Archive for the ‘Faculty Publications’ Category

Vicki Baker

Thursday, January 18th, 2018

Baker, V. L., Lunsford, L. G., & Pifer, M. J. (2017). Developing Faculty in Liberal Arts Colleges: Aligning Individual Needs and Organizational Goals. New Brunswick, NJ: Rutgers University Press.

Abstract:  Developing Faculty Members in Liberal Arts Colleges analyzes the career stage challenges these faculty members must overcome, such as a lack of preparation for teaching, limited access to resources and mentors, and changing expectations for excellence in teaching, research, and service to become academic leaders in their discipline and at these distinctive institutions.  Drawing on research conducted at the thirteen institutions of the Great Lakes Colleges Association, Vicki L. Baker, Laura Gail Lunsford, and Meghan J. Pifer propose a compelling Alignment Framework for Faculty Development in Liberal Arts Colleges to show how these colleges succeed—or sometimes fail—in providing their faculties with the right support to be successful.

Philip Voss

Thursday, January 18th, 2018

Jigmeddorj, B., Garrett, P. E., Andreoiu, C. A., Ball, G. C., Bruhn, T., Cross, D. S., et al. (2017). High-Statistics β+/EC-Decay Study of 122Xe. Physics Procedia, 90(Supplement C), 435-439.

Abstract:  Low-lying excited states of 122Xe have been studied via the β+/EC decay of 122Cs with the 8π γ-ray spectrometer at the TRIUMF Isotope Separator and Accelerator facility. The data collected have enabled the observation of new in-band transitions in the excited 0+ state bands. In addition, the 2+ members of the second 0+ and third 0+ state bands have been firmly confirmed by angular correlation analysis.

Tammy Jechura

Thursday, January 11th, 2018

Woodard, M. A., Jechura, T. J., & Elias, E. P. (2017). Sleep and College Satisfaction. North American Journal of Psychology, 19(3), 573-584.

Abstract: College students face a number of obstacles to achieving proper sleep hygiene and this could have an impact on their overall college experience, as much as on their day-to-day functioning. The current study was designed to assess the relationship between sleep and satisfaction with overall college experience. It was hypothesized that poorer sleep, including fewer hours of sleep and lower quality of sleep, would be correlated with a more negative view of one’s college experience. Students currently enrolled in a small midwestern college (n=74; 52 females) were assessed for sleep quantity and quality using a modified version of the Pittsburgh Sleep Quality Index (adapted from Buysse et al., 1988). A second questionnaire, adapted from the Satisfaction with Life Scale and the Index for Job Satisfaction (Brayfield & Rothe, 1951; Diener et al., 1985), was used to measure satisfaction with college experience. Results revealed that individuals with better sleep hygiene also had higher college satisfaction levels. Additionally, a mediational regression showed that mood mediates the relationship between sleep and college satisfaction. This implies that greater sleep disturbance leads to a more negative mood in students which, in turn, leads to less satisfaction with college experience.

Abigail Cahill

Monday, January 8th, 2018

Cahill, A. E., De Jode, A., Dubois, S., Bouzaza, Z., Aurelle, D., Boissin, E., et al. (2017). A multispecies approach reveals hot-spots and cold-spots of diversity and connectivity in invertebrate species with contrasting dispersal modes. Molecular Ecology, 26(23), 6563-6577.

Abstract: Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50 km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (1) Species without larvae showed higher levels of genetic structure than species with free-living larvae but the role of larval type (lecithotrophic or planktotrophic) was negligible. (2) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (3) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related with local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.

Holger Elischberger, Eric Hill and Lynn Verduzco-Baker

Monday, January 8th, 2018

Elischberger, H. B., Glazier, J. J., Hill, E. D., & Verduzco-Baker, L. (2018). Attitudes Toward and Beliefs about Transgender Youth: A Cross-Cultural Comparison Between the United States and India. Sex Roles, 78, 142-160.

