Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of clay minerals on the morphology of fungal pellets

The objective of this study was to assess the influence of clay minerals on the morphology of mycelial pellets produced under submerged conditions as a prelude to the development of biomineral sorbents for toxic metals. The macro- and microscopic morphology of fungal pellets of melanin-containing microfungi Cladosporium cladosporioides, C. herbarum and Humicola grisea grown in liquid clay-containing medium was studied using scanning electron microscopy. It was found that the inclusion of clay minerals (bentonite, palygorskite and kaolinite) in the liquid medium influenced size, shape and structure of the mycelial pellets produced. In general, a reduction of pellet size, an increase in the length of surface hyphae of the pellets (except for H. grisea ), and a reduction in exopolymer production were observed with increasing clay mineral concentrations up to 5 % (w/v). For C. herbarum , an increasing concentration of bentonite changed the normal pelleted growth form to diffuse star-like growth, which was also observed for C. cladosporioides in the presence of kaolinite. The presence of bentonite and kaolinite in the medium for H. grisea and palygorskyte for C. cladosporioides led to the formation of numerous bulbous hyphae in pellets. However, bentonite decreased such bulbous growth in C. herbarum compared to control pellets which grew as bulbous mycelium. The dynamics of C. cladosporioides growth and pellet formation in the presence of bentonite (0.5% (w/v)) was investigated. It was found that the clay particles were involved in the formation of pellet structure at all stages of fungal growth. The porosity of a growing pellet (evaluated as the ratio of surface hyphae length to pellet radius) increased during early growth (17–24 h) and then decreased up to the stationary phase. A general model of the structure of a fungal pellet grown in clay-containing medium is proposed. The pellets consist of three main layers: a central core, with densely packed mycelium aggregated with solid clay minerals or a matrix of clay/polysaccharides; a middle layer with looser mycelium mixed with clay mineral flakes; and an outer, or ‘hairy’ zone, with loose hyphae surrounded by clay mineral flakes. The relevance of these studies to fungal growth and morphology, and to the development of biomineral sorbents for metal removal is discussed.
Combining Data with Different Distributions of Among-Site Rate Variation

As the number of molecular studies continues to grow, so does the problem of how to analyze multiple data sets. The importance of this problem is indicated by the flurry of recent papers (reviewed by de Queiroz et alv 1995) addressing philosophical and practical considerations facing systematists fortunate enough to have several pertinent data sets on hand. Perhaps the most rigorous practical treatment was that of Bull et al. (1993), who argued against combining data when there is demonstrable heterogeneity among the different data sets in the processes governing character evolution. These authors showed that combining simulated data sets generated from the same topology but with different rates of evolution leads to less accurate estimation of phylogeny than does analysis of the more slowly evolving data set alone. Although the validity of these results is not in question for the models tested, the models used in these simulations may not be very realistic. Specifically, Bull et al. used two single-rate models to generate data sets, one with a uniform high rate and one with a uniform low rate of evolution. Chippindale and Wiens (1994) demonstrated that down-weighting rapidly evolving characters resulted in increased accuracy in combined analyses of
Plunging Behaviour in Chick-rearing Brown Boobies

ABSTRACT Brown Boobies (Sula leucogaster) obtain prey by plunge dives. In order to investigate the foraging behaviour of Brown Boobies underwater, we attached acceleration data loggers to chick-rearing Brown Boobies at Nakanokamishima Island in Japan. We documented, for the first time, Brown Boobies performing many rapid and shallow V-shaped dives and some W-shaped dives during the daylight period. The average and maximum dive depth and duration were 1.03 m and 3.81 m and 1.83 s and 21 s, respectively. Furthermore, Brown Boobies used buoyancy to ascend to the water surface. Our data suggest that Brown Boobies mainly depend on shallow-plunging, contrary to the pursuit divers such as gannets, due to their ecological and/or physiological constraints.
Buttress characteristics in relation to topography and crown eccentricity in planted and naturally-regenerated Shorea leprosula trees.

