Joshua Kruchten

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Joshua Kruchten is a former graduate student of English and American literature at New York University and was recently selected as an Erasmus Mundus student of European Literary Cultures in Strasbourg and Bologna until 2019. Josh has previously studied at Northeastern University and the American University of Paris, and has held research positions at the Harvard NeuroDiscovery Center and Weill-Cornell Medical College. He has also been awarded funding for independent research at both Northeastern University and New York University. As a former researcher in cell and molecular biology, his research interests are far-ranging and interdisciplinary, with a growing interest in intersection points between early modern literature, art, philosophy, and science. Interests include botany, genetics, cartography, and discovery. He is particularly interested in the history of books, reading, and writing, and the relationship between books, animals, and the natural world. Josh has recently finished a thesis on beekeeping and book-keeping in early modern England, and is working on a thesis on apiary representations in early modern France and Italy.

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Articles by Joshua Kruchten

Scholars Love Books (?)

An essay for the Revue de la BNU about my relationship with book history and material culture stu... more

The Casebooks Project

ride, 2017

This essay reviews The Casebooks Project, an ambitious attempt to digitize 80,000 astrological me... more This essay reviews The Casebooks Project, an ambitious attempt to digitize 80,000 astrological medical records from early modern England. The Casebooks Project exemplifies the possibilities of using digital technologies to understand early modern cultural and intellectual history, and offers us insight into the process of creating such a project. However, it remains unclear who the project's audience is, whether to see it purely as a 'dataset' or as a textual-based digital edition, and how public-facing the project wants to be. This review seeks to use the digital edition and Dr. Lauren Kassell's ongoing scholarly and public reflections on the project to highlight the project's successes and suggest further possibilities it may inspire.

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Structure–function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring

A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direc... more A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure–function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein–RNA and protein–protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not.

format_quoteDefined a stereotype triad of Sm protein-RNA interactions, pivotal for understanding binding dynamics in RNA processing.format_quote

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Transcription Factors and DNA Repair Enzymes Compete for Damaged Promoter Sites

Transcriptional regulation is a tightly regulated, vital process. The transcription factor (TF) C... more Transcriptional regulation is a tightly regulated,
vital process. The transcription factor (TF)
CREB1 controls ~25% of the mammalian
transcriptome by binding the CRE sequence
(TGACGTCA). DNA lesions within CRE
modulate CREB1 binding negatively and
positively. Because appropriate DNA lesions
also interact with base excision repair (BER)
proteins, we investigated whether CREB1 and
repair glycosylases compete with each other. We
incubated 39-mer CRE-containing ds
oligonucleotides with recombinant CREB1 alone
or with UNG2 or OGG1, followed by
electrophoretic mobility shift assay (EMSA).
The CpG islet within CRE was modified to
contain a G/U or 8-oxoG (oG)/C mispair. OGG1
and CREB1 reversibly competed for CRE
containing an oG/C pair. Also, OGG1 blocked
CREB1 from dimerizing by 69%, even when
total CREB1 binding was reduced only by 20%-
30%. In contrast, bound CREB1 completely
prevented access to G/U-containing CRE by
UNG2, and, therefore, to BER repair, while
UNG2 exposure prevented CREB1 binding.
CREB1 dimerization was unaffected by UNG2
when CREB1 bound to CRE, but was greatly
reduced by prior UNG2 exposure. To explore
physiological relevance, we microinjected
zebrafish embryos with the same
oligonucleotides, as a sink for endogenous
CREB1. As predicted, microinjection with
unmodified or lesion-containing CRE, but not
scrambled CRE or scrambled CRE with a G/U
mispair, resulted in increased embryo death.
However, only the G/U mispair in native CRE
resulted in substantial developmental
abnormalities, thus confirming the danger of
unrepaired G/U mispairs in promoters. In
summary, CREB1 and DNA glycosylases
compete for damaged CRE in vitro and in vivo,
thus blocking DNA repair and resulting in
transcriptional misregulation leading to
abnormal development.

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Conference Presentations by Joshua Kruchten

Transcription Factors Obstruct DNA Repair

Oxidative damage, deamination, and formation of abasic sites require repair by the base-excision ... more Oxidative damage, deamination, and formation of abasic sites require repair by the base-excision repair (BER) pathway. This pathway is partially regulated by the important transcription factor cyclic AMP-responsive element-binding protein (CREB), which regulates approximately 25% of the human genome. DNA damage repaired by BER enhances or represses CREB’s ability to bind to its consensus sequence (CRE) and dimerize. In particular, the presence of uracil appears to have an enhancing effect, while other lesions in the pathway, including 8-oxo-G, appear to have a diminishing effect. Protein competition assays have shown that human UNG2, the major DNA glycosylase responsible for uracil excision, is not as efficient at uracil removal when CREB is bound to a CRE sequence containing uracil, nor does UNG2 seem to completely displace CREB. We further examined these experiments to determine if UNG2 and OGG1 cleavage was altered in the presence of CREB. We repeated previous binding experiments, exposing CREB and UNG2 or OGG1 to a 5’-radiolabeled double-stranded CRE-substrate containing a G/U mispair or a °G/C. We then isolated the DNA by chloroform:phenol extraction and resolved fragments by denaturing gel electrophoresis. We conclude that CREB prevents base removal both by UNG2 and OGG1, blocking further repair of the damaged base. Since UNG2, but not OGG1, turn over rapidly, some cleavage by UNG2 but not OGG1 is manifest.

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Translations by Joshua Kruchten

Plan for LGBT Citizens (Plan de Ciudadanía LGBT, Segunda Edición)

Translation developed as part of an internship project at the Federación Argentina LGBT in Spring... more Translation developed as part of an internship project at the Federación Argentina LGBT in Spring 2013, generously supported by Northeastern University and the FALGBT. This English translation strove to provide to an English-speaking audience an understanding of the current social, legal, and political realities of LGBT Argentinians, encompassing both their recent successes and efforts that still needed to be made. This final translation was presented to the Argentine Congress in late spring 2013.

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Joshua Kruchten

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