Biology Commons^™

The Role Of Semaphorins In Response To Injury In C. Elegans Neurons, Maria Belen Harreguy Alfonso

Dissertations

When neural tissue is injured by trauma, delicate neuronal processes such as axons and dendrites are prone to lesion damage and often disconnect. The molecular, cellular, and circuit mechanisms that underlie the regrowth and reconnection of these processes and the recovery of behavior are major challenges in the fields of neuroscience, regeneration, and resilience. At the molecular and cellular levels, signaling pathways that mediate neuronal growth cone guidance during development can play a role in neuronal regeneration and recovery from injury. One family of signaling proteins involved in this process comprises the highly conserved semaphorins and their receptors, the plexins. …

Brainless But Smart: Investigating Cognitive-Like Behaviors In The Acellular Slime Mold Physarum Polycephalum, Subash Kusum Ray

Dissertations

Evolutionary pressures to improve fitness, have enabled living systems to make adaptive decisions when faced with heterogeneous and changing environmental and physiological conditions. This dissertation investigated the mechanisms of how environmental and physiological factors affect the behaviors of non-neuronal organisms. The acellular slime mold Physarum polycephalum was used as the model organism, which is a macroscopic, unicellular organism, that self-organizes into a network of intersecting tubules. Without using neurons, P. polycephalum can solve labyrinth mazes, build efficient tubule networks, and make adaptive decisions when faced with complicated trade-offs, such as between food quality and risk, speed and accuracy, and exploration …

Flexibility Vs Consistency: Quantifying Differences In Neuromodulatory Elicited Patterns Of Activity, Elizabeth M. Cronin

Dissertations

Central pattern generating circuits underly fundamental behaviors such as respiration or locomotion and are under the influence of neuromodulators. The presence of neuromodulators is thought to confer flexibility to these circuits to generate distinct patterns of activity to meet distinct behavioral needs. Network output flexibility can be achieved by distinct classes of neuromodulators, those which have convergent cellular actions but divergent circuit actions or by those which have divergent cellular actions but convergent circuit actions.

Both classes of neuromodulator exist in the stomatogastric nervous system of the crab Cancer borealis and influence the activity of a central pattern generating circuit …

Repeated Low-Level Blast Induces Chronic Neuroinflammation And Neurobehavioral Changes In Rat Models, Arun Reddy Ravula

Dissertations

Blast-induced neurotrauma (bTBI) is a signature medical concern for military personnel when they are exposed to explosions in active combat zones. However, soldiers as well as law enforcement personnel are also repeatedly exposed to low-level blasts during training sessions with heavy weaponries as part of combat readiness. Service personnel who sustain brain injuries from repeated low-level blasts (rLLBs) do not display overt pathological symptoms immediately but rather develop cognitive impairments, attention deficits, anxiety, and sleep disturbances over time. An improved rat model of rLLB was developed in this thesis by applying controlled low-level blast pressures (10 psi) repeated five times …

The Interplay Of The Physical Landscape And Social Dynamics In Shaping Movement Of African Savanna Elephants (Loxodonta Africana), Maggie Wisniewska

Dissertations

Free ranging African savanna elephants (Loxodonta africana) are increasingly impacted by human-induced habitat loss and poaching for ivory. Because elephants live in tightly knit groups, this combination of threats not only reduces the size of their populations but also degrades their social interactions. Long-term relationships with socially competent individuals, such as experienced seniors, benefit the ability of other group members to access limiting resources and avoid danger. Understanding how anthropogenic pressure may affect persistence of elephant populations is important, because elephants are an economically important keystone species. This doctoral thesis characterizes how individual elephants influence the movement of their social …

These Fish Were Made For Walking: Morphology And Walking Kinematics In Balitorid Loaches, Callie Hendricks Crawford

Dissertations

Terrestrial excursions have been observed in multiple lineages of marine and freshwater fishes. These ventures into the terrestrial environment may be used when fish are searching out new habitat during drought, escaping predation, laying eggs, or seeking food sources. The physiological demands for life under water and on land are vastly different and require different functional adaptations. Fish with terrestrial excursions must be capable of dealing with the stresses of both aquatic and terrestrial environments for varying periods of time. To deal with these stresses, amphibious fishes exhibit many morphological and behavioral adaptations. These adaptations have led to a range …

Development Of Deep Learning Neural Network For Ecological And Medical Images, Shaobo Liu

