Miracle-dz/UniFAR-FTUs huggingface dataset:
The Long and Short of It: Genetic Variation and Population Structure of the Anchialine Atyid Shrimp Caridina rubella on Miyako-Jima, Japan

ABSTRACT One of the most threatened ecosystems on many islands may be anchialine habitats, or coastal land-locked water bodies with no surface connection to the sea yet containing brackish water that fluctuates with the tides. To better manage these habitats, it is important to develop a broader understanding of the biodiversity within them since such knowledge plays critical roles in establishing conservation strategies. In this study, the genetic variation and population structure of an anchialine atyid shrimp, Caridina rubella Fujino and Shokita, 1975 was investigated in the Southern Ryukyu Archipelago, Japan. Given a planktotrophic larval stage and its potential amphidromous life cycle, populations of C. rubella on the island of Miyako-jima (to which it is apparently restricted) were hypothesized to have little to no structure across the island. To test this, 61 individuals were collected from four anchialine caves and sequence variation examined at the cytochrome c oxidase subunit I (COI) region of the mitochondrial DNA (mtDNA). Surprisingly, significant genetic structure was exhibited across distances ranging from <20 m to > 10 km. Additionally, deep (∼17% p-distance) genetic divergence correlating with distinct variation in rostrum lengths was found between closely situated, but more-or-less completely isolated, populations. This implies “C. rubella” may actually represent two distinct species on Miyako-jima. Given that this atyid is already listed as a threatened species by the Japanese government, the results presented here are useful in the formulation and implementation of future conservation plans for populations of C. rubella on Miyako-jima.
Phylogeny of anaerobic rumen Chytridiomycetes inferred from small subunit ribosomal RNA sequence comparisons

The 18S-like rRNA sequences of four recently isolated strains of rumen anaerobic phycomycetes (Neocallimastix frontalis MCH3, Piromonas communis FL, Sphaeromonas communis FG, and Neocallimastix joyonii NJ1) were analyzed and compared to examine the phylogenetic relatedness of the four isolates to each other and to other eukaryotes. The rumen chytrids characterized demonstrated very high 18S-like rRNA sequence similarities (97–99%). They are more closely related to the true fungi than to any other eukaryotes. Key words: phylogeny, anaerobic fungi, rumen, chytrids, Chytridiomycetes, Neocallimastix.
A Study on The Synthesis, Characterization and Photocatalytic Activity of CaO Nanoparticle Against Some Selected Azo Dyes

The Calcium oxide (CaO) nanoparticle was synthesized by solution combustion method using urea as a fuel. CaO nanoparticle was characterized by Scanning Electron Micrograph (SEM), X-Ray Diffraction (XRD) and UV-absorption spectroscopy. The average crystallite size was found to be 36nm and the band gap energy of CaO nanoparticle was 4.9eV. The photocatalytic degradation of Coralene Navy Blue 3G, Coralene Violet 3R and Disperse Blue 2BL in aqueous solution was investigated by using CaO nanoparticle by varying different parameters such as catalyst concentration, solution pH and dye concentration. All the experiments were conducted in presence of natural sun light. The highest degradation i.e., 99.79 % (0.2g/100ml catalyst dose), 99.34 % (0.4g/100ml catalyst dose) and 87.46% ( 0.3g/100ml catalyst dose ) was achieved at pH 3 for Coralene Navy Blue 3G, Coralene Violet 3R and Disperse Blue 2BL in aqueous medium at 30ppm concentration of dyes.
Genotype by environment interactions affecting grain sorghum. I. Characteristics that confound interpretation of hybrid yield

