Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of Seaweed Chemical Defenses by Amphipod Grazing

Grazing by the generalist amphipod Ampithoe longimana induced increased concentrations of defensive secondary metabolites in the brown alga Dictyota menstrualis and made the seaweed less susceptible to further attack by the amphipod. Although A. longimana preferentially consumes D. menstrualis, its feeding rates can be reduced sig- nificantly by high concentrations of diterpenoid dictyols produced by the alga. In 1991, D. menstrualis from sites with high numbers of A. longimana had higher levels of grazing scars, higher concentrations of dictyols, and were less palatable to A. longimana than plants from sites with few amphipods. Among-site differences in palatability to amphipods did not correlate with plant differences in protein, nitrogen, or carbon content. Within a site, plants that had apparent amphipod grazing scars were significantly less palatable to A. Iongimana than neighboring undamaged plants. Controlled field experiments manipulating A. longimana densities supported the hypothesis that feeding by this amphipod induced elevated chemical defenses in the alga. Compared to undamaged control plants, amphipod- damaged plants had 19-34% more of three diterpenoid secondary metabolites and were 50% less palatable to amphipods. Soluble protein and thallus toughness were unaffected by amphipod grazing and thus could not have caused the differences in palatability. High- pressure liquid chromatography evaluation of adventitious branches growing from blade margins at sites of amphipod grazing scars showed that these branches had significantly elevated levels of two diterpenoids relative to normal blade apices or middles. Thus, the amphipod-induced resistance to further attack occurs through an increase in chemical de- fenses, and these defenses are, to some extent, localized within the plant thallus. Among- site differences in amphipod densities, grazing scars, seaweed defensive chemistry, and plant palatability that we documented in 1991 varied considerably during 1992 and 1993, suggesting that these interrelationships may be complex. In 1992, A. longimana densities did not differ between sites, and there were no between-site differences in palatability or concentrations of deterrent secondary metabolites. In 1993, however, A. Iongimana densities did differ between sites, but between-site differences were less dramatic than in 1991. Some secondary metabolites were slightly, but significantly, increased at the site with higher densities of A. longimana, but this had no effect on A. longimana feeding. It has been long recognized that marine herbivores are active participants in seaweed- herbivore interactions and can greatly influence the structure of benthic algal communities. Our findings suggest that seaweeds are not passive participants in these interactions, but can actively alter their susceptibility to herbivores in ecological time. Induced responses to herbivory help explain both spatial (i.e., within-thallus, within-site, and among-site) and temporal variation in the chemical defenses of D. menstrualis.
Effect of commercial processing stages of apple juice on patulin, fumaric acid and hydroxymethylfurfural (HMF) levels

The effects of different stages of commercial apple juice production on the patulin, fumaric acid and hydroxymethylfurfural (HMF) contents of apple juice were investigated. Heat treatment and activated charcoal were effective for the reduction of patulin. The average reduction of patulin were 13.4% and 22.9% for heat treatment and activated charcoal, respectively. Statistical analysis showed no significant differences (P<0.05) in the presence of fumaric acid between different treatments. Filtration and heat treatment caused an apparent increase in the HMF content, while activated charcoal caused a decrease. The average increments of HMF were 40.4% and 38.0% for separation and heat treatment, respectively, while the average reduction of HMF was 23.7% for activated charcoal. Spiking of samples with known amounts of patulin and fumaric acid revealed respective recovery rates of 96.4% and 95.9%.
Infrared‐Warmed and Unwarmed Wheat Vegetation Indices Coalesce Using Canopy‐Temperature–Based Growing Degree Days

To determine the likely effects of global warming on field-grown wheat (Triticum aestivum L.), a “Hot Serial Cereal” experiment was conducted—so-called “Cereal” because wheat was the crop, “Serial” because the wheat was planted about every 6 wk for 2 yr, and “Hot” because infrared heaters were deployed on six of the planting dates in a temperature free-air controlled enhancement (T-FACE) system, which warmed the canopies of the Heated plots. During the experiment, measurements of canopy reflectance were made two to five times per week from which values of normalized difference vegetation index (NDVI) were calculated. As expected, curves of NDVI from the Heated plots vs. time and vs. growing degree days (GDD) computed from air temperatures generally were ahead of those from Reference plots. However, when plotted against GDD computed from canopy temperatures the curves coalesced, which gives confidence that the infrared-heater treatment simulates natural warming and will produce plant responses not unlike those expected with future global warming. Biomass and grain yields were correlated with the areas under the NDVI vs. GDD curves for the air-temperature-based GDDs, but high variability prevented such a correlation to be detected using canopy-temperature-based GDD. Large differences existed between the total amounts of air or canopy temperature-based GDDs required for wheat to mature in our irrigated fields in an arid region. This implies that GDD based on air temperatures should be regarded only as a local guide to plant development rates, whereas those based on canopy temperatures would be more universal.
Myrtaceae fossil leaves from the Río Turbio Formation (Middle Eocene), Santa Cruz Province, Argentina