Abstract: Using an internet-based survey, we examined attitudes toward transgender youth in the United States and India, two cultures with differences in conceptualizations of gender and treatment of transgender individuals in society, law, and religion. We found generally positive attitudes toward transgender youth in our U.S. (n = 218), but moderately negative ones in our Indian (n = 217), sample. Consistent with the literature on prejudice against transgender adults in many Western societies, general social conservatism in the form of religious beliefs and political ideology, gender-specific conservatism in the form of gender binary belief, and endorsement of environmental rather than biological causes of transgender identity were the best predictors of U.S. participants’ attitudes, although personal contact with gender and sexual minorities also played a role at the bivariate level. These findings suggest that the processes underlying prejudice against transgender youth are similar to those that foster adult-directed transphobia in that cultural context. In contrast, religion-based disapproval and environmental causal attributions were the best predictors of Indian respondents’ attitudes, whereas gender binary belief played only a minor role, and political conservatism and personal contact no role at all. Our regression analyses accounted for considerably more of the variability in U.S. than in Indian participants’ attitudes, highlighting the need for additional (qualitative) work to identify the factors that promote transprejudice in India. We discuss these findings in light of cross-cultural differences between the two countries in terms of our predictors and consider implications for efforts to reduce prejudice against transgender youth.

Albion College Student Co-Author: Jessica Glazier, ’16

Joseph Ho

Friday, November 17th, 2017

Charles, B., & Ho, J. W. (Eds.). (2017). War and occupation in China : the letters of an American missionary from Hangzhou, 1937-1938. Lanham, Maryland: Lehigh University Press.

Mareike Wieth

Thursday, November 9th, 2017

Burns, B. D., Zhang, Y., Wieth, M., & Touyz, S. (2017). An exploratory study of creativity and eating disorders. Journal of Eating Disorders, 5(1), 45.

Abstract: We examined whether cognitive rigidity associated with having an eating disorder generalized to creativity. One hundred twelve participants from the participant pool of an Australian university were given a measure of disordered eating (EDE-Q), asked if they had ever had a diagnosis of an eating disorder (16 reported yes), and given 3 min to generate alternative uses for a paper-clip. The alternative uses task yielded measures of creative fluency, originality, elaboration and flexibility. A logistic regression found that only lower flexibility predicted a self-reported ED diagnosis. Across the spectrum of disordered eating behaviour there was no association between creativity measures and EDE-Q global scores. Our results were consistent with previous findings of an association between cognitive inflexibility and having an ED. However we found no evidence that cognitive inflexibility generalized to creativity more broadly. Our results may lend support to Cognitive Remediation Therapy, but further study is required.

Vicki Baker

Thursday, November 2nd, 2017

Baker, V., & Terosky, A. (2017). Early Career Faculty Mentoring: Career Cycles, Learning and Support. In D. A. Clutterbuck, F. K. Kochan, L. Lunsford, N. Dominguez & J. Haddock-Millar (Eds.), The SAGE Handbook of Mentoring: SAGE Publishing.

Philip Voss

Friday, October 20th, 2017

Voss, P., Drake, T. E., Starosta, K., Andreoiu, C., Ashley, R., Ball, G. C., et al. (2017). Doppler-shift attenuation lifetime measurement of the  36Ar 21+ level. Physical Review C, 96(2), 024305.

Abstract:

At TRIUMF, the TIGRESS Integrated Plunger device and its suite of ancillary detector systems have been implemented for charged-particle tagging and light-ion identification in coincidence with γ-ray spectroscopy for Doppler-shift lifetime studies and low-energy Coulomb excitation measurements. As a test of the device, the lifetime of the first 2+ excited state in 36Ar was measured from the γ-ray line shape of the 2+1 →0+g.s. transition using the Doppler-shift attenuation technique following Coulomb excitation. The line-shape signatures, vital for precision lifetime measurements, were significantly improved by enhanced reaction-channel selectivity using a complementary approach of kinematic gating and digital rise-time discrimination of recoiling charged particles in a silicon PIN diode array. The lifetime was determined by comparisons between the data and simulated line shapes generated using our TIGRESS Coulomb excitation code as an input to the Lindhard method, which was then extended and included as a class in geant4. The model-independent lifetime result of 490±50 fs corresponds to a reduced quadrupole transition strength of B(E2;2+1 →0+g.s.)=56±6 e2 fm4 and agrees well with previous intermediate energy Coulomb excitation measurements, thereby resolving reported discrepancies in the 2+1 level lifetime in this self-conjugate nucleus.

