Browsing by Subject "Translation"

Brother Is a Street Musician – Viewing the Landscape of Modernity Through Popular Songs by Zhang Eujeong was originally published in Korean in 2006. Described as a “fascinating journey upstream into the past to understand where the current will bring the future of Korean pop music,” (Busan Ilbo Review, 2009) Brother Is a Street Musician does not deal with contemporary K-Pop; rather, it visits the first chapter of Korea’s popular music history, which coincided with Japanese colonization in the first half of the 20th century. Combining archival research with a critical analysis of the earliest popular songs, the early recording industry, the first modern era musicians and composers, and the first formation of the consumer masses, Zhang’s book seeks to address the essential question – how did a colonized people construct their own, unique form of popular culture? Today, popular music from Korea has established itself as a formidable, global cultural phenomenon, garnering the interest of not only the power players in the global music industry, but also scholars in many cross-disciplinary fields. As an academic inquiry into the first moment in the history of popular music from Korea, an English translation of this book will be an essential resource in today’s lively conversations around the emerging field of Korean popular music. Furthermore, as a companion to more books coming from Korea to meet the growing demand for resources with diverse perspectives in the study of popular music and culture from the periphery, this book can spur on thoughtful discussions about how dialogue between English academia and the academia of host-language countries/regions, facilitated by translation, can progressively enrich the way we expand knowledge about transnational phenomena as they flow across time, borders, and languages.

This dissertation explores the particular significance of South Asia to international literary and political spheres, beginning with the formative moments of modernist internationalism. At the height of the Harlem Renaissance, W. E. B. Du Bois interrupted his work with the NAACP and the pan-African congresses to write Dark Princess: a Romance. Du Bois's turn to the romance and to India forms the point of departure for my dissertation, for India, both real and imagined, offered modernist intellectuals a space of creative possibility and representative impossibility. The fiction of Cornelia Sorabji, for instance, obfuscates and allegorizes practices of women's seclusion, both to refute imperial feminist solutions and to support her legal activism. From the imperial romance to the anti-racist one, the misrepresentation endemic to the romance genre enables the figuration of a discrepant globe. This modernist practice of transfiguring India, usually in the service of a global political vision, is undertaken both within India as well as outside of it. Rabindranath Tagore, for example, interrupted his leading role in the anti-colonial movement to write Gora, a novel of mistaken identity and inappropriate love, and to mistranslate his own poetry, particularly his Nobel-Prize-winning collection Gitanjali. If realism aims to translate cultural difference, to faithfully carry meaning across boundaries, the romances I consider in my dissertation work instead to mistranslate those differences, to produce a longed-for object beyond cultural specificity. In conversation with postcolonial theorists of Anglophone literary practice, as well as debates around translation in comparative literature, I suggest that we should think about intercultural texts in terms of transfiguration: not the carrying across of meaning from one sign system to another, but the reshaping of culturally specific materials, however instrumentally and inaccurately, in the service of internationalist goals.

Electrical stimulation and block of peripheral nerves hold great promise for treatment of a range of disease and disorders, but promising results from preclinical studies often fail to translate to successful clinical therapies. Differences in neural anatomy across species require different electrodes and stimulation parameters to achieve equivalent nerve responses, and accounting for the consequences of these factors is difficult. In Chapter 2, we describe the implementation, validation, and application of a standardized, modular, and scalable computational modeling pipeline for biophysical simulations of electrical activation and block of nerve fibers within peripheral nerves. The ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds) pipeline provides a suite of built-in capabilities for user control over the entire workflow, including libraries for parts to assemble electrodes, electrical properties of biological materials, previously published fiber models, and common stimulation waveforms. We validated the accuracy of ASCENT calculations, verified usability in beta release, and provide several compelling examples of ASCENT-implemented models. ASCENT will enable the reproducibility of simulation data, and it will be used as a component of integrated simulations with other models (e.g., organ system models), to interpret experimental results, and to design experimental and clinical interventions for the advancement of peripheral nerve stimulation therapies.

