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Micronutrients Status Among Human Immunodeficiency Virus-Infected Children In Southern India, Sangeetha Sivasubramanian, Janardhan Shenoy, Sowmini P. Kamath, Vaman Kulkarni

Open Access archive

Introduction: Deficiencies of micronutrients play a role in human immunodeficiency virus (HIV) infection and its severity. Identifying the micronutrient status would guide supplementation, thus altering the disease progression and severity. Material and methods: A cross-sectional hospital-based study was conducted in Southern India on hundred HIV-infected children. Estimation of serum micronutrient levels (zinc, copper, and iron) and comparison of the deficient micronutrients with clinical stages, immunological categories, CD4 counts, and nutritional status was performed. Results: Among 100 HIV-infected children, zinc deficiency was the most common (62%), whereas copper and iron deficiency was present in 2% and 1%, respectively. Mean age of …

Atfkbp53: A Chimeric Histone Chaperone With Functional Nucleoplasmin And Ppiase Domains, Ajit Kumar Singh, Aritreyee Datta, Chacko Jobichen, Sheng Luan

Open Access archive

FKBP53 is one of the seven multi-domain FK506- binding proteins present inArabidopsis thaliana, and it is known to get targeted to the nucleus. It has a conserved PPIase domain at the C-terminus and a highly charged N-terminal stretch, which has been reported to bind to histone H3 and perform the function of a histone chaperone. To better understand the molecular details of this PPIase with histone chaperoning activity, we have solved the crystal structures of its terminal domains and functionally characterized them. The C-terminal domain showed strong PPIase activity, no role in histone chaperoning and revealed a monomeric five-beta palm-like …

Crop And Weed Discrimination Using Laws’ Texture Masks, Radhika Kamath, Mamatha Balachandra, Srikanth Prabhu

Open Access archive

Computers have become an integral part of human lives. Computers are used in almost every field even in agriculture. Technologies like computer vision-based pattern recognition are being used to detect diseases and pests like weeds affecting the crop. The Weeds are unwanted plants growing among crops competing for nutrients, water, and sunlight. It can significantly reduce the quality and yield of the crops incurring a huge loss to the farmers. This paper investigates the use of texture features extracted from Laws’ texture masks for discrimination of Carrot crops and weeds in digital images. Laws’ texture method is one of the …

Detection Of Torque Teno Virus (Ttv) And Ttvlike Minivirus In Patients With Presumed Infectious Endophthalmitis In India, Poonam Naik, Vivek Pravin Dave, Joveeta Joseph

Open Access archive

Human anelloviruses (Torque Teno Virus (TTV) and TTV Like Mini Virus (TLMV)) are now being reported at a high prevalence across the world, with a controversial disease-inducing potential. The aim of this study was to investigate the role of these anellovirus in vitreous of patients with presumed infectious endophthalmitis. After informed consent, vitreous fluid from patients with endophthalmitis (n = 103) and non-infectious pathologies (n = 102) were analyzed for the presence of TTV and TLMV DNA by qPCR with the limit of quantification defined as 100 copies per reaction. Among the patients clinically diagnosed with endophthalmitis, 29 of the …

Pattern-Corrected Mitotic Activity Index (Pmai): A Novel Prognosticator Of Oral Squamous Cell Carcinoma, Nunna Sai Chitra, Karen Boaz, N. Srikant, Amitha J. Lewis

Open Access archive

Objective: The main aim was to assess the efficiency of the Mitotic Activity Index (MAI) and a novel index devised by us, the Pattern-Corrected Mitotic Activity Index (PMAI) in prognostication of Oral Squamous Cell Carcinoma in terms of lymph node involvement, margin, recurrence and survival status. Material and Method: The study group consisted of 60 cases of histologically-proven Oral Squamous Cell Carcinoma with known status of prognostic indicators. Hematoxylin and eosin stained sections of the tumor proper were utilized for assessment of mitotic activity and pattern of invasion. The Mitotic Activity Index and Pattern-Corrected Mitotic Activity Index were then calculated …

