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Full Issue: Volume 5, Issue 1
Get PDFThe first issue in the fifth volume of the Swarthmore Undergraduate History Journal
Locus-Specific Differential Expression Of Human Satellite Sequences In The Nuclei Of Cancer Cells And Heat-Shocked Cells
Get PDFHuman satellites (HSats) are pericentric, tandemly repeating satellite DNA sequences in the human genome. While silent in normal cells, a subset of HSat2 noncoding RNA is expressed and accumulates in the nucleus of cancer cells. We developed a FISH-based approach for identification of the distribution of three subfamilies of HSat2 (A1, A2, B) sequences on individual human chromosomes. Further, using the HSat subfamily annotations in the T2T completed centromere satellite (CenSat) sequence, we isolated, defined and mapped differentially expressed sequence variants of nuclear-restricted HSat2 and HSat3 RNA from cancer cell lines and heat-shocked cells. We identified chromosome-specific and subfamily-specific expression of HSat2 and HSat3 and established a computational pipeline for differential expression analysis of tandemly repeated satellite sequences. Results suggest the differential expression of chromosome-specific HSat2 arrays in the human genome may underlie their accumulation in cancer cells and that specific HSat3 loci are upregulated upon heat shock
Random-Effects Substitution Models For Phylogenetics Via Scalable Gradient Approximations
Get PDFPhylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate gradient enables scaling of sampling-based inference, namely Bayesian inference via Hamiltonian Monte Carlo, under random-effects substitution models across large trees and state-spaces. Applied to a dataset of 583 SARS-CoV-2 sequences, an HKY model with random-effects shows strong signals of nonreversibility in the substitution process, and posterior predictive model checks clearly show that it is a more adequate model than a reversible model. When analyzing the pattern of phylogeographic spread of 1441 influenza A virus (H3N2) sequences between 14 regions, a random-effects phylogeographic substitution model infers that air travel volume adequately predicts almost all dispersal rates. A random-effects state-dependent substitution model reveals no evidence for an effect of arboreality on the swimming mode in the tree frog subfamily Hylinae. Simulations reveal that random-effects substitution models can accommodate both negligible and radical departures from the underlying base substitution model. We show that our gradient-based inference approach is over an order of magnitude more time efficient than conventional approaches
\u3cem\u3eLhx3/4\u3c/em\u3e Initiates A Cardiopharyngeal-Specific Transcriptional Program In Response To Widespread FGF Signaling
Get PDFIndividual signaling pathways, such as fibroblast growth factors (FGFs), can regulate a plethora of inductive events. According to current paradigms, signal-dependent transcription factors (TFs), such as FGF/MapK-activated Ets family factors, partner with lineage-determining factors to achieve regulatory specificity. However, many aspects of this model have not been rigorously investigated. One key question relates to whether lineage-determining factors dictate lineage-specific responses to inductive signals or facilitate these responses in collaboration with other inputs. We utilize the chordate model Ciona robusta to investigate mechanisms generating lineage-specific induction. Previous studies in C. robusta have shown that cardiopharyngeal progenitor cells are specified through the combined activity of FGF-activated Ets1/2.b and an inferred ATTA-binding transcriptional cofactor. Here, we show that the homeobox TF Lhx3/4 serves as the lineage-determining TF that dictates cardiopharyngeal-specific transcription in response to pleiotropic FGF signaling. Targeted knockdown of Lhx3/4 leads to loss of cardiopharyngeal gene expression. Strikingly, ectopic expression of Lhx3/4 in a neuroectodermal lineage subject to FGF-dependent specification leads to ectopic cardiopharyngeal gene expression in this lineage. Furthermore, ectopic Lhx3/4 expression disrupts neural plate morphogenesis, generating aberrant cell behaviors associated with execution of incompatible morphogenetic programs. Based on these findings, we propose that combinatorial regulation by signal-dependent and lineage-determinant factors represents a generalizable, previously uncategorized regulatory subcircuit we term “cofactor-dependent induction.” Integration of this subcircuit into theoretical models will facilitate accurate predictions regarding the impact of gene regulatory network rewiring on evolutionary diversification and disease ontogeny
Jews Under Tsars And Communists: The Four Questions