RUSLANDI, JATMOKO, JAPRIANTO, PURNOMOSIDI, BUDIARTO S, HARDIANSYAH G, INADA T, PURNOMO S & PUTZ FE. 2015. Buttress characteristics in relation to topography and crown eccentricity in planted and naturally-regenerated Shorea leprosula trees. In logged-over stands in Central Kalimantan, Indonesia, in which Shorea leprosula seedlings were planted along cleared lines 14–15 years before this study, buttress heights and total surface areas were measured on naturally-regenerated and planted trees 20–40 cm diameter at 1.3 m height. Maximum buttress heights were 0.14 m (41%) higher on naturallyregenerated trees. Contrary to our expectations, the tallest buttresses were not concentrated on the uphill sides of tree bases nor on the opposite side of the trunk from the longest crown radius but crowns did extend farthest downslope. These findings suggest some minor adjustments to timber yield projections if the buttressed portions of the lowermost logs are not harvested.
The Phosducin-Like Protein PhLP1 Is Essential for Gβγ Dimer Formation in Dictyostelium discoideum

ABSTRACT Phosducin proteins are known to inhibit G protein-mediated signaling by sequestering Gβγ subunits. However, Dictyostelium discoideum cells lacking the phosducin-like protein PhLP1 display defective rather than enhanced G protein signaling. Here we show that green fluorescent protein (GFP)-tagged Gβ (GFP-Gβ) and GFP-Gγ subunits exhibit drastically reduced steady-state levels and are absent from the plasma membrane in phlp1− cells. Triton X-114 partitioning suggests that lipid attachment to GFP-Gγ occurs in wild-type cells but not in phlp1 − and gβ − cells. Moreover, Gβγ dimers could not be detected in vitro in coimmunoprecipitation assays with phlp1 − cell lysates. Accordingly, in vivo diffusion measurements using fluorescence correlation spectroscopy showed that while GFP-Gγ proteins are present in a complex in wild-type cells, they are free in phlp1 − and gβ − cells. Collectively, our data strongly suggest the absence of Gβγ dimer formation in Dictyostelium cells lacking PhLP1. We propose that PhLP1 serves as a cochaperone assisting the assembly of Gβ and Gγ into a functional Gβγ complex. Thus, phosducin family proteins may fulfill hitherto unsuspected biosynthetic functions.
FLORISTIC STUDY OF DALAB WOODLANDS, NORTH-EAST OF ILAM PROVINCE, WEST IRAN

The present survey deals with the floristic study of Dalab Woodlands, located in Manesht and Ghelarang protected area, western Iran. It covers an area of 4335 ha. In total, 224 vascular plant species belonging to 46 families and 156 genera were identified. The largest families are Asteraceae (29 species), Fabaceae (23 species), Poaceae (22 species), and Apiaceae (18 species). Astragalus (13 species), Centaurea (9 species), Onosma (6 species), Bromus (5 species) and Amygdalus (3 species) are the most diverse genera of the region. The life form spectrum includes: hemichryptophytes (36.6 %), therophytes (33 %), cryptophytes (13.8 %), chamaephytes (8.9 %) and phanerophytes (7.6 %). From the chorological point of view, the largest proportion of the flora belongs to the Irano-Turanian (68.7 %) elements. About 22.32 % of the Dalab Woodlands species are endemic to Iran and six rare species including Alrawia bellii, Arum giganteum, Cousinia cylindracea, Echinops kotschyi, Thymbra spicata and Zeugandra iranica are also identified in this region.
Observations on an Irruption Event of the Moth Achaea catocaloides (Lepidoptera: Erebidae) at Kakamega Forest, Kenya

ABSTRACT The moth Achaea catocaloides Guenee (Lepidoptera: Erebidae, formerly Noctuidae) experiences periodic population irruptions in tropical Africa. Large numbers of adult moths were observed in the Kakamega Forest, Western Kenya in March 2012. Estimated densities of adult moths flying in surveyed forest areas were 6.8 individuals per square metre. Roosting moth density was estimated at 12.7 individuals per 50 cm long branch on two common forest tree species: Croton megalocarpus and Bridelia micrantha. Based on scaled-up data from transect counts we conservatively estimate that this irruption contained 800 million - 1.5 billion moths. The Achaea moths were common throughout the indigenous forest and were being preyed on by birds and monkeys. These population irruptions occur periodically in African forests, but the underlying causes and factors driving them remain undetermined. DNA barcodes of Achaea catocaloides, Achaea catella and Achaea lienardi are provided to facilitate identification of future irruption events.
Manipulation of dietary preferences by the infusion of propionic acid into the rumen of dairy cows in different body condition

