Biology Commons^™

Elucidating The Priming Mechanism Of Clpxp Protease By Single-Domain Response Regulator Cpdr In Caulobacter Crescentus, Kimberly E. Barker

Masters Theses

In Caulobacter crescentus, progression through the cell cycle is regulated by the AAA+ protease ClpXP, and there are several classes of cell-cycle substrates that require adaptors in order to be degraded. CpdR, a single domain-response regulator, binds the N-terminal domain of ClpXP and primes the protease for degradation of downstream factors (Lau et al., 2015). The ability of CpdR to bind ClpX is regulated by its phosphorylation state. In the unphosphorylated state, CpdR binds ClpXP and guides its localization to the cell pole during the swarmer to stalked transition, where CpdR is mediates degradation of substrates such as PdeA. …

Beyond The Fat: Protein Metabolism And Muscle Function As Part Of The Migratory Syndrome Of Songbirds, Cory R. Elowe

Doctoral Dissertations

Migration allows animals to seasonally exploit favorable habitats that are geographically disparate, and migratory animals have a suite of adaptations to complete their extraordinary journeys. This “migratory syndrome” of traits is comprised of seasonally-responsive adaptations that together result in changes to metabolism, body composition, and reproductive status, all of which act to increase the probability of a successful migration. The focus of my dissertation is to investigate the suite of changes in metabolism and muscle function that enable birds to undertake long-duration flights. In chapter 1, I compare fuel use in flight between two related migratory warbler species that migrate …

The Genomic Dynamics Of Fermented Food Microbes, Katherine Chacón-Vargas

Doctoral Dissertations

Along with the agriculture and domestication revolution, humans have utilized bacteria, yeasts, and molds for millennia in the production of traditionally fermented foods and beverages. Fermentation is a very ancient practice of high relevance nowadays since it contributes with a great variety of foods worldwide. Microbial fermentation allows metabolic transformation of the raw food materials leading to biochemical changes that played a key role in food preservation, health benefits, nutrition, flavors, and texture, among others. Food fermentation practices could diverge from traditional artisanal spontaneous fermentation to industrialize methods with specialized microbial starters and although fermented environments tend to be very …

Bioinformatics Lab: A Course-Based Undergraduate Research Experience Curriculum, Kristen M. Deangelis, Mallory Choudoir, Ashley Eng, Maureen A. Morrow

Microbiology Educational Materials

This is a computer lab course intended to give students technical and practical experience in analyzing sequencing data. We focus on bacterial genomes from recently isolated bacteria, so there is a possibility of discovery of new microbial diversity. Collaborative learning will be encouraged, but students will work individually to assemble, annotate, and analyze a bacterial genome.

Each week will begin with a review on the topic to be covered for that week. When applicable, there will be pre-recorded lectures to introduce lab topics, and students are expected to have watched these before coming to class. Our time in class will …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

Changes In Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping To Fac-Sorted Bacteria, Christopher A. Colvin

Masters Theses

Soil microbiomes play pivotal roles to the health of the environment by maintaining metabolic cycles. One question is how will climate change affect soil bacteria over time and what could the repercussions be. To answer these questions, the Harvard Forest Long-Term Warming Experiment was established to mimic predicted climate change by warming plots of land 5℃ above ambient conditions. In 2017, 14 soil core samples were collected from Barre Woods warming experiment to mark 15 years since the establishment of the soil warming in that location. These samples underwent traditional metatranscriptomics to generate an mRNA library as well as a …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

Flexible Phenotypes, Energetics, And Whole-Animal Performance Of Migratory Songbirds, Michael Griego

Doctoral Dissertations

Animal life has evolved innumerable strategies to adapt to a great range of environmental conditions present on earth. The physiology of free-living animals has thus been shaped to allow for maximal performance under challenging conditions and has given rise to traits that enable animals to overcome daunting ecological pressures. Few life history stages in the animal kingdom rival the intensity of annual avian migration: the extreme metabolic requirements of long-distance flight coupled with navigating vast and hostile ecological barriers results in enormously high mortality for young birds. It is therefore the main focus of this thesis to identify physiological traits …

