Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural stabilization of GTP-binding domains in circularly permuted GTPases: Implications for RNA binding

GTP hydrolysis by GTPases requires crucial residues embedded in a conserved G-domain as sequence motifs G1–G5. However, in some of the recently identified GTPases, the motif order is circularly permuted. All possible circular permutations were identified after artificially permuting the classical GTPases and subjecting them to profile Hidden Markov Model searches. This revealed G4–G5–G1–G2–G3 as the only possible circular permutation that can exist in nature. It was also possible to recognize a structural rationale for the absence of other permutations, which either destabilize the invariant GTPase fold or disrupt regions that provide critical residues for GTP binding and hydrolysis, such as Switch-I and Switch-II. The circular permutation relocates Switch-II to the C-terminus and leaves it unfastened, thus affecting GTP binding and hydrolysis. Stabilizing this region would require the presence of an additional domain following Switch-II. Circularly permuted GTPases (cpGTPases) conform to such a requirement and always possess an ‘anchoring’ C-terminal domain. There are four sub-families of cpGTPases, of which three possess an additional domain N-terminal to the G-domain. The biochemical function of these domains, based on available experimental reports and domain recognition analysis carried out here, are suggestive of RNA binding. The features that dictate RNA binding are unique to each subfamily. It is possible that RNA-binding modulates GTP binding or vice versa. In addition, phylogenetic analysis indicates a closer evolutionary relationship between cpGTPases and a set of universally conserved bacterial GTPases that bind the ribosome. It appears that cpGTPases are RNA-binding proteins possessing a means to relate GTP binding to RNA binding.
Australian Legume Research – synthesis and future directions

Abstract. The Australian Legumes Symposium was the first in a planned series of regular technical symposia organised by the Australian Grasslands Association. The aim was to provide researchers with the opportunity to interact, present up-to-date reviews on topics related to pasture legume science, present results of current research and participate in planning of future research and development relevant to pasture legumes. This paper is intended to be the key output of the forum – a summary of findings and highlights from review and contributed research papers as well as identifying key research priorities for the future. In terms of the former, reviews presented at the symposium provided an overview of the development and role of pasture legumes in temperate farming systems. Closely related topics – nitrogen (N) fixation, N balance of farming systems and management of legume inoculation provided a focus on the importance of legumes in terms of N input and overall productivity. International perspectives on lucerne – its improvement and adoption provided a noticeable contrast to the apparent paucity of research into this species in Australia – despite its widespread use in temperate farming systems. In terms of content, there were many other papers delivered dealing with a wide diversity of relevant issues. On one hand the diversity of work in pasture legume research and development may stem from the wide array of expertise available in Australia and New Zealand, while on the other it might suggest that research and development inputs are being thinly spread over a large number of species. With respect to determining research priorities, it was surprising that participants were most concerned with how research is funded and conducted and the need to address this by reconsidering current arrangements. A greater role for economic analysis in determining research priorities was foreshadowed. The identification and management of acid-tolerant perennial legumes for higher rainfall zone permanent pastures was nominated as a major research priority, as was the need to address problems related to pre-inoculation of legume seed. The clear message from the symposium was that there needs to be a reorganisation of pasture legume improvement in order for gains to be effectively realised, and to maintain research and development capacity.
Effect of Nitrogen on Nodulation and Yield of Soybean

SUMMARY Nitrogen fertilizer applied to the surface of the soil in the field did not increase the yield of Bragg soybeans, and at higher levels reduced it, but may or may not significantly reduce soybean nodulation and plant height. In a pot experiment, there was evidence that deeply applied N increased plant height and dry weight of a non-nodulating isoline of Clark soybeans 46 days after planting.
Gas Exchange, Water Status, and Growth of Pepper Seedlings Exposed to Transient Water Deficit Stress are Differentially Altered by Antitranspirants

