Messenger RNA half-life measurements in mammalian cells.

The recognition of the importance of mRNA turnover in regulating eukaryotic gene expression has mandated the development of reliable, rigorous, and user-friendly methods to accurately measure changes in mRNA stability in mammalian cells. Frequently, mRNA stability is studied indirectly by analyzing the steady-state level of mRNA in the cytoplasm; in this case, changes in mRNA abundance are assumed to reflect only mRNA degradation, an assumption that is not always correct. Although direct measurements of mRNA decay rate can be performed with kinetic labeling techniques and transcriptional inhibitors, these techniques often introduce significant changes in cell physiology. Furthermore, many critical mechanistic issues as to deadenylation kinetics, decay intermediates, and precursor-product relationships cannot be readily addressed by these methods. In light of these concerns, we have previously reported transcriptional pulsing methods based on the c-fos serum-inducible promoter and the tetracycline-regulated (Tet-off) promoter systems to better explain mechanisms of mRNA turnover in mammalian cells. In this chapter, we describe and discuss in detail different protocols that use these two transcriptional pulsing methods. The information described here also provides guidelines to help develop optimal protocols for studying mammalian mRNA turnover in different cell types under a wide range of physiologic conditions

Negative feedback control of jasmonate signaling by an alternative splice variant of JAZ10

The plant hormone jasmonate (JA) activates gene expression by promoting ubiquitin-dependent degradation of JAZ transcriptional repressor proteins. A key feature of all JAZ proteins is the highly conserved Jas motif, which mediates both JAZ degradation and JAZ binding to the transcription factor MYC2. Rapid expression of JAZ genes in response to JA is thought to attenuate JA responses, but little is known about the mechanisms by which newly synthesized JAZ proteins exert repression in the presence of the hormone. Here, we show that desensitization to JA is mediated by an alternative splice variant (JAZ10.4) of JAZ10 that lacks the Jas motif. Unbiased protein-protein interaction screens identified three related bHLH transcription factors (MYC2, MYC3, and MYC4) and the co-repressor NINJA as JAZ10.4-binding partners. We show that the N-terminal region of JAZ10.4 contains a cryptic MYC2-binding site that resembles the Jas motif, and that the ZIM motif of JAZ10.4 functions as a transferable repressor domain whose activity is associated with recruitment of NINJA. Functional studies showed that expression of JAZ10.4 from the native JAZ10 promoter complemented the JA-hypersensitive phenotype of a jaz10 mutant. Moreover, treatment of these complemented lines with JA resulted in rapid accumulation of JAZ10.4 protein. Our results provide an explanation for how the unique domain architecture of JAZ10.4 links transcription factors to a co-repressor complex, and suggest how JA-induced transcription and alternative splicing of JAZ10 pre-mRNA creates a regulatory circuit to attenuate JA responses.Fil: Moreno, Javier Edgardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina. Michigan State University; Estados UnidosFil: Shyu, Christine. Michigan State University; Estados UnidosFil: Campos, Marcelo L.. Michigan State University; Estados UnidosFil: Patel, Lalita C.. Michigan State University; Estados UnidosFil: Chung, Hoo Sun. Michigan State University; Estados UnidosFil: Yao, Jian. Michigan State University; Estados UnidosFil: He, Sheng Hang. Michigan State University; Estados UnidosFil: Howe, Gregg A.. Michigan State University; Estados Unido

An interdisciplinary intervention for older Taiwanese patients after surgery for hip fracture improves health-related quality of life