Constraints Of The Imagination: How Phenotypes Are Shaped Through Genetics, The Environment, And Development, Michelle Gilbert

Doctoral Dissertations

Phenotypic constraints are ubiquitous throughout nature, being found throughout all stages of life and at multiple different biological levels including cellular, genetic, environmental, behavioral, evolutionary, and developmental. These constraints have shaped, not only the natural world, but the way that we perceive what is possible, or impossible, an observation made clear by François Jacob in his 1977 paper “Evolution and Tinkering”. This is reflected in the literature, repeatedly, by the regular occurrence of densely packed visualization of phenotypic space that seemingly always have large areas that go unoccupied. Despite constrained regions of space being observable across countless taxa, identifying the …

Tracking And Modulating Circadian Rhythms In Cell Culture Models, Sujeewa Sampath Lellupitiyage Don

Doctoral Dissertations

Circadian rhythms are 24–hour activity cycles that exist for all organisms, from yeast and bacteria to mammals. Epidemiological data has shown that disruptions to circadian rhythms are associated with various diseases, including cancers. Circadian rhythms are regulated at the cellular level by a "molecular clock,” whose oscillations in protein transcription and translation control a range of downstream pathways. However, the connections between altered rhythms and diseases at the molecular level is unclear. Therefore, in this project, I tracked circadian rhythms in a high-resolution manner and thoroughly analyzed them to more completely reflect circadian behaviors and clock functioning at the molecular …

Screening For Binding Partners And Protein-Protein Interactions Of A Fungal Transcription Factor- Xdr1, Nishadi Punsara Gallala Gamage

Masters Theses

Clarireedia spp. (formerly Sclerotinia homoeocarpaF.T. Bennett) is the causal agent dollar spot, the most economically important turfgrass disease impacting golf courses in North America. The most effective strategy for dollar spot control is repeated application of multiple classes of fungicides. However, reliance on chemical application has led to resistance to four classes of fungicides as well as multidrug resistance (MDR). Fungi are known to detoxify xenobiotics, like fungicides, through transcriptional regulation of three detoxification phases: modification, conjugation and secretion. Little is known, however, of the protein-protein interactions that facilitate these pathways. Following next-generation RNA sequencing of Clarireedia spp., a …

Drivers And Direct Impacts Of Lean Mass Dynamics On The Stopover Ecology And Migratory Pace Of Nearctic-Neotropical Migrant Songbirds In Spring, Mariamar Gutierrez Ramirez

Doctoral Dissertations

Annual migration in songbirds is one of the most demanding life-history stages. It represents a period of high mortality, yet there is still much unknown about the ecological correlates that influence its successful completion. After long non-stop migratory flights, birds require a stopover period to rest and replenish depleted energy reserves. Birds use fat as the primary fuel to power long-distance flights. However, birds also burn lean tissue, which results in significant reductions in muscle and organ masses. The discovery and quantification of lean mass catabolism represented a paradigm shift in migration ecology because non-fat components were thought to remain …

A Tipping Point In The Ecuadorian Amazon Rainforest: Current And Future Land-Use And Climate Change Trends, Alula Shields

Masters Theses

Many regions of the Amazon are experiencing drastic changes as deforestation and climate change drive the world’s largest continuous rainforest towards a ‘tipping point’. These disturbances are changing natural cycles that once past a critical threshold, will mark an unstoppable transition to an altered ecosystem. Losing areas of the Amazon rainforest will have implications for the global climate, global carbon budget, and global hydrological regimes. Scholars have projected these tipping points for areas of the eastern Amazon rainforest, but much less scholarship focuses on the headwaters of the Western Amazon, an area of great cultural and biological importance. Ecuador is …

Functional Morphology, Biomechanics, And Evolution Of Ruminant Mammals, Abby Vander Linden

