Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased taxon and character sampling reveals novel intergeneric relationships in the Cracidae (Aves: Galliformes)

The Cracidae is one of the most endangered bird families in the World. Several studies have been published recently on the evolution and conservation of cracids. Phylogenetic analyses using a fragment of 661 bp of the mitochondrial cytochrome b gene for 39 different species of cracids corroborated most relationships found in previous studies. The present work attempts to refine the former phylogenetic hypothesis by increasing taxon sampling and combining molecular with osteological, integumentary and behavioural characters using Maximum Parsimony (MP) and Bayesian analyses. We present both separate and combined total evidence analyses with our molecular data, 152 osteological and 74 integumentary + behavioural characters. While supporting most aspects of the molecular-based hypotheses, the tree based on the combined matrix suggests several modifications of the generic composition for each of the two subfamilies: Penelopinae and Cracinae, and supports the merging of the genera Pipile with Aburria and Mitu with Pauxi. These results suggest that increased taxon and character sampling from a diversity of sources may be at least as important as increased sampling of only one type. Besides, of a total of 891 characters we had 437 parsimonyinformative sites (almost half of the analyzable sites) proving the efficiency of a total-evidence approach.
Low-concentration diffusible molecules affect the formation of biofilms by mixed marine communities

Abstract Biofilm formation is a major concern in any venture in the marine environment and often precedes the establishment of fouling by macro-organisms. In this study, the effects of three known cell-to-cell signalling molecules, nitric oxide (NO), cis-2-decenoic acid (CDA) and patulin, on the formation of marine biofilms were investigated. Each of the molecules has been shown to affect biofilms and this is the first study to investigate their effect on mixed communities of marine biofilm-forming micro-organisms. Studies of the biomass of those biofilms grown in the presence of the molecules showed that all three reduced biofilm formation by marine communities, with both NO and patulin reducing biofilm formation by more than 90% at the highest concentrations studied. However, colony counts revealed that the effect of patulin is likely due to toxicity. Analyses of the biofilm communities were also carried out using DGGE to determine whether there was any variation in the effects of each molecule on different bacterial taxa. No effect was seen on the communities and the biofilms appeared to form according to a neutral community model. Further investigations are recommended to study biofilms at a functional level.
Application of a Bioenergetics Model for Hatchery Production: Largemouth Bass Fed Commercial Feeds

Abstract Fish bioenergetics models based on natural prey items have been widely used to address research and management questions. However, few attempts have been made to evaluate and apply bioenergetics models to hatchery-reared fish receiving commercial feeds that contain substantially higher energy densities than natural prey. In this study, we evaluated a bioenergetics model for age-0 largemouth bass Micropterus salmoides reared on four commercial feeds. Largemouth bass (n ≈ 3,504) were reared for 70 d at 25°C in sixteen 833-L circular tanks connected in parallel to a recirculation system. Model performance was evaluated using error components (mean, slope, and random) derived from decomposition of the mean square error obtained from regression of observed on predicted values. Mean predicted consumption was only 8.9% lower than mean observed consumption and was similar to error rates observed for largemouth bass consuming natural prey. Model evaluation showed that the 97.5% joint confidence region inc.
An investigation to find out the reasons for adoption of agroforestry by farmers in district Faisalabad.

Forests play an important role in Pakistan's economy. These are the important sources for provision of timber, fuel wood, fodder and shelter for livestock. The significance of wood produced on farmlands has increased sharply during the last two decades. The cultivated fields are the best places to grow trees along with crops. The objective of this study was to investigate the reasons and the factors, which are responsible for the adoption of agroforestry by farmers in district Faisalabad. A sample of 125 respondents from five randomly selected rural union councils of tehsil Faisalabad were interviewed through a structured interview schedule in person and the data were analyzed by using computer software to draw conclusions. It was concluded that the farmers were adopting agroforestry practices mainly to meet their fodder and fuel wood requirements. They highly preferred Delibergia sissoo and Acacia nilotica for better economic returns.
Stellifer rastrifer (Pisces: Sciaenidae): first Uruguayan records and a 1200 km range extension

