Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungal Systematics and Evolution

: Ophiopogon japonicus ( Asparagaceae ) is a perennial grass species which can be cultivated as an ornamental and medicinal plant. From April 2021 to September 2022, a serious leaf blight disease of O. japonicus was discovered in Rizhao City, Shandong Province, China. The initial disease symptoms were small yellow spots, finally developing as tip blight, often associated with many small, black, semi-immersed pycnidial conidiomata formed in lesions. To obtain isolates of the causal agent for this disease, samples were randomly collected from O. japonicus diseased leaves in Rizhao City. In total 97 Phyllosticta isolates were obtained from samples, and studied using morphological features and multi-locus phylogenetic analyses of a combined dataset using the internal transcribed spacers (ITS), the 28S large subunit of ribosomal RNA (LSU), and partial translation elongation factor 1-alpha ( tef ), actin ( act ) and glyceraldehyde-3-phosphate dehydrogenase ( gapdh ) loci. Phylogenetically, these Phyllosticta isolates formed a clade in the P. concentrica species complex, and clustered with P. pilospora and P. spinarum . Morphologically, isolates in this clade differed from P. pilospora and P. spinarum by the size of conidiogenous cells and conidia, and the absence of an apical conidial appendage. As a result, these isolates were described as a novel species Phyllosticta rizhaoensis . Pathogenicity was confirmed using Koch’s postulates, which showed that P. rizhaoensis could induce leaf blight symptoms on O. japonicus in China .
DIFFERENTIATION OF BREWING YEAST

Current methods for the differentiation of brewing yeasts are described and their performance critically discussed. Although these methods are widely used they are non-specific and require confirmation by other tests. Emergent approaches such as pyrolysis gas chromatography or the use of gene cloning techniques are considered and their application reviewed. It is concluded that development of such methods could offer a unique ‘fingerprint’ for each brewing yeast based on a single test.
Structural investigations by in silico modeling for designing NR2B subunit selective NMDA receptor antagonists

Glutamate N-methyl-D-aspartate (NMDA) receptors are widely distributed throughout the mammalian central nervous system (CNS). They play key roles in many brain disorders, such as brain trauma, seizures, pain, Parkinson's and Huntington's disease. NMDA receptors are co-assemblies of four subunits. The selectivity of ligands for the NR2B subunit, out of the others, has shown the best side effect profile. The objective of the current studies is to establish the structural requirements for pyrazine and related derivatives for being NR2B selective NMDA receptor antagonists. 2D- and 3D-QSAR models have been developed. 2D-QSAR analyses revealed the key role of Baumann's alignment independent topological descriptors, such as T_2_F_7, T_C_O_7 and T_T_T_6, in biological activity prediction. Furthermore, 3D-QSAR analyses showed that steric and electrostatic molecular descriptors have significant influence in the optimization of pyrazine and related lead compounds as NR2B selective NMDA receptor antagonists. 3D points generated using a 3D-QSAR study have been studied to uncover minimum structural requirements of pyrazine derivatives. The significantly high prediction power of the best QSAR model supports the mechanism of NMDA receptor antagonism through NR2B subunit selectivity. A molecular docking study of the most active compound 18 revealed important structural insights needed to optimize pyrazine derivatives for use as NR2B selective NMDA receptor antagonists. Moreover, a putative structure-based pharmacophore model was established, having features of two aromatic rings, one hydrogen bond donor and one hydrogen bond acceptor. This pharmacophore model could be used as a query for virtual screening of commercially available chemical databases to identify new hits, and 2D- and 3D-QSAR models could be used to predict the activities of identified hits.
Conceptual Model Development for Invasive Species and a Regional Risk Assessment Case Study: The European Green Crab, Carcinus maenas, at Cherry Point, Washington, USA

