Miracle-dz/UniFAR-FTUs huggingface dataset:
The Molecular Chaperoning and GEF Functions of Ric-8 in Heterotrimeric G protein Signaling

Resistance to inhibitors of cholinesterase 8A (Ric-8A) is a non-receptor guanine nucleotide exchange factor (GEF) that stimulates the exchange of guanine nucleotide (GDPàGTP) for heterotrimeric G protein alpha subunits (Gα). In cells, active G proteins (Gα-GTP) alter numerous signaling pathways to provoke biological responses. Overexpression of Ric-8B enhances G protein signaling in cell culture systems, and it has long been postulated, but never been shown to be a Gα GEF. We found that Ric-8B proteins were Gαs GEFs, but the catalysis of nucleotide exchange was GTP dependent. This phenomenon is unusual for a GEF. At low GTP levels, Ric-8B potently inhibited Gαs steady state GTP consumption (catalysis), but at high GTP levels, Ric-8B proteins are Gαs activators. We conclude that at cellular GTP levels, Ric-8B catalyzes nucleotide exchange for Gαs in a forward direction to produce Gα-GTP in cells. Although Ric-8 is a Gα activator in vitro, the actual function of Ric-8 GEF activity in cells was not known. We found that co-overexpression of Ric-8 and Gα baculoviruses in insect cells dramatically enhanced our production of functional purified Gα proteins. With this method, unprecedented quantities of representatives of each Gα class were obtained. We showed that Ric-8 proteins were molecular chaperones that direct nascent G protein α subunits membrane association. To determine the function of Ric-8 in G protein biosynthesis, cell free translation systems were used to ascertain the effect of Ric8 on G protein folding. In Ric-8A immuno-depleted rabbit reticulocyte lysate (RRL), Gα
Ageing bias and precision for deep‐water snappers: evaluating nascent otolith preparation methods using novel multivariate comparisons among readers and growth parameter estimates

&NA; Tropical deep‐water snappers (Etelinae) support valuable fisheries across the Indo‐Pacific, with stock assessments reliant on age‐based information in the absence of reliable catch and effort statistics. These long‐lived species have been considered notoriously difficult to age. However, nascent developments in ageing protocols, particularly thinner transverse sections of otoliths (˜180‐200 &mgr;m), are providing improvements in growth zone clarity, interpretation and repeatability of annuli counts. At a recent international workshop, thin sectioned otoliths from three deep‐water snappers were read under reflected light by eight fisheries scientists from across the Indo‐Pacific, with various levels of fish‐ageing experience. Precision and bias were assessed using traditional ageing precision metrics (index of average percent error, IAPE; and coefficient of variation, CV), and a novel approach using multivariate analyses (metric multidimensional scaling, mMDS) based on Euclidean dissimilarity among readers' counts and subsequent von Bertalanffy (vB) growth parameter estimates. Annuli counts between the primary reader and all other readers were within two for 80% of estimates, with uniform variation across a wide age range for Etelis carbunculus (intraclass correlation coefficient (ICC) = 0.924, n = 20, 3‐25 annuli) and Etelis sp. (ICC = 0.933, n = 15, 2‐27 annuli). In contrast, annuli counts for Pristipomoides filamentosus (n = 14, 4‐49) were less precise (i.e. ICC = 0.835, 66% of counts within two of primary reader) with a bias toward greater variation in younger, pre‐maturational life stages (≤5 annuli). Traditionally accepted ageing precision (IAPE ≤ 5.5%, CV ≤ 7.6%) was achieved for each species, but was commensurate with reader experience. The multivariate mMDS ordination was more informative in identifying both distance (i.e. dissimilarity) and direction (i.e. form) of variations in annuli counts and vB growth parameter estimates among readers. The acceptable level of ageing precision and bias achieved among most readers indicated that deep‐water snappers can be aged precisely when appropriate otolith preparation methods are used. This study contributes towards ageing protocols that can be used to (i) interrogate bias and precision of age data for stock assessments, and (ii) standardise comparisons of age‐based life history characteristics across a species range.
Effects of milk somatic cell count on physical and chemical characteristics of mozzarella cheese