Abstract Background The effects of intervention programs on health-related quality of life (HRQOL) of patients with hip fracture have not been well studied. We hypothesized that older patients with hip fracture who received our interdisciplinary intervention program would have better HRQOL than those who did not. Methods A randomized experimental design was used. Older patients with hip fracture (N = 162), 60 to 98 years old, from a medical center in northern Taiwan were randomly assigned to an experimental (n = 80) or control (n = 82) group. HRQOL was measured by the SF-36 Taiwan version at 1, 3, 6, and 12 months after discharge. Results The experimental group had significantly better overall outcomes in bodily pain (β = 9.38, p = 0.002), vitality (β = 9.40, p < 0.001), mental health (β = 8.16, p = 0.004), physical function (β = 16.01, p < 0.001), and role physical (β = 22.66, p < 0.001) than the control group at any time point during the first year after discharge. Physical-related health outcomes (physical functioning, role physical, and vitality) had larger treatment effects than emotional/mental- and social functioning-related health outcomes. Conclusions This interdisciplinary intervention program may improve health outcomes of elders with hip fracture. Our results may provide a reference for health care providers in countries using similar programs with Chinese/Taiwanese immigrant populations. Trial registration NCT01052636http://deepblue.lib.umich.edu/bitstream/2027.42/78259/1/1471-2474-11-225.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78259/2/1471-2474-11-225.pdfPeer Reviewe

A seasonal, density-dependent model for the management of an invasive weed

Author Posting. © Ecological Society of America, 2013. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 23 (2013): 1893-1905, doi:10.1890/12-1712.1.The population effects of harvest depend on complex interactions between density dependence, seasonality, stage structure, and management timing. Here we present a periodic nonlinear matrix population model that incorporates seasonal density dependence with stage-selective and seasonally selective harvest. To this model, we apply newly developed perturbation analyses to determine how population densities respond to changes in harvest and demographic parameters. We use the model to examine the effects of popular control strategies and demographic perturbations on the invasive weed garlic mustard (Alliaria petiolata). We find that seasonality is a major factor in harvest outcomes, because population dynamics may depend significantly on both the season of management and the season of observation. Strategies that reduce densities in one season can drive increases in another, with strategies giving positive sensitivities of density in the target seasons leading to compensatory effects that invasive species managers should avoid. Conversely, demographic parameters to which density is very elastic (e.g., seeding survival, second-year rosette spring survival, and the flowering to fruiting adult transition for maximum summer densities) may indicate promising management targets.This work was supported by the National Science Foundation (grant DEB-0816514), the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service (grant 05-2290), the Alexander von Humboldt Foundation, and the Academic Programs Office at WHOI

BTG/TOB factors impact deadenylases.

BTG/TOB factors are a family of antiproliferative proteins whose expression is altered in numerous cancers. They have been implicated in cell differentiation, development and apoptosis. Although proposed to affect transcriptional regulation, these factors interact with CAF1, a subunit of the main eukaryotic deadenylase, and with poly(A)-binding-proteins, strongly suggesting a role in post-transcriptional regulation of gene expression. The recent determination of the structures of BTG2, TOB1 N-terminal domain (TOB1N138) and TOB1N138-CAF1 complexes support a role for BTG/TOB proteins in mRNA deadenylation, a function corroborated by recently published functional characterizations. We highlight molecular mechanisms by which BTG/TOB proteins influence deadenylation and discuss the need for a better understanding of BTG/TOB physiological functions

Design and evaluation of a personal digital assistant-based alerting service for clinicians

Purpose: This study describes the system architecture and user acceptance of a suite of programs that deliver information about newly updated library resources to clinicians’ personal digital assistants (PDAs). Description: Participants received headlines delivered to their PDAs alerting them to new books, National Guideline Clearinghouse guidelines, Cochrane Reviews, and National Institutes of Health (NIH) Clinical Alerts, as well as updated content in UpToDate, Harrison's Online, Scientific American Medicine, and Clinical Evidence. Participants could request additional information for any of the headlines, and the information was delivered via email during their next synchronization. Participants completed a survey at the conclusion of the study to gauge their opinions about the service. Results/Outcome: Of the 816 headlines delivered to the 16 study participants’ PDAs during the project, Scientific American Medicine generated the highest proportion of headline requests at 35%. Most users of the PDA Alerts software reported that they learned about new medical developments sooner than they otherwise would have, and half reported that they learned about developments that they would not have heard about at all. While some users liked the PDA platform for receiving headlines, it seemed that a Web database that allowed tailored searches and alerts could be configured to satisfy both PDA-oriented and email-oriented users.Includes bibliographical references

