tRNA splicing

Introns interrupt the continuity of many eukaryal genes, and therefore their removal by splicing is a crucial step in gene expression. Interestingly, even within Eukarya there are at least four splicing mechanisms. mRNA splicing in the nucleus takes place in two phosphotransfer reactions on a complex and dynamic machine, the spliceosome. This reaction is related in mechanism to the two self-splicing mechanisms for Group 1 and Group 2 introns. In fact the Group 2 introns are spliced by an identical mechanism to mRNA splicing, although there is no general requirement for either proteins or co-factors. Thus it seems likely that the Group 2 and nuclear mRNA splicing reactions have diverged from a common ancestor. tRNA genes are also interrupted by introns, but here the splicing mechanism is quite different because it is catalyzed by three enzymes, all proteins and with an intrinsic requirement for ATP hydrolysis. tRNA splicing occurs in all three major lines of descent, the Bacteria, the Archaea, and the Eukarya. In bacteria the introns are self-splicing (1-3). Until recently it was thought that the mechanisms of tRNA splicing in Eukarya and Archaea were unrelated as well. In the past year, however, it has been found that the first enzyme in the tRNA splicing pathway, the tRNA endonuclease, has been conserved in evolution since the divergence of the Eukarya and the Archaea. Surprising insights have been obtained by comparison of the structures and mechanisms of tRNA endonuclease from these two divergent lines

Category-specific enhancement of retrieval due to field perspective

Two memory perspectives have been distinguished: A field perspective where events are re-experienced in the first person, and an observer perspective where events are witnessed in the third person. Two experiments examined the influence of memory perspective on objective memory performance. In both experiments participants were presented with a series of verbal passages, each of which contained several different categories of information. For four of these categories (pertaining to affective reactions, physical sensations, psychological states, and associated ideas), recall was significantly higher when a field perspective was adopted than when an observer perspective was adopted, but for the five other categories (pertaining to physical actions, personal appearance, fine details, spatial relations, and peripheral details) there was no significant effect of perspective upon recall. The study is examined in the context of mental models and imagined episodic events

Impact of Land Management on House Mice and Red Imported Fire Ants

Understanding of mechanisms that limit the abundance and distribution of species is central to ecology. The failure of mechanisms to regulate populations can result in population outbreaks. There have been two outbreaks of house mice in the past decade in central Florida. In my study, I examine the efficacy of landscape management in the form of mowing and plowed soil barriers to limit or prevent outbreaks of house mice in a former agricultural area. House mouse populations were highly variable, but were unaffected by mowing or plowed soil barriers. Red imported fire ants were ubiquitous in the study area regardless of land management treatments. Control of fire ants did not result in more house mice on treated plots

Why bayesian “evidence for H1” in one condition and bayesian “evidence for H0” in another condition does not mean good-enough bayesian evidence for a difference between the conditions

Psychologists are often interested in whether an independent variable has a different effect in condition A than in condition B. To test such a question, one needs to directly compare the effect of that variable in the two conditions (i.e., test the interaction). Yet many researchers tend to stop when they find a significant test in one condition and a nonsignificant test in the other condition, deeming this as sufficient evidence for a difference between the two conditions. In this Tutorial, we aim to raise awareness of this inferential mistake when Bayes factors are used with conventional cutoffs to draw conclusions. For instance, some researchers might falsely conclude that there must be good-enough evidence for the interaction if they find good-enough Bayesian evidence for the alternative hypothesis, H1, in condition A and good-enough Bayesian evidence for the null hypothesis, H0, in condition B. The case study we introduce highlights that ignoring the test of the interaction can lead to unjustified conclusions and demonstrates that the principle that any assertion about the existence of an interaction necessitates the direct comparison of the conditions is as true for Bayesian as it is for frequentist statistics. We provide an R script of the analyses of the case study and a Shiny app that can be used with a 2 × 2 design to develop intuitions on this issue, and we introduce a rule of thumb with which one can estimate the sample size one might need to have a well-powered design

SSB-1 of the yeast Saccharomyces cerevisiae is a nucleolar-specific, silver-binding protein that is associated with the snR10 and snR11 small nuclear RNAs

SSB-1, the yeast single-strand RNA-binding protein, is demonstrated to be a yeast nucleolar-specific, silver-binding protein. In double-label immunofluorescence microscopy experiments antibodies to two other nucleolar proteins, RNA Pol I 190-kD and fibrillarin, were used to reveal the site of rRNA transcription; i.e., the fibrillar region of the nucleolus. SSB-1 colocalized with fibrillarin in a double-label immunofluorescence mapping experiment to the yeast nucleolus. SSB-1 is located, though, over a wider region of the nucleolus than the transcription site marker. Immunoprecipitations of yeast cell extracts with the SSB-1 antibody reveal that in 150 mM NaCl SSB-1 is bound to two small nuclear RNAs (snRNAs). These yeast snRNAs are snR10 and snR11, with snR10 being predominant. Since snR10 has been implicated in pre-rRNA processing, the association of SSB-1 and snR10 into a nucleolar snRNP particle indicates SSB-1 involvement in rRNA processing as well. Also, another yeast protein, SSB-36-kD, isolated by single- strand DNA chromatography, is shown to bind silver under the conditions used for nucleolar-specific staining. It is, most likely, another yeast nucleolar protein

Facilitating Equitable Access and Retention for Underrepresented Students at the University of Mary Washington