Abstract The goal of this article was to generate a method of regional scale ecological risk assessment using an adaptation Relative Risk Model (RRM). As a case study we performed a quantitative, regional risk assessment of an invasive species, the European green crab (Carcinus maenas) at Cherry Point, Washington, USA. The conceptual model was modified from the RRM and incorporates the structure of the hierarchical patch dynamic paradigm. The ranks and filters were integrated to determine the relative contribution of each source of C. maenas to risk as well as the risk to selected biological endpoints, habitats and sub-regions for two source scenarios: (1) current conditions (2004) and (2) future conditions during an El Nino year. The results suggest that the habitat and endpoint with the greatest risk are the eelgrass habitat and the juvenile Dungeness crab, respectively. The Cherry Point subregion was identified as the area having the most risk in the first source scenario, while the Lummi Bay sub-region is most at risk during an El Nino event. The risk of impacts is substantially higher for all endpoints, habitats and sub-regions when El Nino–driven current dispersal is considered. The methodology applied in this case study can be modified and applied to determine the risk of introduction and impacts of other invasive species to the Strait of Georgia, Puget Sound, and other coastal areas.
A new set of microsatellite markers for the peach palm (Bactris gasipaes Kunth): characterization and across-taxa utility within the tribe Cocoeae.

A (GA)n microsatellite-enriched library was constructed and a new set of 18 nuclear simple sequence repeat loci was isolated in Bactris gasipaes var. gasipaes. The loci were found to be highly variable in the target species and readily transferable to related Bactris species as well as to the Astrocaryum and Elaeis genera of the same Cocoeae tribe. These microsatellite resources are made available to study the genetic diversity and gene flow within the Bactris complex for a better understanding of the domestication process of the peach palm and for further Cocoeae genetics
Proteolytic cleavage of vitellogenin and yolk proteins during vitellogenin uptake and oocyte maturation in barfin flounder (Verasper moseri)

Vitellogenin (Vg) and vitellogenin-derived yolk proteins of growing oocytes and ovulated eggs were purified and characterized to evaluate structural changes of yolk proteins during oocyte growth and maturation in barfin flounder, Verasper moseri, a marine teleost which lays pelagic eggs. Native circulating vitellogenin, estimated to be a 520 kDa protein using Superose 6 column chromatography, cleaved into the 410 kDa major yolk protein, lipovitellin (Lv), in vitellogenic oocytes. An additional minor yolk protein at 19 kDa in native form, which was immunoreactive to an antiserum raised against Vg, and a highly phosphorylated 38 kDa band of phosvitin (Pv) in SDS-PAGE with reduction were also identified in vitellogenic oocytes. Analysis of the amino acid composition of the 19 kDa yolk protein showed it to be similar to the β′-component of egg yolk from salmonid fish. The 410 kDa Lv in vitellogenic oocytes was proteolytically cleaved into an 170 kDa major yolk protein during final oocyte maturation. The close similarity of amino acid composition between the two proteins combined with the results of lipid analysis suggested that the 410 kDa Lv cleaved into two homologous 170 kDa monomeric Lv. Both 19 kDa yolk protein (β′-component) and Pv became undetectable after oocyte maturation. We propose that the three classes of yolk proteins (Lv, Pv, and β′-component) are products of Vg cleavage, and that all of them undergo proteolysis again during oocyte maturation. © 1995 Wiley-Liss, Inc.
Genetic relationships among different breeds of Chinese gamecocks revealed by mtDNA variation.

There are currently five primary breeds of Chinese gamecock, the Henan, Luxi, Tulufan, Xishuangbanna and Zhangzhou. Though there is historical evidence of cockfighting in China dating as far back as 2,800 years, the origin and genetic relationships of these breeds are not well understood. We used sequence variation from the mtDNA cytb gene and control region (1,697 bp) to examine the domestication history and genetic relationship of the Chinese gamecock. From 75 samples (14-16 per breed) we found 34 haplotypes, and 45 variable nucleotides. Phylogenetic reconstruction indicated multiple origins of the gamecock breeds. The breeds in the north and center of China, Tulufan, Luxi and Henan, clustered together in a haplogroup and may have the same ancestor. However the southern breeds, Zhangzhou and Xishuangbanna clustered into two isolated haplogroups, suggesting another two origins of Chinese gamecock. Meanwhile, extensive admixture was also found because samples from different breeds, more or less, were always grouped together in the same clades. Based on these results, we discuss the possibilities of multiple origins of gamecock breeds, from both ancestral gamecocks as well as other domestic chickens and red jungle fowl.
Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain.

