Miracle-dz/UniFAR-FTUs huggingface dataset:
The crystal structure of leucyl-tRNA synthetase complexed with tRNA Leu in the post-transfer-editing

Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing activity directed against mischarged isoleucine and similar noncognate amino acids. We describe the post-transfer-editing and product complexes of Thermus thermophilus LeuRS (LeuRSTT) with tRNA Leu at 2.9- to 3.3-Aresolution. In the post-transfer-editing configuration, A76 binds in the editing active site exactly as previously found for the adenosine moiety of a small-molecule editing-substrate analog. The 60 C-terminal residues of LeuRSTT, unseen in previous structures, fold into a compact domain flexibly linked to the rest of the molecule and interacting with the G19-C56 tertiary base pair of tRNA Leu . LeuRS recognition of tRNA Leu depends essentially on tRNA shape rather than base-specific interactions. The structures show that considerable domain rotations, notably of the editing domain, accompany the tRNA-3¢ end dynamics associated successively with aminoacylation, post-transfer editing and product release.
Studies on Variation with Ophiobolus Graminis

Variations were studied in the monosporous Fl progeny ot an isolate of Ophiobolus graminis from wheat. All Fl ascospores from perithecia on living host tissue were strongly pathogenic, but half from a perithecium in culture were weakly pathogenic. Perithecia were formed in culture and on host tissue only by strongly pathogenic progeny. Strongly pathogenic progeny survived well on artificially infected wheat straw buried in unsterilized soil, but weakly pathogenic progeny did not. Survival of all isolates was increased by nitrate enrichment of soil.
Mutagenecity testing of phamarceutical effluents on Allium cepa root tip meristems

Using macro analysis of root growth parameters and micro assay of the root tip meristems through the estimation of the mitotic indices and aberrant cells of Allium cepa root meristems, a study was conducted on three Pharmaceutical effluents discharged into agricultural lands. The chemical analysis of the effluents showed the presence of some potential mutagenic heavy metals (Pb, Cu and Zn) and Cyanide. The experimental design was a factorial in completely randomized design (CRD). The results obtained showed significant reduction in the number of roots and the length of roots grown on the effluents and their dilutions. Highly reduced cell reproduction was observed in all the effluents. The mitotic index (MI) ranged from 49.2 - 2.95, 52.6 - 1.77 and 48.8 - 2.63 in Jutrim, Flu-J and Ampiclox effluents, respctively. Both concentration of the effluents and treatment time had significant effect on the mitotic index. The MI as a percentage of the control at undiluted effluent concentrations and at 24 h exposure time were below 22% of the control value ranging from 6.02, 3.6 and 5.4% in Jutrim, Flu-J and Ampiclox effluents, respectively. Aberrant cells oberved ranged from a mild C-mitotic effect to anaphase bridge and even an induction of multiple nuclei in a cell. The effects of the cytotoxic and genotoxic substances in these wastewaters discharged into the environment on biolife are discussed in this report.
Low larval densities in northern populations reinforce range expansion by a Mediterranean damselfly

Contemporary climate change triggers a poleward range shift in many species. A growing number of studies document evolutionary changes in traits accelerating range expansion (such as growth rate and dispersal-related traits). In contrast, the direct impact of decreasing conspecific densities towards the very edge of the expansion front has been neglected. Density effects may, however, have a profound direct impact on traits involved in range expansion and influence range dynamics. In this study, we contrast the effects of high conspecific larval density typical for established populations and low larval density typical for newly founded populations at the edge of the expansion front on a set of larval traits that may affect the range dynamics in the poleward moving damselfly Coenagrion scitulum. We therefore ran an outdoor mesocosm experiment with a low- and high-density treatment close to the species' northern expansion front. Density effects on survival, growth rate and body size are scored both during the pre-winter growth period and during the subsequent winter period. Additionally, foraging activity was scored at the end of the pre-winter period and body condition [size-corrected body mass, fat content and activity of phenoloxidase (PO)] was scored at the end of the winter period. The low-density treatment had strong direct positive effects on survival, growth rate and body size of larvae before winter indicating relaxed competition. Lower foraging activity at the low-density treatment indicated higher food availability at low conspecific densities. Interestingly, the initial density treatment had stronger effect than densities experienced at the time of quantification on survival during the pre-freezing winter period and body condition estimates at the end of the experiment, indicating also delayed effects of the initial density treatment. Survival throughout a freezing period indicated extreme winter conditions are not likely a limiting factor in the range expansion of this Mediterranean species. The increased survival and individual growth rates (through causing shifts in voltinism) at low conspecific density will translate in increased population growth rates. Furthermore, nutritional advantages at low conspecific density may increase investment in dispersal ability. Together, these direct and delayed density-dependent effects that gradually increase towards the expansion front are expected to accelerate range expansion.
Species composition determines resistance to drought in dry forests of the Great Lakes – St. Lawrence forest region of central Ontario