Dissertations

Deep learning in computer vision and image processing has attracted attentions from various fields including ecology and medical image. Ecologists are interested in finding an effective model structure to classify different species. Tradition deep learning model use a convolutional neural network, such as LeNet, AlexNet, VGG models, residual neural network, and inception models, are first used on classifying bee wing and butterfly datasets. However, insufficient data sample and unbalanced samples in each class have caused a poor accuracy. To make improvement the test accuracy, data augmentation and transfer learning are applied. Recently developed deep learning framework based on mathematical morphology …

Efficient Approximations For Stationary Single-Channel Calcium Nanodomains, Yinbo Chen

Dissertations

Mathematical and computational modeling plays an important role in the study of local Ca2+ signals underlying many fundamental physiological processes such as synaptic neurotransmitter release and myocyte contraction. Closed-form approximations describing steady-state distribution of Ca2+ in the vicinity of an open Ca2+ channel have proved particularly useful for the qualitative modeling of local Ca2+ signals. This dissertation presents several simple and efficient approximants for the equilibrium Ca2+ concentration near a point source in the presence of a mobile Ca2+ buffer, which achieve great accuracy over a wide range of model parameters. Such approximations provide an efficient method for estimating Ca2+ …

Genetic Population Structure And Microbiome Of German Cockroaches In Urban Environments, Xueyang Fan

Dissertations

Pests of human habitats may harbor and disperse pathogens that cause human disease. One such pest is the German cockroach (Blattella germanica), which is known to harbor numerous pathogens, including Klebsiella and Pseudomonas. The aim of this study is to reveal the importance of the German cockroach as a potential vector of human medically important diseases. To do so, this study investigates German cockroach population structure and their associated bacterial microbiome in urban residential environments. Ninety German cockroaches are collected from three residential apartment buildings in three New Jersey cities. Samples are caught by glue traps and stored at -20°C. …

Plant Evolution And Urbanization: Quantifying The Effects Of Natural Selection In Shaping Shepherd’S Purse (Capsella Bursa-Pastoris) Populations In New York City, Rebecca Panko

Dissertations

The aim of this study is to quantify the effects of natural selection in shaping Capsella bursa-pastoris populations along an urban-rural gradient in New York City.

A reciprocal transplant experiment with 168 lab-germinated C. bursa-pastoris seedlings from both urban and rural populations are grown in eight paired home and away sites distributed throughout the New York metropolitan area. Sites are visited approximately thirteen times to record plant fitness. There is evidence for local adaptation of urban populations: urban plants have longer reproductive durations and produce more seed pods in urban environments. These findings suggest that urban plants are better adapted …

The Roles Of Inhibition In C. Elegans Locomotion, Lan Deng

Dissertations

Inhibition plays important roles in modulating neural activities at different levels from small synapses to brain regions, and different systems from sensory to motor. To achieve translocation, locomotor systems produce alternation of antagonist muscles, including axial posture and limb movement and alternation. In the nematode C. elegans, a cross-inhibition circuit, involving excitatory cholinergic and inhibitory GABAergic motoneurons, is believed to generate the dorsoventral alternation of body-wall muscles that supports backward undulatory locomotion. This dissertation challenges this prevalent hypothesis, delves into studying different roles of inhibition, and depicts the expression pattern and functional role of ionotropic GABAA receptor, UNC-49, in motoneurons …

Mitochondria Imaging And Targeted Cancer Treatment, Tinghan Zhao

Dissertations

Mitochondria are essential organelles as the site of respiration in eukaryotic cells and are involved in many crucial functions in cell life. Dysfunction of mitochondrial metabolism and irregular morphology have been frequently found in human cancers. The capability of imaging mitochondria as well as regulating their microenvironment is important both scientifically and clinically. Mitochondria penetrating peptides (MPPs), certain peptides that are composed of cationic and hydrophobic amino acids, are good candidates for mitochondria targeting. Herein, a novel MPP, D-argine-phenylalanine-D-argine-phenylalanine-D-argine-phenylalanine-NH₂ (rFrFrF), is conjugated with a rhodamine-based fluorescent chromophore (TAMRA). The TAMRA-rFrFrF probe exhibits advantageous properties for long-term mitochondria tracking of …

Methods To Improve The Remediation Of Polycyclic Aromatic Hydrocarbons (Pahs) In Aerobic And Anaerobic Environments, Brian Wartell