Carrie Booth Walling

Thursday, October 12th, 2017

Deloffre, M. Z., & Walling, C. B. (2017). Contentious Politics in the United States: What Role for Political Scientists? . PS: Political Science and Politics, 50(4), 985-989.

 

Ola Olapade

Monday, October 2nd, 2017

Olapade, O. A. (2017). Community Composition and Diversity of Coastal Bacterioplankton Assemblages in Lakes Michigan, Erie, and Huron. Microbial Ecology.

Abstract: The Laurentian Great Lakes, including Lakes Superior, Michigan, Huron, Erie, and Ontario, located in the eastern part of North America are considered the largest of freshwater lakes in the world; however, very little is known about the diversity and distribution of indigenous microbial assemblages within these vast bodies of freshwater systems. Therefore, to delineate the microbial structure and community composition in these aquatic environments, combinations of high-throughput sequencing and fluorescent in situ hybridization (FISH) approaches were utilized to quantitatively characterize the occurrence, diversity, and distribution of bacterioplankton assemblages in six different sites located along the coastal regions of Lakes Michigan, Huron, and Erie. Phylogenetic examination showed a diverse bacterial community belonging to 11 different taxonomic groups. Pyrosequencing results revealed that the majority of the sequences were clustered into four main groups, i.e., Proteobacteria, Bacteriodetes, Actinobacteria, and Cyanobacteria, while fluorescent in situ hybridization also showed the numerical dominance of members of the Gammaproteobacteria and the Cytophaga-Flavobacterium in the six lake sites examined. Overall, the assemblages were shown to be quite diverse in distribution among the lake sites examined, comprising mostly of various heterotrophic populations, with the exception of the Lake Erie-Sandusky Bay site with more than 50% domination by autotrophic Cyanobacteria. This indicates that combinations of factors including water chemistry and various anthropogenic disturbances as well as the lake morphometric characteristics are probably influencing the community structure and diversity of the bacterial assemblages within the systems.

Nicolle Zellner

Friday, September 22nd, 2017

Huang, Y. H., Minton, D. A., Hirabayashi, M., Elliott, J. R., Richardson, J. E., Fassett, C. I., Zellner, N.E.B. (2017). Heterogeneous impact transport on the Moon. Journal of Geophysical Research-Planets, 122(6), 1158-1180.

Abstract: Impact cratering is the dominant process for transporting material on the Moon’s surface. An impact transports both proximal material (continuous ejecta) locally and distal ejecta (crater rays) to much larger distances. Quantifying the relative importance of locally derived material versus distal material requires understandings of lunar regolith evolution and the mixing of materials across the lunar surface. The Moon has distinctive albedo units of darker mare basalt and brighter highland materials, and the contacts between these units are ideal settings to examine this question. Information on the amount of material transported across these contacts comes from both the sample collection and remote sensing data, though earlier interpretations of these observations are contradictory. The relatively narrow (similar to 4-5 km wide) mixing zone at mare/highland contacts had been interpreted as consistent with most material having been locally derived from underneath mare plains. However, even far from these contacts where the mare is thick, highland material is abundant in some soil samples (>20%), requiring transport of highland material over great distances. Any model of impact transport on the Moon needs to be consistent with both the observed width of mare/highland contacts and the commonality of nonmare material in mare soil samples far from any contact. In this study, using a three-dimensional regolith transport model, we match these constraints and demonstrate that both local and distal material transports are important at the lunar surface. Furthermore, the nature of the distal material transport mechanism in discrete crater rays can result in substantial heterogeneity of surface materials.

Allison Harnish

Friday, September 22nd, 2017

Graddy-Lovelace, G., Harnish, A., & Hazlewood, J. A. (2016). World Is Burning, Sky Is Falling, All Hands on Deck! Reflections on Engaged and Action-Oriented Socio-Environmental Scholarship. In N. Haenn, R. Wilk & A. Harnish (Eds.), The Environment in Anthropology: A Reader in Ecology, Culture, and Sustainable Living (Second edition ed., pp. 445-481). New York: New York University Press.

Ken Saville

Thursday, September 7th, 2017

Leung, W., Shaffer, C. D., Chen, E. J., Quisenberry, T. J., Ko, K., Braverman, J. M., et al. (2017). Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3-Genes Genomes Genetics, 7(8), 2439-2460.