During a recent nematode survey in natural environments of the Los Alcornocales Regional Park narrow valleys, viz . , the renowned 'canutos' excavated in the mountains that maintain a humid microclimate, in southern Spain, an amphimictic population of Xiphinema globosum was identified. Morphological and morphometric studies on this population fit the original and previous descriptions and represent the first report from Spain and southern Europe. Molecular characterisation of X. globosum from Spain using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS1-rRNA is provided and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships within X. globosum and other Xiphinema species. A supertree solution of the different phylogenetic trees obtained in this study and in other published studies using rDNA genes are presented using the matrix representation parsimony method (MRP) and the most similar supertree method (MSSA). The results revealed a closer phylogenetic relationship of X. globosum with X. diversicaudatum , X. bakeri and with some sequences of unidentified Xiphinema spp. deposited in GenBank.
Isolation and characterization of cDNA encoding cinnamyl alcohol dehydrogenase (CAD) in sorghum (Sorghum bicolor (L.) Moench)

The gene encoding cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195), which catalyzes the final step in the biosynthesis of monolignol, was isolated and characterized in sorghum. The nucleotide sequence of sorghum CAD (SbCAD) cDNA is approximately 1457 bp in length encoding a polypeptide of 365 amino acids. A comparison of sorghum CAD amino acid sequence with those of other species showed highly homology to monocot CAD cDNA. DNA gel blot analysis revealed one or two strong signals, suggesting that a single CAD gene was present in sorghum. Expression analysis using the total RNA with a SbCAD cDNA probe demonstrates that the transcripts of the CAD gene are more abundant in the lower stem than the upper stem. It was not possible to detect any signal in the leaf tissue because it exhibits a low level of lignification.
Further Characterization of Intra-Acrosomal MN7 and MC41 Antigens, with Special Reference to Immunoelectron Microscopic Comparison of Releasing Process during the Acrosome Reaction in the Mouse

Mouse intra-acrosomal antigens, recognized by monoclonal antibodies, MN7 and MC41, were analyzed by SDS-PAGE and Western blotting. Both the MN7- and MC41-antigens were glycoproteins of 90kDa and 200kDa, respectively. However, the two antigens exhibited different biochemical properties; the MN7-antigen was extracted only in the acidic condition (pH 3.0), while the MC41-antigen was detectable in both acidic and neutral conditions. The releasing process during the acrosome reaction was examined by immunoelectron microscopy. The MN7-antigen, which was initially distributed uniformly in the entire acrosome, gradually disappeared from the acrosome, being localized once at the cortex-medulla border region at the middle stage, and dispersed without close contact with the vesiculated membrane. By contrast, the MC41-antigen, which was initially restricted to the cortical region of the anterior acrosome, was localized on the electrondense materials lining closely to the fenestrated membrane at the middle stage, and dispersed keeping in close contact with the vesicles. These findings indicate that the antigens originally segregated into different subdomains can be differentially released during the acrosome reaction.
Nutrient reserves of breeding Ring-necked Ducks (Aythya collaris)

We studied carcass composition of Ring-necked Ducks, Aythya collaris, collected on breeding areas in Beltrami County, Minnesota. Females collected before they had commenced rapid growth of ovarian follicles apparently stored body lipid and body protein. For every gram of egg lipid produced, somatic lipid stores declined by 0.48 g at all stages of rapid follicle growth, irrespective of the daily rate of egg lipid production. A decline in body protein coincided with increased daily requirements for clutch proteins. However, females increased their protein reserves from mid to late rapid follicle growth, resulting in no difference between reserves of females starting and terminating rapid follicle growth. We suggest that observed patterns of lipid storage by Ring-necked Ducks, and possibly by other species of temperate-nesting ducks, have evolved to allow supply of clutch lipids at a rate in line with the ease with which we suspect that breeding hens are able to procure dietary protein; the high daily protei.
The intra‐ and interspecific relationships between abundance and distribution in helminth parasites of birds

