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

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

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

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 of Stainless Steel and a High Pressure - High Temperature Constraint on Thermal Diffusivity of Al_2O_3

Time dependent shock temperatures were measured for stainless steel (SS) films in contact with transparent anvils. The anvil/window material was the same as the driver material so that there would be symmetric heat flow from the sample. Inferred Hugoniot temperatures, T_h , of 5800–7500 K at 232–321 GPa are consistent with previous measurements in SS. Temperatures at the film‐anvil interface (T_i ), which are more directly measured than T_h , indicate that T_i did not decrease measurably during the approximately 250 ns that the shock wave was in Al_2O_3 or LiF anvils. Thus an upper bound is obtained for the thermal diffusivity of Al_2O_3 at the metal/anvil interface at 230 GPa and 6000K of κ≤0.00096 cm_2/s. This is a factor of 17 lower than previously calculated values, resulting in a decrease of the inferred T_h by 730 k. The observed shock temperatures are combined with temperatures calculated from measured Hugoniots and are used to calculate thermal conductivities of Al_2O_3. Also we note that since there was no measurable intensity decrease during the time when the shock wave propagated through the window, we infer from this that Al_2O_3 remained transparent while in the shocked state. Thus sapphire is a good window material to at least 250 GPa for shock temperature measurements for metals

Investigation of extended blinks and interblink intervals in subjects with and without dry eye

Background: The purpose of this study was to investigate the occurrence and duration of extended blinks ≥ 70 msec and their associated interblink intervals in normal subjects and in subjects with mild to moderate dry eye. Methods: This single-center, prospective, double-blind study included 11 subjects with dry eye and eight subjects with normal eyes. Extended blinks were defined as lid closure in at least two successive video frames (≥70 msec). Digital video imaging of each subject’s eyes was recorded while the subject viewed a 10-minute documentary. The subjects did not know that blink was the outcome being measured. Following capture, the videos were manually analyzed in a masked fashion for the occurrence of extended blinks. The length of the interblink interval (ie, time between blinks) before and after these extended blinks (the interblink interval ratio) was calculated, as well as differences in lid contact times. Results: The dry eye group had a median extended blink duration which was 2.53 times longer than that of the normal group. For subjects with dry eye, interblink intervals post-extended blink were significantly longer than interblink intervals pre-extended blink (P < 0.001). Interblink intervals did not lengthen significantly in normal subjects. In both groups, the duration of the extended blink was significantly (P = 0.001) and positively correlated with interblink interval ratio (post-extended to pre-extended blink interblink interval), such that for each doubling of extended blink duration, the interblink interval ratio increased by 10%. Blinks longer than one second in duration occurred almost exclusively in subjects with dry eye. Conclusion: This study reports three central findings: blink duration tended to be longer in subjects with dry eye; a lengthening of the interblink interval after an extended blink occurred in subjects with dry eye but not in those without dry eye; and a longer blink duration was associated with a significantly increased interblink interval ratio in all subjects

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

Blink patterns and lid-contact times in dry-eye and normal subjects

Purpose To classify blinks in dry eye and normal subjects into six subtypes, and to define the blink rate and duration within each type of blink, as well as the total lid-contact time/minute. Materials and methods This was a single-centered, prospective, double-blind study of eleven dry-eye and ten normal subjects. Predefined subjects watched a video while blinks were recorded for 10 minutes. Partial blinks were classified by percentage closure of maximal palpebral fissure opening: 25%, 50%, 75%. Complete blinks were characterized as full (>0 seconds), extended (>0.1 seconds), or superextended (>0.5 seconds). The mean duration of each type of blink was determined and standardized per minute as total lid-contact time. Results: Total blinks observed were 4,990 (1,414 normal, 3,756 dry eye): 1,809 (50.59%) partial and 1,767 (49.41%) complete blinks among dry-eye subjects versus 741 (52.90%) partial and 673 (47.60%) complete blinks among normal subjects. Only superextended blinks of ≥0.5-second duration were significantly more frequent in dry-eye subjects than normals (2.3% versus 0.2%, respectively; P=0.023). Total contact time was seven times higher in dry-eye subjects than normals (0.565 versus 0.080 seconds, respectively; P0.1 second), the average contact time (seconds) was four times longer in dry-eye versus normal subjects (2.459 in dry eye, 0.575 in normals; P=0.003). Isolating only superextended blinks (>0.5 seconds), average contact time was also significantly different (7.134 in dry eye, 1.589 in normals; P<0.001). The contact rate for all full closures was 6.4 times longer in dry-eye (0.045 versus 0.007, P<0.001) than normal subjects. Conclusion: Dry-eye subjects spent 4.5% of a minute with their eyes closed, while normal subjects spent 0.7% of a minute with their eyes closed. Contact time might play a role in the visual function decay associated with increased blink rates

Tourist choice processing: evaluating decision rules and methods of their measurement

A detailed understanding of decision rules is essential in order to better explain consumption behavior, yet the variety of decision rules used have been somewhat neglected in tourism research. This study adopts an innovative method, greedoid analysis, to estimate a noncompensatory type of decision rule known as lexicographic by aspect (LBA). It is quite different from the weighted additive (WADD) model commonly assumed in tourism studies. By utilizing an experimental research design, this study enables the evaluation of the two types of decision rules regarding their predictive and explanatory power. Additionally, we introduce a novel evaluation indicator (“cost”), which allows further investigation of the heterogeneity in the use of decision rules. The results suggest that although the out-of-sample accuracy is lower, the LBA model has a better explanatory performance on respondents’ preference order. Moreover, the different perspective provided by the LBA model is useful for obtaining managerial implications