Germline Genetic Determination Of Cancer Outcome, Benjamin N. Ostendorf

Student Theses and Dissertations

Immunotherapy has transformed the treatment of melanoma patients. However, despite the enormous promise of immunotherapy, a major fraction of patients with advanced melanoma still succumb to this deadly disease. In addition, systemic immunotherapy can lead to relevant toxicities. Therefore, it is an unmet need to identify the factors that modulate the outcome and response to therapy of melanoma patients. One major factor accounting for individual differences in the host response to cancer is the genetic makeup of the germline. A thorough assessment of the role of germline genetics in melanoma outcome is lacking, partly because of the difficulty in assessing …

Small-Molecule Activation Of Yap For Inner-Ear Regeneration – And Beyond, Nathaniel Kastan

Student Theses and Dissertations

Hippo signaling is an evolutionarily conserved pathway that restricts organ growth during development and suppresses regeneration in mature organs. Using a highthroughput phenotypic screen, we have identified a potent, non-toxic, and reversible inhibitor of Hippo signaling. An ATP-competitive inhibitor of Lats kinases, the compound causes Yap-dependent proliferation of murine supporting cells in the inner ear, murine cardiomyocytes, and human Müller glia in retinal organoids. The compound promotes the initial stages of the proliferative regeneration of hair cells, a process thought to be permanently suppressed in the adult mammalian inner ear. In conjunction with the Tri- Institutional Therapeutics Discovery Institute, we …

Cas9-Primed Adaptive Immunity During The Crispr-Cas Response, Philip M. Nussenzweig

Student Theses and Dissertations

Prokaryotes have developed numerous defense strategies to combat the constant threat of viruses (bacteriophages) that endanger them. Clustered, regularly interspaced short palindromic repeats (CRISPR) loci provide archaea and bacteria with adaptive immune systems that allow them to counteract these rapidly evolving genetic parasites. These diverse systems all generally contain two components: a set of CRISPR-associated (cas) genes and a series of repetitive DNA elements intercalated with variable sequences known as spacers. Following viral infection, these sequences are acquired from the viral genome and integrated in the CRISPR array as new spacers. Spacers are then transcribed into CRISPR RNAs (crRNAs) that …

Cell Memory And Fate In Human Development, Anna Kresovich Yoney

Student Theses and Dissertations

Development of a single cell, the fertilized egg, into an entire organism is a fascinating example of biological organization that gives rise to many forms of multicellular life. Cell-cell signaling is central to development, particularly in organisms such as vertebrates, where embryonic cells become progressively restricted in their potential through a hierarchy of decision points guided by the signals they receive. All cells contain the same genetic information in the form of DNA, and we now know that the DNA is modified epigenetically to impart distinct functions to each adult cell type. However, we are just beginning to uncover how …

Hybridization In Ants, Ian Butler

Student Theses and Dissertations

Interspecific hybridization is a relatively common occurrence within all animal groups. Two main factors make hybridization act differently in ants than in other species: eusociality and haplodiploidy. These factors serve to reduce the costs of interspecific hybridization in ants while simultaneously allowing them to take advantage of certain benefits. Eusociality may mitigate the effects of hybridization by allowing hybrids to be shunted into the worker caste, potentially reducing the effects of hybrid sterility. In haplodiploid species, males do not have a father. They instead develop from unfertilized eggs as haploid clones of their mother. This means that interspecifically mated queens …

Diverse Kappa Opioid Receptor Agonists: Relationships Between Signaling And Behavior, Amelia Dunn

Student Theses and Dissertations

The opioid system, comprised mainly of the three opioid receptors (kappa, mu and delta) and their endogenous neuropeptide ligands (dynorphin, endorphin and enkephalin, respectively), mediates mood and reward. Activation of the mu opioid receptor is associated with positive reward and euphoria, while activation of the kappa opioid receptor (KOR) has the opposite effect. Activation of the KOR causes a decrease in dopamine levels in reward-related regions of the brain, and can block the rewarding effects of various drugs of abuse, making it a potential drug target for addictive diseases. KOR agonists are of particular interest for the treatment of cocaine …

Structural And Functional Studies Of The Unconventional Proteobacterial Transcription Activator Crl In Complex With The Transcription Machinery, Alexis Jaramillo Cartagena