Abstract: The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (similar to 5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 59 ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

Vicki Baker

Thursday, September 7th, 2017

Baker, V. L., Terosky, A. L., & Martinez, E. (2017). Faculty Members’ Scholarly Learning Across Institutional Types (ASHE Higher Education Report, Volume 43, Number 2): Jossey-Bass.

Philip Voss

Tuesday, August 1st, 2017

Pore, J. L., Cross, D. S., Andreoiu, C., Ashley, R., Ball, G. C., Bender, P. C., et al. (2017). Study of the β decay of 116m1In: A new interpretation of low-lying 0+ states in 116Sn. The European Physical Journal A, 53(2), 27.

Abstract: The 116Sn nucleus contains a collective rotational band originating from proton π 2p-2h excitations across the proton Z = 50 shell gap. Even though this nucleus has been extensively investigated in the past, there was still missing information on the low-energy interband transitions connecting the intruder and normal structures. The low-lying structure of 116Sn was investigated through a high-statistics study of the β decay of 116m1In with the 8π spectrometer and its ancillary detectors at TRIUMF. These measurements
are critical in order to properly characterize the π 2p-2h rotational band. Weak γ-decay branches are observed utilizing γ-γ coincidence spectroscopy methods, leading to the first direct observation of the
85 keV 2+2 → 0+3 γ ray with a transition strength of B(E2) = 99.7(84) W.u. The analysis of these results strongly suggests that the 2027 keV 0+3 state should replace the previously assigned 1757 keV 0+2 state as the band-head of the π 2p-2h rotational band.

Nicolle Zellner

Tuesday, August 1st, 2017

Zellner, N. E. B. (2016). Lunar Regolith: Materials. In B. Cudnik (Ed.), Encyclopedia of Lunar Science (pp. 1-7). Springer International Publishing.

Brad Chase

Tuesday, August 1st, 2017

Abhayan, G. S., Joglekar, P. P., Rajesh, S. V., Aswathy, G. S., Chase, B., Ajithprasad, P., et al. (2016). Fish Otoliths from Navinal, Kachchh, Gujarat: Identification of Taxa and Its Implications. Heritage: Journal of Multidisciplinary Studies in Archaeology, 4, 218-227.

Abstract: Among archaeological fauna, considerable amounts of fish remains have been reported from several archaeological sites in Gujarat especially from the Harappan context. Fish remains have not received due attention in faunal studies conducted in South Asia in general owing to several factors. This paper is a preliminary study on fish otoliths from the surface collection at the Harappan site of Navinal, Kachchh, Gujarat. A total of 2257 numbers of otoliths were collected and studied from the site. Identification of taxa was done using comparative modern reference collection of fishes. Six species of fish were identified from the otolith assemblage from Navinal which belong to two families namely Ariidae and Sciaenidae. Fishery practices of the Harappans are assumed on the basis of the identified fish species.

Ashley Miller

Tuesday, August 1st, 2017

Miller, A. (2016). Speech paralysis : ingestion, suffocation, and the torture of listening. In L. M. Voskuil (Ed.), Nineteenth-century energies : literature, technology, culture. Abingdon, UK ; New York: Routledge.

David Reimann

Tuesday, August 1st, 2017

Reimann, D. A. (2016). Snub Polyhedral Forms Constructed from Flexible 60-120 Degree Rhombic Tiles. Proceedings of Bridges 2016: Mathematics, Music, Art, Architecture, Education, Culture, 443-444.

Abstract: We construct snub polyhedral forms using rhombi made from paper-backed wood veneer which are connected pairwise at corners using split-pin fasteners. Combining pairs of adjacent triangular faces into roughly 60°-120° rhombi result in polyhedron with even degree vertices. The flexibility of the materials allows the final closing of the object into a roughly spherical shape, despite eliminating the dihredral angle between the adjacent paired triangles. The open lattice construction yields elegant chiral symmetric forms with visual movement.

Holger Elischberger and Eric Hill

Tuesday, July 18th, 2017

Foster, S. D., Elischberger, H. B., & Hill, E. D. (2017). Examining the Link Between Socioeconomic Status and Mental Illness Prejudice: The Roles of Knowledge About Mental Illness and Empathy. Stigma and Health.