Question Predicted changes in the frequency of short-term drought events raise concerns about potential effects of climate change on forest ecosystems. Few experiments have investigated the effects of tree species richness and composition in forest assemblages exposed to drought, and general conclusions for these systems are currently lacking. We tested the hypothesis that different species richness and composition affects community-level stability during a severe short-term drought event across a gradient of tree species assemblages typical of temperate forest ecosystems on dry substrates. Location Great Lakes – St. Lawrence forest region, central Ontario, Canada. Methods The study assemblages spanned a gradient of 15 different combinations of species richness and composition of four tree species. The drought occurred in 2005 and was characterized by high growing season temperature and low precipitation. Plots (n = 63) representing replicate assemblages were selected to collect increment cores (n = 1193) and examine growth responses to past drought at the community and population levels. Cross-dated tree ring measurements were used to reconstruct basal area increment (BAI) and calculate indices of resistance, resilience and productivity over the drought period. We used hierarchical analysis of variance models to estimate the effects of species richness and composition on drought responses. Results We identified a significant effect of species composition on community-level resistance and productivity. White pine (Pinus strobus) abundance was associated with lower community resistance and white birch (Betula papyrifera) abundance with higher resistance. Assemblages with greater productivity were often characterized by the high abundance of trembling aspen (Populus tremuloides). There was no overall effect of the assemblage gradient on the population-level stability; however, red pine (Pinus resinosa) productivity was higher in combination with trembling aspen and white birch. Conclusion Our study demonstrated that species richness had no effect on the community-level stability of growth during a drought in temperate forests on dry substrates. Instead, there were important compositional effects that determine some aspects of stability during drought events. If pine forests were managed to maintain a component of deciduous species, the capacity to dampen the community-level effects of more frequent drought would increase.
Growth and function of Stegosaurus plates: evidence from bone histology

Histological examination of Stegosaurus dorsal bony plates shows a thin wall of incompletely remodeled bone surrounding a large cancellous region containing some large “pipes” delineated by thin bony walls. Growth proceeded mainly from the basal region of the plates. Histological observations provide a test against which several functional interpretations of the plates are checked. While some interpretations (e.g., plates as armor) are clearly falsified, others (linked to thermoregulatory functions) seem to be more robust, although by no means can they be viewed as clearly vindicated on the basis of the evidence presently available.
Decoupled Seasonal Stress as an Indication of Chronic Stress in Montastraea cavernosa and Porites astreoides Inhabiting the Florida Reef Tract

Although mass mortality from disease and climate anomalies are largely to blame for rapid losses in coral cover along the Florida reef tract, the failure of extant populations to recolonize the offshore zone is puzzling given improvements to water quality and narrower range in seawater temperature compared to the inshore patch reef zone. Using existing data from the Coral Reef Environmental Monitoring Program (CREMP) and from an inshore and offshore site established to compliment this dataset we identified significantly increased abundance and diversity of scleractinian coral from inshore to offshore across the Florida reef tract. Applying exploratory statistical methods we identified two abundant species, Montastraea cavernosa and Porites astreoides , inhabiting both zones to varying degrees. Following reciprocal transplantation of conspecifics between a representative offshore and inshore reef (6 m depth), we monitored monthly coral colony brightness (a measurement related to endosymbiotic dinoflagellate density) over a two-year period to examine symbiont loss, a common stress response in scleractinian corals. Although species-specific stress patterns were not identified, zone-specific variation was evident. Trigonometric regression of stress level by month revealed a significant relationship supporting an annual stress and recovery period at the inshore patch reef zone. Contrary to this result, conspecifics transplanted to the offshore zone did not display recovery resulting in a continued chronically bleached state over the two-year period. Our results implicate alleviation or decreased stress at inshore sites and the importance of extending greater protection to reefs within this zone.
Preferential binding of ATR protein to