Next, in Chapter 3 we demonstrated how ASCENT can be applied to simulate accurately nerve responses to electrical stimulation. We simulated vagus nerve stimulation (VNS) for humans, pigs, and rats. We informed our models using histology from sample-specific or representative nerves, device design features (i.e., cuff, waveform), published material and tissue conductivities, and realistic fiber models. Despite large differences in nerve size, cuff geometry, and stimulation waveform, the models predicted accurate activation thresholds across species and myelinated fiber types. However, our C fiber model thresholds overestimated thresholds across pulse widths, suggesting that improved models of unmyelinated nerve fibers are needed. Our models of human VNS yielded accurate thresholds to activate laryngeal motor fibers and captured the inter-individual variability for both acute and chronic implants. For B fibers, our small-diameter fiber model underestimated threshold and saturation for pulse widths >0.25 ms. Our models of pig VNS consistently captured the range of in vivo thresholds across all measured nerve and physiological responses (i.e., heart rate, Aδ/B fibers, Aγ fibers, EMG, and Aα fibers). In rats, our smallest diameter myelinated fibers accurately predicted fast fiber thresholds across short and intermediate pulse widths; slow unmyelinated fiber thresholds overestimated thresholds across shorter pulse widths, but there was overlap for pulse widths >0.3 ms. We elevated standards for models of peripheral nerve stimulation in populations of models across species, which enabled us to model accurately nerve responses, demonstrate that individual-specific differences in nerve morphology produce variability in neural and physiological responses, and predict mechanisms of VNS therapy and side effect.

Lastly, in Chapter 4 we investigated how previous efforts to translate VNS therapies (e.g., for stroke, heart failure, and rheumatoid arthritis) have not accounted for individual and species-specific differences in nerve responses while selecting stimulation parameters, which could explain why clinical outcomes have not reproduced promising results from preclinical animal studies. We used previously validated computational models of VNS based on individual-specific nerve morphologies for populations of rats, pigs, and humans from Chapter 3 to show that a range of thresholds exists to achieve a target nerve response within and across species. We found that applying the same parameters across individuals of a species and recycling or linear scaling of stimulation parameters across species produces a large range of nerve responses. Our work highlights the need for systematic approaches to select stimulation parameters that account for individual- and species-specific differences in nerve responses to stimulation, which may be required to achieve higher response rates and greater therapeutic benefit from VNS therapies.

In the following document, I will describe two distinct strategies that poliovirus

(PV) deploys to manage host antiviral responses. In the first section, I report on a role of

the constitutive repressor of eIF2α phosphorylation (CReP) in translation of PV and the

endoplasmic reticulum (ER)-resident chaperone binding immunoglobulin protein (BiP)

at the ER. Functional, proximity-dependent labeling and cell fractionation studies

revealed that CReP, through binding of the eukaryotic translation initiation factor eIF2α,

anchors translation initiation machinery at the ER and enables protein synthesis in this

compartment. This ER site was protected from the suppression of cytoplasmic protein

synthesis by acute stress responses. I propose that partitioning of translation initiation

machinery at the ER enables cells to maintain active translation of PV during stress.

In the second section, I report that PV 2A protease cleaves all three members of

the YTHDF protein family, cytosolic N6-methyladenosine (m6A) ‘readers’ that regulate

target mRNA fate. These cleavages occurred early during infection, and preemptive

YTHDF3 depletion enhanced viral replication. This corresponded with diminished type-

I interferon (IFN) receptor (IFNAR) expression and IFN-stimulated gene induction,

while IFN production was not significantly changed. I propose that 2A protease cleaves

YTHDF proteins, in part, to interfere with IFNAR expression and antagonize the host

antiviral response.

Signaling pathways converge on the translation machinery and influence protein synthesis globally or specifically on certain classes of transcripts. The experiments described in this thesis focus on regulation of translation initiation through the cap-binding protein eIF4E.

