Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome‐wide association studies in elite varieties of German winter barley using single‐marker and haplotype‐based methods

Genome-wide association studies (GWAS) became a widely used method to map qualitative and quantitative traits in plants. We compared existing single-marker and haplotype-based methods for GWAS with a focus on barley. Based on German winter barley cultivars, four different single-marker and haplotype-based methods were tested for their power to detect significant associations in a large genome with a limited number of markers. We identified significant associations for yield and quality-related traits using the iSelect array with 3886 mapped single nucleotide polymorphism (SNP) markers in a structured population consisting of 109 genotypes. Genome simulations with different numbers of genotypes, marker densities and marker effects were used to compare different GWAS methods. Results of simulations revealed a higher power in detecting significant associations for haplotype- than for single-marker approaches, but showed a higher false discovery rate for SNP detection, due to lack of correction for population structure. Our simulations revealed that a population size of about 500 individuals is required to detect QTLs explaining a small trait variance (<10%).
Biochemical Studies on a Virus Associated with Egg Drop Syndrome 1976

Summary A number of hitherto undescribed, serologically identical viruses have been isolated from a syndrome of depressed egg production in broiler breeder flocks (Egg Drop Syndrome 1976). One of these, 127 virus, was purified after growth in chick embryo liver cells. Three particle types B1, B2 and B3 with densities of 1.32, 1.30 and 1.28 g/ml, respectively, were separated in CsCl equilibrium density gradients. B1 and B2 particles possessed infectivity and were labelled with 3H-thymidine. However, they differed morphologically and B2 particles agglutinated chicken erythrocytes whereas B1 particles did not. B3 particles were not infectious, were not labelled with 3H-thymidine but agglutinated chicken erythrocytes. They were penetrated by stain when examined by electron microscopy and probably correspond to empty particles. B1, B2 and B3 particles differed in their polypeptide compositions; seven of the polypeptides in B1 and B2 particles had counterparts in purified fowl adenovirus type 1. The soluble haemagglutinin from 127 virus, which did not sediment under centrifugation conditions sufficient to pellet virus particles, was purified using DEAE cellulose chromatography and gel filtration. Purified soluble haemagglutinin contained two polypeptides (mol. wt. 67000 and 65000), which co-migrated in polyacrylamide gels with two of those present in purified 127 virus particles. The soluble haemagglutinin sedimented heterogeneously (20 to 50S) in sucrose density gradients and had a density of 1.24 g/ml in CsCl. It was inactivated by trypsin, urea and pyridine. Electron microscopy of purified soluble haemagglutinin showed rod-like structures with lengths of 25 to 30 nm, which radiated from a central area measuring approx. 10 nm in diam. It is suggested that 127 virus is an adenovirus.
Effects of Fall Fertilization on Cold Resistance, Color, and Growth of Kentucky Bluegrass1

Fall fertilization of turf is usually avoided because it is thought to reduce cold resistance of plants composing the sward. Turf receiving N during this season exhibits color longer in fall and earlier in spring. The effects of periodic fall nitrogenous fertilization on the cold resistance, color, and growth of Kentucky bluegrass (Poa pratensis L.) were measured from September, 1970, to June, 1971, to ascertain if there is a period during the fall when N may be applied to produce color longer, yet not predispose plants to cold injury. Determinations of the cold resistance of crown tissue were made utilizing conductivity techniques for measurement of solutes diffused after cold treatment. Nitrogen at 2 kg N/200 m² (as NH₄NO₃) was applied to different plots on October 1 and 15, November 1 and 15, and December 1 and 15, 1970. An additional treatment received 1 kg N/200 m² on each date. The cold resistance of all treatments increased through the fall and early winter, peaked near the end of January, decreased slowly through February, and was lost rapidly in March and April. Early fall fertilization (through November 1) resulted in the greatest reduction in cold resistance in the fall, while late fall fertilization (after November l) resulted in the greatest reduction in the spring. Fertilization up until November 1 resulted in a color increase (i.e., chlorophyll increase) shortly after fertilization, and maintenance of color into early winter. Fertilization after November 1 did not produce substantial fall green-up. All treatments produced good spring green-up by mid-March; however, late fall fertilized plots (after November 1) had a higher chlorophyll content by mid-April. No treatment produced any measurable topgrowth from the end of November until May. Plots fertilized before November 1 produced additional yields in the fall, while plots fertilized later produced additional yields in the spring.
Natural phytosanitary products effects on Bacillus Thuringiensis SUBSP. Kurstaki (Berliner)