The ATR protein is a member of the phosphoinositide 3-kinaserelated kinase family and plays an important role in UV-induced DNA damage checkpoint response. Its role as a signal transducer in cell cycle checkpoint is well established, but it is currently unclear whether ATR functions as a damage sensor as well. Here we have purified the ATR protein and investigated its interaction with DNA by using biochemical analysis and electron microscopy. We find that ATR is a DNA-binding protein with higher affinity to UVdamaged than undamaged DNA. In addition, damaged DNA stimulates the kinase activity of ATR to a significantly higher level than undamaged DNA. Our data suggest that ATR may function as an initial sensor in the DNA damage checkpoint response.
Photic Stress in Symbiont-Bearing Reef Organisms: Analyses of Photosynthetic Performance

As populations of Acropora spp. and Orbicella spp. have declined along the Florida reef tract, populations of the scleractinians, Siderastrea siderea and Montastraea cavernosa, and the zoanthid, Palythoa caribaeorum, have remained relatively stable. The objective of this study was to assess temporal variability in photochemical efficiencies (Fv/Fm) of the dinoflagellate Symbiodinium symbionts in these three “survivor” species. Anthozoan colonies with no visual indication of disease or bleaching were assessed quarterly during the years 2012 and 2013, at sites at 6 and 18 m depths at Tennessee Reef. Colonies were dark-acclimated for at least 20 minutes prior to measurements using pulse-amplitude modulated fluorometry. The mean Fv/Fm values for Palythoa caribaeorum at 6 m were consistently the lowest (0.59; 0.2 SE), and were significantly different between summer and autumn of 2012. Siderastrea siderea from the 6 m site revealed no significant differences in Fv/Fm (0.64; 0.2 SE) across the sampled months, and were significantly lower than for those living at 18 m depth (0.68; 0.2 SE). Colonies of Montastraea cavernosa at 18 m showed no significant differences in mean quantum yields over time (0.68; 0.2 SE). This study found no strong temporal/seasonal influence in the Fv/Fm in the examined species, supporting previous evidence for photoprotective mechanisms that allow them
The Struggle of Existence.G. F. Gause

(1) In the two preceding chapters our attention has been concentrated on the indirect competition, and we have to turn now to an entirely new group of phenomena of the struggle for existence, that of one species being directly devoured by another. The experimental investigation of just this case is particularly interesting in connection with the mathematical theory of the struggle for existence developed on broad lines by Vito Volterra. Mathematical investigations have shown that the process of interaction between the predator and the prey leads to periodic oscillations in numbers of both species, and all this of course ought to be verified under carefully controlled laboratory conditions. At the same time we approach closely in this chapter to the fundamental problems of modern experimental epidemiology, which have been recently discussed from a wide viewpoint by Greenwood in his Herter lectures of 1931. The epidemiologists feel that the spread of microbial infection presents a particular case of the struggle for existence between the bacteria and the organisms they attack, and that the entire problem must pass from the strictly medical to the general biological field.
Preclinical toxicity and safety evaluation of Althaea officinalis L. extract as naturopathic medicine in common carp (Cyprinus carpio L.): Hematological and biochemical study