Successful field establishment of vegetable transplants often depends on the ability of young seedlings to tolerate various biotic and abiotic stresses after transplanting. Treatments that limit transpirational water loss could improve plant survival and stand establishment. In this study we evaluated growth and physiological responses of pepper (Capsicum annuum L.) seedlings to foliar application of chemical plant regulators [abscisic acid (ABA) and aminoethoxyvinylglycine (AVG)] or physical film-forming barriers [AntiStress (AS), Transfilm (TF), and Vapor Gard (VG)] during transient 4-day water deficit cycles. During two 4-day water deficit cycles, stomatal conductance (g(s)) and net CO2 assimilation rate (A(CO2)) were unaffected by the application of physical materials, but differed for ABA and AVG. Compared with untreated control plants, ABA reduced gs (47% to 69%) and A(CO2) (37% to 57%) by the end of the second water deficit cycle, whereas AVG increased gs (27% to 60%) during the first desiccation cycle. Leaf (psi(lf)) and stem (psi(st))xylem water potential of plants treated with film-forming materials generally decreased at the same rate as those of untreated plants, whereas application of AVG caused earlier and more pronounced decline of psi(lf). Application of ABA enabled the maintenance of psi(lf) and psi(st) during two desiccation cycles, and thus prevented an increase of electrolyte leakage and leaf abscission. Growth rates of all plant components were reduced after ABA applications. However, allometric relationships showed similar patterns of dry matter allocation in leaves and shoots among ABA, TF, VG, and untreated control plants. Application of AS reduced allocation of dry matter to leaves, whereas AVG enhanced it at the expense of roots. These data indicate that water deficit tolerance of pepper seedlings only occurred with foliar application of ABA. This effect was associated with improved plant water relations, increased cell membrane stability, reduced leaf abscission, and a transient reduction in plant growth rates.
Range and Ecology of Helenium virginicum in the Missouri Ozarks

Abstract Helenium virginicum (Virginia sneezeweed) is a federally listed threatened herb found at unshaded sites in seasonally inundated ponds in the Shenandoah Valley of Virginia and in the Ozark Highlands of Missouri. In the Ozarks, one population of H. virginicum was discovered in the 1950s, though it was thought to be a hybrid of Helenium flexuosum and Helenium autumnale until genetics work resolved its identity in 2000. Since that time, it was the only known population outside of Virginia. In this study, we systematically identified potential H. virginicum habitat in the Ozarks by using topographic maps and aerial photographs and surveyed these areas for H. virginicum. Our objectives were to locate new populations of the plant and to better define its ecology in Missouri. By the end of the growing season of 2004, we had located 42 new populations of H. virginicum in the lower Missouri Ozarks—more populations than are currently known in the state of Virginia. The results of this study greatly expand the known range of H. virginicum in Missouri and provide important information regarding its ecology.
Ecologia da polinização do maracujá-amarelo, na região do vale do submédio São Francisco

This study describes aspects of floral biology and the reproductive system of Passiflora edulis f. flavicarpa (Passifloraceae), including foraging patterns of the floral visitors in the region of Sao Francisco Valley. The study was carried out in irrigated orchards in the Manicoba Project, in Juazeiro-BA, during 2005 and 2006. The floral anthesis occurred between midday and 1 pm. Flower closing started at 6 pm and finished around 1 am. The time for style deflexion was 71,4 ± 12,4 min, about 5% of the flowers remained with the style undefexed. The stigmas were receptive during the entire anthesis and the pollen grains presented 94% viability. The nectar volume was in average 100 µL, with 48% of sugar concentration . The average number of pollen grains/flower was 140,595 ± 34,175 and 426 ± 77 of ovules/ovary. The highest rates were obtained after manual crossed pollination (74%), confirming the existence of a system of self-incompatibility. We registered 10% of flowers with four stigmas, which when manually pollinated, produced bigger fruits with a higher number of seeds (477,7 ± 76,8). We found a positive correlation between the number of seeds and the weight of the fruits. The flower visitors were Apis mellifera, Trigona spinipes, Xylocopa grisescens, X. frontalis and X. cearensis. A. mellifera and T. spinipes being pollen and nectar robbers, respectively. Bees of the genus Xylocopa were more frequent during the dry season and A. mellifera during the wet season. The effective pollinators were X. grisescens and X. frontalis. We found that they were limited in number in the studied areas. However they were found to be more frequent in other plant species during the rainy season which indicates that these plant species compete with the passion fruit for pollination service.
Does the telemetry technology matter? Comparing estimates of aquatic animal space-use generated from GPS-based and passive acoustic tracking