Aberrant regulation of eIF4E has important roles in several pathologies and, most notably, in tumorigenesis. Nevertheless, the understanding of the molecular con-sequences of changes in eIF4E activity remains incomplete. We employ a cell-free system to demonstrate that eIF4E function is required for efficient cap-dependent translation but inhibitory for translation of both cellular and viral RNAs relying on cap-independent mechanisms. Furthermore, we show that phosphorylation of eIF4E favors cap-independent translation in vitro.

To verify that our findings in the cell-free system are representative of an in vivo system, we also analyzed growth of an oncolytic poliovirus, relying purely on cap-independent translation, in the context of varying activity of signaling pathways. Data obtained from this virus helps to confirm that phosphorylation of eIF4E does indeed result in increased cap-independent translation. Additionally, these experiments provide important information for the clinical application of this oncolytic poliovirus, as they help to explain virus specificity and might allow for rational patient selection.

The endoplasmic reticulum (ER) is an organelle that exists as a patchwork of

functional membrane domains with unique protein components. The rough ER is one

such domain characterized by associated ribosomal particles and is known as the site of

translation for secretory and membrane proteins (SMPs). This has since been extended

to include the translation of the entire transcriptome and other diverse functions

including autophagosome assembly and miRNA silencing, however, little is known

about the macromolecular organization of these complex biochemical processes. Using

a proximity labeling technique, BioID, four ribosome associated membrane proteins

(RAMPs) were selected to create a rudimentary map of translation on the rough ER by

combining the BioID nonspecific biotin‐labeling with streptavidin pulldowns and mass

spectrometry. This revealed distinct environments surrounding each RAMP in addition

to overlap that established spatial organization of these domains with each other. Of the

four selected, only two, LRRC59 and Sec61β of the Sec61 translocon, labeled ribosomes

in vivo. Identification of the mRNAs associated with these labeled ribosomes revealed

that translation was spatially distinct between the two sites. This supports the existence

of complex sorting mechanisms within this domain that extend to sites of optimized

protein synthesis for sub‐groups of mRNAs.

Since organisms exist within changing environments and stressors, the next step

was to determine if macromolecules associated with the ER during homeostasis change

their localization during stress, namely the unfolded protein response (UPR).

Combining DTT treatment for UPR stimulation with smFISH for ER chaperones

transcriptionally upregulated during this stress, it was determined that only specific

transcripts, e.g. GRP94, are localized to cytoplasmic granules during stress while others,

e.g. BiP, are not. Combining these observations with the existing literature, the working

hypothesis is that transcripts, such as BiP, able to recruit ribosomes during times of

inefficient cap‐dependent translation, can escape stress granules while the nascent

transcript RBP environment, such as that on GRP94, is responsible for its recruitment to

these granules. Whether this observation is generalizable to all transcripts being made

upon UPR stimulation is the subject of further study.

RAS is a small GTPase that helps to convert extracellular cues into intracellular actions. It is the most commonly mutated oncogene and is found in an active mutant form in 90% of pancreatic cancers. Therefore, study of how this protein is made and then how this protein signals in the cell could provide the foundation for novel approaches to treat RAS-driven malignancies.

First I demonstrate that the level of protein expressed from the gene KRAS, but not the highly homologous gene HRAS, is limited in mammalian cells by an abundance of underrepresented (rare) codons in the encoding mRNA. KRAS mRNA from both ectopic plasmids as well as from the endogenous cellular gene is subject to slowed translation due to these rare codons within its coding sequence. This has consequences for tumorigenesis, as replacement of the rare codons with commonly used codons accelerates RAS driven tumor growth. This may extend beyond HRAS and KRAS, as many other homologous gene pairs show a high divergence in codon usage and protein expression, suggesting that this could be a wider phenomenon used by mammalian cells to regulate protein levels.

