Miracle-dz/UniFAR-FTUs huggingface dataset:
Aluminium tolerance is achieved by exudation of citric acid from roots of soybean (Glycine max)

Fourteen soybean (Glycine max [L.] Merr.) cultivars were analysed and found to differ considerably in aluminium (Al) resistance. The cultivars Suzunari (Al-resistant) and Shishio (Al-sensitive) were selected for further analysis of physiological mechanisms of Al resistance. The relative root growth of Shishio was 48% compared to 76% for Suzunari in response to 15 μM Al (24 h). Aluminium accumulation and Al-induced callose formation in root apices were 50 and 25% of that in Suzunari, respectively. Al inhibited both Suzunari and Shishio during the first 6 h of exposure. However, the root growth inhibition was further increased in Shishio but not in Suzunari, suggesting an Al-induced Al-resistant mechanism operating in Suzunari. Organic acid analysis in root exudates of both cultivars revealed that they specifically exuded citrate in response to Al. However, the citrate exudation rate was significantly higher in Suzunari during the 6 h/24 h Al treatment, which was 52/330 compared to Shishio's 26/118 (nmol [g root fresh weight] -1 [6 h] -1 ), respectively. This Al-induced citric acid exudation was found to be specific for Al, as several other metals failed to induce citrate exudation in both cultivars. Fourteen days of P deficiency did not elicit citrate excretion in both cultivars, while application of Al to P-deficient plants rapidly induced citrate exudation in both cultivars, confirming the specificity of the response of these soybean cultivars to Al. To our knowledge, this is the first report demonstrating an Al-exclusion mechanism in soybean cultivars, which is conferred by enhanced and specific Al-induced exudation of citrate.
A transgenic zebrafish model of signaling through toll-like receptors

Toll-like receptors (TLRs), members of the innate immune system, recognize distinctive components of pathogens to initiate cellular signaling pathways. These pathways lead to the production of inflammatory proteins such as tumor necrosis factor alpha (TNFα), a cytokine that activates immune cells to fight the infection. When infections disseminate into the bloodstream, TLR-signaling is activated systemically and the excessive release of cytokines, chemokines, and other inflammatory mediators produces a life-threatening condition known as septic shock. The majority of drugs recently developed to treat septic shock were beneficial in animal and in vitro models, but were ineffective in human clinical trials. One possible solution to resolve this disparity is to use the new animal model Danio rerio (zebrafish) whose unique characteristics allow for high-throughput, large-scale screening of chemicals and for exclusive study of the innate immune system. We undertook three different approaches to establish a functioning transgenic zebrafish model that facilitates visualization of TNFα expression as an indicator of TLR signaling and pathologic immune response. The first expression clone contains the human TNFα (hTNFα) enhancer and the enhanced green fluorescent (EGFP) reporter gene under control of the basal carp β-actin promoter. The second expression clone contains all elements of the first clone with the addition of a red fluorescent reporter gene, DsRed, under control of a lens-specific promoter, the Xenopus laevis γ-crystallin
47 EFFECT OF L-CARNITINE TREATMENT DURING OOCYTE MATURATION ON THE POST-THAW DEVELOPMENT OF PORCINE EMBRYOS VITRIFIED AT THE PRONUCLEAR STAGE