ABSTRACT This study was conducted to evaluate the effects of marshmallow extract (Althaea officinalis L.) administration on blood cells and biochemical parameters of carp liver. A total of 150 carps (Cyprinus carpio, initial body mass of 37.7 ± 4.4 g) were fed diets containing 0.0 (control diet), 2.5, 5, and 10 g marshmallow extract for 60 days. On days 30 and 60 of the experiment blood samples were collected and hematological parameters and liver enzyme activities—aspartate aminotransferase (AST), alanine amino transferase (ALT), lactate dehydrogenase (LDH), and alkaline phosphatase (ALP)—were measured. No significant difference was found (p > .05) in red blood cells (RBC); hemoglobin concentration (Hb); hematocrit (Htc); mean corpuscular volume (MCV); mean corpuscular hemoglobin concentration (MCH); or the percentage of neutrophils, basophils, and eosinophils in fish fed with different concentrations of marshmallow extract on days 30 and 60. However, the white blood cell (WBC) count was increased significantly in the fish fed for 60 days with feed supplemented with 5 g marshmallow extract (p < .05). The MCHC was increased signiﬁcantly in ﬁsh fed with diets supplemented with 2.5 g marshmallow extract for 60 days (p < .05). Administration of marshmallow extract (5 g) significantly increased (p < 0.05) lymphocytes on days 30 and 60. However, dietary intake of 10 g marshmallow extract had significantly decreased the monocyte percentage after 60 days. A significant increase was observed in AST, ALT, ALP, and LDH levels in livers of fish fed with extract 10 g, which may be attributed to cytotoxicity. However, marshmallow extract 2.5 and 5 g did not have adverse effects on liver enzymes. These results indicate that preclinical dietary supplementations of 2.5 and 5 g marshmallow extract per kg diet have no side effects on common carp.
Acute toxicity evaluation of drought-tolerant transgenic rice Agb0103 to Daphnia magna

A drought-tolerant transgenic rice (Agb0103) was developed using a pepper methionine sulfoxide reductase (CaMsrB2) under the control of rice Rab21 promoter with a selection marker, the phosphinothricin acetyltransferase (PAT) gene. Commercialization of genetically modified (GM) crops will require the evaluation of risks associated with the release of GM crops. With the potential problems associated to GM crops safety testing, the investigation of their effects on non-target organisms is necessary for environmental risk research. This study was carried out to assess acute toxicity of a GM crop using the water flea (Daphnia magna) for non-target organism risk evaluation. The effect of acute toxicity on Daphnia magna of Agb0103 rice and a non-GM rice, Ilmibyeo, were investigated at different concentrations (0, 625, 1,250, 2,500, 5,000, and 10,000 ㎎/L). The Agb0103 rice used for the test was confirmed to express the CaMsrB2/PAT gene by the PCR and ELISA. Daphnia magna feeding tests showed no significant differences in cumulative immobility or abnormal response with either Agb0103 rice or non-GM rice. The 48hr-EC 50 values showed no difference between Agb0103 rice (2243 ㎎/L) and non-GM rice (2694 ㎎/L). These results suggest that there is no significant difference in toxicity to Daphnia magna between Agb0103 rice and its non-GM counterpart.
Estimating Summer Squash Leaf Area Nondestructively

Crop leaf area estimates from nondestructive measurements of leaf length and width offer reliable, inexpensive alternatives to leaf area meters (Gamiely et al., 1991; Manivel and Weaver, 1974; Robbins and Pharr, 1987; Wiersma and Bailey, 1975). Additionally, these methods permit repeated sampling of the same plants over time, thus reducing some of the experimental variability associated with destructive sampling procedures. The objective of this research was to determine whether an existing cucumber (Cucumis sativus L.) leaf area model (Robbins and Pharr, 1987) would apply to summer squash (Cucurbita pepo L.) since leaf morphology of these species is similar and, if not, to develop leaf area-estimating functions for summer squash. ‘Sunrise’, ‘Corona’, ‘Dixie’, ‘Lemondrop’, ‘Dark Star’, and ‘Senator’ summer squash were sown in 3.5-liter pots containing commercial potting soil (Metro-Mix 300; W.R. Grace and Co., Cambridge, Mass.) and grown in a greenhouse. At the end of 4 weeks, at least 30 leaf lamina representing the range of leaf sizes present were sampled from each cultivar. Leaf lamina length (L) was measured after the method of Robbins and Pharr (1987), and leaf width (W) was measured at the widest point perpendicular to the lamina midrib. Actual leaf area (A) was determined for each lamina with a LICOR Model 3000 leaf area meter (LI-COR, Lincoln, Neb.). Statistical analyses revealed that the functions of Robbins and Pharr (1987) derived for cucumbers did not satisfactorily fit the squash data from the current experiment, indicating a different model was needed for summer squash. Several combinations of variables and regression equations were evaluated by comparing coefficients of determination (R 2) and error mean squares (MSE); four combinations gave the best results (Table 1). No significant differences (P = 0.05) were found between cultivars. An equation using the product of L and W was the overall best equation in terms of R2 and MSE. However, a model using W2 was similar in precision (Fig. 1). A model based on a single measurement offers the advantages of more efficient data collection and less complex calculations. Summer squash leaf area cannot be estimated using a previously derived model for cucumber, but can be accurately and nondestructively estimated using leaf width. A single equation performed well for several commercial cultivars over a wide range of leaf sizes. Other squash cultivars will likely fit the functions derived in this experiment unless their leaf morphology differs greatly from those used here.
Energetics , Metabolism , and Endothermy in Sharks and Rays