Underwater passive acoustic (PA) telemetry is becoming the preferred technology for investigating animal movement in aquatic systems; however, much of the current statistical tools for telemetry data were established from global positioning system (GPS)-based data. To understand the appropriateness of these tools for PA telemetry, we dual-tagged free-ranging aquatic animals that exist at the air-water interface (Crocodylus porosus, n=14). The location of each animal was simultaneously recorded over a 3-month period by fixed acoustic receivers and satellite positioning. Estimates of minimum travel distance and home range (HR) were then calculated from the PA and GPS datasets. The study revealed significant disparity between telemetry technologies in estimates of minimum travel distance and HR size. Of the five HR measures investigated, the linear distance measure produced the most comparable estimates of HR size and overlap. The kernel utilisation distribution with a reference smoothing parameter function and ad hoc function, however, produced comparable estimates when raw acoustic detections were grouped into periods when animals were within and between receiver detection fields. The study offers guidelines on how to improve the accuracy and precision of space-use estimates from PA telemetry, even in receiver arrangements with large areas of non-detection.
SMALL-PREY PROFITABILITY: FIELD ANALYSIS OF SHOREBIRDS’ USE OF SURFACE TENSION OF WATER TO TRANSPORT PREY

Abstract Previous laboratory studies have shown that Red-necked Phalarope (Phalaropus lobatus), Wilson’s Phalarope (P. tricolor), Western Sandpiper (Calidris mauri), and Least Sandpiper (C. minutilla) use the surface tension of water surrounding a prey item to transport it from bill tip to mouth. Although such experimental work suggests that many species of shorebird may be capable of surface-tension feeding, no field studies have been done that examine this possibility. We studied the occurrence and interspecific variation in the performance of surface-tension transport (STT) in wild shorebirds feeding on identical prey items in shallow water. All shorebirds videotaped—Little Stint (C. minuta), Dunlin (C. alpina), Sanderling (C. alba), Curlew Sandpiper (C. ferruginea), Common Redshank (Tringa totanus), and Black-winged Stilt (Himantopus himantopus)—used STT to feed on small prey items. Individuals employing STT used one or several cycles of jaw spreading to transport the prey contained in a drop of water upward along the bill cavity, an action indicative of STT. Two distinct types of prey transport were observed: (1) use of STT in isolation by calidridine species following the description given in previous studies (i.e., an absence of other feeding mechanisms such as tongue movements, suction, or inertial transport), and (2) STT aided by inertial transport (head jerks) as seen in Common Redshank and Black-winged Stilt. Measured prey-transport variables (number of cycles, total time, and speed of transport) varied among species. The absence of significant relationships between these variables and measures of external morphology (bill length, bill length-to-width ratio, and bill length-to-depth ratio) suggests that some interspecific variations in STT performance may be attributable to differences in internal bill morphology. We show that STT is a common feeding mechanism in small or medium- sized shorebird species that feed on small prey items in shallow water. Birds using STT transported ≤3.6× faster than the theoretical value predicted by a previous model and can achieve high intake rates when foraging on high densities of available small prey items. Ventajas de las Presas Pequeñas: Análisis de Campo del Uso de la Tensión Superficial del Agua por las Aves Playeras para Transportar las Presas
Crying out in pain—A systematic review into the validity of vocalization as an indicator for pain

Vocalization is often used to assess pain, sometimes combined with other behaviours such as facial expressions. Contrary to facial expressions, however, for vocalization, there is little evidence available on the association with pain. The aim of this systematic review was to critically analyse the association between vocalization and pain, to explore if vocalizations can be used as a “stand‐alone” indicator for pain.
Catheter ablation of atrial fibrillation in cardiac amyloidosis