Abstract: Unlike people suffering from most physical afflictions, those with mental illness often face prejudice. This study examines the interplay of several key social and personal predictors of mental illness prejudice: SES, empathy, mental illness knowledge, and personal acquaintance with the mentally ill. As expected, analyses showed that higher subjective (although not objective) SES, lower levels of empathy, and lower levels of knowledge about mental illness all predicted increased prejudice against people suffering from clinical depression and nondescript mental illness—although not against people suffering from schizophrenia. Path analyses showed evidence for a mediating role of knowledge and empathy in the link between SES and prejudice. Implications of these findings for ways to diffuse mental illness prejudice are discussed.

Allison Harnish

Monday, July 17th, 2017

Haenn, N., Wilk, R. R., & Harnish, A. (Eds.). (2016). The Environment in Anthropology (Second Edition): A Reader in Ecology, Culture, and Sustainable Living. New York: NYU Press.

Drew Christopher

Thursday, June 29th, 2017

Christopher, A. N. (2017). Interpreting and using statistics in psychological research. Thousand Oaks, California: SAGE Publications.

Jess Roberts

Monday, June 26th, 2017

Roberts, J. (2016). “hear the bird”: Sarah Piatt and the Dramatic Monologue. In A. Socarides & J. Putzi (Eds.), A History of Nineteenth-Century American Women’s Poetry (pp. 345-358). Cambridge: Cambridge University Press.

Abstract: For much of the latter half of the nineteenth century, American poet Sarah Piatt wrote and published poems that gave voice to women and children, that grieved the loss of loved ones and moral certainty, and that revealed an unnerving inclination for self-conscious complexity. Some of the most culturally influential periodicals of her time – Atlantic Monthly, Harper’s Weekly, Scribner’s – circulated hundreds of her poems, as well as reviews of the many collections of these poems in book form. These reviews were, by turns, delighted and discomfited by what they called Piatt’s “distinctiveness,” heralding her as one of America’s geniuses even as they cautioned her against apparently unbecoming subtlety and obscurity.

Among the things that distinguished Piatt was her obvious interest in the contextual dynamism of spoken language and the poetic genre that seemed particularly well suited to capitalize on and examine it: the dramatic monologue. Over the course of her career, Piatt wrote more dramatic monologues than any other nineteenth-century American poet. Though many Piatt scholars have addressed dramatic monologues in the context of essays about Piatt’s irony or ambivalence, and in terms of her place among Confederate poets or in postbellum magazine culture, no one has yet read her dramatic monologues primarily through the lens of genre. That is what I do here. In the pages that follow, I describe the generic conventions of the dramatic monologue that are integral to Piatt’s experiments with it, building an interpretive framework out of the doubleness inherent to the genre. I ground that analysis in Piatt’s fifth collection, Dramatic Persons and Moods (1879), because it provides the poems I address with a shared print context, the very title of which directs the reader’s eye to genre. What emerges is a clear picture of how Piatt manipulated the particular conventions of the dramatic monologue in order to anatomize the way women maintained and disrupted the very conventions that restricted their range of experience and expression in their roles as mothers and daughters, readers and writers.

Nicolle Zellner

Friday, June 23rd, 2017

Zellner, N. E. B. (2017). Cataclysm No More: New Views on the Timing and Delivery of Lunar Impactors. Origins of Life and Evolution of Biospheres, 1-20.

Abstract: If properly interpreted, the impact record of the Moon, Earth’s nearest neighbour, can be used to gain insights into how the Earth has been influenced by impacting events since its formation ~4.5 billion years (Ga) ago. However, the nature and timing of the lunar impactors – and indeed the lunar impact record itself – are not well understood. Of particular interest are the ages of lunar impact basins and what they tell us about the proposed “lunar cataclysm” and/or the late heavy bombardment (LHB), and how this impact episode may have affected early life on Earth or other planets. Investigations of the lunar impactor population over time have been undertaken and include analyses of orbital data and images; lunar, terrestrial, and other planetary sample data; and dynamical modelling. Here, the existing information regarding the nature of the lunar impact record is reviewed and new interpretations are presented. Importantly, it is demonstrated that most evidence supports a prolonged lunar (and thus, terrestrial) bombardment from ~4.2 to 3.4 Ga and not a cataclysmic spike at ~3.9 Ga. Implications for the conditions required for the origin of life are addressed.