Student Theses and Dissertations

The σ^S subunit of RNA polymerase (RNAP) is the master regulator of stress responses in many Gram-negative bacteria. This alternative σ factor assembles with the core RNA polymerase to initiate the transcription of genes needed to survive different environmental changes. Crl is a small protein that activates the transcription of σ^S-dependent genes. In contrast to most transcription activators, Crl does not bind DNA to help recruit RNA polymerase and instead interacts directly with σ^S. At the outset of my research, little was known about how the binding of Crl to σ^S leads to transcription …

Blood-Derived Plasminogen Modulates The Neuroimmune Response In Both Alzheimer's Disease And Systemic Infection Models, Sarah K. Baker

Student Theses and Dissertations

Alzheimer's disease (AD) is a progressive neurodegenerative disease that affects 44 million people worldwide. To date, there are no effective treatments that prevent progression or death from the disease. It is clear that AD development is multifactorial and can arise from genetic or lifestyle factors and that vascular dysfunction and inflammation play a role in the progression of the disease. Many cardiovascular factors associated with an increase in systemic infection have been linked to a risk of AD development and progression. However, the link between vascular risk factors, systemic inflammation, and the neuroinflammation characteristic of AD are not fully understood. …

Time-Restricted Feeding Extends Longevity In Drosophila Melanogaster, Daniel Cabrera

Student Theses and Dissertations

Time-restricted feeding (TRF) is a dietary intervention in which daily feeding patterns align with behavioral patterns, synchronizing feeding times with periods of higher activity, e.g. humans eating only during the day or rodents (nocturnal animals) at night. TRF has been shown to improve cardiac health in Drosophila melanogaster, reduce metabolic markers in rodent models, and reduce glycemic indices in prediabetic men. However, the mechanism and long-term effects of this intervention remain elusive. To understand the effect of TRF on longevity we used the fruit fly Drosophila melanogaster, which is a useful model for longevity, sleep and circadian studies because of …

Dissection Of Neurons And Circuits Involved In Regulating Innate Behaviors, Movement And Higher Cognitive Functions In Mice, Luca Parolari

Student Theses and Dissertations

Elucidating the mechanisms through which brain circuits influence behavior is a fundamental tenet of Systems Neuroscience. Advancements in this field are critical to help us understand the inner workings of our brains, and eventually who we are as humans. Describing the physiologic functioning of neural circuits is also necessary to recognize their malfunctions, and to develop strategies to correct them. In many cases, however, alterations in the activity of brainwide circuits can be traced back to specific neuronal populations, and acting selectively upon these cells can restore the normal activity within the system, ultimately correcting the aberrant behavior. Thus, understanding …

Testing The T-Loop Model Of Telomeric End Protection, Leonid Alexeevich Timashev

Student Theses and Dissertations

Telomeres are the key structures that protect the ends of linear chromosomes. Although they are often thought about in the context of cellular aging, their most important role is actually to protect the end of the DNA from being mis-interpreted as a site of DNA damage. Telomeres are thought to accomplish this through the action of shelterin. Shelterin is a multi-protein complex where each subunit is dedicated to a specific role in repressing a form of DNA damage signaling, repair, or recruiting telomerase to extend the telomere end. One of the critical anchor points of shelterin is a protein known …

Chemical Biology Of Dynein, Cristina C. Santarossa

Student Theses and Dissertations

Cytoplasmic dynein is a AAA (ATPase Associated with various Activities) motor protein that transports cellular cargoes towards the microtubule minus-end. Despite its essential role in intracellular transport, dynein remains the least understood cytoskeletal motor. With speeds >25 μm/min in cells, dynein's cellular functions are challenging to study using genetic approaches, such as CRISPR and RNA interference, as the perturbation timescales far exceed those of dynein action. Fast-acting small molecule probes can be powerful tools to study dynein's many cellular mechanisms, but the design of potent and selective inhibitors of dynein remains challenging. Inhibitors of dynein's motor domain have been reported, …

Ddi1/2 And Rtf2-Dependent Regulation Of Rnase H2 At The Replisome Ensures Genome Stability, Brooke A. Conti

