Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana.

Low linear energy transfer (LET) gamma rays and high LET HZE (high atomic weight, high energy) particles act as powerful mutagens in both plants and animals. DNA damage generated by HZE particles is more densely clustered than that generated by gamma rays. To understand the genetic requirements for resistance to high versus low LET radiation, a series of Arabidopsis thaliana mutants were exposed to either 1GeV Fe nuclei or gamma radiation. A comparison of effects on the germination and subsequent growth of seedlings led us to conclude that the relative biological effectiveness (RBE) of the two types of radiation (HZE versus gamma) are roughly 3:1. Similarly, in wild-type lines, loss of somatic heterozygosity was induced at an RBE of about a 2:1 (HZE versus gamma). Checkpoint and repair defects, as expected, enhanced sensitivity to both agents. The "replication fork" checkpoint, governed by ATR, played a slightly more important role in resistance to HZE-induced mutagenesis than in resistance to gamma induced mutagenesis

High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments.

Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as "collateral" damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe(26+) high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the "DSB response" were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing "extended night." This response was not apparent in gamma-irradiated plants

A Conflict Resolution Model Amenable to Sociological Practice

Social connectedness constrains individuality in favor of relationship. Group affiliation contributes to a tension between self and social motivation. Often, it becomes difficult to find mutually acceptable solutions to common problems In such cases, conflicts may emerge which require professional intervention to resolve. This article presents a model of conflict resolution which draws resource from sociological theory, research, and practice It delineates an adaptable strategy applicable to a wide range of social structures and concomitant relational problem

Two-stage coarsening mechanism in a kinetically constrained model of an attractive colloid

We study an attractive version of the East model using the real-space renormalization group (RG) introduced by Stella et al. The former is a kinetically constrained model with an Ising-like interaction between excitations, and shows striking agreement with the phenomonology of attractive colloidal systems. We find that the RG predicts two nonuniversal dynamic exponents, which suggests that in the out-of-equilibrium regime the model coarsens via a two-stage mechanism. We explain this mechanism physically, and verify this prediction numerically. In addition, we find that the characteristic relaxation time of the model is a non-monotonic function of attraction strength, again in agreement with numerical results.Comment: 10 page

Un[bracketed]: Phenomenological Polyethnography

Purpose Because of limitations to the purpose and practice of both phenomenological and duoethnographic research methodologies, our purpose in this paper was to propose phenomenological polyethnography as a hybrid qualitative methodology, which would guide skilled researchers in conducting phenomenological exploration of an emergent experience as insiders. Design/methodology/approach A hybridization approach to phenomenology and duoethnography as two distinct qualitative research traditions. Findings Employing a poststructuralist perspective, researcher-participants with relevant difference co-investigate a phenomenological question together. Borrowing elements from both hermeneutic phenomenology and duoethnography, this methodology involves the consideration of a phenomenon, the use of authors with relevant difference who have both special insight into that phenomenon as participants and skill as qualitative researchers, the intentional collection of prereflective data while all researcher-participants are experiencing the phenomenon or immediately after, the subsequent reflection upon and interpretation of the phenomenon as it was similarly and differently experienced by the researcher-participants, and the description of both the essence and meaning of the phenomenon. Research limitations/implications This new, hybrid qualitative methodology will enable researchers to more efficiently analyze and disseminate the research of insider knowledge on emergent phenomena in higher education and other settings. Originality/value As a new methodology, it may be used to investigate events and provide rich, thick description in a way not before seen

RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals

Double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi). Using a recently developed Drosophila in vitro system, we examined the molecular mechanism underlying RNAi. We find that RNAi is ATP dependent yet uncoupled from mRNA translation. During the RNAi reaction, both strands of the dsRNA are processed to RNA segments 21-23 nucleotides in length. Processing of the dsRNA to the small RNA fragments does not require the targeted mRNA. The mRNA is cleaved only within the region of identity with the dsRNA. Cleavage occurs at sites 21-23 nucleotides apart, the same interval observed for the dsRNA itself, suggesting that the 21-23 nucleotide fragments from the dsRNA are guiding mRNA cleavage

A Duoethnographic Exploration of Persistent Technological Failures in Synchronous Online Education

While higher education becomes increasingly reliant upon technology to deliver instruction, technological failures profoundly affect faculty members and students. We used duoethnography to explore the student-instructor dynamic during persistent technological failures within a synchronous online course, which occurred during a semester-long, qualitative research methods course. Duoethnography allowed us to first explore our own experiences and then engage in a continuous dialogue to interrogate the same event without privileging one voice over the other. We provide a series of dialogues of our shared understandings and different perspectives, taken from discussions and reflections on the experience. We then provide deeply personal insight into how faculty members and students may be affected by technological failures in distance education

RCMAT: a regularized covariance matrix approach to testing gene sets

<p>Abstract</p> <p>Background</p> <p>Gene sets are widely used to interpret genome-scale data. Analysis techniques that make better use of the correlation structure of microarray data while addressing practical "n<p" concerns could provide a real increase in power. However correlation structure is hard to estimate with typical genomics sample sizes. In this paper we present an extension of a classical multivariate procedure that confronts this challenge by the use of a regularized covariance matrix.</p> <p>Results</p> <p>We evaluated our testing procedure using both simulated data and a widely analyzed diabetes data set. We compared our approach to another popular multivariate test for both sets of data. Our results suggest an increase in power for detecting gene set differences can be obtained using our approach relative to the popular multivariate test with no increase in the false positive rate.</p> <p>Conclusion</p> <p>Our regularized covariance matrix multivariate approach to gene set testing showed promise in both real and simulated data comparisons. Our findings are consistent with the recent literature in gene set methodology.</p

Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism

Polycistronic transcripts are considered rare in the human genome. Initiation of translation of internal ORFs of eukaryotic genes has been shown to use either leaky scanning or highly structured IRES regions to access initiation codons. Studies on mammalian viruses identified a mechanism of coupled translation termination-reinitiation that allows translation of an additional ORF. Here, the ribosome terminating translation of ORF-1 translocates upstream to reinitiate translation of ORF-2. We have devised an algorithm to identify mRNAs in the human transcriptome in which the major ORF-1 overlaps a second ORF capable of encoding a product of at least 50 aa in length. This identified 4368 transcripts representing 2214 genes. We investigated 24 transcripts, 22 of which were shown to express a protein from ORF-2 highlighting that 3' UTRs contain protein-coding potential more frequently than previously suspected. Five transcripts accessed ORF-2 using a process of coupled translation termination-reinitiation. Analysis of one transcript, encoding the CASQ2 protein, showed that the mechanism by which the coupling process of the cellular mRNAs was achieved was novel. This process was not directed by the mRNA sequence but required an aspartate-rich repeat region at the carboxyl terminus of the terminating ORF-1 protein. Introduction of wobble mutations for the aspartate codon had no effect, whereas replacing aspartate for glutamate repeats eliminated translational coupling. This is the first description of a coordinated expression of two proteins from cellular mRNAs using a coupled translation termination-reinitiation process and is the first example of such a process being determined at the amino acid level