Stellifer rastrifer, a coastal fish species that inhabits the tropical and south-western Atlantic Ocean is reported for the first time from the Uruguayan coast. Its geographic distribution range is extended southward more than 1200 km. Population descriptors such as a length frequency distribution (LFD) and a length-weight relationship are presented. Some warm circulation events are suggested as a putative factor explaining the occurrence of the fish in the area.
Identification, characterization and high-resolution mapping of resistance genes to Phytophthora infestans in potato

The devastating late blight pathogen Phytophthora infestans infects foliage as well as tubers of potato. To date, resistance breeding has often focused on foliage blight resistance, but tuber blight resistance is becoming more and more important in cultivated potatoes. In this study, a reliable tuber assay for resistance assessment was developed and foliage and tuber blight resistance (R) was compared in four mapping populations. In the RH4X-103 population, tuber blight resistance inherited independently from foliage blight resistance. Three specific R genes against P. infestans were segregating. The Rpi-abpt and R3a genes function as foliage-specific R genes, whereas the R1 gene acts on both foliage and tuber. In the segregating populations SHRH and RH94-076, tuber and foliage blight resistance correlated significantly, which suggests that resistance in foliage and tuber is conferred by the same gene (could be R3b) and QTL, respectively. In the CE population neither tuber nor foliage resistance was observed.
Livestock grazing behavior and inter- versus intraspecific disease risk via the fecal–oral route

Livestock herbivores are at risk of parasite/pathogen exposure from livestock and wild mammal feces during grazing. Livestock exposure to parasites/pathogens will be dependent on the behavioral contact processes between grazing livestock and host animal (both livestock and wild mammal) feces at the bite scale. Here we use 2 grazing experiments to determine the affect of feces from different species and in different defecation patterns on the grazing response of cattle. In experiment 1, there were 4 plots, each with 4 replicates of 5 patch treatments of different fecal contamination (240 g/m-super-2 of Eurasian badger feces, cattle feces, fallow deer feces, Eurasian rabbit feces, and noncontaminated control patches). In experiment 2, there were 3 treatment patterns of badger fecal contamination (one 1-m-super-2 circular patch contaminated with 960 g of badger feces; two 1-m-super-2 circular patches each contaminated with 480 g of badger feces; and four 1-m-super-2 circular patches each contaminated with 240 g of badger feces), divided into 2 plots per treatment. The cattle's grazing response was determined by measuring sward depletion at each of the treatment patches. In experiment 1, cattle-grazed control and rabbit fecal--contaminated patches the most, whereas badger-contaminated patches were grazed the least. In experiment 2, cattle grazed the treatment with the greatest number of fecal-contaminated patches the most. We conclude that cattle vary their grazing response to feces from different host species and to feces in different spatial patterns. Quantifying these behavioral responses to feces is a key step toward quantifying infection risk to herbivores via the fecal--oral route in grazing systems. Copyright 2009, Oxford University Press.
Patterns in microphytobenthic primary productivity: Species‐specific variation in
migratory rhythms and photosynthetic efficiency in mixed‐species biofilms

The importance of temporal changes in the vertical distribution of microphytobenthic algae on the overall functioning of intertidal biofilms were investigated with low‐temperature scanning electron microscopy and high‐resolution single‐cell fluorescence imaging of photosystem II efficiency (estimated by the fluorescence parameter F’q/F’m) in intact cores maintained in tidal mesocosms. Early morning biofilms consisted of smaller naviculoid and nitzschioid taxa or euglenoid species. By midday, Gyrosigma balticum and Pleurosigma angulatum were dominant. Some taxa (e.g., Plagiotropis vitrea) disappeared from surface layers after midday. Species composition continued to change toward the end of the photoperiod, with G. balticum dominating in diatom‐rich biofilms. In Euglena‐rich biofilms, initial dense surface films of euglenids became progressively dominated by smaller diatoms. F’q/F’m (measured at a photosynthetically active photon flux density (PPFD) of 220 µmol m−2 s−1) of individual cells of all taxa declined significantly after midday, but increased toward dusk. There were significant differences in F’q/F’m between species, particularly after midday. F’q/F’m versus irradiance curves and relative electron transport rate (rETRmax) showed higher efficiencies and rETRmax for euglenids, whereas G. balticum, Nitzschia dubia, and small Nitzschia sp. were shade‐adapted with low values of F’q/F’m, rETRmax, and Esat. G. balticum, P. vitrea, and N. dubia showed rapid vertical migration away from the surface with increasing irradiance. Euglenids, P. angulatum, and N. dubia exhibited their highest rETRmax values at midday. Esat for algal cells was between 500 and 600 µmol m−2 s−1, except for N. dubia and small Nitzschia sp. , which had an Esat of 300 µmol m−2 s−1. Differences in behavioral and photophysiological traits between microphytobenthic taxa could be a form of niche separation and need to be incorporated into conceptual models of daily patterns of production in intertidal biofilms.
Observations on the Feeding Ecology of Estuarine Nematodes