The aim of the present study was to investigate the physical and chemical characteristics of mozzarella cheese manufactured from cows milk containing somatic cell counts (SCC) at low ( 800,000 cells/mL) levels. Cheeses were manufactured according to the following sequence: milk pasteurisation (65°C, 30 min), inoculation with starter culture (3%) and calcium chloride, followed by mixing and incubation (34°C, 60 min), addition of rennet, mixing and incubation (34°C, 35 min). The coagulum was cut, drained and stored (4°C, 12-16 h, until pH 5.2). Next, the curd was stretched and kneaded (80-85°C, 5 min), salted in brine (20°B, 20 h) at 10°C and dried (5°C, 48 h). The cheeses were vacuum packed in plastic bags and stored at 4°C for 30 days. Cheese samples were analysed on days 2, 9, 16, 23 and 30 after production. Analyses in cheese included titratable acidity, pH, dry matter, fat dry matter, ash, total protein, casein, extent and depth of proteolysis, lipolysis (expressed as free fatty acids, FFA) and instrumental texture parameters (hardness, springiness an chewiness). SCC in milk did not affect (p>0.05) the yield and the physical parameters of mozzarella cheese over 30 days of storage. However, the total protein and casein decreased, and the FFA content increased in cheese manufactured from high SCC milk (p 800,000 cells/mL) in order to avoid protein losses and a higher lipolysis ratio in the cheese during 30 days of storage.
Shell sculpture as a defensive adaptation in ammonoids

Quantification of Paleozoic, Triassic, Jurassic, and Cretaceous ammonoid shell ornamentation shows that commonality and roughness of ornamentation increased throughout the geologic range of the ammonoids. The two major hypotheses concerning the function of ammonoid shell ornamentation are that 1) ornament served a protective (defensive) function against shell breakage by predators, and 2) it increased hydrodynamic efficiency of the shell during swimming. The heavily ribbed and spined ammonoid shells of the late Mesozoic have ornamentation too coarse to have served any hydrodynamic purpose. The increasing proportion of such shells during the Jurassic and Cretaceous may have been in response to increased numbers of late Mesozoic shell crushing predators and “better armed” ammonoid prey. This trend parallels adaptive trends of other invertebrate groups during the “Mesozoic marine revolution” as defined by Vermeij (1977).
Phylogenetic relationships of the largest lungless tetrapod (Gymnophiona, Atretochoana) and the evolution of lunglessness in caecilians

Atretochoana eiselti is the largest extant lungless tetrapod. This species is one of the fully aquatic caecilian amphibians of the family Typhlonectidae. It is unique within Gymnophiona in lacking lungs and having sealed choanae, a snake‐like postoccipital jaw articulation, and some other greatly divergent features. Phylogenetic relationships of the five typhlonectid genera have been estimated only once previously, in an analysis of morphological data. Here we infer for the first time integrating molecular and morphological data, the relationships of all typhlonectid genera. Although Atretochoana and Potomotyphlus share several derived character states in morphology, some of which linked to a reduction of the pulmonary importance in respiration, Potomotyphlus is more closely related to Typhlonectes than to Atretochoana. Consequently, we conclude that evolutionary loss of lungs or gradual reduction of their importance in respiration in Atretochoana and Potomotyphlus was convergent within this poorly known group of amphibians.
Does seed coat structure modulate gut-passage effects on seed germination? Examples from Miconieae DC. (Melastomataceae)