Este trabalho objetivou avaliar o efeito dos produtos fitossanitarios naturais (PFN) sobre esporos e sobre a toxicidade dos cristais de Bacillus thuringiensis subespecie kurstaki – HD1 (Btk). Para tal foram usados os produtos comerciais (Agromos, Biogermex, Bovemax, Calda Bordalesa, Ecolife®, Dalneen, Matan Plus, Pironin e Stuble –Aid®) em tres diferentes concentracoes. O efeito dos PFN sobre esporos foi avaliado comparando-se suspensoes de Btk + PFN com agua destilada esterelizada (ADE) e suspensoes com caldo nutriente (CB), inoculadas em agar nutriente (AN), em placas de Petri quantificando-se o numero de unidades formadoras de colonias (UFC / mL), 18 h apos a inoculacao e incubacao. O efeito dos PFN sobre cristais foi avaliado com suspensoes de Btk + ADE + PFN adicionados a dieta artificial fornecida para Anticarsia gemmatalis Hub. (Lepidoptera: Noctuidae), quantificando-se o numero de lagartas mortas nos tempos 24, 48 e 72 h. Matan Plus foi o unico produto natural que nao apresentou efeito sobre esporos. Todos os outros produtos, independentemente da concentracao, diminuiram significativamente as UFC/mL. Com relacao aos cristais, a Calda Bordalesa foi o unico produto que reduziu significativamente a atividade inseticida de Btk nas tres concentracoes.
The habitats of the land snail Cepaea nemoralis (L.) on downland and their ecogenetic significance

Population densities of adult Cepaea nemoralis (L.) were estimated for nine chalk grassland sites on the South Downs. Estimates of cover, species composition and height of vegetation were also obtained. The density of C. nemoralis was positively associated with Bromus erectus cover, and negatively with Festuca spp. cover. This finding, confirmed by an earlier survey, suggests that the density of C. nemoralis in chalk grassland is directly or indirectly governed by mammalian grazing pressure, and not by the availability of suitable food. Intensely grazed downland is an unsuitable, or at best a marginal habitat for C. nemoralis. This conclusion is discussed with particular reference to ‘area effects’ in the shell character polymorphism, often found in downland populations of C. nemoralis.
Differences in gene flow in a twofold secondary contact zone of pond turtles in southern Italy (Testudines: Emydidae: Emys orbicularis galloitalica, E. o. hellenica, E. trinacris)

Using virtually range‐wide sampling for three pond turtle taxa (Emys orbicularis galloitalica, E. o. hellenica, E. trinacris), we analyse gene flow across their southern Italian contact zone. Based on population genetic analyses of 15 highly polymorphic microsatellite loci and a mitochondrial marker, we show that the general genetic pattern matches well with the current taxon delimitation. Yet, single individuals with conflicting genetic identity suggest translocation of turtles by humans. In addition, we identify in south‐western France and the vicinity of Rome populations being heavily impacted by introduced turtles. Cline analyses reveal that the major genetic break between E. o. galloitalica and E. o. hellenica corresponds well with the currently accepted intergradation zone in southern Italy. However, introgression is largely unidirectional from E. o. galloitalica into E. o. hellenica. In the distribution range of the latter subspecies, genetic footprints of E. o. galloitalica are evident along most of the Italian east coast. Our results corroborate that E. o. galloitalica was introduced long ago in Corsica and Sardinia and naturalized there. Gene flow between E. orbicularis and E. trinacris is negligible, with the Strait of Messina matching well with the narrow cline centre between the two species. This contrasts with other Mediterranean freshwater turtle species with extensive transoceanic gene flow. Compared to the two subspecies of E. orbicularis, the Sicilian E. trinacris shows an unexpectedly strong population structuring, a finding also of some relevance for conservation. The differences between the two taxon pairs E. orbicularis/E. trinacris and E. o. galloitalica/E. o. hellenica support their current taxonomic classification and make them attractive objects for follow‐up studies to elucidate the underlying mechanisms of speciation by comparing their properties.
Identification of Quantitative Trait Loci in Rice for Yield, Yield Components, and Agronomic Traits across Years and Locations