An experiment using 16 cows (ranging from 11 to 127 days since the cessation of milk production) investigated how varying propionic acid concentration in rumen fluid influenced preference for chaff flavoured with either anise or vanilla. After an initial flavour preference test, cows were allocated among 4 treatments: 0, 5, 10, or 15% of daily maintenance ME requirements supplied by an intraruminal infusion of propionic acid. Cows received an infusion on alternate days in combination with a specific chaff flavour. After 10 days, each cow was offered both flavours simultaneously for 20 min and preference for the flavour associated with the infusion was calculated as the cows’ final preference for the infusion flavour (% of total DM intake) minus the initial preference for that same flavour. Concentration of propionic acid in ruminal fluid ranged between 10 and 50 mmol/L and was significantly correlated with treatment (100r 2 = 92.1). Preference for the flavour associated with elevated rumen fluid propionic acid was related to condition score (P = 0.057, 100r 2 = 23.4), liveweight (P = 0.042, 100r 2 = 26.3), and number of dry days prior to the experiment (P = 0.016, 100r 2 = 34.6). Lighter cows generally preferred the infusion flavour, and heavy cows, the alternative flavour, indicating that cows can discriminate between feeds based on rumen fluid propionic acid concentration, but preference is influenced by physiological state.
Bioresponsive nanoparticles based on poly(amidoamine)s for protein delivery

This study describes the design and development of multifuctional poly(amidoamine)s (PAAs) capable to form self-assembled nanocomplexes with peptides and proteins, as functional bioresponsive vectors for protein delivery to targeting cells in vitro and in vivo. The representative examples of this novel family of water-soluble PAAs have very promising properties to function as vectors for highly potent and non-toxic intracellular protein delivery. The synthesis procedure of these polymers is compatible with the use of a variety of functionalized amine monomers, allowing large variation in the structure of the polymers, and tuning of the chemical and biophysical properties that are of significance for efficient protein delivery. We have designed PAAs able to form nanosized complexes at neutral pH by a self-assembly process with model proteins, such as β-galactosidase, lysozyme, human serum albumin, ovalbumin, p24 and human insulin, and a model peptide for brain therapy. These nanocomplexes are stable at physiological pH and efficiently protect protein integrity (i.e. no denaturation occurs). Upon acidification of the solution after endosomal uptake, the pH decrease and consequently the change of charge lead to decreased protein-polymer interaction and thus a tendency for the nanoparticles to destabilize. Moreover, for nanocomplexes made from PAAs containing disulfide linkages in their polymeric backbone (SS-PAAs), fast disintegration of the complexes and release of the protein payload is observed in reductive solution, mimicking the intracellular environment. Profection experiments showed that proteins encapsulated in PAA nanoparticles were successfully internalized into the cells with remaining activity and excellent cell-viability. In addition of providing intracellular bioreduction, the presence of the disulfide groups also increased the mucoadhesive properties of the nanoparticles. In the presence of mucus secreting cells, we showed that the SS-PAA-based nanocomplexes were capable to successfully internalize protein into the cell cytosol with a much higher extent than nanoparticles based on PAAs lacking disulfide linkages. The results described in this thesis indicate that PAAs should create opportunities for novel applications in protein delivery for oral and nasal administration, as well as delivery to the brain.
SUBSPECIFIC AND TEMPORAL VARIATION IN THE STRUCTURALLY BASED COLORATION OF THE ULTRAMARINE GROSBEAK

Abstract ABSTRACT Ultramarine Grosbeaks (Cyanocompsa brissonii) possess a striking sexual dichromatism, with males dark blue and females brown. There are two subspecies in Argentina: the larger-bodied C. b. argentina, which is common in shrubs and semiopen areas, and the smaller C. b. sterea that inhabits forests. We measured reflectance spectra of six plumage patches from study skins to evaluate the possibility of color differences between males of each subspecies and temporal variation in plumage coloration. We found differences between subspecies in color brightness, hue, saturation, and UV chroma in the plumage patches of more conspicuous coloration, which could be related to ambient light differences between the environments that each subspecies inhabits. We also documented temporal color variation in some plumage patches, in particular a gradual decrease of UV reflectance and a gradual increase in hue after molting, possibly attributable to feather wear.
PHYLOGENETIC RELATIONSHIPS AMONG NINE SCALLOP SPECIES (BIVALVIA: PECTINIDAE) INFERRED FROM NUCLEOTIDE SEQUENCES OF ONE MITOCHONDRIAL AND THREE NUCLEAR GENE REGIONS

