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Migrations : Ireland in a global world
This edited collection explores Ireland's complex relationship with migration in novel and innovative ways. The contributors - leading scholars of migration from the disciplines of anthropology, geography, history, media studies, sociology, sociolinguistics and women's studies - draw on new research to provide insights into emigration from and immigration to Ireland, both past and present.
Book
Characterizing primary transcriptional responses to short term heat shock in Down syndrome
Heat shock stress induces genome-wide changes in transcription regulation, activating a coordinated cellular response to enable survival. We noticed many heat shock genes are up-regulated in blood samples from individuals with trisomy 21. We characterized the immediate transcriptional response to heat shock of two lymphoblastoid cell lines derived from brothers with and without trisomy 21. The trisomy 21 cells displayed a more robust heat shock response after just one hour at 42°C than the matched disomic cells.
Journal Article
Train students to navigate ethical swamps
A protocol can help with the tricky conversations essential to responsible research conduct, says Mary A. Allen.
A protocol can help with the tricky conversations essential to responsible research conduct, says Mary A. Allen.
“A responsible researcher needs to be able to navigate conflicts and tricky situations.”
Journal Article
Alexander L. George : a pioneer in political and social sciences
Alexander L. George was one of the most productive and respected political scientists of the late twentieth century. He and his wife, Juliette George, wrote one of the first psychobiographies, and Professor George went on to write seminal articles and books focusing on political psychology, the operational code, foreign policy decisionmaking,case study methodology, deterrence, coercive diplomacy, policy legitimacy, and bridging the gap between the academic and policymaking communities. This book is the first and only one to contain examples of the works across these fields written by Alexander George and several of his collaborators.
Book
Etiology of Viral Gastroenteritis in Children <5 Years of Age in the United States, 2008-2009
Background. Although rotavirus and norovirus cause nearly 40% of severe endemic acute gastroenteritis (AGE) in children <5 years of age in the United States, there are limited data on the etiologic role of other enteric viruses in this age group. Methods. We conducted active population-based surveillance in children presenting with AGE to hospitals, emergency departments, and primary care clinics in 3 US counties. Stool specimens from these children and from age-matched healthy controls collected between October 2008 and September 2009 were tested for enteric adenovirus, astrovirus, sapovirus, parechovirus, bocavirus, and aichivirus. Typing was performed by sequencing and phylogenetic analysis. Results. Adenovirus, astrovirus, sapovirus, parechovirus, bocavirus, and aichivirus were detected in the stool specimens of 11.8%, 4.9%, 5.4%, 4.8%, 1.4%, and 0.2% of patients with AGE and 1.8%, 3.0%, 4.2%, 4.4%, 2.4%, and 0% of healthy controls, respectively. Adenovirus (type 41), astrovirus (types 1, 2, 3, 4, and 8), sapovirus (genogroups I and II), parechovirus (types 1, 3,4, and 5), and bocavirus (types 1, 2, and 3) were found cocirculating. Conclusions. Adenovirus, astrovirus, and sapovirus infections were detected in 22.1% of the specimens from children <5 years of age who had medical visits for AGE and tested negative for rotavirus and norovirus. No causal role for parechovirus and bocavirus was found.
Journal Article
TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks
TF Profiler is a method of inferring transcription factor (TF) regulatory activity, i.e., when a TF is present and actively participating in the regulation of transcription, directly from nascent sequencing assays such as PRO-seq and GRO-seq. While ChIP assays have measured DNA localization, they fall short of identifying when and where the effector domain of a transcription factor is active. Our method uses RNA polymerase activity to infer TF effector domain activity across hundreds of data sets and transcription factors. TF Profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
Journal Article
Transcription dosage compensation does not occur in Down syndrome
Background
The increase in DNA copy number in Down syndrome (DS; caused by trisomy 21) has led to the DNA dosage hypothesis, which posits that the level of gene expression is proportional to the gene’s DNA copy number. Yet many reports have suggested that a proportion of chromosome 21 genes are dosage compensated back towards typical expression levels (1.0×). In contrast, other reports suggest that dosage compensation is not a common mechanism of gene regulation in trisomy 21, providing support to the DNA dosage hypothesis.
Results
In our work, we use both simulated and real data to dissect the elements of differential expression analysis that can lead to the appearance of dosage compensation, even when compensation is demonstrably absent. Using lymphoblastoid cell lines derived from a family with an individual with Down syndrome, we demonstrate that dosage compensation is nearly absent at both nascent transcription (GRO-seq) and steady-state RNA (RNA-seq) levels. Furthermore, we link the limited apparent dosage compensation to expected allelic variation in transcription levels.
Conclusions
Transcription dosage compensation does not occur in Down syndrome. Simulated data containing no dosage compensation can appear to have dosage compensation when analyzed via standard methods. Moreover, some chromosome 21 genes that appear to be dosage compensated are consistent with allele specific expression.
Journal Article
Economic Values for Coral Reef Conservation and Restoration in Florida
Florida’s coral reef is the third-largest barrier reef system in the world and provides valuable ecosystem services, such as recreation and tourism, erosion protection, and other services. Florida’s reefs have been declining due to impacts from climate change, pollution, and other pressures. In response, various conservation strategies have been implemented, including education and outreach, growing corals in nurseries and transplanting them to degraded reef sites, and deploying artificial reefs. However, few studies have estimated an explicit value for different strategies to attain conservation goals. Understanding economic values for reef restoration and enhancement is needed to help inform decision-making and support marine policy. This study conducted a stated preference choice experiment survey to examine the way U.S. residents make economic trade-offs among different restoration strategies, including increasing coral cover, deploying artificial reefs, and limiting visitor access to reef sites. The results suggest that, on average, the economic value of increasing coral cover is about twice as high as the value of increasing the number of artificial reef sites. Economic values for reducing visitation were similar to values for increasing the number of artificial reefs. These results provide essential information to policy analysts concerning reef use, reef importance, and economic values for reef restoration.
Journal Article
Detecting Differential Transcription Factor Activity from ATAC-Seq Data
Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases.
Journal Article