquid waste. This study used a randomized block design of eight treatments with four replications. Parameters observed were soil chemical properties after application of Biomix-N (Na-ex, total N, EC, Cd, and pH), rice plant growth (plant height and tiller number), Cd concentration in the plant, and relative agronomic effectiveness (RAE). …

Measures And Models Of Visual Acuity In Epipelagic And Mesopelagic Teleosts And Elasmobranchs, Eleanor M. Caves, Tracey Sutton, Eric J. Warrant, Sönke Johnsen

Marine & Environmental Sciences Faculty Articles

Eyes in low-light environments typically must balance sensitivity and spatial resolution. Vertebrate eyes with large "pixels" (e.g., retinal ganglion cells with inputs from many photoreceptors) will be sensitive but provide coarse vision. Small pixels can render finer detail, but each pixel will gather less light, and thus have poor signal relative-to-noise, leading to lower contrast sensitivity. This balance is particularly critical in oceanic species at mesopelagic depths (200–1000 m) because they experience low light and live in a medium that significantly attenuates contrast. Depending on the spatial frequency and inherent contrast of a pattern being viewed, the viewer’s pupil size …

Targeted Sequencing Of The Panicum Miliaceum Gene Space And Genotyping Of Variant Sites From Population Genetics Studies, Combined In A Single Assay, As A Tool For Broomcorn Millet Assisted Breeding, Gabriele Magris, Serena Foria, Silvano Ciani, Dipak K. Santra, Ombretta Polenghi, Virna Cerne, Michele Morgante, Gabriele Di Gaspero

Department of Agronomy and Horticulture: Faculty Publications

Broomcorn millet (Panicum miliaceum L.) is a prehistorical cereal, today cultivated as a minor crop with low yields but with a renewed interest for its high water use effciency and gluten-free grains. To reverse the downward trend in broomcorn millet cultivation, the crop needs genetic improvement and creation of novel genetic variation to increase productivity. In order to facilitate genomics-assisted breeding, we designed a reduced representation genome-sequencing assay that investigates 1.8% of the nuclear DNA in a targeted and reproducible way, with an intensity of genomic sampling that is a direct function of local recombination rate. We used this …

The Directional Effect Of Target Position On Spatial Selective Auditory Attention, Heesung Park

Dissertations, 2020-current

Spatial selective auditory attention plays a crucial role in listening in a mixture of competing speech sounds. Previous neuroimaging studies have reported alpha band neural activity modulated by auditory attention, along with the alpha lateralization corresponding to attentional focus. A greater cortical representation of the attended speech envelope compared to the ignored speech envelope was also found, a phenomenon known as 'neural speech tracking’. However, little is known about the neural activities when attentional focus is directed on speech sounds from behind the listener, even though understanding speech from behind is a common and essential aspect of daily life. The …

Characterizing Cancer Metabolism From Bulk And Single-Cell Rna-Seq Data Using Metaflux, Yuefan Huang, Vakul Mohanty, Merve Dede, Kyle Tsai, May Daher, Li Li, Katayoun Rezvani, Ken Chen

Faculty, Staff and Student Publications

Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing metabolic reprogramming in the tumor microenvironment (TME) is of emerging importance in cancer research and patient care. However, recent technologies only measure a subset of metabolites and cannot provide in situ measurements. Computational methods such as flux balance analysis (FBA) have been developed to estimate metabolic flux from bulk RNA-seq data and can potentially be extended to single-cell RNA-seq (scRNA-seq) data. However, it is unclear how reliable current methods are, particularly in TME characterization. Here, we present a computational framework METAFlux (METAbolic Flux balance analysis) …

Lvpt: Lazy Velocity Pseudotime Inference Method, Shuainan Mao, Jiajia Liu, Weiling Zhao, Xiaobo Zhou

Faculty, Staff and Student Publications

The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the probability and direction of cell differentiation. LVPT shows better and comparable performance of …

Mutation-Induced Changes In The Stability, B-Cell Epitope, And Antigenicity Of The Sars-Cov-2 Variant Spike Protein: A Comparative Computational Stud, Nira Meirita Wijayanti, Muhammad Hermawan Widyananda, Lailil Muflikhah, Nashi Widodo

Karbala International Journal of Modern Science

The spike (S) protein is a major antigenicity site that targets neutralizing antibodies and drugs. The growing number of S protein mutations has become a severe problem for developing effective vaccines. Here, we investigated four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that were the most infectious and widespread during the COVID-19 pandemic to determine the trends and patterns of mutation-induced changes in the stability, B-cell epitope, and antigenicity of the SARS-CoV-2 S protein. The data showed that the Beta and Gamma variants had three mutations on the receptor-binding domain (RBD), which is the specific site on the S …