The extreme cryo-sensitivity of porcine oocytes and embryos is attributed to their endemically high content of cytoplasmic lipid droplets. In attempts to improve the cryo-tolerance of porcine embryos, various strategies have been used to reduce the amount of lipid droplets present in the cytoplasm before vitrification. Recently, the cryo-tolerance of bovine oocytes vitrified at the metaphase II stage was improved by supplementing in vitro maturation (IVM) medium with l-carnitine (LC), a stimulator of lipid metabolism (Chakitisakul et al. 2013 Theriogenology 79, 590–598). The objective of this study was to determine the effect of supplementing IVM medium with LC on the post-thaw development of porcine embryos vitrified at the pronuclear stage. Oocytes recovered from the ovaries of prepubertal gilts were matured in modified porcine oocyte medium supplemented with 0 (control) or 12 mM LC during the final 22 h of IVM. Following IVF, presumptive zygotes were cultured in porcine zygote medium-3. At the pronuclear stage, cohorts of embryos from each group were either vitrified using a solid surface vitrification procedure (Somfai et al. 2009 Biol. Reprod. 80, 42–49) or cultured for 7 d without being vitrified. Vitrified zygotes were subsequently warmed and cultured for 7 d. The rates of cleavage, blastocyst formation, and hatching were recorded, and all blastocysts were stained to determine the total cell numbers. Three replicates were performed. Proportional data were arcsine transformed and subjected to ANOVA, and cell number data were analysed by t-test. The post-thaw survival rates of the embryos that were vitrified did not differ between the groups (control: 95.7%; LC: 97.1%; P > 0.05). There were no significant effects of LC treatment or vitrification on the rates of cleavage, blastocyst formation, and hatching (Table 1). Vitrified embryos derived from LC-treated oocytes produced blastocysts with fewer cells than vitrified embryos derived from untreated oocytes (Table 1; P < 0.05). In contrast to previous findings in other species, the results indicate that supplementing IVM medium with LC did not enhance the post-thaw development of porcine embryos vitrified at the pronuclear stage. Table 1.Effect of l-carnitine (LC) treatment and vitrification on porcine embryo development C. Grupen was supported by an OECD Fellowship.
Highly efficient visual selection of transgenic rice plants using green fluorescent protein or anthocyanin synthetic genes

Visual selection enables transformation in plants that are sensitive to the stress of antibiotic selection. Furthermore, we proposed a method of isolating transformed cells in which the gene of interest is expressed at high level using visual selection. However, visual selection was inefficient and laborious because of the technical difficulties involved in clonal propagation of transformed calli selected using GFP (9.4–20.5% in the model japonica rice variety Nipponbare in our previous report). Very recently, we have discovered that an indica model cultivar, Kasalath, is very highly competent for Agrobacterium-mediated transformation compared to Nipponbare, suggesting that visual selection would be achieved more efficiently in Kasalath than in Nipponbare. We confirmed that the number of transformed cells emitting green fluorescence in Agrobacterium co-cultivated callus of Kasalath under no antibiotic pressure was >50-fold higher than the number obtained in Nipponbare. We succeeded in clonal propagation of GFP emitting cells at a frequency of 62.2–85% in Kasalath. Moreover, we showed that anthocyanin, that is an intrinsic pigmentation and thus might be more acceptable to consumers, can be used as an intrinsic marker in visual selection of rice. Thus, we propose that combination of the use of cultivar which has high transformation competency and visual selection system could enhance efficient production of transgenic rice expressing foreign gene product at higher level.
Studies of morphological parameters affecting ungulate locomotion in snow

We deal with possible morphological adaption to varied snow conditions by four North American ungulate species. Chest heights and weight loads on track are key parameters in estimating capabilities of species, and of age and sex classes within species, to cope with snow. Methods believed suitable for measuring those parameters in replicable fashion are discussed. Comparative studies of bison (Bison bison), moose (Alces alces), wapiti (Cervus elaphus), and white-tailed deer (Odocoileus virginianus) are described. There are pronounced differences in both parameters between species and between some age and sex classes within species. Chest heights of the three cervids differed by a fixed interval suggesting that differential ability to use varied snow depths may play a role in resource partitioning. Differential winter mortality may be related to sex and age class differences in ability to cope with snow. Morphological differences relate to regional distributions by determining species suitability for surviv.
Host Suitability for Insect Parasitoids