Student Theses and Dissertations

Proteasome shuttle proteins, DNA Damage Inducible 1 (DDI1) and DNA Damage Inducible 2 (DDI2), are active in the replication stress response (Kottemann et al., 2018). Under conditions of replication stress, DDI1/2 function to remove Replication Termination Factor 2 (RTF2) from the replisome. Persistence of RTF2 at the replisome compromises the replication stress response, resulting in accumulation of single-stranded DNA, inefficient replication fork restart, genome instability, and cell death. During unperturbed replication, RTF2 travels with the replication fork (Kottemann et al., 2018). Here we examine the function of RTF2 and address why RTF2's removal from the replisome is necessary for recovery …

Cryo-Em Studies Of Bacterial Rna Polymerase, James Chen

Student Theses and Dissertations

In bacteria, a single RNA polymerase (RNAP) performs all transcription. The overall structure of bacterial RNAP resembles a crab claw with pincers comprising the β' and β subunits and a large cleft where the active site sits. Structural information about this essential enzyme has mainly been provided by X-ray crystal structures of stable transcription complexes. RNAP crystal structures are difficult to obtain and the captured states may not always represent physiological states of the enzyme due to crystal packing artifacts. Recent advances in electron detectors and software enable near-atomic resolution structures of large biological complexes to be determined by single …

Mechanisms Of Evasion: Anti-Tumor Immune Suppression & Trna-Dependent Growth In Cancer Metastasis, Lisa Brooke Noble

Student Theses and Dissertations

Metastatic disease presents diverse therapeutic challenges for cancer patients, clinicians, and scientists. Cancer cells have developed sophisticated mechanisms of evasion to survive the selective pressures provided by the metastatic cascade. Two themes of success encompass modulating their surrounding microenvironment, or manipulating cell autonomous regulatory programs not intended for differentiated somatic cells. Both challenges are addressed in this body of work which focus on gastrointestinal and breast cancer metastasis. During cancer progression, tumour cells employ mechanisms that suppress both adaptive and innate immune responses. While our understanding of the molecular basis of adaptive immune suppression by cancer cells has led to …

A Role For Mindbomb 1 In Adenovirus Genome Delivery, Stephanie Sarbanes

Student Theses and Dissertations

The journey from plasma membrane to nuclear pore is a critical step in the lifecycle of DNA viruses, many of which must successfully deposit their genomes into the nucleus for replication. Viral capsids strategically navigate this vast distance (and all subsequent lifecycle steps) through the coordinated hijacking of a number of cellular proteins subsequently termed host factors. Given the virus' dependence on these proteins, host factors therefore represent valuable targets for therapeutic interventions. Still, the identity and function of many of these factors remains unknown. In this body of work, I will detail our own journey from initial identification to …

Crispr/Caste: Functional Genomic Studies Of The Major Evolutionary Innovations Of Ants, Waring Trible

Student Theses and Dissertations

Ants are social organisms that live in groups and depend intimately on their nestmates for growth and survival. Ants have evolved a number of highly sophisticated, social phenotypes that allow them to form coherent colonies. This thesis explores two particularly derived features of ant biology: complex chemical communication and caste plasticity. To study these features, I had a particular focus on generating and characterizing germ-line mutants. I believe that the study of mutants, and applying molecular biology methods more generally, can lead to insights in ant biology that would not be possible with more traditional methods. I first describe my …

Representations Of Reward And Movement In Drosophila Dopaminergic Neurons, Aryeh Zolin

Student Theses and Dissertations

The neuromodulator dopamine is known to influence both immediate and future behavior, motivating and invigorating an animal's ongoing movement but also serving as a reinforcement signal to instruct learning. Yet it remains unclear whether this dual role of dopamine involves the same dopaminergic pathways. Although reward-responsive dopaminergic neurons display movement-related activity, debate continues as to what features of an individual's experience these motor-correlates correspond and how they influence concurrent behavior. The mushroom body, a prominent neuropil in the brain of the fruit fly Drosophila melanogaster, is richly innervated by dopaminergic neurons that play an essential role in the formation of …

Identification Of Gene Expression Changes In Sleep Mutants Associated With Reduced Longevity In Drosophila, Zikun Wang

Student Theses and Dissertations

Sleep deprivation has become a common problem in modern society, yet the physiological consequences of sleep deprivation remain poorly understood. Sleep disruption has been shown to shorten lifespan in multiple animal species. In my thesis study, I investigated the relationship between sleep and longevity using Drosophila melanogaster. By analyzing the sleep and longevity profiles from a panel of sleep mutants, I discovered a robust positive correlation between daily sleep time and median longevity. This discovery led to my hypothesis that sleep disruption as a result of genetic mutation would elicit certain gene expression changes that ultimately would lead to shortened …

