Viruses represent the most abundant biological entities on earth where, they are able to interact with all kingdoms of life. Yet their diversity, ecology and evolutionary aspects are only beginning to be fully elucidated, mainly due to technical limitations. The vast majority of the microbial world remains elusive to culture; more than 90% of genome sequenced viral isolates infect only 5 of the 54 prokaryotic phyla that are currently recognized. In contrast, viral metagenomics bypasses the need for cultures by directly sequencing fragmented genetic material of environmental viral communities. This dissertation uses viral metagenomics by applying well-tested bioinformatic protocols and expanding them to compare and contrast patterns of diversity, richness and specialization of large viral metagenomic datasets, in both local and global scales. First I demonstrate the utility of a functional-based perspective by adopting the protein cluster environment to estimate global viral diversity. Then, I use this PC approach to analyze metagenomes from two ecologically different environments, which by uncovering local gene specialization showcases the adequacy of a gene-centered workflow. Then I continue to expand upon this PC framework to study the Tara Oceans virome analyses of these data reveal patters of diversity that support a seed bank model. Finally, in search of a more meaningful ecological unit, I move from a gene-centered standpoint towards a population-based frame. We adopted a novel metagenomic technique that allowed me to uncover the discontinuity in the genomic sequence space, thus empirically defining a population. This final contribution will allow to sort and count viral communities, the first step to applying ecological and evolutionary theory.

Hypertrophic cardiomyopathy (HCM) is a primary disease of the myocardium. 4-11% of HCM is caused by mutations in cardiac troponin T (cTnT) and 65% of them are within the tropomyosin (TM)-binding TNT1 domain. Two of the known mutational hotspots within TNT1 are in the N and C-terminal domains. Unlike the N-terminal domain; no high-resolution structure exists for the highly conserved C-terminal domain limiting both our ability to understand the functional role of this extended domain in myofilament activation and molecular mechanism(s) of HCM. The Δ160E mutation is an in-frame deletion of a glutamic acid residue at position 160 of cTnT. This TNT1 C-terminal mutation is associated with an especially poor prognosis. The Δ160E mutation is located in a putative "hinge region" immediately adjacent to the unstructured flexible linker connecting the TM-binding TNT1 domain to the Ca²⁺-sensitive TNT2 domain. Unwinding of this α-helical hinge may provide the flexibility necessary for thin filament function. Previous regulated in vitro motility assay (R-IVM) data showed mutation-induced impairment of weak actomyosin binding. Thus, we hypothesized that the Δ160E mutation repositions the flexible linker which impairs weak electrostatic binding and ultimately leads to severe cardiac remodeling. The goal of our studies is two-fold: 1) to gain high-resolution insight into the position of the cTnT linker with respect to the C-terminus of TM, and 2) to identify Δ160E-induced positional changes using Fluorescence Resonance Energy Transfer (FRET) in a fully reconstituted thin filament. To this end, residues in the middle and distal regions of the cTnT linker were sequentially cysteine-substituted (A168C, A177C, A192C and S198C) and labeled with the energy donor IAEDANS. The energy acceptor, DABMI was attached to cysteine 190 (C190) in the C-terminal region of TM and FRET measurements were obtained in the presence and absence of Ca²⁺ and myosin subfragment 1 (S1). An all-atom thin filament model in the Ca²⁺–on state was employed to predict the pathogenic effects of the Δ160E mutation on the structure and the dynamics of the cTnT linker region. Our data suggest that the linker domain runs alongside the C-terminus of TM and is differentially repositioned by calcium, myosin and the Δ160E mutation. The Δ160E mutation moves the linker closer to the C-terminus of TM. The in silico model supported this finding and demonstrated a mutation-induced decrease in linker flexibility. Moreover, the model predicted a pathogenic change in the orientation of the middle region of the linker and in the position of the Ca²⁺-sensitive TNT2 domain and the TM-binding TNT1 domain in response to Δ160E mutation. Collectively, our findings suggest that the Δ160E mutation-induced changes in the structure, position and dynamics of the linker region cause steric blocking of weak myosin binding sites on actin and subsequent impairment of contraction and disruption of sarcomeric integrity. These studies, for the first time, provided information regarding the role of the extended linker in both myofilament activation and disease.