Cardiac amyloidosis is a progressive infiltrative disease involving deposition of amyloid fibrils in the myocardium and cardiac conduction system that frequently manifests with heart failure (HF) and arrhythmias, most frequently atrial fibrillation (AF), atrial flutter (AFL), and atrial tachycardia (AT).
Critical role of divalent cations and Na+ efflux in Arabidopsis thaliana salt tolerance

Detrimental effects of salinity on plants are known to be partially alleviated by external Ca2+. Previous work demonstrated that the Arabidopsis SOS3 locus encodes a Ca2+-binding protein with similarities to CnB, the regulatory subunit of protein phosphatase 2B (calcineurin). In this study, we further characterized the role of SOS3 in salt tolerance. We found that reduced root elongation of sos3 mutants in the presence of high concentrations of either NaCl or LiCl is specifically rescued by Ca2+ and not Mg2+, whereas root growth is rescued by both Ca2+ and Mg2+ in the presence of high concentrations of KCl. Phenocopies of sos3 mutants were obtained in wild-type plants by the application of calmodulin and calcineurin inhibitors. These data provide further evidence that SOS3 is a calcineurin-like protein and that calmodulin plays an important role in the signalling pathways involved in plant salt tolerance. The origin of the elevated Na : K ratio in sos3 mutants was investigated by comparing Na+ efflux and influx in both mutant and wild type. No difference in Na+ influx was recorded between wild type and sos3; however, sos3 plants showed a markedly lower Na+ efflux, a property that would contribute to the salt-oversensitive phenotype of sos3 plants.
Variation in Male Advertisement Calls in the Neotropical Frog Physalaemus enesefae

Abstract I described the advertisement call of Physalaemus enesefae in the time and spectral domains and analyzed the relationship between male body size, mass and condition, and call characteristics. I also estimated among-male and within-male variation in seven call traits and their repeatabilities. For the population under study, male calls were 720 ms long, had a dominant frequency of 898 Hz, and were repeated at 3.8-sec intervals, on average. Weak but significant correlations existed between male mass and three call traits: dominant frequency, initial frequency, and final frequency of the call. There was ample among-male variation in all call traits analyzed. In relation to within-male variation, the intercall interval had the highest coefficients of variation, and the initial and the final frequency of the call had the lowest. All the call traits analyzed were static except for intercall interval, which was dynamic. Intercall interval had the lowest repeatability of all call traits analyzed. Thus, call traits with the lowest within-male variation had the highest repeatabilities and vice versa. Individual variation in call traits and high repeatabilities set the stage for the evolution of most call traits. Selection on intercall interval, however, might have a limited evolutionary effect as a consequence of its low repeatability.
Population dynamics, allometric relationships and reproductive status of Microcosmus sabatieri (Tunicata: Ascidiacea) in the Aegean Sea

The Mediterranean ascidian Microcosmus sabatieri is among the conspicuous benthic invertebrates, forming dense populations on moderately inclined cliffs. It is an edible species, commercially harvested at the southern part of the Aegean Sea. Considering that the biology of this species has not been adequately studied, a three-year survey was carried out focusing on population structure, allometric relationships and reproductive status of M. sabatieri stocks in Astypalea Island (Dodecanese, south Aegean). Population density showed insignificant temporal variation and lower values at the steeper station, while the pattern of dispersion was random. All measured biometric characters showed high plasticity, especially those related to siphons. All the examined morphometric relationships follow negative allometry. Ascidian length was a good predictor of biomass, and a strong relation was observed between mantle and tunic characters. Gonad somatic index showed a single spawning season per year, in winter. Length–frequency distribution analysis revealed the presence of one mode of medium sized individuals, implying that M. sabatieri stocks are under moderate fishing pressure in the study area.
Control of Guignardia citricarpa by Bacillus subtilis and Trichoderma spp.