Observations on living estuarine nematodes show that previous feeding type classifications do not accurately represent the trophic structure of an intertidal mudflat in the Westerschelde Estuary (Netherlands). A new scheme with six major nematode feeding guilds is proposed: (1) microvores; (2) ciliate feeders; and (3) deposit feeders sensu stricto are all nematodes without a distinct buccal armature. In the first two groups bacteria and protozoa, respectively are the major particulate food sources, while other items are included in the diet of the third. The three other categories are recognized among the nematodes with a buccal armature: (4) epigrowth feeders; (5) facultative predators; and (6) predators. Diatoms and other microalgae are an important particulate food for many epigrowth feeders. The importance of bacteria as a food source for these nematodes remains poorly documented. A strictly or mainly predatory behaviour has been described for only few species from the study area. Several nematodes, however, are facultative predators. The predatory strategy of Calyptronema maxweberi, as described in this paper, suggests the use of a paralysing or lethal secretion in prey capture, which, to our knowledge, is the first report for aquatic nematodes. Furthermore, the importance of sources other than particulate food in free-living aquatic nematodes is stressed. Our observations show that many aquatic nematodes are in fact opportunistic feeders, which may change feeding strategies in response to available food.
AN INVESTIGATION OF THE SUGARS PRESENT IN THE NECTAR OF FLOWERS OF VARIOUS SPECIES

Several investigations of variations in the quantity and sugar concentration of nectar secreted by the flowers of different plant species have been carried out; but, except for the work of Beutler (I930), few determinations of the constituent sugars have been made. From the flowers of many species it has been difficult to obtain adequate samples of nectar for qualitative analysis by the available chemical methods. However, application of the micro-analytical technique of paper-partition chromatography developed by Consden, Gordon & Martin (1944) has now made possible the separation and identification of sugars present in extremely small quantities of nectar. From observations of the foraging behaviour of honeybees, Vansell (I934, I942), Kleber (I935) and Butler (I945) concluded that the selective visits of nectar-gathering bees to various species growing in any area are influenced by both the quantity and sugar concentration of nectar present in the different flowers. Wykes (I950) also found that, when offered equal amounts of sugar solutions of the same total concentration but consisting of different sugars, honeybees exhibit decided preferences for solutions containing a mixture of sucrose, glucose and fructose. Thus it appears probable that the individual sugars present, in addition to the amount and sugar concentration, may contribute to the relative attractiveness of specific nectars to honeybees. It was therefore decided to determine the constituent sugars present in nectar secreted by flowers of a wide range of species and, by examining samples of nectar collected at different times during the flowering period, to establish whether the individual sugars in nectar from any one species remain constant.
Increasing GLP-1–Induced β-Cell Proliferation by Silencing the Negative Regulators of Signaling cAMP Response Element Modulator-α and DUSP14