Dissertations

Oil spills occur regularly in terrestrial environments and crude oil can contain many compounds that are highly resistant to degradation. Among these compounds are high levels of polycyclic aromatic hydrocarbons (PAHs) which are not only toxic but can also be carcinogenic and/or mutagenic. The first chapter of this dissertation includes an extensive review chapter on the variables affecting the anaerobic degradation of hydrocarbons, with a particular focus on PAHs. Electron acceptors, electron donors, temperature, salinity, pH all play key roles in determining the possibility effective of effective degradation occurring. Thus, by addressing solutions, such as biostimulation, improving environmental variables for …

Direct And Indirect Controls On Bee Community Composition, Caroline Marie Devan

Dissertations

Bees are important pollinators, critical for the continued survival of plants in both natural and agricultural ecosystems. Diverse bee communities have been shown to increase richness in plant communities and plant reproduction depends upon bee community richness. Yet there is growing concern that pollinators, especially bees, are declining globally. This dissertation focuses on evaluating the mechanisms responsible for bee community composition in order to promote bee conservation in natural systems and their restoration in human-dominated urban and agricultural landscapes.

Bee populations are impacted directly by three things: floral resources, nesting resources and risk, primarily from natural enemies. Bees are indirectly …

Regulation Of Voltage-Gated K+ Currents In Motor Neurons: Activity-Dependence And Neuromodulation, Dalia Salloum

Dissertations

Neuronal output is shaped by extrinsic modulation as well as modulation of intrinsic properties of individual neurons, mediated by activity-dependent changes in the expression levels of voltage-gated ionic currents. Activity-dependent regulation of ionic currents is a mechanism by which electrical output of a neuron feeds back onto the expression of its own ion channels to alter cellular excitability in response to stimuli. Neurons alter their intrinsic properties to achieve long lasting changes involved in development, learning and memory formation and vital functions of organ systems such as locomotion and digestion. At the same time, plasticity of neuronal excitability driven by …

Biophysical Mechanisms Of Frequency-Dependence And Its Neuromodulation In Neurons In Oscillatory Networks, David Michael Fox

Dissertations

In response to oscillatory input, many isolated neurons exhibit a preferred frequency response in their voltage amplitude and phase shift. Membrane potential resonance (MPR), a maximum amplitude in a neuron’s input impedance at a non-zero frequency, captures the essential subthreshold properties of a neuron, which may provide a coordinating mechanism for organizing the activity of oscillatory neuronal networks around a given frequency. In the pyloric central pattern generator network of the crab Cancer borealis, for example, the pacemaker group pyloric dilator neurons show MPR at a frequency that is correlated with the network frequency. This dissertation uses the crab …

Regulation Of Mtorc1 By Homocysteine And Its Effects On Autophagy In Human And Mouse Neuronal Tissues, Khoosheh Khayati

Dissertations

The molecular mechanisms leading to and responsible for age-related, sporadic Alzheimer’s disease (AD) remain largely unknown. It is well documented that aging patients with elevated levels of the amino acid metabolite homocysteine (Hcy) are at high risk of developing AD. The impact of Hcy on molecular clearance pathways in mammalian cells, including in-vitro cultured induced pluripotent stem cell-derived forebrain neurons and in-vivo neurons in mouse brains is investigated in this research project. Exposure to high Hcy levels results in up-regulation of the mechanistic target of rapamycin complex 1 (mTORC1) activity, one of the major kinases in cells that is tightly …

Determining How Stable Network Oscillations Arise From Neuronal And Synaptic Mechanisms, Diana Martinez

Dissertations

Many animal behaviors involve the generation of rhythmic patterns and movements. These rhythmic patterns are commonly mediated by neural networks that produce an oscillatory activity pattern, where different neurons maintain a relative phase relationship. This thesis examines the relationships between the cellular and synaptic properties that give rise to stable activity in the form of phase maintenance, across different frequencies in a well-suited model system, the pyloric network of the crab Cancer borealis. The pyloric network has endogenously oscillating ‘pacemaker’ neurons that inhibit ‘follower’ neurons, which in turn feed back onto the pacemaker neurons. The focus of this thesis …