Doctoral Dissertations

Ruminant mammals, including the families Bovidae, Cervidae, Tragulidae, Moschidae, Antilocapridae, and Giraffidae, display incredible past and present diversity in morphology, ecology, and behavior. They inhabit an impressive range of environments across North and South America, Europe, Asia, and Africa, and compel the fascination of naturalists and researchers alike with their charismatic social behavior and conspicuous cranial appendages. I explore the drivers and consequences of this spectacular diversity through a comparative morphological framework, biomechanical modeling approaches, and semi-parametric and likelihood-based methods for estimating state-dependent diversification rates across the ruminant phylogeny. Together, these investigations provide evidence for adaptation via correlated evolution of …

The Time Course And Neuroanatomy Of Rhinophore Regeneration In The Nudibranch Berghia Stephanieae, Ani Maroyan

Masters Theses

Within five weeks, the nudibranch, Berghia stephanieae (Gastropoda, Mollusca) can regenerate a severed rhinophore, the main olfactory appendage, such that it is indistinguishable from a non-lesioned rhinophore. The rhinophore is a 2 mm long stalk with lateral sides covered in ridges and the distal third covered in fluorescent pigmentation. Its internal morphology is dominated by longitudinal musculature, overlaid by a complex neuronal plexus, which contains neurons that express various neuroactive substances including serotonin and small cardioactive peptide (SCP). Two large nerves originate in the rhinophore ganglion at the base of the rhinophore and run the length of the rhinophore. To …

Development Of A New Behavioral Assay For Juvenile Berghia Stephanieae, Kelly E. Fischer

Masters Theses

Developing robust behavioral assays to study olfactory-driven behaviors allows for greater insight into the neural mechanisms behind them. Oftentimes, olfactory behavioral assays require a two-choice design, consistent variables, and controlled stimulus application. This can be challenging when working with marine dwelling organisms such as nudibranchs. Extensive work shows the importance of olfaction in both pre-metamorphic larval development and adult stage nudibranchs (Gastropoda, Mollusca). However, there is little research investigating how olfaction plays a role in rapidly developing, post-metamorphic juvenile nudibranchs such as Berghia stephanieae. To study olfactory-associated behaviors in juvenile Berghia, a novel behavioral microfluidic chip was designed which …

Monitoring Mammals At Multiple Scales: Case Studies From Carnivore Communities, Kadambari Devarajan

Doctoral Dissertations

Carnivores are distributed widely and threatened by habitat loss, poaching, climate change, and disease. They are considered integral to ecosystem function through their direct and indirect interactions with species at different trophic levels. Given the importance of carnivores, it is of high conservation priority to understand the processes driving carnivore assemblages in different systems. It is thus essential to determine the abiotic and biotic drivers of carnivore community composition at different spatial scales and address the following questions: (i) What factors influence carnivore community composition and diversity? (ii) How do the factors influencing carnivore communities vary across spatial and temporal …

Diversity And Evolution Of Human Eccrine Sweat Gland Density, Andrew W. Best

Doctoral Dissertations

Human eccrine density is highly derived. However, little is known about contemporary variation in this trait, what shapes it, and how it influences heat dissipation. This project explores 3 questions: 1) Is variation in functional eccrine density (FED) explained by childhood climate? 2) Is this variation patterned by geographic ancestry? 3) Is variation in FED associated with differences in heat dissipation capacity? We measured FED and sweat production in 6 body areas via pharmacological stimulation and impressions of sweating skin in 72 participants. Childhood climate variables were taken from the WorldClim database and geographic ancestry was estimated with 23andMe tests. …

Mechanisms Of Mitotic Checkpoint Silencing By The Disordered Kinetochore Protein Spc105, Margaux Audett

Doctoral Dissertations

The kinetochore protein Spc105R (DmSpc105R) is a large intrinsically disordered protein (IDP) that recruits spindle assembly checkpoint (SAC) proteins and is required for SAC signaling in a conserved manner. Chromosome biorientation satisfies the SAC and while it has been proposed that SAC satisfaction may require the establishment of stable kinetochore-MT (KT-MT) attachments and tension generation, the question of whether tension directly regulates SAC signaling is unresolved and controversial. Here we present data in support of Spc105R as a tension-sensing IDP that directly regulates checkpoint protein localization and signaling independent of the establishment of stable KT-MT attachments. The N-terminus of DmSpc105R …

Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos

Masters Theses

Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate …

Dynamic Evolution In The Leucine-Rich Repeat Receptor-Like Kinase (Lrr-Rlk) Family Of Receptors, Jarrett Man

Doctoral Dissertations

Cells in multicellular organisms must gauge their environmental conditions, including neighboring cells, during development. In plants, the Leucine-Rich Repeat Receptor-like Kinases (LRR-RLKs) encode a family of membrane-bound receptors that transduce such cell-to-cell signals and are required for many aspects of plant development. Very little is known about the function of most of these genes, and the evolutionary history of the family is difficult to infer because of its size and complexity. Several factors contribute to this difficulty, including genetic redundancy, challenging bioinformatic detection, exceptionally large family size, and high copy number variation among species. In this dissertation, I characterize some …

Genomics And Transcriptomics Yields A System-Level View Of The Biology Of The Pathogen Naegleria Fowleri, Emily K. Herman, Alex Greninger, Mark Van Der Giezen, Michael L. Ginger, Immaculada Ramirez-Macias, Haylea C. Miller, Matthew J. Morgan, Anastasios D. Tsaousis, Katrina Velle, Romana Vargová

Biology Department Faculty Publication Series

The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. Results Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains …

Hp1Α Is A Chromatin Crosslinker That Controls Nuclear And Mitotic Chromosome Mechanics, Amy R. Strom, Ronald J. Biggs, Edward J. Banigan, Xiaoto Wang, Katherine Chiu, Cameron Herman, Jimena Collado, Feng Yue, Joan C. Ritland Politz, Leah J. Tait

Biology Department Faculty Publication Series

Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1 alpha (CBX5) is unknown. We used a novel HP1 alpha auxin-inducible degron human cell line to rapidly degrade HP1 alpha. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1 alpha is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1 alpha(I)(165E) indicate that chromatin crosslinking via …

Membrane-Partitioned Cell Wall Synthesis In Mycobacteria, Alam García-Heredia, Takehiro Kado, Caralyn E. Sein, Julia Puffal, Sarah H. Osman, Julius Judd, Todd A. Gray, Yasu S. Morita, M. Sloan Siegrist

Microbiology Department Faculty Publication Series

Many antibiotics target the assembly of cell wall peptidoglycan, an essential, heteropolymeric mesh that encases most bacteria. In rod-shaped bacteria, cell wall elongation is spatially precise yet relies on limited pools of lipid-linked precursors that generate and are attracted to membrane disorder. By tracking enzymes, substrates, and products of peptidoglycan biosynthesis in Mycobacterium smegmatis, we show that precursors are made in plasma membrane domains that are laterally and biochemically distinct from sites of cell wall assembly. Membrane partitioning likely contributes to robust, orderly peptidoglycan synthesis, suggesting that these domains help template peptidoglycan synthesis. The cell wall-organizing protein DivIVA and the …

Neural Representation Of Abstract Task Structure During Generalization, Avinash R. Vaidya, Henry M. Jones, Johanny Castillo, David Badre

Psychological and Brain Sciences Faculty Publication Series

Cognitive models in psychology and neuroscience widely assume that the human brain maintains an abstract representation of tasks. This assumption is fundamental to theories explaining how we learn quickly, think creatively, and act flexibly. However, neural evidence for a verifiably generative abstract task representation has been lacking. Here, we report an experimental paradigm that requires forming such a representation to act adaptively in novel conditions without feedback. Using functional magnetic resonance imaging, we observed that abstract task structure was represented within left mid-lateral prefrontal cortex, bilateral precuneus, and inferior parietal cortex. These results provide support for the neural instantiation of …

Spatio-Temporal Associations Between Deforestation And Malaria Incidence In Lao Pdr, Francois Rerolle, Emily Dantzer, Andrew A. Lover, John M. Marshall, Bouasy Hongvanthong, Hugh J. W. Sturrock, Adam Bennett