7.1 Energetics . 211 7.1. 1 Size . 211 7.1. 2 Temperature . 212 7.1. 3 Acclimation . 212 7.1. 4 Experimental Apparatus . 212 7.1. 5 Metabolic Rates . 213 7.1. 5.1 Sharks. 213 7.1. 5.2 Rays . 218 7.1. 6 Temperature Effects . 218 7.1. 7 Muscle Metabolic Biochemistry. 218 7.1. 8 Metabolic Rates in the Field . 218 7.1. 9 Anaerobic Metabolism . 219 7.2 Behavioral Thermoregulation of Ectothermic Elasmobranchs . 220 7.2. 1 Foraging and Digestion . 220 7.2. 2 Reproduction . 221 7.3 Endothermy . 221 7.3. 1 Myotomal Muscle Endothermy . 221 7.3. 2 RM Endothermy and Movement Patterns . 227 7.3. 3 Eye and Brain Endothermy . 228 7.3. 4 Visceral Endothermy and Homeothermy . 229 7.3. 5 Endothermy and Blood-Oxygen Binding . 230 7.4 Summary . 232 Acknowledgments . 232 References . 232
A g-Tocopherol-Rich Mixture of Tocopherols Maintains Nrf2 Expression in Prostate Tumors of TRAMP Mice via Epigenetic Inhibition of

Nuclear factor-erythroid 2-related factor 2 (Nrf2) plays a pivotal role in maintaining cellular redox homeostasis and eliminating reactive toxic species. Nrf2 is epigenetically suppressed due to CpG hypermethylation in prostate tumors from the transgenic adenocarcinoma of the mouse prostate (TRAMP) model. We previously showed that dietary feeding of a gtocopherol–rich mixture of tocopherols (g-TmT) suppressed prostate tumorigenesis in TRAMP mice associated with higher Nrf2 protein expression. We hypothesized that g-TmT may maintain Nrf2 through epigenetic inhibition of promoter CpG methylation. In this study, 8-wk-old male TRAMP mice were fed 0.1% g-TmT or a control diet for 16 wk. The methylation in the Nrf2 promoter was inhibited in the prostate of the g-TmT group compared with the control group. Protein expressions of DNA methyltransferase (DNMT), including DNMT1, DNMT3A, and DNMT3B, were lower in the prostate of the g-TmT group than in the controls. TRAMP-C1 cells were treated with 30 mmol/L of g-TmT or blank medium for 5 d. The methylation in the Nrf2 promoter was inhibited in the g-TmT–treated cells compared with the untreated cells at d 5, and mRNA and protein expressions of Nrf2 and NAD(P)H:quinone oxidoreductase 1 were higher. Interestingly, only DNMT3B was inhibited in the g-TmT–treated cells compared with the untreated cells. In the aggregate, our findings demonstrate that g-TmT could inhibit CpG methylation in the Nrf2 promoter in the prostate of TRAMP mice and in TRAMPC1 cells, which might lead to higher Nrf2 expression and potentially contribute to the prevention of prostate tumorigenesis in this TRAMP model. J. Nutr. 142: 818–823, 2012.