No full textTracing the evolving nature of popular and official beliefs about the purported nature of the Jews from the 18th century onwards, Russia and the Jewish Question explores how perceptions of Jews in late Imperial Russia and the Soviet Union shaped the regimes\u27 policies toward them. In so doing Robert Weinberg provides a fruitful lens through which to investigate the social, economic, political, and cultural developments of modern Russia. Here, Weinberg reveals that the \u27Jewish Question\u27 – and, by extension anti-Semitism – emerged at the end of the 18th century when the partitions of Poland made hundreds of thousands of Jews subjects of the Russian crown. He skillfully argues the phrase itself implies the singular nature of Jews as a group of people whose religion, culture, and occupational make-up prevent them from fitting into predominantly Christian societies. The book then expounds how other characteristics were associated with the group over time: in particular, debates about rights of citizenship, the impact of industrialization, the emergence of the nation-state, and the proliferation of new political ideologies and movements contributed to the changing nature of the \u27Jewish Question\u27. Its content may have not remained static, but its purpose consistently questions whether or not Jews pose a threat to the stability and well-being of the societies in which they live and this, in a specifically Russian context, is what Weinberg examines so expertly
LHS 475 b: A Potential Venus Analog Orbiting A Nearby M Dwarf
No full textBased on photometric observations by TESS, we present the discovery of a potential Venus analog transiting LHS 475, an M3 dwarf located 12.5 pc from the Sun. The mass of the star is 0.274 ± 0.015 M☉. The planet, originally reported as TOI 910.01, has an orbital period of 2.0291010 ± 0.0000017 days and an estimated radius of 0.975 ± 0.058 R⊕. We confirm the validity and source of the transit signal with MEarth and Las Cumbres Observatory Global Telescope ground-based follow-up photometry. We present radial velocity data from CHIRON that rule out massive companions. In accordance with the observed mass–radius distribution of exoplanets as well as planet formation theory, we expect this planetary companion to be terrestrial, with an estimated radial velocity semiamplitude of 1.1 m s⁻¹. LHS 475 b is likely too hot to be habitable but is a suitable candidate for emission and transmission spectroscopy
Does It Stick? A Longitudinal Study Of Introductory Physics For Life Sciences At A Small College
No full textAt Swarthmore College, we began developing an Introductory Physics for Life Sciences (IPLS) course nearly 20 years ago. The electricity, magnetism and optics semester was launched in 2008 and both semesters have been offered regularly since Fall 2015. Two primary goals of this curriculum are (1) to prepare students to effectively use physical models and quantitative reasoning in biological and biomedical contexts, and (2) for students to come to view physics as relevant to the life sciences. To evaluate whether these goals are achieved, we conducted a longitudinal interdisciplinary study assessing students\u27 abilities to use what they learned from IPLS in later biology and chemistry courses, as well as students\u27 long-term attitudes toward physics. We found that IPLS students were more likely than non-IPLS students to reason quantitatively and mechanistically about particular biophysical phenomena, even up to two years after leaving the IPLS course, and were significantly more successful at building a physical model that combined ideas in a manner novel to them. We also found that positive changes in IPLS students\u27 attitudes about the relevance of physics to the life sciences persisted for at least two years after the course ended. The specific methods and findings of this study have been reported elsewhere. In this paper, we describe how our IPLS curriculum leverages the rich network of interdepartmental faculty relationships at small institutions to support students to recognize the connections between physics and their other science classes, and describe how the opportunities for close relationships between students and faculty made possible a decade of research into the curriculum outcomes. By identifying and tracking student trajectories over time and across disciplines, we were able to identify student reasoning and attitudes that were specifically associated with prior or concurrent enrollment in IPLS
TOI-1994b: A Low-Mass Eccentric Brown Dwarf Transiting A Subgiant Star
No full textWe present the discovery of TOI-1994b, a low-mass brown dwarf transiting a hot subgiant star on a moderately eccentric orbit. TOI-1994 has an effective temperature of 7700 +720/-410 K, V magnitude of 10.51 mag and log(g) of 3.982 +0.067/-0.065. The brown dwarf has a mass of 22.1 +2.6/-2.5 MJ, a period of 4.034 days, an eccentricity of 0.341 +0.054/-0.059, and a radius of 1.220 +0.082/-0.071 RJ. TOI-1994b is more eccentric than other transiting brown dwarfs with similar masses and periods. The population of low-mass brown dwarfs may have properties similar to planetary systems if they were formed in the same way, but the short orbital period and high eccentricity of TOI-1994b may contrast this theory. An evolved host provides a valuable opportunity to understand the influence stellar evolution has on the substellar companion\u27s fundamental properties. With precise age, mass, and radius, the global analysis and characterization of TOI-1994b augments the small number of transiting brown dwarfs and allows the testing of substellar evolution models