Attraction And Risk In Urban Bird Habitats, Megan E. Litwhiler

Dissertations

Urban expansion is an increasing threat to native bird populations. Consequently, maintaining and developing safe urban habitat space is necessary for conservation. Birds living in, or migrating through, urban areas utilize a variety of managed green-spaces such as parks, gardens, college campuses, and cemeteries. In addition to managed habitats, birds may use abandoned property that has been reclaimed by vegetation and associated spontaneous, biological communities. Such urban habitats may provide valuable resources for birds and other wildlife; however, these sites often contain high densities of non-native plants and can be polluted, potentially imparting a greater risk than benefit to the …

E Pluribus Unum: What Individual Whales Can Tell Us About Enigmatic Species Distribution And Social Organization, Tanya Marie Lubansky

Dissertations

Large whales have historically been difficult to study and many aspects of their ecology remain unknown especially at the long -term population level. The ability to identify individual whales based on natural markings provides the opportunity to track individuals over time and space; this data may offer more insight into the ecology of whales than previously imagined. This study demonstrates use of photo-identification data to model both social structure and habitat selection, minimizing the need for invasive research and greatly increasing the sample size used in such endeavors. A conditional logistic model is written for a 20-year sightings dataset on …

Astrocytes Modulate Microglial Phenotype And Dendritic Cell-Like Properties, Nischal K. Padala

Dissertations

Microglia are the resident immune cells of the CNS. In the healthy CNS, they express negligible levels of MHC II molecules as well as co-stimulatory molecules CD40, CD80 and CD86 necessary for antigen presentation to and activation of T cells. Co-stimulatory molecule expression can be induced in isolated microglia in vitro by sequential treatment with granulocyte monocyte colony-stimulating factor (GM-CSF) followed by lipopolysaccharide (LPS). Upon such treatment, they become mature dendritic cells (DCs), capable of activating T cells. However, microglia are not isolated in life, but rather exist in an environment enriched by other cells, notably astrocytes.

Therefore, to determine …

Consequences Of Stochastic Mrna Synthesis In A Gene Regulatory Pathway, Khyati Shah

Dissertations

Gene expression is a stochastic process, with elements of randomness present in both transcription and translation. This stochasticity results in cell-to-cell variation in the amounts of gene products, mRNAs and proteins, and is observed in organisms ranging from bacteria and yeast to higher eukaryotes. Randomness in the activation and inactivation of a gene is the preliminary cause of this variation. At the level of proteins, these variations are buffered compared to levels of mRNA, due to the longer lifespan of proteins. Nevertheless, there is substantial variation observed at the level of proteins, resulting in phenotypic diversity among genetically identical cells. …

Mechanisms Of Ionic Current Changes Underlying Rhythmic Activity Recovery After Decentralization, Olga E. Khorkova Sherman

Dissertations

Neuronal networks capableof generating rhythmic output in the absence of patterned sensory or central inputs are widely represented in the nervous system where they support a variety of functions, from learning and memory to rhythmic motor activity such as breathing. To perfectly function in a living organism, rhythm-generating networks have to combine the capability of producing a stable output with the plasticity needed to adapt to the changing demands of the organism and environment. This dissertation used the pyloric network of the crab Cancer borealis to identify potential mechanisms that ensure stability and adaptation of rhythm generation by neuronal networks …

Bioinformatics Study Of Mammalian Mrna Polydenylation, Haibo Zhang

Dissertations

Messenger RNA polyadenylation is one of the key post-transcriptional events in mammalian cells, which have influences on many aspects of mRNA metabolism. Several human diseases have been shown to associate with abnormal polyadenylation, highlighting the importance of this process. The availability of the complete sequence of human and mouse genomes, together with their gene expression data provides valuable resources to study mRNA polyadenylation on a system level. This dissertation addresses the following issues of mammalian mRNA polyadenylation through bioinformatics approaches: (1) the extensive documentation of several key aspects of polyadenylation sites in humans and mice on a genomic level; (2) …

Non-Parametric Algorithms For Evaluating Gene Expression In Cancer Using Dna Microarray Technology, Virginie Aris

Dissertations

Microarray technology has transformed the field of cancer biology by enabling the simultaneous evaluation of tens of thousands mRNA expression levels in a single experiment. This technology has been applied to medical science in order to find gene expression markers that cluster diseased and normal tissues, genes affected by treatments, and gene network interactions. All methods of microarray data analysis can be summarized as a study of differential gene expression. This study addresses three questions, 1) the roles of selectively expressed genes for the classification of cancer, 2) issues of accounting for both experimental and biological noise, and 3) issues …