Past sorghum hybrid trials in north-eastern Australia have detected substantial genotype by environment (GxE) interactions for yield in sampling a variable target population of environments (TPE) that is affected by spatial and seasonal differences in crop water supply. Three datasets, comprising yields of commercial and final stage experimental hybrids and covering 9-17 years (Y) and up to 30 locations (L), were analysed to quantify variance components for trial error, genotypic (sigma(g)(2)), and GxE (sigma(gl)(2), sigma(gy)(2), and sigma(gly)(2)) interaction effects. Whereas trial means varied 2-3-fold across seasons, a greater range was estimated for variance components of trial error (range of 0.05-0.5), G (0->0.3), and GxL interaction (0.05->1.0). There was substantial seasonal variation in the ratio of sigma(g)(2) to (sigma(g)(2)+sigma(gl)(2)), and in two datasets, 73% of the seasonal sigma(gl)(2) was due to poor genetic correlations among locations. This implies that any given set of hybrids in a random set of locations would be ranked differently from season to season. Analysis of locations over years detected 90% of the total GxE interaction as GxLx Y, rather than GxL or GxY, although this was reduced by accounting for genotype maturity. To achieve repeatabilities of >80%, trials would need to be conducted over at least 5 years and 20 locations per year. The variable and unpredictable nature of much of the GxE interaction in the region implies that broad adaptation to different water regimes is required, unless prior knowledge of the seasonal weather can be used to choose 'narrowly adapted' cultivars. With current approaches, a large sample of environments is needed to identify such hybrids, and testing across locations and years is equally important. Alternative breeding strategies based on classifying environment types are discussed.
Plant‐associated Bacillus spp. alter life‐history traits of the specialist insect Brevicoryne brassicae L.

Numerous soil‐dwelling Bacillus species form mutualistic relationships with plants, in which the hosts derive an array of benefits, including the alteration of nutrient and chemical content. Despite such ubiquitous and intimate Bacillus–plant associations, the role of these bacteria in affecting the performance of specialist foliage‐feeding insects is largely unknown. We studied the effects of individual and mixed treatments of Bacillus cereus, Bacillus subtilis and Bacillus amyloliquefaciens on calabrese growth and important life‐history characteristics and the population dynamics of the specialist phloem‐feeding aphid Brevicoryne brassicae. All Bacillus species negatively affected the life‐history traits and supressed the populations of B. brassicae in varying magnitudes. The differences in aphid populations and number of leaves infested increased swiftly towards the end of the experiment and peaked 71 days after sowing. Bacillus cereus was the most effective treatment in reducing B. brassicae growth rates, followed by the mixture of species, B. amyloliquefaciens and B. subtilis treatments. However, no synergistic or additive effects of bacteria were found. Overall, plant growth promoting Bacillus species significantly suppress the growth and development of B. brassicae and show great potential for use in an integrated biological control programme for this pest.
Comparison of early- and late-senescence near-isogenic barley germplasm : proteomics and biochemistry shed new light on an old problem

Before plants die they undergo the essential process of senescence, a coordinated recovery and translocation of mobile nutrients from vegetative tissues (e.g., leaves) to surviving tissues (e.g., reproducing seeds). In the case of important monocarpic cereals (such as maize, wheat, rice, and barley), the timing and efficiency of senescence has a major impact on crop yield as it is intimately linked to nutrient metabolism. To further investigate this process, a proteomic comparison of near-isogenic barley germplasm, latesenescence/low-grain protein (GPC) parental variety ‘Karl’ and a near-isogenic earlysenescence/high-GPC line, ‘10_11’, was performed by label-free quantitative mass spectrometry-based (shotgun) and two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) proteomic techniques. Analyzing the differences between senescent flag leaf proteomes of line ‘10_11’ and variety ‘Karl’ at 14 and 21 days after anthesis,, a total of 17 proteins (7 at 14 dpa and 10 at 21 dpa) were found to be 30 significantly (and >1.5-fold) upregulated in line ‘10_11’ as compared to variety ‘Karl’ by 2D-DIGE, while 49 additional proteins (9 at 14 dpa and 49 at 21 dpa) were identified as significantly (again >1.5-fold) upregulated in line ‘10_11’ by the shotgun approach, indicating that the two techniques are complementary. Conspicuously, a number of proteins with putative roles in plant-pathogen interactions were upregulated in line ‘10_11’. These included membrane receptors, a cyclic nucleotide-gated ion channel, glucanases, pathogenesis-related and disease resistance proteins. Additionally, enzymes and proteins involved in protein degradation (including a family S8 serine protease and a tripeptidyl protease) and organic/amino acid metabolism (citrate synthase, glutamine synthetase) were upregulated, as may be expected in early-senescing germplasm involved in nitrogen remobilization. These data shed new light on senescence regulation, on the importance of plant pathogen defense during senescence, and possibly on crosstalk between senescence regulation and pathogen defense.
Assimilation of Fe and carbon by marine copepods from Fe-limited and Fe-replete diatom prey