OBJECTIVE—Glucagon-like peptide-1 (GLP-1) is a growth and differentiation factor for mature β-cells and their precursors. However, the overall effect of GLP-1 on increasing β-cell mass in both in vivo and in vitro conditions is relatively small, and augmenting this effect would be beneficial for the treatment or prevention of type 1 and type 2 diabetes. Here, we searched for cellular mechanisms that may limit the proliferative effect of GLP-1 and tested whether blocking them could increase β-cell proliferation. RESEARCH DESIGN AND METHODS—We examined GLP-1–regulated genes in βTC-Tet cells by cDNA microarrays. To assess the effect of some of these gene on cell proliferation, we reduced their expression using small heterogenous RNA in β-cell lines and primary mouse islets and measured [3H]thymidine or 5′-bromo-2′-deoxyuridine incorporation. RESULTS—We identified four negative regulators of intracellular signaling that were rapidly and strongly activated by GLP-1: the regulator of G-protein–signaling RGS2; the cAMP response element-binding protein (CREB) antagonists cAMP response element modulator (CREM)-α and ICERI; and the dual specificity phosphatase DUSP14, a negative regulator of the mitogen-activated protein kinase (MAPK)/extracellular signal–regulated kinase 1/2 (ERK1/2) pathway. We show that knockdown of CREMα or DUSP14 or expression of a dominant-negative form of DUSP14 increased β-cell line proliferation and enhanced the GLP-1–induced proliferation of primary β-cells. CONCLUSIONS—Together, our data show that 1) the cAMP/protein kinase A/CREB and MAPK/ERK1/2 pathways can additively control β-cell proliferation, 2) β-cells have evolved several mechanisms limiting GLP-1–induced cellular proliferation, and 3) blocking these mechanisms increases the positive effect of GLP-1 on β-cell mass.
Optimal conditions for production of extracellular alkaline protease from a newly isolated Bacillus subtilis strain AKRS3

A new strain of alkaline protease producing Bacillus bacterium was isolated from an alkaline soil sample and was characterized. The bacterium was identified as Bacillus subtilis based on 16S rRNA sequencing and phylogenetic tree analysis. The organism was coded as B. subtilis AKRS3. The growth curve of the organism was elucidated by culturing in a basal medium in shake flasks under ambient shaking conditions. The optimal conditions for alkaline protease production were studied by following the monofactorial methodology. Enzyme yield was found to be optimum close to 24 hours, which coincided with the commencement of the stationary phase of the bacterium. A pH of 9.0, temperature of 37o C and agitation speed of 125 rpm were also identified to be optimum for enhanced enzyme yields in shake flasks. An inoculum of 4% v/v with 24 hrs of age was also identified to be ideal for inoculation. Xylose at 2 g/l concentration and beef extract at 1.5 g/l concentration were preferred by the organism for optimum enzyme productivity in the broth. The organism displayed an NaCl tolerance of upto 1 % as optimum. Fe2+ salts at 0.01 % concentration was the preferred metal component in the medium.
Measuring and interpreting trait‐based selection versus meta‐community effects during local community assembly

Questions (1) How can one quantify the relative importance of meta-community processes related to immigration, local trait-based habitat filtering, and demographic stochasticity using the Community Assembly by Trait Selection (CATS) model in a general context? (2) How can this generalization be used to detect different strengths and directions in trait selection at the meta-community and local community levels? Methods I describe a decomposition of the deviance between observed and predicted relative abundances based on a maximum entropy model including a meta-community prior (CATS) and generalize a previous decomposition of relative abundance using this model; corrections to avoid negative explained proportions of deviance are presented. Simulations of community assembly are used to explore its properties and elucidate its interpretation. In particular, this method quantifies the proportion of the total deviance between observed and predicted relative abundances attributed to: (1) pure trait-based local selection, (2) dispersal mass effect from the meta-community, (3) joint contributions of (1) and (2) that cannot be separated; and (4) residual deviance due to demographic stochasticity. Results and Conclusions The previous decomposition, while giving correct values in that particular data set, requires modification in order to avoid nonsensical negative values. When the modifications described in this paper are made, the decomposition provides correct values. Furthermore, positive or negative values of the joint composition inform us of the importance and direction of correlations between local trait-based selection and processes occurring in the larger meta-community.
A Review of the Surface Lipids of Grapes and Their Importance in the Drying Process