Second, I demonstrate that RAS driven tumors partially depend on eNOS for growth. Using genetically engineered mouse models that recapitulate the spontaneous development of pancreatic cancer, I demonstrate that the protein eNOS is progressively upregulated as tumors develop. I then demonstrate that genetic ablation of eNOS partially blocks the development of preinvasive pancreatic lesions in these mice, and trends toward increasing survival in mice that develop lethal pancreatic adenocarcinoma. Furthermore, I then show that inhibition of eNOS using the clinically tested small molecule L-NAME can also slow the development of preinvasive neoplasia and nonsignificantly increase survival, although not to the level of eNOS genetic ablation. These findings are applicable to a clinical setting, as in conjunction with others I show that L-NAME treatment of human pancreatic cancer xenografts halves their growth, even when the main side effect of L-NAME, hypertension, is treated.

Together, these studies provide a better understanding of how RAS functions within the cell, and thus, ultimately, how RAS driven cancers may be treated.

Nearly thirty percent of all newly synthesized polypeptides are targeted for rapid proteasome-mediated degradation. These rapidly degraded polypeptides (RDPs) are the primary source of antigenic substrates for the major histocompatibility complex (MHC) class I presentation pathway, allowing for the immunosurveillance of newly synthesized proteins by cytotoxic T lymphocytes. Despite the recognized role of RDPs in MHC class I presentation, it remains unclear what molecular characteristics distinguish RDPs from their more stable counterparts. It has been proposed that premature translational termination products may constitute a form of RDP; indeed, in prokaryotes translational drop-off products are normal by-products of protein synthesis and are subsequently rapidly degraded.

To study the cellular fate of premature termination products, the antibiotic puromycin was used to modulate prematurely terminated polypeptide production in human cells. At low concentrations, puromycin doubled the fraction of rapidly degraded polypeptides, with enhanced degradation predominantly affecting small polypeptides, consistent with rapid degradation of truncated translation products. Immunoprecipitation experiments using anti-puromycin antisera demonstrated that the majority of peptidyl-puromycins are rapidly degraded in a proteasome-dependent manner. Low concentrations of puromycin increased the recovery of cell surface MHC class I-peptide complexes, indicating that prematurely terminated polypeptides can be processed for presentation via the MHC I pathway. In the continued presence of puromycin, MHC I export to the cell surface was inhibited, coincident with the accumulation of polyubiquitinated proteins. The time- and dose-dependent effects of puromycin suggest that the pool of peptidyl-puromycin adducts differ in their targeting to various proteolytic pathways which, in turn, differ in the efficiency with which they access the MHC class I presentation machinery. These studies highlight the diversity of cellular proteolytic pathways necessary for the metabolism and immunosurveillance of prematurely terminated polypeptides which are, by their nature, highly heterogeneous.

Multiple signaling pathways control protein synthesis by modulating translation initiation factors. Map Kinase Integrating Kinase 1 (Mnk1) relays signals to its major downstream target eIF4E. Activation of Mnk1 and subsequent phosphorylation of eIF4E results in changes in translation rates for subsets of mRNAs. Both the Erk1/2 and p38 MAPK pathways activate Mnk1 meaning that Mnk1 responds to growth signals through Erk1/2 and stress signals through p38 MAPK. However, it is not clear how Mnk1 mediates translational changes specific to each pathway. We investigated the activation of Mnk1 by stress and cytokines through the p38 MAPK pathway. We found that of the four different p38 MAPK isoforms, p38α alone controls acute stress and cytokine signaling to translation machinery. Furthermore, this regulatory axis is greatly diminished in neurons. We discovered that p38α expression is repressed in the brain due to two neuron-selective microRNAs, miR-124 and -128. Next, we investigated the mechanism of p38α mediated Mnk1 activation to see if it differed from Erk1/2 mediated activation. Looking at the induced binding of Mnk1 to eIF4G, we found that the dissociation rate varies depending on the activating pathways. This shows that Mnk1 is not a true convergence point of p38 and Erk1/2 MAPK pathways resulting in identical downstream effects, but that Mnk1 mediates pathway specific effects on translation factors.