Previous studies have demonstrated that growth of marine phytoplankton, bacteria and protozoa can be limited by the availability of Fe. We report evidence that the amount of Fe assimi- lated by crustacean grazers is affected by the Fe status of their prey. 59 Fe and 14 C radiotracers were used to follow the fate of Fe and carbon (C) during trophic transfer from diatoms to copepods. Fe assimilation efficiency was higher for copepods ingesting Fe-limited Thalassiosira weissflogii (17%) compared to diatoms that were not limited by Fe (10%), but assimilated Fe was lost more rapidly by copepods ingesting Fe-limited prey. Fe:C assimilation ratios were lower in copepods (5-12 µmol Fe:mol C) than the cellular ratios of the phytoplankon prey (17-35 µmol Fe:mol C), suggesting that copepods do not accumulate Fe relative to C during grazing. The largest single fate for Fe and C after grazing was regeneration to dissolved pools. Fe:C ratios in dissolved pools were approximately equal to the ratios in the original prey, but Fe:C ratios were higher in particulate pools (largely fecal pellets), which should facilitate the export of Fe from the euphotic zone relative to C. Although copepod grazing does recycle cellular Fe and C, our results indicate that grazing may also tend to enhance Fe stress for lower trophic levels by removing Fe from the euphotic zone faster than C.
The Use ofNicotiana benthamianaas an Herbaceous Receptor Host for Closteroviruses From Leafroll-Affected Grapevines

In vitro shoot tip cultures from four leafroll-affected grapevines, Vitis vinifera Limberger, Kadarka, Muller-Thurgau, and Schwarz Riesling, were ground in a nicotine-containing buffer, and the extracts were rubinoculated into Nicotiana benthamiana . The N. benthamiana plants inoculated with extracts from the first two cultivars showed an auxiliary vein clearing which eventually progressed into an interveinal chlorosis with darker primary vein banding. Only one type of closterovirus, identified by immunosorbent electron microscopy (ISEM) as grapevine virus A (GVA), was detected in these plants. The N. benthamiana plants inoculated with extracts from Muller-Thurgau or Schwarz Riesling showed a flecking which developed into a pronounced interveinal chlorosis with dark vein banding. These N. benthamiana plants contained two types of closterovirus-like particles. One type was identified as GVA by ISEM. The other closteroviruslike particles were not decorated in ISEM preparations using antisera prepared against the closteroviruses GVA, NY-1, GLRV-1, or GLRV-3. These results illustrate that other closterovirus-like particles, as well as GVA, can be mechanically transmitted from grapevine into N. benthamiana and are consistent with the view that grapevine leafroll disease has a complex etiology.
Rapid estimate of earthquake source duration: application to tsunami warning.

The source duration is not directly injected in the numerical simulations of tsunami, because the cinematic of the source is presently totally ignored (Jamelot and Reymond, 2015). But in the case of a tsunami-earthquake that occurs in the shallower part of the subduction zone, we have to consider a source in a medium of low rigidity modulus; consequently, for a given seismic moment, the source dimensions will be decreased while the slip distribution increased, like a ’compact’ source (Okal, Hébert, 2007). Inversely, a rapid ’snappy’ earthquake that has a poor tsunami excitation power, will be characterized by higher rigidity modulus, and will produce weaker displacement and lesser source dimensions than ’normal’ earthquake.
Impact of Banks Grass Mite1 Damage to Yield and Quality of Maize Silage

Abstract. Banks grass mite, Oligonychus pratensis (Banks), is a major pest of maize, Zea mays L. , causing significant economic loss of yield of maize grown for grain. However, damage and economic loss to maize grown for silage are not well documented. This study evaluated damage associated with infestation by different numbers of mites (noninfested check, low, medium, and large) and subsequent effects on yield and quality of maize harvested for silage. Mite densities in each of the designated infested treatments steadily increased weekly, but at different level, until after Aug 10. Weekly changes in damage rating level corresponded to the increases of mite densities that occurred in each of the infested treatments. The population decline of mites after this date was associated with increasing predator densities. No significant differences in silage yields were detected between noninfested (80.21 Mt/ha), low (82.38 MT/ha), and medium (78.87 MT/ha) infestations, but significant differences occurred with the high-infested (70.43 MT/ha) treatment. Regression analysis between mite damage and yield by plot showed losses occurred after the cumulative damage was >20. Economic loss from maize infested with large numbers of mites ranged for -$97.80 to -489.00 when silage prices ranged from $10.00 to 50.00 per ha. Damage to maize by any of the mite-infested levels did not detrimentally affect the nutritional quality of maize cut for silage. The data indicated a threshold could be developed for making management decisions. Impact of predators in managing spider mites also is discussed.
Structure and Function in Bacteriophage Phi6