The parasitic mode of life is very productive and has evolved in numerous orders of arthropods. Many parasitic insects differ from other parasitic organisms in that the adults of parasitic insects are free living, a limited number of progeny develop per host, and the host does not survive the encounter. These parasitic insects have been referred to as parasitoids to distinguish them from other parasitic organisms in which the adults and their progeny are parasitic, many individuals of different generations may occur on the same host, and the host is usually not killed. Unlike the parasite-host relationship, the evolution of the parasitoid-host relationship is of little consequence for the host, which does not survive the association to pass on its genetic information (203). The coevolution of the parasitoid and host has resulted in a number of unique associations. There are a number of steps necessary for the success of the parasitoid­ host relationship. Doutt (44) divided the events into four steps: (a) host habitat location, (b ) host location, (c) host acceptance, and (d ) host suit­ ability. Vinson (203) added a fifth step, referred to as host regulation. Whether a parasitoid is able to develop within a host may depend on the ability or inability of the parasitoid to regulate the host's physiology. The
Short Note: Circumpolar distribution of the pycnogonid-ectoparasitic gastropod Dickdellia labioflecta (Dell, 1990) (Mollusca: Zerotulidae)

The Antarctic gastropod Dickdellia labioflecta (Dell, 1990) (originally described as Laevilittorina (Corneolittorina) labioflecta) is an obligate parasite of pycnogonids, which exploits their body fluids through the cuticular gland holes (Lehmann et al. 2007) and lays its eggs on the pycnogonid's legs where embryos complete their life cycle (Hedgpeth 1964, Sirenko 2000, Lehmann et al. 2007). The ecology of D. labioflecta appears to be unique, as no other examples of such a specialized parasitic behaviour on pycnogonids are known. This life-style and the related anatomical specializations (gut and digestive gland morphology), prompted the erection of a new genus, Dickdellia Warén & Hain, 1996 provisionally included in the family Zerotulidae (Warén & Hain 1996). Although information is quite scant, to date, two pycnogonid host species are known for Dickdellia: Colossendeis megalonyx megalonyx Fry & Hedgpeth, 1969 (Lehmann et al. 2007) and Nymphon isabellae Turpaeva, 2000 (Sirenko 2000).
Targeting the Sortase A Transpeptidase to Tackle Gram-positive Pathogens

The virulence factors include the cell-wall associated proteins called MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) that can promote the adhesion to host proteins, for example, the fibronectin that is very common in host tissues. The cellwall associated proteins are necessary for host colonization, invasion, immune evasion and biofilm formation [4]. The biofilms, multistratified bacterial communities that grow on a biological or artificial surface, are responsible for chronic infectious diseases and for device or biomaterial associated infections, and are more resistant to host immune defence system and to conventional antibiotics [5].
Aspects of the biology of the giant form of Sthenoteuthis oualaniensis (Cephalopoda ommastrephidae) from the Arabian Sea

An investigation was carried out on the recently discovered ‘giant’ extra large (XL) form of the squid Sthenoteuthis oualaniensis from the Arabian Sea. The sample consisted of 2 males, which have not been previously described, and 13 females. Diet composition, parasite loading, sucker ring dentition, biolumi-nescence and sexual dimorphism were examined and compared to known parameters of the medium (M) form. Reproductive strategy, potential fecundity, egg size distribution in the ovary and oviducts were examined in mature XL females. Evidence of multiple spawning in the giant form was also investigated. Overall body shape, bioluminescent structures and coloration of the giant form were similar to the M form, though the XL form had a smaller fin angle than the M form. The mature female XL form has a dorsal mantle length about twice that of a mature female M form. Adult females of the XL form have a dorsal mantle length about twice that of adult males of the same form. Differences between males and females were found in arm sucker ring dentition and parasite load, suggesting a difference in diet. This could be linked to size differences between the sexes. A strong correlation between ovary mass and mantle length was found (r2 = 0.64). Poor correlation was found between mantle length and oviduct mass (r2 = 0.128) and potential fecundity (r2 = 0.07). Potential fecundity ranged between 2–5 million eggs and the holding capacity of the oviducts was approximately 300, 000 eggs. This combined with the presence of spermatangia and the presence of food in the stomach suggest that the XL form is a multiple spawner. S. oualaniensis appears to have a plastic phenotype and has adapted to the Arabian Sea conditions by evolving the capacity to grow to a giant size.
Mineral composition of corn and soybean meal