The causes of Amyotrophic Lateral Sclerosis (ALS), a fatal neurodegenerative disease that results in skeletal muscle paralysis, remain unclear. However, a nuclear DNA and RNA binding protein called TAR DNA binding protein 43 (TDP-43) has emerged as a critical marker of ALS pathology. A previous drug screen conducted in the Zarnescu laboratory showed that anti-diabetic drugs can rescue lethality in a fruit fly model of ALS based on TDP-43. These results suggested that the insulin signaling pathway might be altered in motor neurons in a TDP-43 dependent manner. Therefore, we hypothesized that the insulin pathway is interacting with TDP-43 in vivo and may be contributing to TDP-43neurotoxicity. Using genetic interaction approaches in flies we found that TDP-43dependent locomotor defects are sensitive to the levels of insulin receptor activity. In addition, genetic interaction data suggest that Akt is hyperactivated in motor neurons expressing TDP-43, possibly as a compensatory mechanism to enable survival. Finally, upregulating protein synthesis through S6K and 4EBP appears to have beneficial effects. These findings support our hypothesis and provide insights into potential therapeutic strategies to help treat this devastating disease.

Experts in the field of molecular and cellular biology (MCB) use domain-specific reasoning strategies to navigate the unique complexities of the phenomena they study and creatively explore problems in their fields. One primary goal of instruction in undergraduate MCB is to foster the development of these domain-specific reasoning strategies among students. However, decades of evidence-based research and many national calls for undergraduate instructional reform have demonstrated that teaching and learning complex fields like MCB is difficult for instructors and learners alike. Therefore, how do students develop rich understandings of biological mechanisms? It is the aim of this dissertation work to explore features of expertise and knowledge building in undergraduate MCB by investigating knowledge organization and problem-solving strategies. Semi-structured clinical think-aloud interviews were conducted with introductory and upper-division students in MCB. Results suggest that students must sort ideas about molecular mechanism into appropriate mental categories, create connections using function-driven and mechanistic rather than associative reasoning, and create nested and overlapping ideas in order to build a nuanced network of biological ideas. Additionally, I characterize the observable components of generative multi-level mechanistic reasoning among undergraduate MCB students constructing explanations about in two novel problem-solving contexts. Results indicate that like MCB experts, students are functionally subdividing the overarching mechanism into functional modules, hypothesizing and instantiating plausible schema, and even flexibly consider the impact of mutations across ontological and biophysical levels. However "filling in" these more abstract schema with molecular mechanisms remains problematic for many students, with students instead employing a range of developing mechanistic strategies. Through this investigation of expertise and knowledge building, I characterize several of the ways in which knowledge integration and generative explanation building are productively constrained by domain-specific features, expand on several discovered barriers to productive knowledge organization and mechanistic explanation building, and suggest instructional implications for undergraduate learning.

Mayer-Rokitansky-Kuster-Hauser Syndrome is a congenital disorder of the female reproductive tract due to impaired Müllerian duct development. There are three known categorical presentations: isolated, atypical, and MURCS association. Several developmentally significant factors including inappropriate AMH/AMHR interaction, and mutations in the WNT gene family and HOXA7-13 cluster have been studied. There has also been investigation into an autosomal dominant pattern of inheritance in families with multiple cases of the syndrome. Due to the presence of multiple subsets of patients with similar genetic abnormalities, it seems unlikely that a single etiology will be discovered.

Mutations in MCOLN1, which encodes the cation channel protein TRPML1, result in the neurodegenerative lysosomal storage disorder Mucolipidosis type IV. Mucolipidosis type IV patients show lysosomal dysfunction in many tissues and neuronal cell death. The orthologue of TRPML1 in Caenorhabditis elegans is CUP-5; loss of CUP-5 results in lysosomal dysfunction in many tissues and death of developing intestinal cells that results in embryonic lethality. We previously showed that a null mutation in the ATP-Binding Cassette transporter MRP-4 rescues the lysosomal defect and embryonic lethality of cup-5(null) worms. Here we show that reducing levels of the Endosomal Sorting Complex Required for Transport (ESCRT)-associated proteins DID-2, PHI-33, and ALX-1/EGO-2, which mediate the final de-ubiquitination step of integral membrane proteins being sequestered into late endosomes, also almost fully suppress cup-5(null) mutant lysosomal defects and embryonic lethality. Indeed, we show that MRP-4 protein is hypo-ubiquitinated in the absence of CUP-5 and that reducing levels of ESCRT-associated proteins suppresses this hypo-ubiquitination. Thus, increased ESCRT-associated de-ubiquitinating activity mediates the lysosomal defects and corresponding cell death phenotypes in the absence of CUP-5.