1. Positive correlations between local abundance and distribution on a larger spatial scale are commonly observed among related species. 2. Within parasite species, the same relationship may be expected between prevalence and intensity of infection across host species used. Across parasite species, a positive relationship is expected between average abundance in a host population and the number of host species that can be exploited based on the resource breadth hypothesis. Trade-offs between the ability to exploit many host species and the potential for heavy infections, however, could result in a negative relationship. 3. Intraspecifically, using data on 51 helminth species parasitic in birds, prevalence and intensity of infection among host species used are generally only weakly correlated. Only in nematodes is there an overall positive relationship between prevalence and intensity. 4. A comparative analysis was performed on data from 389 species of cestodes, trematodes and nematodes parasitic in birds to determine how host specificity covaries interspecifically with abundance, measured both as prevalence and intensity of infection. 5. After controlling for phylogenetic influences and sampling effort, the number of host species used correlated positively with prevalence in all three parasite taxa, and with intensity of infection in trematodes only. 6. These results do not support the existence of a trade-off between abundance and the use of many host species, as has been found for fish parasites. Instead, whatever makes helminth parasites of birds abundant within a host population may facilitate their successful colonization of new host species.
Preharvest aflatoxin contamination of corn and other grain crops grown on the U.S. Southeastern Coastal Plain

Preharvest aflatoxin contamination of grain grown on the U.S. Southeastern Coastal Plain is provoked and aggravated by both biotic and abiotic stress factors that influence infection by the Asperigillus group. Asperigillus flavus, Link ex Fr. , is one of the principal toxigenic fungi of summer grains grown in the region, and the hot, humid weather patterns along with suboptimal summer rainfall favor the development of this organism. An array of arthropod species also contributes to the dispersal of this fungus as they attack and feed on the developing grain. Research on summer grains grown on the Coastal Plain has the expressed goal of reducing, and perhaps eliminating aflatoxin contamination in adapted germplasm using classical crop improvement methods to deploy host plant resistance. This research is complimented and enhanced by molecular techniques that have proven invaluable in the identification and development of superior germplasm. It also emphasizes the need to fully understand the biological interactions between fungus, arthropods, crops, and the environmental conditions that govern the aflatoxin contamination. Alternative cropping systems that avoid contamination are also integrated into this summary of this research progress.
The effects of nitrogen stress on the stable carbon isotope composition, productivity and water use efficiency of white spruce (Picea glauca (Moench) Voss) seedlings

The effect of nitrogen stress on needle δ 13 C, water-use efficiency (WUE) and biomass production in irrigated and dry land white spruce (Picea glauca (Moench) Voss) seedlings was investigated. Sixteen hundred seedlings, representing 10 controlled crosses, were planted in the field in individual buried sand-filled cylinders. Two nitrogen treatments were imposed, nitrogen stressed and fertilized. The ranking of δ 13 C of the crosses was maintained across all combinations of water and nitrogen treatments and there was not a significant genetic versus environmental interaction. The positive relationships between needle δ 13 C, WUE and dry matter production demonstrate that it should be possible to use δ 13 C as a surrogate for WUE, and to select for increased WUE without compromising yield, even in nitrogen deficient environments. Nitrogen stressed seedlings had the lowest needle δ 13 C in both irrigated and dry land conditions. There was a positive correlation between needle nitrogen content and δ 13 C that was likely associated with increased photosynthetic capacity. There was some indication that decreased nitrogen supply led to increased stomatal conductance and hence lower WUE. There was a negative correlation between intrinsic water use efficiency and photosynthetic nitrogen use efficiency (NUE). This suggests that white spruce seedlings have the ability to maximize NUE when water becomes limited. There was significant genetic variation in NUE that was maintained across treatments. Our results suggest that in white spruce, there is no detectable effect of anaplerotic carbon fixation and that it is more appropriate to use a value of 29‰ ('Rubisco only') for the net discrimination against 13 C during CO 2 fixation. This leads to excellent correspondence between values of C l /C a derived from gas exchange measurements or from δ 13 C.
Gaze-contingent ocular parallax rendering for virtual reality