Myrtaceae, the gum tree family, is a large angiosperm clade of 5671 species mostly distributed in tropical and subtropical regions of the world. In the southernmost tip of South America (Santa Cruz province) where the fossils analysed in this study come from (Río Turbio Formation), this family is virtually absent and the extant vegetation is largely dominated by deciduous Nothofagus pumilio and Nothofagus antarctica. During the early Paleogene, however, the Myrtaceae were an important element in southern Patagonian floras. Here, we report and describe ten taxa related to the extant genera Eugenia, Myrcia, Psidium, Myrcianthes and possible Eucalyptus and Campomanesia. The presence of a high diversity of Myrtaceae during the Eocene in one of the southernmost regions of the world could be thought as unusual. However, during this period of time (45 Ma), a number of other tropical lineages also reached these high latitudes probably as a consequence a warming climatic trend. In fact, through the Paleocene–Early Eocene interval, climatic conditions were the warmest of the Cenozoic. After this period of time, a progressive decline in temperature forced the migration of megathermal elements towards lower latitudes and, at the same time, led to the expansion of forest dominated by Nothofagus which predominate the region today.
Purification and characterization of endoxylanase Xln-2 from Aspergillus niger B03

An extracellular multiple form of endoxylanase was isolated from the xylanolytic complex of Aspergillus niger B03. The enzyme was purified to a homogenous form using ultrafiltration, anion exchange chromatography, and gel filtration. It was a nonglycosylated protein with a molecular weight of 20,000 Da as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and 21,000 Da as determined by gel filtration. The optimal pH for the enzyme action was 5.0 and the optimal temperature was 55 °C. Endoxylanase stability was significantly improved in the presence of glycerol and sorbitol. The enzyme activity was activated by Mn2+ and Co2+, and it was inhibited by Ag+, Cu2+, Fe3+, Fe2+, and Pb2+. The substrate specificity and the product profile of the enzyme suggested that it was an endoxylanase. The enzyme showed a synergism with another endoxylanase from Aspergillus niger B03 in xylan hydrolysis.
Temporal niche of acoustic activity in anurans: interspecific and seasonal variation in a neotropical assemblage from south-eastern Brazil

Sympatric anuran species tend to differ in their temporal niche breadth and may also have considerable seasonal variation in diel activity patterns. We studied the temporal niche breadths of six anuran species during 24 consecutive months in an area of secondary forest at the Brazilian Atlantic Rainforest. Along hourly intervals, at each of three observation points along a stream, the number of calling males of Adenomera marmorata , Eleutherodactylus parvus , Physalaemus signifer , Aplastodiscus eugenioi , Scinax hayii and S. trapicheiroi was recorded. The influence of rainfall, air humidity and temperature on the variation in the niche breadth of each species was analysed. Mean niche breadth differed for all species. Scinax trapicheiroi had the broadest niche and S. hayii had the smallest. Temporal niche breadth varied seasonally for all species. Two species ( E. parvus and S. hayii ) showed strong variation in the temporal niche when compared to the other species. Eleutherodactylus parvus , A. eugenioi and S. hayii were significantly affected by rainfall, air humidity and temperature. Niche overlap among species pairs also varied annually with mean temporal niche overlap being greater during the rainy season than during the dry season.
Selection for resistance to fusarium root rot, and associations among resistances to six diseases in alfalfa