IV ACKNOWLEDGEMENT AND DEDICATION.V CHAPTER 1: INTRODUCTION.1 1.1 BACTERIOPHAGE Φ6 AS A MODEL ORGANISM. 1 1.2 BACTERIOPHAGE Φ6 DESCRIPTION . 4 1.3 BACTERIOPHAGE Φ6 LIFE HISTORY. 5 1.4 GENETIC EXCHANGE, CYSTOVIRIDAE AND REASSORTMENT OF SEGMENTED GENOMES. 7 CHAPTER 2: EVIDENCE FOR A FUNCTIONAL ROLE IN THE 3’ UTR OF THE SMALL SEGMENT OF BACTERIOPHAGE Φ6. 11 ABSTRACT: . 11 2.
Availability of building roosts for bats in four towns in southwestern Ontario, Canada

Sites for roosting and areas for foraging are vital to the survival of bats (Grindal and Brigham, 1999; Fenton, 2003), but the relative importance of these two kinds of resources remains unclear (Fenton, 1997). Building roosts provide some species of bats with superior climatic conditions for some situations (Lausen and Barclay, 2002) and access to building roosts may be critical to successful reproduction by some bats (Lausen and Barclay, 2006). In Southern Ontario, Canada, buildings are common roost sites for two species (Myotis lucifugus, Eptesicus fuscus); occasional roosts for two (Pipistrellus subflavus, Myotis septentrionalis) and rarely by another (Myotis leibii) (Van Zyll de Jong, 1985). At least half of Ontario’s bat species make frequent or occasional use of building roosts but in spite of this situation, there are few data about the incidence of bats in different kinds of buildings. There is an indication that bats roost more often in older buildings located closer to parkland/woodland and bodies of water compared to randomly selected, unoccupied buildings (Brigham and Fenton, 1987; Entwistle et al., 1997; Williams and Brittingham, 1997; Gaisler et al., 1998). The incidence of bats roosting in buildings could reflect the availability of buildings and/or adjacent habitats for foraging. To assess this, we compared the incidence of bat roosts in buildings in four communities in Southwestern Ontario which are surrounded by different matrices of urban, forest/park and agricultural lands. Using responses to a questionnaire, we located bat roosts in buildings. By visiting each roost we determined how bats gained access, and compared buildings used as roosts with a random selection of buildings in each community.
Ultrastructural cytochemistry as a tool for studying transcriptional mechanisms

Ultrastructural cytochemistry is a powerful tool for investigating the biology of the cell nucleus. Thanks to its very high resolution, it has been possible to localize with extreme accuracy the sites of transcription, splicing and maturation of both mRNA and rRNA, their precise location as well as their movements. By means of immunocytochemical techniques, many nuclear proteins have been given a specific role in the transcriptional mechanisms, with the possibility of precisely mapping their location on a single RNA fibril. Starting from the 70s, the techniques have evolved from the resolution of autoradiography to that of gold-coupled antibodies, reaching a resolution of few nanometers. The use of correlative microscopy techniques as well as of electron tomography has also allowed the 3D imaging of ribonucleoprotein-containing structures in situ, in the nucleus. The association of a biological mechanism with the cytochemical localization of a specific molecule has been crucial in defining the functional organization of the cell nucleus, and has been invaluable for the understanding of many biological processes.
Impact of Soil Moisture and Mowing Height on Ataenius spretulus (Coleoptera: Scarabaeidae) Selection of Golf Course Turf Habitat in Choice Tests