A population of 164 recombinant inbred lines (RILs) of rice (Oryza sativa L.) derived from a cross between Milyang23 and Gihobyeo was evaluated for nine phenotypic characters over three years and two regions in Korea. The population had been previously mapped using 414 molecular markers. Genotype x environment (G x E) interaction was analyzed for six grain yield-related traits and three agronomic traits across years and locations using the AMMI model. The quantitative trait loci (QTLs) were detected by interval mapping and composite interval mapping. A total of 75 QTLs were identified for the nine traits across five environments and they were categorized as (i) 29 QTLs with main effect, (ii) 18 QTLs with minor effect, (iii) 13 QTLs with G x E interaction effect, (iv) six QTLs with both main effect and G x E interaction effect, and (v) nine potential QTLs with low log of the odds (LOD) scores. The AMMI model explained from 68.6% to 84.7% of the interaction effect and 19 QTLs were significantly associated with G x E interaction. Culm length had the least G x E, while the maximum G x E interaction was exhibited for spikelets per panicle (39.7%) and percent ripened grain (35.3%). Markers closely linked to main effect QTLs will be most useful for marker-assisted breeding.
The Secretory Cells of the Goat Oviductal Epithelium: An Ultrastructural Study.

Ultrastructural features of the secretory cells of the goat's oviduct were studied at the early follicular phase, the follicular phase, the early luteal phase, the mid-luteal phase, and the late luteal phase. The secretory cells began to regenerate at the early follicular phase. At the follicular phase, numerous secretory granules of various size and electron density were seen in the secretory cells. At the early luteal phase, maximum secretory activity by exocytosis was apparent especially in the ampulla. At the mid-luteal and the late luteal phase, many ampullar secretory cells had large cytoplasmic protrusions which often contained nuclei. The pinching-off of protrusion was observed at these phases. Apoptosis-like fragments were seen in the ampullar epithelium at the late luteal phase, when the secretory cells were atrophied.
PGE1 Inhibits the Expression of PAI-1 mRNA Induced by TNF-α in Human Mesangial Cells

: We examined the effect of PGE1 on the expression of plasminogen activator inhibitor-1 (PAI-1) mRNA induced by tumor necrosis factor-alpha (TNF-alpha) in human mesangial cells, because PAI-1 is one of major factors for the progression of glomerulosclerosis. The expression of PAI-1 mRNA was increased after stimulation with TNF-alpha, and it was diminished by pre-incubation with PGE1. Next, we examined the effect of PGE1 on the phosphorylation of mitogen activated protein kinase (MAPK) family and Akt. TNF-alpha activated the phosphorylation of p44/42 MAPK, p38 MAPK, SAPK/JNK and Akt in mesangial cells. PGE1 inhibited the TNF-alpha induced phosphorylation of SAPK/JNK and Akt, but not p44/42 MAPK and p38 MAPK. The TNF-alpha induced expression of PAI-1 mRNA was not affected by PD98059, an inhibitor of MEK, SB203580, an inhibitor of p38 MAPK, nor LY294002, an inhibitor of PI3 K. However, DMAP, an inhibitor of SAPK/JNK, inhibited the expression of PAI-1 mRNA, suggesting that the TNF-alpha induced expression of PAI-1 mRNA is regulated by the SAPK/JNK dependent pathway in human mesangial cells. By the incubation with H8, an inhibitor of PKA, the inhibitory effect of PGE1 on the expression of PAI-1 mRNA was abolished, suggesting that PGE1 inhibited the PAI-1 mRNA expression via the PKA pathway. Our results suggest that the inhibition of PAI-1 synthesis by PGE1 in human mesangial cells may have therapeutic implications for glomerulosclerosis such as occurs in diabetic nephropathy.
Density-dependence in habitat utilisation by wood mice in a Sitka spruce successional mosaic: the roles of immigration, emigration, and variation among local demographic parameters