Fusarium root and crown rot in New York, caused mostly by Fusarium avenaceum (Fr.:Fr.) Sacc. , F. oxysporum Schlechtend. :Fr. , and F. solani (Mart.) Sacc. , reduces longevity and productivity of alfalfa (Medicago sativa L.). The research objectives were to determine correlations among six alfalfa diseases and progress from recurrent phenotypic selection for resistance to fusarium root rot. From alfalfa half-sib progenies, phenotypic and additive genetic correlation coefficients were estimated among resistances to disease caused by the three Fusarium spp. and three common vascular diseases, bacterial wilt (BW) [caused by Clavibacter michiganense subsp. insidiosum (McCull.)], verticillium wilt [caused by Verticillium albo-atrum (Reinke & Berthier], and fusarium wilt [caused by F. oxysporum Sch. ex Fr. f. sp. medicaginis (J.L. Weimer)] [. ]
Ethylene Production and 1‐Aminocyclopropane‐1‐Carboxylate (ACC) Synthase Gene Expression in Tomato (Lycopsicon esculentum Mill.) Leaves Under Enhanced UV‐B Radiation

Tomato (Lycopsicon esculentum Mill.) plants grown in a greenhouse were irradiated with two different levels of UV-B, namely 8.82 (T1) and 12.6 kJ/m2 per day (T2). Ethylene production, 1-aminocyclopropane-1-carboxylate (ACC) content, 1-(malonylamino) cyclopvopane-1-carboxylic acid (MACC) content, gene expression of ACC synthase (EC 4.4.1.14), and ACC oxidase activity in tomato leaves were determined. The results indicated that ACC content, the activity of ACC synthase and ACC oxidase, and ethylene production increased continuously under low doses of UV-B radiation, whereas at high doses of radiation these parameters increased during the first 12 d and then started to decrease. The MACC content increased continuously over 18 d under both doses of UV-B irradiation. The changes in ACC content, ACC synthase activity, ACC oxidase activity, the transcriptional level of the ACC synthase gene, and ethylene production were consistent with each other, suggesting that ACC synthase was the key enzyme in ethylene biosynthesis and that ethylene production in tomato leaf tissues under UV-B radiation could be regulated by the expression of the ACC synthase gene. The results also indicate that the change in ethylene metabolism may be an adaptive mechanism to enhanced UV-B radiation. (Managing editor: Ping He)
Isolation and Physiological Functionality of Yeasts from Wild Flowers in Seonyudo of Gogunsanyeoldo, Jeollabuk-do, Korea

전라북도 고군산열도 선유도 일대에서 2014년 4월에 개화한 야생화들로부터 효모들을 분리한 후 이들의 26S rDNA의 D1/D2 부위의 염기서열을 결정한 다음 NCBI의 BLAST database에 등록되어 있는 효모들과의 상동성을 비교 분석하여 동정하였다. 야생화 51점에서 21종의 효모들을 61 균주 분리하였고, 이들 중 Cryptococcus aureus SY1-4 등의 Cryptococcus 속 균들이 가장 많았고, Metschnikowia reukaufii SY20-1등 Metschnikowia 속 균과 Rhodotorula ingeniosa SY1-1등 Rhodotorula 속 균들도 비교적 많이 분리되었다. 이들 61 균주들의 배양상등액과 무세포추출물을 제조한 후 생리기능성을 측정한 결과 M. reukaufii SY44-6의 배양상등액이 각각 49.6%의 XOD 저해활성과 38.4%의 미백성 Tyrosinase 저해활성을 보여 우수하였다. 【Sixty one yeast strains of 21 species were isolated from wild flowers in Gogunsanyeoldo, including Seonyudo of Jeollabuk-do, Korea, and identified by comparison of nucleotide sequences for PCR-amplified D1/D2 region of 26S rDNA using BLAST. Among them, Cryptococcus sp. including C. aureus SY1-4 were found to be dominant, and Metschnikowia sp. including M. reukaufii SY20-1 and Rhodotnula sp. such as R. ingeniosa SY1-1 were also abundantly isolated. Some physiological functionalities of the culture broth and cell-free extracts from 61 yeast strains were determined. Supernatant from Metschnilowia reukaufii SY44-6 showed anti-gout xanthine oxidase inhibitory activity of 49.6% and whitening tyrosinase inhibitory activity of 38.4%, respectively. 】
Computationally Identifying Novel NF-κB-Regulated Immune Genes in the Human Genome