Abstract Fruits of Melastomataceae constitute a key resource for Neotropical frugivores. However, the mechanisms determining gut-passage effects on seed germination are poorly known. Here, we determine how bird gut-passage affects seed germination in three species of Miconieae by running germination experiments, examining changes in seed coat structure and determining germination inhibition by fruit extracts. Mature fruits of Clidemia urceolata, Leandra aurea and Miconia rubiginosa were sampled in south-eastern Brazil and seeds were submitted to treatments evaluating gut-passage effects and different concentrations of fruit extracts. Light and scanning electron microscopy were used to compare seed coat structure and thickness of control and gut-passed seeds. We found minor effects of gut passage on seed germination. However, changes in seed coat structure of gut-passed seeds of L. aurea may have been related to a decrease in germination. Our data also support the idea that germination inhibitors in fruit pulp may contribute to the inhibition effect. Our study corroborates the idea that changes in the seed coat following gut passage modulate the complex fruit–frugivore interactions, especially between plants and generalist dispersers, and that seed cleaning is a key factor determining seedling establishment in Neotropical Melastomataceae.
Extreme Landscapes Decrease Taxonomic and Functional Bird Diversity but Promote the Presence of Rare Species

Abstract. Human activities may generate geometrical landscape (i.e. composed of rectilinear and repetitive landscape units) structures that can significantly influence the spatial distribution of birds. While bird distribution in various landscape types has been extensively studied, the role played by landscape configuration and composition in different facets of bird diversity remains unclear. Here, these two main components of landscape characteristics (i.e. configuration and composition) are disentangled and their relative influence on three different facets of bird assemblages: taxonomic and functional characteristics, and the presence of rare species, is tested. We chose four large coastal salinas of Western France as a relevant model of geometrical and human-dominated landscapes where each landscape unit can be easily identified and mapped. The landscape characteristics of these sites were mapped and quantified. Then, terrestrial breeding birds were sampled in 172 point-counts using a standardized protocol. 69 diurnal terrestrial bird species were detected and considered in analyses (waterbirds and owls excluded). Landscape composition was found to have a higher influence on bird communities than landscape configuration, which fits with the “landscape composition hypothesis”. More specifically, the most “extreme” landscapes — those with low terrestrial surface areas, low landscape richness and diversity, low cohesion, and very patchy landscapes with complex geometrical shapes — host the lowest bird taxonomic abundance, richness and diversity and functional richness, but are characterized by the presence of rare species (mainly wetland specialist species, e.g. Reed Bunting Emberiza schoeniclus and species with restricted ranges e.g. Bluethroat Luscinia svecica namnetum). Our results suggest that conservation plans in such geometrical and human-dominated habitats should not only focus on one aspect of landscape characteristics or one aspect of biological diversity but also consider the adverse effects of landscape characteristics on these different facets.
The diet of Cerulean Warbler (Setophaga cerulea) nestlings and adult nest provisioning behaviors in southern Indiana

ABSTRACT We studied the diet of nestling Cerulean Warblers (Setophaga cerulea) and the provisioning behaviors of parents in southern Indiana. The Cerulean Warbler, a small insectivorous passerine breeding in eastern North American deciduous forests, is one of the fastest declining Neotropical wood warblers. Our primary objectives were to determine the importance of specific prey items in the diet of nestling Cerulean Warblers, and to assess whether the proportion of lepidopteran larvae (caterpillars) in the diet changed during the breeding season. We also describe general nest provisioning behavior, including differences between females and males, and assess breeding success across years. We video-taped provisioning behavior to determine the prey types (insects and arachnids) that parent Cerulean Warblers fed their young during the breeding season in 2013 and compared the proportions of lepidopteran larvae in the diet to that in the environment. The proportion of lepidopteran larvae in the nestling diet was 53% (n = 194/366) across the entire breeding season in 2013 and 83% during the peak nestling period which occurred in late May to early June. The proportion of lepidopteran larvae in the diet was 3.8 times greater than the proportion of lepidopteran larvae available. The proportion of lepidopteran larvae in the nestling diet decreased during the breeding season and was 80% reduced for the last nest of the season compared to the first nest. Additional observations from 2011 and 2012 were similar where lepidopteran larvae composed 65% (n = 15/23) and 44% (n = 8/18) of the diet, respectively. The mean length of arthropods in the diet was 15 mm compared to a mean length of 6 mm in the environment. Other prey items fed to nestlings included Orthoptera, Diptera, Neuroptera, Arachnida, Coleoptera, Hemiptera, and Phasmida. The average feeding rate during 2011–2013 was 4.31 ± 0.34 deliveries/30 mins, and males fed more frequently than females. Mayfield nest success was 35% in 2011 (n = 12), 6% in 2012 (n = 12), and 33% (n = 27) in 2013. We conclude that lepidopteran larvae were the main food source for nestling Cerulean Warblers and that the proportion of lepidopteran larvae in their diet was the highest during peak numbers of nestlings at the end of May and early June.
Estimation of interrelationships among some quality factors of jute seeds