Monogenic Defects Of The Type I Interferons Signaling Pathway In Humans: Molecular And Clinical Implications, Nicholas Hernandez

Student Theses and Dissertations

The germ theory of disease, which dictates that microorganisms colloquially referred to as "germs" can invade humans or other hosts and cause disease, has remained the dominant conceptualization of infectious disease since the late nineteenth century. Since that time, growing appreciation for the extent of subclinical infections, that is, infections where the germ is detectable in its host without causing overt disease, and the Mendelian inheritance patterns of some infectious diseases have reinvigorated the study of the human genetic basis of infectious disease. This theory, so far demonstrated for a number of bacterial, fungal, and viral infections, holds that germs …

A Network Approach To Understanding Mirna Regulation In Adipose Tissue, Sean O'Connor

Student Theses and Dissertations

Adipose tissue is a complex organ that is essential for lipid storage and energy homeostasis in mammals. While transcription factors that govern adipogenesis, inflammation, non-shivering thermogenesis, and endocrine function in fat tissue have been well-described, comparatively less attention has been given to post-transcriptional regulators. Here, we employ two contrasting approaches to identify miRNAs that influence adipocyte phenotype. First, miRNAs were sequenced from 6 fat pads, primary preadipocytes, and primary mature adipocytes. Comparative analyses of abundance across adipose tissue type and stage of differentiation revealed a number of miRNAs that influence key metabolic processes. miR-335 inhibited adipogenesis, miR-192 promoted pro-thermogenic and …

Sympathy For The Microbiota: How Changes In Gut Microbial Composition Influence The Immune System And Basic Physiology By Way Of The Sympathetic Nervous System, Paul Andrew Muller

Student Theses and Dissertations

The gastro-intestinal tract is the most extensive mucosal surface in mammals and harbors the most numerous immune cell reservoir as well as a complex and autonomous nervous system. The GI tract is continuously exposed to foreign antigen and potentially toxic chemicals through the ingestion of food. In addition, the lumen of the human GI tract is populated with approximately 1013 bacteria, which is equivalent to the number of cells in the entire human body (Sender et al., 2016). The intestinal microbiome, which aids in host metabolism, represents a diverse population of microorganisms separated from the inside of the body by …

Regional Geographies Of The Us-Mexico Border, Kimberly Collins, Mike Kohout

Geography and Environmental Studies Faculty Publications

No abstract provided.

Structural Equation Modeling To Detect Correlates Of Childhood Vaccination: A Moderated Mediation Analysis, Abraham Degarege, Karl Krupp, Vijaya Srinivas, Boubakari Ibrahimou, Purnima Madhivanan

Journal Articles: Epidemiology

OBJECTIVES: This study used a health belief theory derived framework and structural equation model to examine moderators, mediators, and direct and indirect predictors of childhood vaccination.

METHODS: A secondary analysis was conducted using data collected from a cross-sectional survey of a random sample of 1599 parents living in urban and rural areas of Mysore district, India. Applying two-stage probability proportionate-to-size sampling, adolescent girls attending 7th through 10th grades in 23 schools were selected to take home a questionnaire to be answered by their parents to primarily assess HPV vaccine intentions. Parents were also asked whether their children had received one …

Effects Of Facial Features And Styling Elements On Perceptions Of Competence, Warmth, And Hireability Of Male Professionals, Marc Fetscherin, Stacey Tantleff-Dunn, Arne Klumb

Faculty Publications

Few studies investigated the effects of facial characteristics on stereotyping in the business context. Using a 2 (beard/no beard) x 2 (acne/no acne) x 2 (tie/no tie) x 2 (eyeglasses/no eyeglasses) between subjects’ design, two representative samples of 364 and 711 participants rated different stimuli of male subjects on dimensions of competence, warmth and hireability. Based on 4,215 observations, results show acne has a negative and eyeglasses a positive effect on both competence and warmth. Wearing a necktie has a positive effect on competence and a negative effect on warmth. Finally, beardedness has a negative effect on warmth. We also …