Identifying novel NF-κB-regulated immune genes in the human genome is important to our understanding of immune mechanisms and immune diseases. We fit logistic regression models to the promoters of 62 known NF-κB-regulated immune genes, to find patterns of transcription factor binding in the promoters of genes with known immune function. Using these patterns, we scanned the promoters of additional genes to find matches to the patterns, selected those with NF-κB binding sites conserved in the mouse or fly, and then confirmed them as NF-κB-regulated immune genes based on expression data. Among 6440 previously identified promoters in the human genome, we found 28 predicted immune gene promoters, 19 of which regulate genes with known function, allowing us to calculate specificity of 93%–100% for the method. We calculated sensitivity of 42% when searching the 62 known immune gene promoters. We found nine novel NF-κB-regulated immune genes which are consistent with available SAGE data. Our method of predicting gene function, based on characteristic patterns of transcription factor binding, evolutionary conservation, and expression studies, would be applicable to finding genes with other functions.
High β-Secretase Activity Elicits Neurodegeneration in Transgenic Mice Despite Reductions in Amyloid-β Levels

Amyloid-β peptides (Aβ) are widely presumed to play a causal role in Alzheimer disease. Release of Aβ from the amyloid precursor protein (APP) requires proteolysis by the β-site APP-cleaving enzyme (BACE1). Although increased BACE1 activity in Alzheimer disease brains and human (h) BACE1 transgenic (tg) mice results in altered APP cleavage, the contribution of these molecular alterations to neurodegeneration is unclear. We therefore used the murine Thy1 promoter to express high levels of hBACE1, with or without hAPP, in neurons of tg mice. Compared with hAPP mice, hBACE1/hAPP doubly tg mice had increased levels of APP C-terminal fragments (C89, C83) and decreased levels of full-length APP and Aβ. In contrast to non-tg controls and hAPP mice, hBACE1 mice and hBACE1/hAPP mice showed degeneration of neurons in the neocortex and hippocampus and degradation of myelin. Neurological deficits were also more severe in hBACE1 and hBACE1/hAPP mice than in hAPP mice. These results demonstrate that high levels of BACE1 activity are sufficient to elicit neurodegeneration and neurological decline in vivo. This pathogenic pathway involves the accumulation of APP C-terminal fragments but does not depend on increased production of human Aβ. Thus, inhibiting BACE1 may block not only Aβ-dependent but also Aβ-independent pathogenic mechanisms.
A new algorithm to calculate the nestedness temperature of presence–absence matrices

Aim The nestedness temperature of presence–absence matrices is currently calculated with the nestedness temperature calculator (NTC). In the algorithm implemented by the NTC: (1) the line of perfect order is not uniquely defined, (2) rows and columns are reordered in such a way that the packed matrix is not the one with the lowest temperature, and (3) the null model used to determine the probabilities of finding random matrices with the same or lower temperature is not adequate for most applications. We develop a new algorithm, BINMATNEST (binary matrix nestedness temperature calculator), that overcomes these difficulties.
Differential responses of different phenotypes of Microcystis (Cyanophyceae) to UV-B radiation

Abstract: Microcystis can be single celled or colonial under certain conditions, thereby possessing phenotypic plasticity. Differential physiological and biochemical responses of colonial Microcystis aeruginosa FACHB 939 and its single-celled strain to ultraviolet type B radiation (UV-B) exposure were investigated. Results suggested that UV-B exposure exerted a lower inhibitory effect on the growth of colonial Microcystis, and that the single-celled strain had higher ability to recover after exposure to UV-B. Carotenoids/chlorophyll a (Chl a) ratios were increased, whereas phycobilisome/Chl a ratios were decreased by UV-B exposure. The photosynthetic activities of both phenotypes were inhibited, but colonial Microcystis showed higher tolerance and recovery ability to UV-B exposure. The sheath and shading effect, as well as changes of pigments of colonial Microcystis, were believed to play roles in resisting UV-B exposure. UV-B radiation can increase the sinking rate of the single-celled Microcystis and cause colonial Microcystis to shift from a floating to a sinking state. The observed reduction of colony size and increase in total carbohydrate content induced by UV-B radiation presumably caused the decrease in buoyancy in Microcystis. However, the increase in sinking rate is also an important way for Microcystis to avoid damage inflicted by UV-B radiation.
The effect of γ-irradiation on the chemical composition and antioxidant activities of peppermint essential oil and extract

In this study, the effects of gamma irradiation on the chemical constituents and antioxidant activities of peppermint essential oils and hydro alcoholic extract have been investigated. The results indicated that the major compounds of Mentha piperita were menthol, menthone, α-gurjunene, neo-menthol and 1,8-cineole. The oil main components were not considerable changed due to irradiation. Also, the total flavonoid content of the hydro alcoholic extract was unchanged after irradiation. In addition, the antioxidant activities of the oils and extracts stayed at a high level even after irradiation. Therefore, the application of the irradiation process can be suggested for the decontamination of peppermint without changes in the composition and antioxidant properties.
Overexpression of the MYB-related transcription factor GCC7 in Arabidopsis thaliana leads to increased levels of Pi and changed P-dependent gene regulation.