The ability of isolates of Bacillus subtilis and Trichoderma spp. to control citrus black spot (CBS) was investigated in ´Natal´ sweet orange orchards. The first experiment was conducted during the 2001/2002 season and four isolates of B. subtilis (ACB-AP3, ACB-69, ACB-72 and ACB-77), applied every 28 days, alone or in combination were tested and compared with fungicide treatments. Two other experiments were carried out during the 2002/2003 season, where the same isolates of Bacillus and two isolates of Trichoderma (ACB-14 and ACB-40) were tested being applied every 28 days in the second experiment, and every 15 days in the third experiment. In the first experiment, the treatment with ACB-69 differed statistically from the control, but did not differ from other biological control agents or mixture of Bacillus isolates. In the second experiment, the treatments with ACB-69 and ACB-AP3 resulted in smaller disease index compared with the control treatment. However, this result was not repeated in the third experiment, where the isolates were applied every 15 days. Disease severity was high in both evaluated seasons and the fungicide treatment was the most effective for disease control.
Evaluation of Date Palm Cultivars for Rearing the Red Date Palm Weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Abstract Development of red date palm weevil Rhynchophorus ferrugineus (Olivier) was evaluated on 4 popular cultivars of date palm, viz., ‘Khalas’, ‘Sukkary’, ‘Khasab’, and ‘Sillaj’ for 2 consecutive generations. The weevils reared on ‘Sukkary’ showed significantly better growth expressed in most parameters such as length, width and weight at larval, pupal and adult stages. Significantly greater numbers of eggs were laid on cv. ‘Sukkary’ as compared to the other 3 cultivars. This might be because of higher sugar content of cv. ‘Sukkary’. Adult lifespan was significantly longer on cv. ‘Khasab’. Though more cocoons were harvested from ‘Khalas’, frequency of adult emergence was better on ‘Sukkary’. Male to female ratio was similar on all date palm cultivars.
Physicochemical characterization of starches from some Nigerian and Chinese roots and tubers

Physicochemical properties of starches of two popular Nigerian sweet potato (NSP1 and 2) cultivars were studied using those from Chinese sweet potato (CSP), cassava (CC) and potato (CP) widely used for starch production, as references. Moisture, ash, protein, and phosphorus contents of the starches varied from 4.34 to 9.48%, 0.26 to 0.31%, 0.05 to 0.42% and 0.018 to 0.995%, respectively with NSP starches showing significantly (p < 0.05) higher protein and lower ash content. The starches differed in amylose content, granule shapes, mean granule sizes, particle size distribution, enzyme digestibility; swelling power and solubility pattern. Higher retrogradation tendency was observed in NSP1 and CP starch pastes compared to those of CSP and NSP2. Thermal properties varied in the various starches. NSP1 and 2 showed higher gelatinization temperatures (73.17, 71.64°C), lower peak viscosities (2269, 2295 cP) and lower stability ratios (0.49, 0.54), respectively compared to the Chinese starches. Mean granule size and phosphorus content of the starches had substantial effect on their pasting properties. However, variability observed in the properties of the various starches further projected their useful and comparative potentials in food and non-food applications. Key words: Sweet potato, starch, pasting properties, thermal properties, retrogradation, digestibility.
Rethinking the role of many plant phenolics - protection from photodamage not herbivores?

Phenolics have been considered classic defence compounds for protecting plants from herbivores, ever since plant secondary metabolites were suggested to have evolved for that reason. The resource availability and carbon-nutrient balance hypotheses proposed that variation in phenolic levels between and within plant species reflects environmental availability of nutrients and light, and represents a trade-off in allocation by plants to growth and defence against herbivores. In contrast to these concepts, we suggest that (1) the main role of many plant phenolics may be to protect leaves from photodamage, not herbivores; (2) they can achieve this by acting as antioxidants; and (3) their levels may vary with environmental conditions in order to counteract this potential photodamage. We therefore suggest that patterns in phenolic levels, often used to support the concept of trade-off between growth and herbivore defence in relation to resource availability, may actually reflect different risks of photodamage. We suggest that the level of many phenolics is low under some environmental conditions, not because resources to produce them are limited, but simply because the risk of photodamage is low and they are not required. If our photodamage hypothesis is correct, a reassessment of the ecological and evolutionary role of many phenolics in plant defence theory is required.