The storage mycoflora associated with seeds of 21 accessions of Corchorus capsularis L. were isolated and identified. Blotter, Paper towel and Agar plate methods were used to isolate the fungi associated with seeds. A total of ten species of fungi viz. Aspergillus flavus , A. fumigatus , A. niger , A. terreus , Curvularia lunata , Colletotrichum corchori , Fusarium oxysporum, Eurotium sp. , Penicillium sp. and Rhizopus stolonifer were isolated from the selected jute seeds. Aspergillus spp. and Colletotrichum corchori were predominant in most of the jute accessions. Accession No. A-3047 showed the highest fungal incidence and Accession Nos. A-3361, A-2734 and A-877 showed the lowest. Accession No. A-3361 showed the highest seed germination while Accession No. A-3309 showed the lowest. Mortality of seedling showed the highest in Accession No. A-3309 and the lowest in Accession No. A-3361. Physical purity of seed recorded the highest in Accession No. A- 3361 and the lowest in Accession No. A-3309. There were negative correlation between percentage of fungi and percentage of germination and between percentage of fungi and physical purity of seeds. Positive correlation was observed between percentage of fungi and seedling mortality and between purity of seed and germination of seed. Dhaka Univ. J. Biol. Sci. 25(1): 9-17, 2016
Effect of rice husk diluted dietary switching on body weight, carcass yield and digestive tract of adult ganders Einfluss des wechselnden Einsatzes von mit Reisschalen verdünnten Rationen auf das Lebendgewicht, die Schlachtausbeute und das Verdauungssystem von erwachsenen Gantern

Dietary switching has been reported in many birds as an indicator of the structural flexibility of the digestive tract. Some waterfowls switch from seeds to aquatic insects or new plant tissues when preparing for breeding (KRAPU and REINECKE, 1992). Songbirds switch diets from insects to fruits during migration (BAIRLEIN and GWINNER, 1994; BIEBACH, 1996). At the same time, reversible size changes in the gastrointestinal tract in response to changes in diet composition have been reported in red grouses, quails and ducks (MOSS and PARKINSON, 1972; SAVORY and GENTLE, 1976a, b; KEHOE et al., 1988). It is apparent that dietary switching occurs in diets of many birds and it is also a good design to study the nutrition need characteristic of birds. Insoluble fiber is generally considered as a nutrient diluent in poultry diets (HETLAND et al., 2004), although its effects are not well clear. There was no significant difference in growth performance of 0-4 week-old and 5-6 week-old geese while adding 0-15% and 30% leymus chinensis to the diet, respectively (TIMMLER and JEROCH, 1993). Contents of 18% alfalfa, ryegrass and wheat bran in diets can promote growth of goslings of 4-10 weeks (ZHOU, 2004). Dietary inclusion of coarse insoluble fiber has also been reported to promote gizzard development (HETLAND et al., 2003, 2004). The effects of insoluble fiber on the performance of broilers differ depending on fiber particle size (AMERAH et al., 2009b). However, the use of rice husk (RH) in poultry rations is limited for the low CP and high CF content. Reports in geese fed on fibrous diets are less than those in gallinaceous birds, even though both of them can utilize a high-fiber diet (SAVORY and GENTLE, 1976a, b; AMERAH et al., 2009b). The objectives of the present experiment were to evaluate the effects of dietary switching with RH in increasing amounts on body weight (BW), carcass yield and digestive tract of adult geese. Material and methods
Influence of groundnut (Arachis hypogaea) based intercropping under different levels of irrigation on the performance of intercrops