A proper concentration and turnover of inorganic phosphate (Pi) is essential to maintain cellular processes. Consequently, plants have mechanisms to control Pi homeostasis and to alleviate Pi limitation. The MYB-related transcription factor, PHR1, is important for gene induction during Pi starvation. PHR1 belongs to a family, characterised by the presence of a GARP- and a coiled coil domain. We propose that this family, with 15 members in Arabidopsis thaliana (L.) Heynh. , be termed the GCC-family. In this study, transgenic plants overexpressing one member, GCC7, and a T-DNA knockout mutant, gcc7, are characterised. We find overexpressor plants to accumulate more Pi in shoots, irrespective of the Pi supply. Therefore, GCC7 was characterised in relation to Pi starvation. We conclude that GCC7 is not strictly required for a P-starvation response since the gcc7 mutant responds to Pi limitation. However, overexpression of GCC7 strongly interferes with the P-starvation response, abolishing induction of several P-responsive genes including AT4, IPS1 and several P-transporter genes, whereas GCC7 does not directly interfere with the PHR1 (GCC1) dependent regulation of miR399d. Thus GCC7 influences P-accumulation and P-dependent gene regulation, but GCC7 has a function entirely different from PHR1.
Os caranguejos Eriphiidae, Menippidae, Panopeidae e Pilumnidae (Crustacea Brachyura) de águas rasas do litoral do Paraná, com chave pictórica de identificação para as espécies

A pictorial species identification key for crabs of the families Eriphiidae, Menippidae, Panopeidae and Pilumnidae from shallow waters of Parana State coast was elaborated. A description of the recognition characteristics and illustrations of the species are also presented. Crab samples were obtained from mangrove, estuary and oyster farming located in Guaratuba Bay and rocky shore in Matinhos city. Drawings and analyses were based on freshly collected specimens and on those deposited at Natural History Museum of Capao da Imbuia and at Laboratory of Ecology of Crustacea UFPR. A total of 13 species were analyzed, from which nine species of Panopeidae, two Pilumnidae and one of Eriphiidae and Menippidae. This species richness was considered similar to neighboring areas in spite of the short extension of the Parana State coast.
HOST PREFERENCES OF RHUS RADICANS (ANACARDIACEAE) IN A SOUTHERN DECIDUOUS HARDWOOD FOREST

Rhus radicans, a root-climbing liana, is not distributed randomly among potential host tree species in an old-growth mixed mesophytic forest on the southern Cum- berland Plateau of north Alabama, USA. Vines are more abundant than expected on Carya ovata and Quercus rubra, but less abundant than expected on Juglans nigra, Acer sac- charum, and Sassafras albidum. Seed germination and early seedling growth in the presence of bark extracts suggest allelochemical interactions may influence the observed host pref- erences.
Effect of stand density on radial growth of branches of Scots pine in southern and central Finland

Branch growth dynamics in Scots pine (Pinus sylvestris L.) were studied in 19 thinning experiments in southern and central Finland. Data were collected from 229 trees growing on sites of different fertility with different stand density, age, and canopy position. Radial increments were measured from discs from the base of the thickest branch on every fifth living whorl. Branch growth declined gradually from the upper part of the crown towards the crown base. Near the crown base, the effect of stand density was most apparent and branches remained alive without forming annual rings. After the thinnings, branch growth did not increase, but wider spacing delayed the reduction in branch growth and increased branch longevity. Correlation of branch increment between trees was greater in the upper whorls than in the lower crown. Correlation of the radial increment between whorls of different ages was greater between whorls near each other than between whorls from the upper and lower crown. Variation of the annual increments was similar in the stem and branches. A model was developed for predicting branch increment at different heights in the crown. The best independent variables for indicating branch increment were stem radial increment, height/diameter ratio, and branch age.