SUMMARY Levels of several nutritionally significant minerals (P, K, Ca, Mg, Mn, Fe, Al, Cu, Zn, and Na) were determined in 16 samples of yellow corn and 16 samples of soybean meal from the 2009 US harvest. Phosphorus content was of particular interest in view of the widespread use of the enzyme phytase and the increased cost of organic P. An effort was made to ensure a geographic diversity in the origin of these samples. However, no attempt was made to identify the exact area where the respective crops had been cultivated. Phosphorus content of yellow corn averaged 0.23%, which was slightly lower than listed by the NRC but in agreement with other recent studies. The P content of soybean meal (0.67%) was slightly higher than that reported by the NRC.
Herbaceous Response to Canopy Cover, Light Intensity, and Throughfall Precipitation in Coniferous Forests

Measurements of canopy opening, understory light, throughfall precipitation, and understory herb response in leaf surface area per square meter in pine forests on light—textured soils in northern Wisconsin show that the understory herb layer is more responsive to differences in throughfall precipitation determined by canopy opening than to difference in light. Canopy opening controls both the level of light reaching the herb layer and the proportion of total precipitation reaching the litter layer, but the light levels are apparently considerably above the minimum thresholds for these species. On the light—textured soil—moisture recharge in the surface layers, as influenced by canopy opening, exerts the major control over the total cover of herbaceous species. Moisture content of the lower litter layers and upper soil layer, where most of the northern understory herbs are rooted, is greatly influenced by variations in throughfall determined by canopy opening.
Population densities of wheat thrips, Haplothrips tritici Kurdjumov (Thysanoptera: Phlaeothripidae), on different wheat and barley cultivars in the province of Kahramanmara ş , Turkey

Population densities of Haplothrips tritici ( H. tritici ) Kurdjumov (Thysanoptera: Phlaeothripidae) were studied in Kahramanmara ş , Turkey. In 2002, bread wheat cultivars, Bocro 4, Pehlivan and Yüre ğ ir 89, durum wheat cultivars, Balcali 85, Ceylan 95 and Harran 95 and barley cultivars, Esterel and Pacific, were used. In 2003, Sham IV and Firat 93 were used instead of Pehlivan and Ceylan 95. Hege was also added to the barley cultivars. H. tritici (mostly second-stage larvae) population densities on Bocro 4, Pehlivan and Yüre ğ ir 89 on the 6th of June in the first year were 54.8, 59.5 and 33.0/ear, respectively. Populations on durum wheat reached their highest value twice (during the egg and second larvae stages) in the first year. The first one was on the 10th May, when H. tritici densities in Balcali 85, Ceylan 95 and Harran 95, were 42.1, 52.0 and 40.5/ear, respectively, and the second one was on the 6th of June, when they were 47.5, 60.9 and 58.9/ear, respectively. In the second year, H. tritici on Bocro 4 reached their highest level (26.9/ear) on 17th May and H. tritici populations on Sham IV and Yüre ğ ir 89 on 29th May were also at their highest level with 48.4 and 20.1/ear, respectively. Population densities on durum wheat cultivars were not as high as in the first year and changed between 0.2 and 9.7/ear. H. tritici on barley also stayed at low levels for the first (0.1 to 3.2/ear) and second (0.1 to 1.2/ear) years.
Growth Factor-mediated Tumor Progression and Metastasis in Cholangiocarcinoma