A field experiment was conducted during kharif season of 2017 and 2018 to study the influence of intercropping under different levels of irrigation on the performance and nutrient dynamics of groundnut. Groundnut intercrops involving castor, blackgram, sesame and pearlmillet recorded higher plant height, dry matter production, yield attributes and equivalent intercrop yields under irrigation scheduling of IW/CPE ratio of 0.75. The Relative production efficiency favoured the intercropping system over the sole cropping system with values varying from19% to 99.6% over the conventional sole cropping system. Higher relative production efficiency was realised with castor as it outperformed as a companion crop but suppressed the groundnut yields. Application of water at IW/CPE ratio of 0.75 comprising 7 irrigations (excl. sprouting and life irrigation) enhanced the productivity in terms of equivalent intercrop yield as well as sole crop yield.
The effect of early diet on hepatic cholesterol metabolism in piglets

Plasma total, low density lipoprotein (LDL) and high density lipoprotein (HDL) cholesterol concentrations increase immediately following birth. Interestingly, this increase is greater in breast-fed infants than in infants fed formula. The reason(s) why there are differences in plasma cholesterol concentrations between breast-fed and formula-fed infants is not known. However, this difference may be a consequence of the variations in lipid composition between milk and infant formula. Little is known regarding the specific effects of the lipid component(s) of infant diets on the expression of genes involved in hepatic lipid metabolism. The studies presented in this thesis determined whether the addition of cholesterol, arachidonic acid [20:4(n-6)] and docosahexaenoic acid [22:6(n-3)] to formula, and the positional distribution of fatty acids in formula triglycerides increases plasma cholesterol in formula-fed piglets to levels observed in milk-fed piglets. In study #1, piglets were fed from birth to 18 days of age with either a conventional infant formula (conventional formula) or a formula with synthesized triglycerides (TG) (synthesized TG formula). The conventional infant formula had 70% of the total 16:0, representing 23% of total fatty acids, esterified at the sn-1 and 3 positions of the formula triglyceride. The synthesized TG formula contained a similar percentage of 16:0, representing 23% of total fatty acids, but had 47% of the total 16:0 esterified at the centre (sn-2) position of the formula triglyceride. Each of the conventional and synthesized TG formulae were provided either without (<0.10 mM) or with 0.65mM cholesterol added to formula, 0.52mmol/L as unesterified cholesterol and 0.13 mmol/L as cholesterol oleate. A reference group of piglets was also fed sow milk.
The Effect of Growing Location and Harvest Maturity on the Storage Performance and Quality of ‘Hayward’ Kiwifruit

Kiwifruit from 3 growing locations were harvested at 4 maturity levels. Weight, length, width, flesh color, flesh firmness, harvest soluble solids, titratable acidity, respiration, and ethylene production were measured at harvest, and subsequent storage behavior and sensory quality of the fruit were evaluated. The results indicate that a combination of initial soluble solids content at harvest, and flesh firmness, similar to the maturity index for pear, seems promising as a maturity index for kiwifruit.
Influence of plant growth regulators on in vitro micropropagation of Rauwolfia tetraphylla L.

In vitro culture of shoot apices of an introduced and naturalized medicinal plant Rauwolfia tetraphylla on Murashige & Skoog's basal medium, supplemented with α-naphthaleneacetic acid and 6-benzyladenine or indolyl 3-acetic acid and 6-benzyladenine resulted in the formation of 7-15 multiple shoot buds. The use of α-naphthaleneacetic acid and 6-benzyladenine stimulated callus formation at the base of the multiple shoot while indolyl 3-acetic acid and 6-benzyladenine stimulated only multiple shoot buds with no callus interface. Higher levels of 6-benzyladenine with α-naphthaleneacetic acid suppressed shoot elongation but increased the shoot multiplication rate. Murashige & Skoog's medium containing α-naphthaleneacetic acid and indolyl 3-butyric acid induced root formation. Through sequential hardening process well-rooted plantlets could be successfully established in the field.