Abstract Current knowledge of the evolutionary relationships among scallop species (Mollusca: Bivalvia: Pectinidae) in the Indo-Pacific region is rather scanty. To enhance the understanding of the relationships within this group, phylogenies of nine species of scallops with the majority from coastal regions of Thailand, were reconstructed by maximum parsimony, maximum likelihood, and Bayesian methods using sequences of the 16S rRNA of the mitochondrial genome, and a fragment containing the ITS1, 5.8S and ITS2 genes of the nuclear DNA. The trees that resulted from the three methods of analysis were topologically identical, however, gained different levels of support at some nodes. Nine species were clustered into two major clades, corresponding to two subfamilies (Pectininae and Chlamydinae) of the three currently recognized subfamilies within Pectinidae. Overall, the relationships reported herein are mostly in accordance with the previous molecular studies that used sequences of the mtDNA cytochrome oxidase subunit I, and the classification system based on microsculpture of shell features and morphological characteristics of juveniles. Levels of divergences were different among genes (i.e., the 5.8S gene showed the lowest levels of nucleotide divergence at all levels, whereas the 16S rRNA showed the highest level of variation within species, and ITS2 gene revealed the highest level of divergence at higher levels).
Conspecific Brood Parasitism and Host Clutch Size in Common Pochards Aythya ferina

Abstract. Conspecific brood parasitism is an alternative reproductive tactic in which parasitic females lay eggs into the nests of other females of the same species who carry out the subsequent parental care. Conspecific brood parasitism is reported to be common among birds, however detailed information about rates of parasitism based on molecular identification of alien eggs at the population level is still scarce. Here, we used protein fingerprinting of egg albumen to identify eggs laid by parasites in a breeding population of Common Pochard Aythya ferina. Among 42 nests sampled during 3 field seasons, 162 eggs out of 432 (37.5%) were classified as parasitic. Conspecific brood parasitism occurred in total in 39 nests (93%). Average clutch size was about 10 eggs. However, after exclusion of parasitic eggs, the clutch size decreased to about 6 eggs. The number of parasitic females ranged from 1 to 7 and the mean number of parasitic females per clutch was 2.53 ± 0.28. We found a significant negative correlation between the number of parasitic eggs within a clutch and the timing of breeding — parasites laid most of the eggs before the estimated peak of initiated nests. In addition, number of parasitic eggs was negatively related to number of host eggs in the clutch. This observation implies that cost of excessive parasitism might cause clutch size adjustment in the host but other possible explanations are discussed.
THE INABILITY OF THE TEXAS “BROWN TIDE” ALGA TO USE NITRATE AND THE ROLE OF NITROGEN IN THE INITIATION OF A PERSISTENT BLOOM OF THIS ORGANISM 1

A planktonic alga similar in general morphology and pigments to Aureococcus anophagefferens Hargraves and Sieburth has caused persistent and ecologically damaging blooms along the south Texas coast. Experiments using 100 μM NO3−, NO2−, and NH4+ demonstrated that the alga could not use NO3− for growth but could use NO2− and NH4+. Doubling iron or trace metal concentrations did not permit growth on NO3−. Chemical composition data for cultures grown in excess NO3− or NH4+, respectively, were as follows: N·cell−1 (0.88 vs. 1.3 pg), C:N ratio (25:1 vs. 6.4:1), C:chlorophyll a (chl a) (560:1 vs. 44:1), and chl a·cell−1 (0.033 vs. 0.16 pg). These data imply that cells supplied with NO3− were N‐starved. Culture addition of 10 mM final concentration chlorate (a nitrate analog) did not affect the Texas isolate while NO3− utilizing A. anophagefferens was lysed, suggesting that the NO3− reductase of the Texas isolate is nonfunctional. Rates of primary productivity determined during a dense bloom indicated that light‐saturated growth rates were ca. 0.45 d−1, which is similar to maximum rates determined in laboratory experiments (0.58 d−1± 0.16). However, chemical composition data were consistent with the growth rate of these cells being limited by N availability (C:N 28, C:chl a 176, chl a·cell−1 0.019). Calculations based on a mass balance for nitrogen suggest that the bloom was triggered by an input of ca. 69 μM NH4+ that resulted from an extensive die‐off of benthos and fish.
Oleomonas sagaranensis gen. nov., sp. nov., represents a novel genus in the α-Proteobacteria