Greg Saltzman

Friday, June 23rd, 2017

Saltzman, G. M. (2016). Contested Terrain:  Developments in Labor Law Affecting Higher Education Since 2012. In H. S. Wechsler (Ed.), NEA 2016 Almanac of Higher Education (Washington:  National Education Association (pp. 31-38).

Vicki Baker

Thursday, June 22nd, 2017

Baker, V. (2017). Organizational Contexts & Formal Mentoring Programs: Aligning Individual and Organizational Outcomes. In D. A. Clutterbuck, F. K. Kochan, L. Lunsford, N. Dominguez & J. Haddock-Millar (Eds.), The SAGE Handbook of Mentoring: SAGE Publishing.

Christopher Rohlman

Thursday, June 22nd, 2017

Rohlman, C. E., Blanco, M. R., & Walter, N. G. (2016). Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome. In M. Spies & Y. R. Chemla (Eds.), Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods (Vol. 581, pp. 257-283).

Abstract: The spliceosome is a biomolecular machine that, in all eukaryotes, accomplishes site-specific splicing of introns from precursor messenger RNAs (pre-mRNAs) with high fidelity. Operating at the nanometer scale, where inertia and friction have lost the dominant role they play in the macroscopic realm, the spliceosome is highly dynamic and assembles its active site around each pre-mRNA anew. To understand the structural dynamics underlying the molecular motors, clocks, and ratchets that achieve functional accuracy in the yeast spliceosome (a long-standing model system), we have developed single-molecule fluorescence resonance energy transfer (smFRET) approaches that report changes in intra-and intermolecular interactions in real time. Building on our work using hidden Markov models (HMMs) to extract kinetic and conformational state information from smFRET time trajectories, we recognized that HMM analysis of individual state transitions as independent stochastic events is insufficient for a biomolecular machine as complex as the spliceosome. In this chapter, we elaborate on the recently developed smFRET-based Single-Molecule Cluster Analysis (SiMCAn) that dissects the intricate conformational dynamics of a pre-mRNA through the splicing cycle in a model-free fashion. By leveraging hierarchical clustering techniques developed for Bioinformatics, SiMCAn efficiently analyzes large datasets to first identify common molecular behaviors. Through a second level of clustering based on the abundance of dynamic behaviors exhibited by defined functional intermediates that have been stalled by biochemical or genetic tools, SiMCAn then efficiently assigns pre-mRNA FRET states and transitions to specific splicing complexes, with the potential to find heretofore undescribed conformations. SiMCAn thus arises as a general tool to analyze dynamic cellular machines more broadly.

Andy Boyan

Thursday, June 8th, 2017

Sherry, J. L., Boyan, A., Knight, K., Edwards, C., & Hao, Q. (2017). Multiplayer games as the ultimate communication lab and incubator: A multi-media study. In R. Kowert & T. Quandt (Eds.), New Perspectives on the Social Aspects of Digital Gaming: Multiplayer 2. New York: Routledge.

Brad Rabquer

Wednesday, May 31st, 2017

Mor-Vaknin, N., Saha, A., Legendre, M., Carmona-Rivera, C., Amin, M. A., Rabquer, B. J., et al. (2017). DEK-targeting DNA aptamers as therapeutics for inflammatory arthritis. Nature Communications, 8, 14252.

Abstract: Novel therapeutics are required for improving the management of chronic inflammatory diseases. Aptamers are single-stranded RNA or DNA molecules that have recently shown utility in a clinical setting, as they can specifically neutralize biomedically relevant proteins, particularly cell surface and extracellular proteins. The nuclear chromatin protein DEK is a secreted chemoattractant that is abundant in the synovia of patients with juvenile idiopathic arthritis (JIA). Here, we show that DEK is crucial to the development of arthritis in mouse models, thus making it an appropriate target for aptamer-based therapy. Genetic depletion of DEK or treatment with DEK-targeted aptamers significantly reduces joint inflammation in vivo and greatly impairs the ability of neutrophils to form neutrophil extracellular traps (NETs). DEK is detected in spontaneously forming NETs from JIA patient synovial neutrophils, and DEK-targeted aptamers reduce NET formation. DEK is thus key to joint inflammation, and anti-DEK aptamers hold promise for the treatment of JIA and other types of arthritis.