Advances in genetics and fluorescent protein chemistry have enabled us to fuse fluorescent probes directly to biomolecules in stably growing organisms; making it easier to image the precise position and movement of cells in three dimensions. Fluorescent stains and dyes can be employed in a similar fashion to visualize nano-scale fluctuations in active cellular structures without fixation. While informative and exciting on a qualitatively level, microscopy truly becomes powerful when we can extract meaningful quantitative information. To accomplish this, custom MATLAB (Mathworks, Natick, MA) image analysis algorithms were developed to specifically measure the biophysical parameters related to pathogenesis and function in microbes and mammalian cells. These parameters can then be exploited in the development of biophysical models to validate current measurements, and make critical predictions about the system's behavior, often addressing quantities inaccessible by experimental methods. The following research chapters of this dissertation thoroughly describe how these techniques were developed and applied to study the biophysical mechanisms of bacterial and cellular invasion.

This work revealed what is at the core of a particular group of prospective teachers that underlie their commitment to teach in under-resourced schools and districts. Prospective teachers committed to teaching in under-resourced schools have qualities or attributes of recognition and respect for students and families who come from low-income and culturally different backgrounds and experiences. These prospective teachers were able to recognize complex interactions that students and their families face at the individual, social and institutional level. They also sought ways to address their students' learning needs by drawing from students' experiences to make meaningful connections between home and school. To identify students' and families' lived experiences, cultural practices, and language as resources to draw from, are acts of recognition and respect towards students and their families who are, for many prospective teachers, different from themselves. Recognition and respect for difference are essential attributes that underlie a socially just and humanistic pedagogy which can positively impact the learning outcomes for students who are historically poorly served by our public schools. This work highlights a different view that prospective teachers from majority White European backgrounds have about social others. It also provides a new framework using social otherness as a lens to reveal prospective teachers' understandings and knowledge about students and families from low-income backgrounds.

Traditional undergraduate biology courses are content intensive, requiring students to understand and remember large amounts of information in short periods of time. Yet most students maintain little of the material encountered during their education. Poor knowledge retention is a main cause of academic failure and high undergraduate attrition rates. Characterizing strategies that support robust learning is critical for ensuring student success. One such strategy is testing effect, the observation that repeated testing can improve the fidelity and durability of retained knowledge more than an equal quantity of restudy. Numerous investigations have described the nature and boundaries of testing effect. Very few, however, have characterized its efficacy in actual classroom practice. The current study investigated whether repeated testing or repeated study affected student retention and understanding of complex biological concepts. The study was conducted in a large (~320 students) introductory biology class. All study conditions and assessments were required components of the course. Student retention of two fundamental molecular biology "big ideas" was targeted; (1) the relationship between genotype and phenotype, and (2) the relationship between gene expression and cell function. Students were randomly assigned to one of three repeated quiz or study conditions. For four weeks, students encountered various combinations of multiple-choice (MC) questions and review material related to big ideas 1&2 and/or unrelated lecture topics. Five weeks after the last quiz, all students completed identical MC final exam questions related to both big ideas. To determine the quality of "understanding" assessed by the MC questions, a subset of students also completed a short answer (SA) test prior to the final exam. Both question formats assessed the same knowledge (2 big ideas) at the same level (comprehension and application). Final exam performance supported the finding that repeated retrieval improves long-term retention of knowledge relative to repeated study. Novel to other previous work conducted at the undergraduate level, the current findings suggest that repeated testing affects student retention and understanding of sophisticated concepts. Careful design and analysis of parallel multiple-choice and short answer questions demonstrated that each can target and elicit similar qualities and types of knowledge.

This study investigated whether participation in the Partnership for Research and Education in Plants (PREP), a long-term authentic plant research project, in conjunction with explicit verses implicit instruction can change high school students' conceptions of the nature of science (NOS). The participants included a total of 134 students comprised of three groups from 10 total classes over the course of two academic years. Participants in four classes (two each year) participated in PREP and received explicit instruction on NOS. Participants in four other classes (two each year) participated in PREP and received implicit only instruction on NOS. Additionally, two classes (one each year) of high-achieving freshmen participated in PREP and received explicit instruction on NOS. This third group was used as a comparative group to the other two groups, due to their high achievement in middle school math and science. The treatment for all three groups spanned 8 weeks and included participation in an authentic plant research project. An open-ended questionnaire (modified Views of Nature of Science - VNOS), in conjunction with semi-structured interviews, was used to assess students' conceptions before and after the intervention. Results showed that all three groups improved their conceptions of NOS equally. The high-achieving group began with significantly higher-scoring views prior to the completion of the intervention, and improved to the same degree as the other two groups. A comparison of the explicit group to the implicit only group showed that there was no significant difference in their improvement, as both groups improved equally. Implications for the teaching and learning of NOS are discussed.