A framework for automatic semantic video annotation

The rapidly increasing quantity of publicly available videos has driven research into developing automatic tools for indexing, rating, searching and retrieval. Textual semantic representations, such as tagging, labelling and annotation, are often important factors in the process of indexing any video, because of their user-friendly way of representing the semantics appropriate for search and retrieval. Ideally, this annotation should be inspired by the human cognitive way of perceiving and of describing videos. The difference between the low-level visual contents and the corresponding human perception is referred to as the ‘semantic gap’. Tackling this gap is even harder in the case of unconstrained videos, mainly due to the lack of any previous information about the analyzed video on the one hand, and the huge amount of generic knowledge required on the other. This paper introduces a framework for the Automatic Semantic Annotation of unconstrained videos. The proposed framework utilizes two non-domain-specific layers: low-level visual similarity matching, and an annotation analysis that employs commonsense knowledgebases. Commonsense ontology is created by incorporating multiple-structured semantic relationships. Experiments and black-box tests are carried out on standard video databases for action recognition and video information retrieval. White-box tests examine the performance of the individual intermediate layers of the framework, and the evaluation of the results and the statistical analysis show that integrating visual similarity matching with commonsense semantic relationships provides an effective approach to automated video annotation

Development of Standard Criteria to Evaluate the Effectiveness of Helmets at Decreasing the Risk of Concussions

In many sports, such as American football, accumulations of mild traumatic brain injuries have been suggested as a possible link to neurodegeneration and future mental disorders. With head impacts occurring at all levels of competition and in different sports, it is critical to develop an accurate method for quantifying the effects of head impacts and determining the efficacy of helmets. This study examines the derivation of different dimensionless numbers and ascertains the critical factors needed to predict the effects of head impacts, specifically the resulting accelerations from an impact. Given a known force of impact, parameters such as peak translation acceleration and impact duration were collected for a total of 200 impacts at 10 locations around the head. These parameters were used in conjunction with dimensionless numbers to compare various helmet designs across sports. Five input and four output criteria, or π variables, were derived using fundamental variables of total mass, width of neck, and the difference between muscle reaction time and the impact duration. By determining the coefficients of the governing equations for each output π variable, the impulse of impacts had a consistent effect on helmet efficacy, while the masses and radii of helmets contained confounding variables that made it difficult to predict the effectiveness of attenuating the head accelerations

On the bioeconomics of marine reserves when dispersal evolves

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Natural Resource Modeling 28 (2015): 456-474, doi:10.1111/nrm.12075.Marine reserves are an increasingly used and potentially contentious tool in fisheries management. Depending upon the way that individuals move, no-take marine reserves can be necessary for maximizing equilibrium rent in some simple mathematical models. The implementation of no-take marine reserves often generates a redistribution of fishing effort in space. This redistribution of effort, in turn, produces sharp spatial gradients in mortality rates for the targeted stock. Using a two-patch model, we show that the existence of such gradients is a sufficient condition for the evolution of an evolutionarily stable conditional dispersal strategy. Thus, the dispersal strategy of the fish depends upon the harvesting strategy of the manager and vice versa. We find that an evolutionarily stable optimal harvesting strategy (ESOHS)—one which maximizes equilibrium rent given that fish disperse in an evolutionarily stable manner– - never includes a no-take marine reserve. This strategy is economically unstable in the short run because a manager can generate more rent by disregarding the possibility of dispersal evolution. Simulations of a stochastic evolutionary process suggest that such a short-run, myopic strategy performs poorly compared to the ESOHS over the long run, however, as it generates rent that is lower on average and higher in variability.This material is based upon work supported by funding from: The Woods Hole Oceanographic Institution's Investment in Science Fund to MGN; The Recruitment Program of Global Experts to YL; The University of Tennessee Center for Business and Economics Research to SL; and the U.S. National Science Foundation (NSF) through grants OCE-1031256, DEB-1257545, and DEB-1145017 to MGN, CNH-0707961 to GEH, DMS-1411476 to YL; and NSF Graduate Research Fellowships under Grant No. 1122374 to EAM and ES