A Gram-negative bacterium was previously isolated from an oil field in Shizuoka, Japan, and designated strain HD-1. Here we have performed detailed characterization of the strain, and have found that it represents a novel genus. The 16S rRNA sequence of strain HD-1 displayed highest similarity to various uncultured species (86.7∼99.7%), along with 86.2∼88.2% similarity to sequences from Azospirillum, Methylobacterium, Rhizobium, and Hyphomicrobium, all members of the α-Proteobacteria. Phylogenetic analysis revealed that HD-1 represented a deep-branched lineage among the α-Proteobacteria. DNA–DNA hybridization analysis with Azospirillum lipoferum and Hyphomicrobium vulgare revealed low levels of similarity among the strains. We further examined the biochemical properties of the strain under aerobic conditions. Among carbon sources, ethanol, n-propanol, n-butanol, and n-tetradecanol were the most preferred, while acetate, propionate, and pyruvate also supported high levels of growth. The strain could also grow on aromatic compounds such as toluene, benzene and phenol, and aliphatic hydrocarbons such as n-octane and n-tetradecane. In contrast, glycerol and various sugars, including glucose, fructose, maltose, and lactose, failed to support growth of HD-1. Under an anaerobic gas phase with butanol as the carbon source, little increase in cell weight was observed with the addition of several possible electron acceptors. As strain HD-1 represents a novel genus in the α-Proteobacteria, we designated the strain as Oleomonas sagaranensis gen. nov., sp. nov., strain HD-1.
Analysing levels of China's agricultural domestic support with an optimising model

Abstract The paper analyses the impacts of alteration of agricultural domestic supports on state welfare adopting partial equilibrium theory. In order to find out the appropriate levels of agricultural domestic supports in China, a nonlinear programming approach was utilised, based on constraints of the annual financial budget and the Uruguay Round Agreement on Agriculture, to build an optimisation model for levels of China agricultural domestic support was built to aim at the maximum welfare. The result shows that the maximum levels of China “amber box” support are 50 billion dollars from welfare maximisation in the international agricultural product trade. The amber box support is about 174 billion RMB yuan according to the de minimis levels of China with 8.5%. The national annual budgetary expenditure for agriculture was 175.445 billion RMB yuan approximately in 2003, the amber box support of which was only 55.143 billion RMB yuan.
Estimation of the bioenergetic costs of fruit and other organ synthesis in apple

The specific bioenergetic cost of apple fruit (Malus domestica Borkh. cv. Braeburn) growth was calculated from seasonal elemental analysis (for carbon, hydrogen, nitrogen, and sulphur) and ash data. Specific cost changed during fruit development and at harvest was 1.16 g glucose g -1 dry weight of which 0.142 g glucose g -1 dry weight was consumed in growth respiration. Comparisons of those end-of-season values with those from a range of other apple cultivars (early through late maturing, and with a range of sugar/acid ratios) showed little difference, despite variations in elemental composition. Specific costs ranged between 1.15 and 1.16 g glucose g -1 dry weight, and growth respiration between 0.136 and 0.148 g glucose g -1 dry weight. Specific costs were also calculated for leaves (extension and spur), wood (1 and 2 year), and trunk and roots (fine and coarse). Leaves had the greatest cost (mean 1.44 g glucose g -1 dry weight), then wood and trunk (mean 1.38 g glucose g -1 dry weight), and fruit had the smallest. Specific growth costs were also calculated from heats of combustion data. Little difference was observed between the two methods, but the values calculated from the elemental analysis data tended to be higher than those calculated from the heats of combustion data.
Evaluation of electrofishing efficiency in a stream under natural and regulated conditions

Sampling efficiency (p), estimated from the Zippin depletion model and the percentage of fish obtained during first runs (single-pass electrofishing), which is also named relative abundance (C1), calculated as the ratio of C1 to estimated density for a site (Ce), were analysed in five contiguous sites in a small lowland stream in Poland over 23 years. The sampled reach was unregulated during the first decade of the study period, but regulated by weirs and sluices in the latter 13 years. The sites were populated with 17 fish species during this period. Sampling efficiency p calculated for all species did not differ significantly between the five sites in any given year, between benthic and non-benthic species, or between the natural and regulated periods. Differences in p were only observed between some species. C1 differed significantly between large and small species and, except for roach, was not dependent on the number of runs. Results indicate a high stability of both sampling indices in this small stream, despite changes in channel morphology after regulation: information which could be useful for future sampling research in streams.