Different ligands can lead to the activation of epidermal growth factor receptor, and the subsequent signal transduction leads to an increase in cellular motility, proliferation, invasion, and blocking of apoptosis, and all of this contributes to the development and progression of cancer. Our studies clarified; 1) The EGFR expression level is reduced during tumor progression or during ligand-induced EGFR activation. 2) ANXA8 and its regulatory pathway may well be alternative, strategic targets for inhibiting tumor metastasis. 3) The molecular pathway of EphA2 signaling and provide insight into the mechanisms that control cancer progression and metastatic spread in cholangiocarcinoma (CC). Therefore, therapeutic strategies that target EphA2 and its downstream effectors may be useful to control CC. Korean J Pancreatobiliary 2015;20(4):175-189
THE VALUE OF LIFE HISTORY DATA IN THE STUDY OF THE EVOLUTION OF THE AMPHIBIA

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Viruses in soils: morphological diversity and abundance in the rhizosphere

Soil viruses are potentially of great importance as they may influence the ecology and evolution of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Despite this importance, the area of soil virology is understudied. Here, we report the isolation and preliminary characterisation of viruses from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod shaped, filamentous and bacilliform particles were detected in the soil samples. An apparent predominance of small spherical and filamentous bacteriophages was observed, whereas tailed bacteriophages were significantly less abundant. In this report, we also present observations and characterisation of viruses from different soil functional domains surrounding wheat roots: rhizosheath, rhizosphere and bulk soil. In spite of the differences in abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically, there were approximately 1.1―1.2 x 10 9 virions g ―1 dry weight, implicating remarkable differences in virus-to-bacteria ratios in domains close to roots, rhizosphere and rhizosheath (approximately 0.27) and in bulk soil (approximately 4.68).
Anticancer activity of persimmon ( Diospyros kaki L.) calyx extracts on human cancer cells

Natural products are the source of numerous therapeutic agents. Recent progress in the discovery of drugs from natural products has resulted in development of compounds for use in cancer treatment. Results from this study demonstrated that methanolic extracts of persimmon calyx (PCE) have cytotoxic effects in human cancer cells. Through MTT reduction assay, lactate dehydrogenase release assay, morphological assay, and colony formation assay, highly cytotoxic effects were demonstrated in human cancer cells treated with various concentrations of PCE. As expected, PCE inhibited growth of HT-29 cells in a dose-dependent manner. In particular, 500 µg/ml of PCE showed 31.1% inhibition against HT-29 cells. Interestingly, characteristics of apoptosis, including chromatin condensation and sharking, were shown to occur in HT-29 cells 24 h after treatment with 500 µg/ml of PCE. In addition, PCE also showed cytotoxic activity against HeLa and PANC-1 cells, as well as HT-29 cells. These results indicate that PCE contains bioactive materials and that it is a potential candidate for use as a chemotherapeutic agent against human cancer cells. Key words: Natural products, persimmon calyx, cytotoxic effects, cancer cells, apoptosis.
OBSERVATIONS OF NORTHERN FLYING SQUIRREL FEEDING BEHAVIOR: USE OF NON-TRUFFLE FOOD ITEMS

In the Pacific Northwest, the northern flying squirrel, Glaucomys sabrinus, consumes sporocarps of a wide variety of hypogeous mycorrhizal fungi (truffles). Numerous other foods are also consumed but are not well characterized by fecal pellet analysis either because they are more fully digested (seeds, nuts, fruits, vegetation) or because of the similarity among spore types (lichen photobionts, epigeous fungi). Thus, observations of squirrel foraging are important in characterizing non-truffle dietary components. As part of a trapping and telemetry study, we observed G. sabrinus foraging on 63 occasions; 34 were observations of non-truffle consumption. These foods included epigeous fungi, fruits and seeds, and conifer seedlings. We hypothesize G. sabrinus may consume more non-truffle foods than is indicated by fecal pellet analysis, and that such foods may be important nutritional supplements to a low-quality diet as well as substitutes for truffles in times or places of low truffle abundance. By availing themselves of other food sources, G. sabrinus may persist in otherwise marginal habitats, while also contributing to the dispersal of a wide diversity of fungi and increasing genetic diversity of fungal and microbial species.