Current-generation virtual reality (VR) displays aim to generate perceptually realistic user experiences by accurately rendering many perceptually important effects including perspective, disparity, motion parallax, and other depth cues. We introduce ocular parallax rendering, a technology that renders small amounts of gaze-contingent parallax capable of further increasing perceptual realism in VR. Ocular parallax, small depth-dependent image shifts on the retina created as the eye rotates, occurs because the centers of rotation and projection of the eye are not the same. We study the perceptual implications of ocular parallax rendering by designing and conducting a series of user experiments. We estimate perceptual detection and discrimination thresholds for this effect and demonstrate that it is clearly visible in most VR applications. However, our studies also indicate that ocular parallax rendering does not significantly improve depth perception in VR.
How Hormonal Priming of Aged and Nonaged Seeds of Bromegrass Affects Seedling Physiological Characters

Effects of hormonal priming by cytokinin (CK), auxin, and gibberellin (GA) at 0, 25, 50, and 100 ppm of aged and nonaged seeds of bromegrass (Bromus inermis) on some physiological properties of seedlings were evaluated in a pot experiment. The seeds were subjected to accelerated aging to produce aged seeds. Percentage and rate of seedling emergence, seedling vigor, seedling-growth rate (SGR), seedling dry weight, chlorophyll and activity of catalase and peroxidase of seedling decreased following accelerated aging. Auxin priming improved emergence, vigor, SGR, root length, shoot, and seedling height. CK produced largest leaf area, whereas GA-primed seed had the highest concentration of chlorophyll in seedlings. Results suggested that physiological quality of bromegrass seed, especially aged seed, could be improved by hormonal priming. Auxin had the most positive effect on percent emergence, rate of emergence and SGR; CK and GA had positive effects on chlorophyll and leaf area. The three phytohormones in appropriate ratio in the priming solution improved aged seeds of bromegrass physiologically.
A comparative study of migratory behaviour and body mass as determinants of moult duration in passerines

Birds moult to maintain plumage function through life, but the factors that determine moult duration are poorly understood. In temperate areas, variation in moult duration could be largely associated with between-species differences in migratory behaviour (migrants have less time for moulting after breeding), and body mass (because the aerodynamic cost of rapid moult increases allometrically with body size). Moreover, if the energetic cost of transport favours a smaller body size in migratory species, then the effects of migratory behaviour and body mass on moult duration could be confounded. We conducted a comparative study of the duration of adult complete moult in 48 European passerine species, in relation to body mass and migratory behaviour (sedentary, short-distance migrants and long-distance migrants). Lighter and more migratory species moulted faster than heavier and more sedentary species, but migration was not associated with body mass. If accelerated moult compromises the success of migration, changes in the physiology or phenology of moult in migratory birds are better interpreted as adaptive responses to compensate for such costs.
Habitat use by muskoxen (Ovibos moschatus) in winter in an alpine environment

Muskoxen (Ovibos moschatus) were introduced into a relatively snow-rich alpine environment in Norway far outside their natural polar distribution 40 years ago. Habitat choice in winter by the muskoxen was compared with topographical characteristics and snow and vegetation distributions. The density of fecal-pellet groups was approximately 1500/ha in the exclusively used Dryas heath, more than 30 times greater than that observed in the only two other heath communities, lichen heath and Juncus heath. Juncus heath had a standing graminoid biomass of ca. 30 g/m2, but 50-60 cm of hard snow. Lichen heath had shallow snow ( >27°), which offered the only available areas with shallow snow (ca. 20 cm) and available graminoids (ca. 10 g/m2). %Integrated ram hardness% values were <<200 kg cm in Dryas heath compared with 1500-2500 kg cm .