The Flavivirus genus contains several arthropod-borne viruses that pose global health threats, including dengue virus (DENV). We identified two ribosomal proteins, RPLP1 and RPLP2 (RPLP1/2), that are crucial host factors required for translation of flaviviruses and efficient flavivirus infection of human cell lines and Aedes aegypti mosquitoes, which are natural vectors for these viruses. We hypothesized that RPLP1/2 are accessory ribosomal proteins that function to promote translation of specific cellular mRNAs sharing undefined features with the DENV genome. We found that these proteins are not broadly required for cellular translation and but are necessary for efficient accumulation of DENV proteins early in infection and ectopically expressed DENV structural proteins. The ribosome profiling technique allowed us to quantitative map ribosomes across the transcriptome during early DENV infection in human cell lines depleted for RPLP1/2. We observed that local ribosome occupancy is altered in the viral open reading frame with RPLP1/2 knockdown, consistent with a role for RPLP1/2 in promoting translation elongation. The most prominent ribosome pausing site in the DENV RNA was in the 5’ end of the E protein coding sequence which is located 210 nts downstream of two adjacent TMs. We also observed that RPLP1/2 depletion resulted in altered ribosome density in mRNAs encoding two or more transmembrane domains. This work increases our knowledge on DENV translation regulation and sheds light on the function of RPLP1/2 in translation of specific cellular RNAs.

The cerebral cortex is an anatomically complex brain structure that controls our higher cognitive functions such as abstract thought and language. The cortex is largely shaped during embryonic development when radial glial progenitors divide and differentiate to produce neurons. Neurons are organized into 6-layers through migration guided by the structural support of radial glial cells. Disruptions in progenitor proliferation or neuronal migration underly diverse neurodevelopmental disorders with life-long impacts on cognitive, psychiatric, and motor functions. Developmental mechanisms that build the brain are regulated by precise gene-expression networks. Here, we uncover two novel layers of post-transcriptional mRNA regulation in the developing cortex. First, we used model models to describe a widespread phenomenon of mRNA localization to the distal structures—the basal process and endfeet—of radial glial progenitors. With live imaging approaches, we detected active mRNA transport to and local translation within radial glial endfeet. Transcriptomic and proteomic analyses revealed that endfeet contain cytoskeletal, signaling, and proteostasis factors that may be locally and dynamically controlled. The second line of investigation focused on the RNA-helicase DDX3X which is frequently mutated in neurodevelopmental disorders. We discovered that Ddx3x is required both in progenitor differentiation and neuronal migration in the developing mouse cortex. DDX3X mutations varied from loss-of-function to missense alleles, and a subset of missense variants caused severe cortical malformations in patients. Biochemical and cell biological assays revealed that dominant missense mutations reduced DDX3X helicase activity and induced formation of RNA-protein aggregates associated with impaired translation, uncovering novel pathologies underlying developmental disorders. Together, these studies extend our understanding of post-transcriptional regulation in brain development and neurodevelopmental disorders.

The partitioning of translation to the outer membrane of the endoplasmic reticulum is a problem that has been the subject of inquiry since the discovery of the ribosome. The large degree to which ribosomes were found to be tethered to the membrane led to intense investigation of a series of related questions regarding the identity of those mRNAs that are translated on the endoplasmic reticulum, and the functions of that localization in cell stress. In this dissertation, I approach each of these questions in turn and work to reconcile my observations with those models that have been previously proposed. A theme of this work is the application of modern methods, particularly deep sequencing technology, to address problems that had largely been considered solved. The most prominently featured method is ribosome profiling, which is paired with classical biochemical and cell biological techniques. I arrive at several conclusions: 1) a significant fraction of all mRNAs is well represented on the endoplasmic reticulum membrane, 2) the properties of translation diverge substantially between membrane-associated and free ribosomes, and 3) the compartmentalization of translation can serve as an important variable in cell stress.