Biostatistics and Epidemiology Faculty Publications Series

As countries in the Greater Mekong Sub-region (GMS) increasingly focus their malaria control and elimination efforts on reducing forest-related transmission, greater understanding of the relationship between deforestation and malaria incidence will be essential for programs to assess and meet their 2030 elimination goals. Leveraging village-level health facility surveillance data and forest cover data in a spatio-temporal modeling framework, we found evidence that deforestation is associated with short-term increases, but long-term decreases confirmed malaria case incidence in Lao People's Democratic Republic (Lao PDR). We identified strong associations with deforestation measured within 30 km of villages but not with deforestation in the …

Extreme Morphology, Functional Trade-Offs, And Evolutionary Dynamics In A Clade Of Open-Ocean Fishes (Perciformes: Bramidae), Michelle C. Gilbert, Andrew J. Conith, Catherine S. Lerose, Joshua K. Moyer, Steve H. Huskey, R. Craig Albertson

Biology Department Faculty Publication Series

Synopsis When novel or extreme morphologies arise, they are oft met with the burden of functional trade-offs in other aspects of anatomy, which may limit phenotypic diversification and make particular adaptive peaks inaccessible. Bramids (Perciformes: Bramidae) comprise a small family of 20 extant species of fishes, which are distributed throughout pelagic waters worldwide. Within the Bramidae, the fanfishes (Pteraclis and Pterycombus) differ morphologically from the generally stout, laterally compressed species that typify the family. Instead, Pteraclis and Pterycombus exhibit extreme anterior positioning of the dorsal fin onto the craniofacial skeleton. Consequently, they possess fin and skull anatomies that are radically …

Heterogeneous Contributions Of Change In Population Distribution Of Body Mass Index To Change In Obesity And Underweight, Ncd Risk Factor Collaboration

Environmental Health Sciences Faculty Publication Series

From 1985 to 2016, the prevalence of underweight decreased, and that of obesity and severe obesity increased, in most regions, with significant variation in the magnitude of these changes across regions. We investigated how much change in mean body mass index (BMI) explains changes in the prevalence of underweight, obesity, and severe obesity in different regions using data from 2896 population-based studies with 187 million participants. Changes in the prevalence of underweight and total obesity, and to a lesser extent severe obesity, are largely driven by shifts in the distribution of BMI, with smaller contributions from changes in the shape …

Deficient Spermiogenesis In Mice Lacking Rlim, Feng Wang, Maria Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Mary C. Wallingford, Darya A. Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando

Veterinary & Animal Sciences Department Faculty Publication Series

The X-linked gene Rlim plays major roles in female mouse development and reproduction, where it is crucial for the maintenance of imprinted X chromosome inactivation in extraembryonic tissues of embryos. However, while females carrying a systemic Rlim knockout (KO) die around implantation, male Rlim KO mice appear healthy and are fertile. Here, we report an important role for Rlim in testis where it is highly expressed in post-meiotic round spermatids as well as in Sertoli cells. Systemic deletion of the Rlim gene results in lower numbers of mature sperm that contains excess cytoplasm, leading to decreased sperm motility and in …

Mpdb 2.0: A Large Scale And Integrated Medicinal Plant Database Of Bangladesh, Nazmul Hussain, Rony Chanda, Ruhshan Ahmed Abir, Mohsina Akter Mou, Md Kamrul Hasan, M Arif Ashraf

Biology Department Faculty Publication Series

ObjectiveMPDB 2.0 is built to be the continuation of MPDB 1.0, to serve as a more comprehensive data repertoire for Bangladeshi medicinal plants, and to provide a user-friendly interface for researchers, health practitioners, drug developers, and students who wish to study the various medicinal & nutritive plants scattered around Bangladesh and the underlying phytochemicals contributing to their efficacy in Bangladeshi folk medicine.ResultsMPDB 2.0 database (https://www.medicinalplantbd.com/) comprises a collection of more than five hundred Bangladeshi medicinal plants, alongside a record of their corresponding scientific, family, and local names together with their utilized parts, information regarding ailments, active compounds, and PubMed ID …