Density dependence in habitat utilisation by a population of wood mice (Apodemus sylvaticus L.) was investigated within a habitat mosaic produced by the felling of mature Sitka spruce (Picea sitchensis Bong. Carriere). A capture-mark-recapture study was carried out from May 1990 to June 1992, with trapping in five 0.81-ha grids marked in mature forest and clear-fellings of different ages. Intergrid movements were frequent (15.3% of all recaptures). A significant linear negative relationship was found between overall population sizes and degree of heterogeneity in habitat utilisation, although the former explained only about one-quarter of the variation in the latter (r2 = 0.233). Wood mice were more evenly distributed among grids when numbers in the area were high, indicating density-dependence in their habitat utilisation. Demography was studied at subpopulation (grid) level to determine whether the observed pattern was due to movements among grids or to intergrid variation in the balance between recruit.
Genetic differentiation among Atlantic cod in south and south‐east Icelandic waters: synaptophysin (Syp I) and haemoglobin (HbI) variation

Significant differences were found at the synaptophysin (Syp I) locus between two groups of Icelandic cod Gadus morhua; Loftstaoahraun (spawning ground), Reykjanesgrunn and Eyrabakkabugur (feeding grounds) on the one hand and Kantur (spawning ground) and Austfjaroadjup (feeding ground) on the other. There was also a considerable genetic heterogeneity within the former group. The results indicate that the cod in south and south-east Icelandic waters do not belong to one panmictic population.
Overview and Application of QTL for Adult Plant Resistance to Leaf Rust and Powdery Mildew in Wheat

Leaf rust and powdery mildew, caused by Puccinia triticina and Blumeria graminis f. sp. tritici, respectively, are widespread fungal diseases of wheat (Triticum aestivum L.). Development of cultivars with durable resistance is crucially important for global wheat production. This paper reviews the progress of genetic study and application of adult plant resistance (APR) to wheat leaf rust and powdery mildew. Eighty leaf rust and 119 powdery mildew APR quantitative trait loci (QTL) have been reported on 16 and 21 chromosomes, respectively, in over 50 publications during the last 15 yr. More important, we found 11 loci located on chromosomes 1BS, 1BL, 2AL, 2BS (2), 2DL, 4DL, 5BL, 6AL, 7BL, and 7DS showing pleiotropic effects on resistance to leaf rust, stripe rust, and powdery mildew. Among these, QTL on chromosomes 1BL, 4DL, and 7DS also correlate with leaf tip necrosis. Fine mapping and cloning of these QTL will be achieved with the advent of cheaper high-throughput genotyping technologies. Germplasm carrying these potential resistance genes will be useful for developing cultivars with durable multidisease resistance. In addition to its non-NBS–LRR (nucleotide binding site–leucine rich repeat) structure, the senescence-like processes induced by Lr34 could be the reason for durability of resistance; however, more information is needed for a full understanding of the molecular mechanism related to durability. Adult plant resistance genes have been used by CIMMYT for more than 30 yr and have also been transferred to many Chinese wheat varieties through shuttle breeding.
DELAYED OVARIAN DEVELOPMENT AND AESTIVATION IN ADULT FEMALES OF HETERONYMPHA MEROPE MEROPE (LEPIDOPTERA: SATYRINAE)

There are strong indications that in New South Wales there is a delay in ovarian development in females of Heteronympha merope merope (Lepidoptera: Satyrinae) and in addition, under hot conditions, aestivation may occur. A similar delay in ovarian development is indicated in H. mirifica but is probably not accompanied by aestivation. In both species females copulate soon after emergence, and adult males do not aestivate. Delayed ovarian development and aestivation, which have not previously been recorded in Australian Papilionoidea, are discussed in relation to climate.
Imbricacy and stomatal wax plugs reduce maximum leaf conductance in Southern Hemisphere conifers

An examination of the relationship between theoretical maximum leaf conductance as calculated from stomatal dimensions, and measured maximum leaf conductance was undertaken in a group of Southern Hemisphere conifers. The relative effects of stomatal wax plugs, found in most species of conifers in the Southern Hemisphere, and imbricate leaf arrangement were expressed as a percentage inhibition of maximum leaf conductance (gmax) calculated from the ratio of measured gmax to theoretical gmax. Because of the similar stomatal dimensions of all species, measured gmax was proportional to stomatal density in plugged and unplugged species, with species without wax plugs producing maximum leaf conductances on average 91% of calculated gmax, while in species with plugged stomata measured gmax was on average only 35% of theoretical gmax. There was no effect produced by imbricacy in itself, but when combined with epistomy, gmax was significantly reduced to about 17% of theoretical gmax. This is clearly illustrated by comparisons of juvenile–adult foliage, and closely related imbricate and nonimbricate species. The adaptational advantages of imbricacy and wax plugs, and the potential for inferring gmax of fossil taxa are discussed.
Mycorrhizal colonization of transgenic Eucalyptus camaldulensis carrying the mangrin gene for salt tolerance