Higher education institutions are facing increasing pressure to find new ways to attract, retain, and graduate the diverse populations of college students. As a result, colleges and universities need to adapt to the changing demographics of students who benefit from more sustained and engaged forms of support that are responsive to their specific social, cultural, and economic backgrounds. This sequential mixed methods study seeks to understand the ways in which the University of Mary Washington serves its underrepresented students in order to develop strategies to enhance the recruitment and retention of Black, Hispanic/Latinx, low-income, and first-generation college students. Building on the literature on retention and persistence, sense of belonging, and organizational change, researchers developed a student sense of belonging survey, an organizational readiness for change assessment, and conducted focus group discussions with UMW students. In particular, the project sought to understand the current institutional culture regarding inclusion and sense of belonging for underrepresented students. This study\u27s findings inform how the University of Mary Washington can better facilitate the recruitment, retention, and graduation of underrepresented students

An engineered Tetrahymena tRNA(Gln) for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression

A new tRNA, THG73, has been designed and evaluated as a vehicle for incorporating unnatural amino acids site-specifically into proteins expressed in vivo using the stop codon suppression technique. The construct is a modification of tRNAGln(CUA) from Tetrahymena thermophila, which naturally recognizes the stop codon UAG. Using electrophysiological studies of mutations at several sites of the nicotinic acetylcholine receptor, it is established that THG73 represents a major improvement over previous nonsense suppressors both in terms of efficiency and fidelity of unnatural amino acid incorporation. Compared with a previous tRNA used for in vivo suppression, THG73 is as much as 100-fold less likely to be acylated by endogenous synthetases of the Xenopus oocyte. This effectively eliminates a major concern of the in vivo suppression methodology, the undesirable incorporation of natural amino acids at the suppression site. In addition, THG73 is 4-10-fold more efficient at incorporating unnatural amino acids in the oocyte system. Taken together, these two advances should greatly expand the range of applicability of the in vivo nonsense suppression methodology

Shock temperature measurements in metals: New results for an Fe alloy

The temperature of a Fe-Cr-Ni alloy (304 stainless steel) has been measured during shock compression using a high-speed radiometric technique. Experiments were performed on high-quality thick films deposited on sapphire and LiF windows. The samples had no observable porosity or defects and closely meet the ideal criteria for shock temperature measurements. Data obtained with both Al_2O_3 and LiF windows are internally consistent, indicating that they remain transparent to high pressures and are thus suitable windows for shock temperature measurements. Our data yield stainless steel melting temperatures ranging from 4570±310K at 138 GPa to 5710±340 K at 215 GPa, and additionally provide bounds on the initial Hugoniot temperatures of the sample between 5600±340 K at 234 GPa (near the solidus) and 6580±440 K at 283 (in the liquid field). Taken together, these data define a smooth curve for melting of the alloy up to 271 GPa and 5860 K, which should represent a point on the Iiquidus. Melting along the Hugoniot begins at approximately 234 GPa and 5600 K, as compared with 242 GPa and 6400 K for pure Fe. At the pressure of the inner core-outer core boundary, the melting point of 304 stainless steel is lower than that of pure Fe by ≈ 1450 K, as compared with only 110 K at 1 atm. These results demonstrate that upon alloying with Ni and Cr the melting point depression of Fe and thus material likely to comprise the inner core increases with increasing pressure

The Interblink Interval in Normal and Dry Eye Subjects

Purpose: Our aim was to extend the concept of blink patterns from average interblink interval (IBI) to other aspects of the distribution of IBI. We hypothesized that this more comprehensive approach would better discriminate between normal and dry eye subjects. Methods: Blinks were captured over 10 minutes for ten normal and ten dry eye subjects while viewing a standardized televised documentary. Fifty-five blinks were analyzed for each of the 20 subjects. Means, standard deviations, and autocorrelation coefficients were calculated utilizing a single random effects model fit to all data points and a diagnostic model was subsequently fit to predict probability of a subject having dry eye based on these parameters. Results: Mean IBI was 5.97 seconds for normal versus 2.56 seconds for dry eye subjects (ratio: 2.33, P = 0.004). IBI variability was 1.56 times higher in normal subjects (P < 0.001), and the autocorrelation was 1.79 times higher in normal subjects (P = 0.044). With regard to the diagnostic power of these measures, mean IBI was the best dry eye versus normal classifier using receiver operating characteristics (0.85 area under curve (AUC)), followed by the standard deviation (0.75 AUC), and lastly, the autocorrelation (0.63 AUC). All three predictors combined had an AUC of 0.89. Based on this analysis, cutoffs of ≤3.05 seconds for median IBI, and ≤0.73 for the coefficient of variation were chosen to classify dry eye subjects. Conclusion: (1) IBI was significantly shorter for dry eye patients performing a visual task compared to normals; (2) there was a greater variability of interblink intervals in normal subjects; and (3) these parameters were useful as diagnostic predictors of dry eye disease. The results of this pilot study merit investigation of IBI parameters on a larger scale study in subjects with dry eye and other ocular surface disorders

Upgrading Marine Ecosystem Restoration Using Ecological-Social Concepts

Conservation and environmental management are principal countermeasures to the degradation of marine ecosystems and their services. However, in many cases, current practices are insufficient to reverse ecosystem declines. We suggest that restoration ecology, the science underlying the concepts and tools needed to restore ecosystems, must be recognized as an integral element for marine conservation and environmental management. Marine restoration ecology is a young scientific discipline, often with gaps between its application and the supporting science. Bridging these gaps is essential to using restoration as an effective management tool and reversing the decline of marine ecosystems and their services. Ecological restoration should address objectives that include improved ecosystem services, and it therefore should encompass social ecological elements rather than focusing solely on ecological parameters. We recommend using existing management frameworks to identify clear restoration targets, to apply quantitative tools for assessment, and to make the re-establishment of ecosystem services a criterion for success