Ataenius spretulus (Haldeman) (Coleoptera: Scarabaeidae) is the most common grub in golf course fairways in Michigan. Ataenius spretulus grubs are 3- to 10-fold more abundant in golf course fairways (mowed at a height of 1.5 cm) than in the roughs (mowed at a height of 5.0 cm or higher). Predation and infection by Paenibacillus sp. were previously reported to be greater in the rough, and may partially explain outbreaks of A. spretulus grubs in golf course fairways. In addition to natural enemies, cultural practices of irrigation and mowing could also be important factors, especially if A. spretulus prefers to oviposit in the fairway over the rough. In this paper we examine the impact of soil moisture and mowing height on oviposition and habitat selection. In a greenhouse experiment where A. spretulus adults were given a choice of turf maintained at fairway or rough height, no ovipositional preference for one or the other was observed. In three different growth chamber experiments where adults were allowed to choose among fairway or rough turf plugs held in soil at different moisture levels, adults preferred turf plugs in soil at a volumetric moisture content of 13% to 26% over turf plugs in soil at 8% to 9% moisture for their habitat selection. We conclude from these greenhouse and growth chamber experiments that A. spretulus adults do not choose turf habitat based on mowing height, but may be infl uenced by soil moisture levels.
Global diversity of marine macroalgae: environmental conditions explain less variation in the tropics

Aim Marine macroalgae provide an excellent opportunity to test hypotheses about latitudinal diversity gradients because macroalgal richness decreases towards the tropics, contrary to classic patterns, and because three evolutionarily distinct macroalgal clades (Rhodophyta, Chlorophyta, Phaeophyceae) have converged ecologically. Specifically, we determine the extent to which environmental conditions can predict genus richness in macroalgae. We also evaluate whether the magnitude or direction of the effect of environmental factors, or their ability to explain variation in macroalgal diversity, varies geographically. Location Global oceans. Methods We formulated and fitted global spatial regression models and geographically weighted regression (GWR) models to determine the extent to which environmental conditions could predict genus richness in macroalgae. GWR allowed us to determine how the role of environmental conditions varied amongst geographical regions. Results The global regression model showed that sea surface temperature and nutrients were important predictors of macroalgal genus richness at a global scale. However, GWR revealed that environmental factors explained less variability in richness in the tropics than elsewhere. Main conclusions Our results show that whilst environmental conditions influence marine macroalgal diversity, the strength of this influence shows considerable geographical variation. In particular, environmental conditions explain more of the observed variation in diversity at high latitudes than at low latitudes. This finding is consistent with the hypothesis that environmental tolerances influence species distributions more strongly at high latitudes, whereas other factors, such as biotic interactions, play a more prominent role in the tropics.
Investigation of the Seasonal Variation in the Phytoplankton in the Surface Waters of the Gulf of Edremit

The aim of this study was to determine the phytoplankton species existing in the Gulf of Edremit and some environmental conditions affecting them. Samples were collected in July and October 2003 and in January and April 2004 from 3 stations through horizontal tows using a plankton net. After the analysis of plankton samples, 123 species that belong to 5 classes were identified. It was determined that one species (Phalacroma cuneus Schutt, 1895) was a new record for Turkish waters. The species composition mostly consisted of dinoflagellates (53.7%) which were followed by diatoms (43.9%). Most of the species which were identified in this study were similar to those phytoplanktonic algal species which were reported from the Eastern Mediterranean Sea in previous studies. These are neritic, oceanic, temperate and subtropical climate species. It was detected that 10 out of 19 potentially harmful algal species identified in this study were toxic species; however, they did not show an extreme increase. Dinophyceae had the highest cell number in July (1100 cell/L, St.1) and Bacillariophyceae in April (2280 cell/L, St.2). The environmental variables of the seawater such as temperature (13.0-26.5 oC), salinity (35.9-38.5‰) and dissolved oxygen (4.43-8.46 mg/L) were measured in every sampling period. Consequently, the phytoplankton species and their abundances in the Gulf of Edremit were firstly determined with this study, and phytoplankton composition representing oligotrophic sea water characteristic in the Aegean Sea was obtained.
Effect of Aging and Priming on Physiological and Biochemical Traits of Common Bean (Phaseolus vulgaris L.)

Aging and deterioration (artificial aging) are the most effective factors on the seed vigour. In order to study the changes in physiological and biochemical characteristics of common bean under aging and priming treatments a factorial experiment based on completely randomized design conducted with three replications. Seed aging (control, 90 and 80% of control germination) and seed invigoration with priming including control, hydro (distilled water), osmo (PEG 6000), hormone (gibberellic acid) and halo (NaCl) priming were considered as experimental factors. Results showed that osmo-priming had the ability to relatively ameliorate the aging effect and recover some of the seed aspects like germination rate, protein and phytin content for invigorate germination and seedling establishment. Priming indirectly increased seed vigour via germination rate and it can provide homogeny of emergence in the field and obtaining appropriate plant population.