Transgenic products and the creation of new organisms with innovative transgenic traits generally raise risk assessment concerns because of potential risks to nontarget organisms. Cartagena Protocol on Biosafety and Japanese government regulations require scientific environmental risk assessments of living modified organisms prior to release to avoid adverse effects on the environment. Soil microorganisms, such as the arbuscular mycorrhizal fungi, aid in plant nutrient acquisition and protection from environmental stresses such as salt stress. In this study, we used a salt-tolerant transgenic Eucalyptus camaldulensis transformed with the mangrin gene from a mangrove plant and evaluated the interactions between environmental stress-tolerant transgenic plants and arbuscular mycorrhizal fungi. Our results indicated that these transformants were substantially equivalent to nontransformants in terms of arbuscular mycorrhizal fungi colonization under both saline and nonsaline conditions, and that the arbuscular mycorrhizal fungi colonization could potentially enhance the salt tolerance of the transgenic plant.
Expanding Immunology: defensive versus ecological perspectives

the few serious efforts to understand the scienceof immunology theoretically by employing both scientific and philosoph-ical critiques.Elling Ulvestad expertly summarizes diverse and extensive immu-nological science and then offers an ecologically inspired critique, which em-ploys classical philosophical approaches as well as contemporary philosophy ofscience.His basic thesis is that the immune system functions within a larger con-text than the restricted confines of a circumscribed “self” opposing dangerousnon-self challenges.That dichotomy of self and other would be replaced with afully ecological orientation,in which immunity is characterized within a frame-work that includes the organism and its environment in terms of both defensiveand cooperative functions.In other words,beyond characterizing immune reac-tions within the organism, immunology must also situate (contextualize) thoseresponses within the larger environment in which they occur.Assembling a widerange of experimental findings and examining the models that structure them,Ulvestad presents both scientific and philosophical arguments to buttress his the-oretical claims.Because of the demands on the reader to bridge the scientific portrait of the
Overexpression of bacterial catalase in tomato leaf chloroplasts enhances photo‐oxidative stress tolerance

The Escherichia coli gene katE, which is driven by the promoter of the Rubisco small subunit gene of tomato, rbcS3C, was introduced into a tomato ( Lycopersicon esculentum Mill.) by Agrobacterium tumefaciens -mediated transformation. Catalase activity in progeny from transgenic plants was approximately three-fold higher than that in wild-type plants. Leaf discs from transgenic plants remained green at 24 h after treatment with 1 µ M paraquat under moderate light intensity, whereas leaf discs from wild-type plants showed severe bleaching after the same treatment. Moreover, ion leakage from transgenic leaf discs was significantly less than that from wild-type leaf discs at 24 h after treatment with 1 µ M paraquat and 10 m M H 2 O 2 , respectively, under moderate light intensity. To evaluate the efficiency of the E. coli catalase to protect the whole transgenic plant from the oxidative stress, transgenic and wildtype plants were sprayed with 100 µ µ µ M paraquat and exposed to high light illumination (800 µ mol m − 2 s − 1 ). After 24 h, the leaves of the transgenic plants were less damaged than the leaves of the wild-type plants. The catalase activity and the photosynthesis activity (indicated by the F v / F m ratio) were less affected by paraquat treatment in leaves of transgenic plants, whereas the activities of the chloroplastic ascorbate peroxidase isoenzymes and the ascorbate content decreased in both lines. In addition, the transgenic plants showed increased tolerance to the oxidative damage (decrease of the CO 2 fixation and photosystem II activity and increase of the lipid peroxidation) caused by drought stress or chilling stress (4 ° C) under high light intensity (1000 µ mol m − 2 s − − − 1 ). These results indicate that the expression of the catalase in chloroplasts has a positive effect on the protection of the transgenic plants from the photooxidative stress invoked by paraquat treatment, drought stress and chilling stress.