The surface wax (bloom) of the grape berry occurs in amounts of about 0.1 mg/cm 2 and is chemically a mixture of long-chain alcohols, esters of such alcohols and fatty acids, free fatty acids, long-chain aldehydes, and hydrocarbons. The chain length of these compounds is 12 to 35, with a maximum in the range of 24 to 28. The main constituent of grape wax is oleanolic acid, which is absent from the cuticular wax of grapevine leaves. The concentration of surface wax on leaves is about 1/10th that on grape berries. The cuticular wax is the main barrier to the evaporation of water, and careful removal of the surface wax, by vapor of solvents, is almost as effective in promoting evaporation as peeling the berry. The effect of wax and its components in hindering evaporation can be simulated in model systems, i.e., wax-coated plastic membranes. In this system, aldehydes, alcohols, and paraffins were found to be equally effective in inhibiting evaporation. Fatty acids show some activity, whereas oleanolic acid is ineffective when applied in amounts similar to those on the cuticle. The drying rate of grapes can be increased by chemical treatments. Dipping of grapes in hot caustic soda solution removes part of the wax and probably destroys the cuticular structure irreversibly. However, in the cold-dipping process suitable "oils" are reversibly added to the grape surface, whereby the drying rate is increased 2-3 times. The cold-dipping process also has a secondary effect. Grapes that are naturally dried usually darken in color, whereas dipped sultanas stay yellow-green. This is due to inhibition of the action of the polyphenol oxidases by quick drying. In addition to the naturally occurring lipids, during the processing of dried grapes, some lipids are added to prevent stickiness. These added lipids can be detected and determined by chromatographic methods.
Failure of Infused β-Hydroxybutyrate to Decrease Proteolysis in Man

Ketone bodies have been suggested to have a proteinsparing effect, since infusion of Na-β-hydroxybutyrate in man decreases plasma alanine concentrations and urinary nitrogen (N) excretion. To test this hypothesis, six normal postabsorptive volunteers were infused with Na-β-hydroxybutyrate for 3 h. Rates of glucose, leucine carbon, and alanine appearance and disappearance from the plasma space were traced with [3-3H]glucose, L-[6,6,6-2H3]leucine, and [2,3,3,3-2H4]alanine. Rates of leucine N appearance and disappearance and the rate of transfer of leucine N to alanine were assessed with [15N]leucine. During ketone body infusion, plasma alanine decreased (P < 0.05), whereas plasma leucine increased (P < 0.05). Rates of alanine appearance increased (5.3 ± 0.3 to 7.8 ± 0.6 μmol/kg · min), but the increase in its rate of disappearance was sightly greater, accounting for the decrease in plasma alanine concentration. Leucine N flux and the rate and percent of leucine N transferred to alanine increased, whereas leucine carbon flux was unchanged. To determine the effect of the alkalemia induced by Na-β-hydroxybutyrate, four additional subjects were infused with NaHCO3. Alkalemia had no effect on leucine N or carbon flux or on the rate of appearance of alanine, but increased the rate of alanine disappearance, resulting in a decrease in the plasma alanine concentration. Since the rate of appearance of leucine carbon was unaltered during the infusion of Na-β-hydroxybutyrate, it is unlikely that hyperketonemia per se decreases proteolysis in postabsorptive man.
Characterization and genetic mapping of a mutation (ms35) which prevents anther dehiscence in Arabidopsis thaliana by affecting secondary wall thickening in the endothecium

The male sterile mutant, ms35, of Arabidopsis thaliana was produced by X-irradiation of seeds. The mutant produces fertile pollen, but is male sterile because the anthers do not dehisce. Anther development in ms35 plants occurs as in wild-type Arabidopsis until shortly after microspores are released from meiotic tetrads. Thereafter, in the wild type, bands of lignified, cellulosic secondary wall thickenings are laid down around the cells of the anther endothecium. In contrast, wall thickenings are not formed in the endothecium of the ms35 mutant. Development of other lignified tissues, for example the vascular tissue of the stamen, occurs normally in ms35 plants. In mutant anthers, as pollen maturation is completed, the stomium is cleaved but the anther wall does not retract to release pollen. The block in anther dehiscence in ms35 plants is specifically correlated with the absence of endothecial wall thickenings. The ms35 mutation represents the first genetic evidence in support of the proposed role of the endothecium in anther dehiscence. The ms35 gene was mapped to the top arm of chromosome 3 (hy2-(4.17±2.31 cM)-ms35-(32.14±5.45 cM)-gl1).