The ability to rapidly alter gene expression is essential to surviving fluctuating environments. The disjunction between mRNA abundance and mRNA translation is of particular interest in stress responses that elicit large scale gene expression reprogramming. Targeted changes in the translation efficiency of select mRNA, within the standing pool of total mRNA, allow for rapid alterations in the proteome upon environmental cue. Here, I discover large changes in the translational landscape that are independent from the underlying transcriptional dynamics during the early stages of PAMP-Triggered Immunity (PTI) and a coordinated translational response during the later stage Effector-Triggered Immunity (ETI). Certain mRNAs borne features, such as mRNA methylation and uAUGs, which initiate uORFs, that are known to affect mRNA stability and translation activity, yet little is known about how these elements affect mRNA translation during infection stress. Through observations of translation dynamics, I investigated the impact of known and novel mRNA features on local immunity. In addition, I discovered additional facets of the plant immune response including a novel mRNA sequence consensus, which I call the R-motif that induces mRNA translation upon pathogen detection.

This dissertation examines the translation and printing of the Qur'an in the late Ottoman Empire and the early years of the Republic of Turkey (1820-1938). As most Islamic scholars deem the Qur'an inimitable divine speech, the idea of translating the Qur'an has been surrounded with concern since the first centuries of Islam; printing aroused fears about ritual purity and threatened the traditional trade of the scribes. This study examines how Turkish Muslims challenged these concerns and asserted the necessity to print and translate the Qur'an in order to make the text more accessible.

With the spread of the printing press and literacy in the nineteenth and twentieth centuries, Qur'an translations have become increasingly important as means of transmitting the meaning of the text to expanding audiences. I investigate the rise of Qur'an translation through a historical survey of Ottoman and Turkish language translations and an examination of the debates surrounding them waged in periodicals, government archives, and monographs. While Turkish translations have often been construed as a product of nationalism, I argue that the rise of translation began with a renewed emphasis on the Qur'anic theme of intelligibility bolstered by the availability of printed books, the spread of state schools, and increased knowledge of European history and intellectual currents. Turkish nationalists later adopted and advocated the issue, reconstruing the "Turkish Qur'an" as a nationalist symbol.

Over the course of the nineteenth and twentieth centuries, the meaning of Qur'an translation itself has changed and incorporated a variety of new concerns. Asserting translation of the Qur'an in the late Ottoman Empire became synecdoche for a new vision of Muslim authority and modernity that reduced the role of the ulama and created space for interpretive plurality on an unprecedented scale. Meanwhile, some Turkish intellectuals came to appreciate the symbolic value of Turkish renderings for the assertion of national identity in the Islamic sphere. While the notion of translation as replacement has withered, in practice, translations have come to play a robust role in Turkish Muslim life as supplement and counterpoint to the Qur'anic text.

microRNAs (miRNAs) downregulate the expression of numerous mRNAs and are involved in almost every biological process where they have been examined. Inherent sequence or cis-elements located in mRNA termini and 5' and 3' UTRs likewise influence post-transcriptional gene regulation. We delineate the relative importance of the 5' m7G-cap, the 3' poly(A) tail, and Internal Ribosome Entry Sites (IRESs) in miRNA-mediated repression. mRNA targets must contain a m7G-cap to be repressed, are repressed to a greater extent when containing a poly(A) tail, and are not precluded from repression when translating via an IRES.

miRNAs can inhibit translation and / or induce mRNA decay. While the core effector proteins are established, mechanistic details of how miRNAs interfere with mRNA translation and stability remain elusive. Contrary to the repressive effects of miRNAs, the poly(A)-binding protein (PABP) (through binding to the poly(A) tail and eIF4G) can increase both translation and mRNA stability independently. We elucidate a functional role for the PABP in miRNA repression; manipulation of `active' PABP levels affects repression conversely in part by inhibiting miRNA-induced deadenylation. Furthermore, we find that expression changes in the PABP binding partner PABP interacting protein 2 (Paip2) modulates both miRNA repression and PABP protein complex formation. Additionally, we establish Paip2 as a bona fide miR-128 target, and demonstrate miR-128 de-repression of non-miR-128 target mRNAs through this targeting event.