Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Phylogeny of Nepenthaceae Based on Cladistic Analysis of Plastid trnK Intron Sequence Data

Nepenthaceae are an exceptional family with regard to carnivo ry and the uniformity of characters. This makes it dif- ficult to resolve phylogenetic relationships due to conv ergent evolution of morphological features. Using comparative se- quencing of the chloroplast trnK intron, the monophyly of this complex family and hypoth eses of infrageneric relationships were tested. Sequences from 71 Nepenthes taxa, representing all groups and two taxa of the closely related Ancistrocladaceae and Dioncophyllaceae as outgroup, were determined and ana- lysed using maximum parsimony methods. Results of this analy- sis show that the isolated taxa N. distillatoria (Sri Lanka) and N. pervillei (Seychelles) are the most basal, clearly separated from the Madagascan taxa N. madagascariensis and N. masoalensis which are placed in a distinct subclade. This corresponds with some plesiomorphic character s shared by these taxa. N. khasi- ana (North India) has an intermediate position between these relic Western species and the remaining taxa. The species of the Malay Archipelago can be referred to three distinct lineages which indicate a correlation to biogeography . Thus the recent disjunct distribution of Nepenthes is interpreted as a result of an incisive extinction of progenitors, a process of migration and a subsequent diversification on the islands of Borneo, Sumatra, Sulawesi and New Guinea. Based on our molecular data, two in- terpretations concerning the origin of Nepenthes are possible: i) evolution in the Northern Tethys which is suppor ted by fossil pollen records from the European Focene, or , ii) a Gondwana- land origin at a time when the Indian plate was separated from Madagascar. Molecular data indicate that colonization of SE Asia started from an ancient Indian stock. Subsequently, in the Malay Archipelago a new secondary centre of diversity developed. Ma- dagascar, the Se ychelles and New Caledonia were probably reached by migration via land bridges, starting from widespead common ancestors with subsequent extinction leaving the cur- rent taxa. There is no evidence for long-distance dispersal. Cur- rent infragenic classification of Nepenthes is only partly in accordance with the phylogen y inferred from trnK intron data.
Emerging technologies / Technologies naissantes Real-time polymerase chain reaction: applications to studies on soilborne pathogens

Real-time, or quantitative, polymerase chain reaction (Q-PCR), offers a rapid, sensitive, and specific method for the diagnosis of plant pathogens in soil, water, air, and plant samples. Fluorescence is used to monitor the accumulation of the PCR product after each PCR cycle. The fluorescence data are used to extrapolate the amount of target DNA present in the sample before amplification so that detection and quantification are achieved in a single assay. Detection limits are generally in the femtogram range for purified pathogen DNA, in the picogram range for pathogen DNA in plant samples, and one to several spores for soil samples. Quantification is reliable over a dynamic range of five to seven orders of magnitude of target DNA, in which differences of two fold or more in target DNA can be detected. Real-time PCR has already been recognized as a valuable tool for epidemiological studies, disease management, detection of emerging pathogens, evaluation of resistance and tolerance to disease, and phytosanitary screens. In this review, we compare four major real-time chemistries that have been used for the detection and quantification of soilborne plant pathogens and discuss the advantages and limitations of TaqManTM and SYBRTM green I, the most widely used chemistries. Current applications of real-time PCR to the diagnosis of plant pathogens in soil and plant samples, considerations for assay development, and variations in measurements are also discussed.
Comparison of the absorption efficiency of α- and β-cryptoxanthin in female Wistar rats

Xanthophylls, such as lutein and zeaxanthin, have received increasing interest in recent years because of positive correlations between their consumption and the prevention of eye diseases. Numerous human intervention studies have been conducted with lutein to estimate the bioavailability from different formulations. The present study was designed to obtain basic data on the absorbance efficiency of the monohydroxylated counterparts of lutein and zeaxanthin: α- and β-cryptoxanthin. A corn-oil-based diet comprising ß-cryptoxanthin from papaya purée and α-cryptoxanthin from green carrot leaves was fed to five female Wistar rats for 8 consecutive days at a rate of 17·3 nmol/d and 9·2 nmol/d, respectively. The identity of the xanthophylls in the supplement was ascertained by LC-(APCI)MS analyses, and xanthophylls present in liver and plasma samples were determined by HPLC/diode array detector (DAD). The β-cryptoxanthin concentrations of rat livers in the treatment group were statistically distinguishable (P < 0·01) from those present in the livers of the control group that were fed a basic diet. α-Cryptoxanthin, the second xanthophyll present in the supplement, was not found in rat livers in the treatment group. Plasma samples were free of xanthophylls. This is the first report proving that β-cryptoxanthin has a higher absorption efficiency than α-cryptoxanthin in rats, at least from a minimally processed oil-based xanthophyll supplement.
Host Specificity of Altica carduorum Guer. Chrysomelidae: Coleoptera , a Defoliator of Cirsium arvense L. Scop. Asteraceae from North-western China

Traditionally, insects are not approved for release in North America as agents for the biological control of weeds if the larvae complete development on desirable plants in no-choice tests. This criterion excludes the use of the leaf-feeding beetle Altica carduroum Guer. since it can complete development on all Cirsium spp. , including rare North American species, although in nature it is only known from the target weed Cirsium arvense. Host suitability is the result of a sequence of selection factors, and this study shows that most discrimination between thistle species is the result of host finding and egg production, and not larval developmental ability. In no-choice tests, the larvae completed development on 18 Cirsium species in five sections of the genus that were tested and on Silybum marianum, but not on other genera in the tribe Cardueae or more distantly related Asteraceae. The adult food consumption on C. arvense was two to eight times greater than on other Cirsium species, many of which, such a.
Cnidae variability in Balanophyllia europaea and B. regia (Scleractinia: Dendrophylliidae) in the NE Atlantic and Mediterranean Sea

Traditionally and for practical reasons, skeleton structure has been the main source of taxonomic characters for scleractinian systematics, whereas information from soft tissues has been comparatively neglected. However, skeleton variability may leave species identification uncertain. The use of characters from soft tissues (e.g. polyp anatomy, cnidae size) is routine in the study of other (“soft”) hexacorallian orders. This contribution aims to determine whether cnidae characters are useful in taxonomic studies of scleractinians. The cnidae composition of two congeneric species— Balanophyllia europaea (Risso, 1826) and Balanophyllia regia Gosse, 1860 have been studied throughout a wide geographical area. The data obtained show consistent qualitative and quantitative differences between the two species. This study shows that the cnidae characters can be useful taxonomic criteria for distinguishing congeneric species.
What can modern statistical tools do for limnology

Freshwater ecology and limnology is no stranger to experiments and data collected at large spatial and temporal scales. Nor is it a stranger to the molecular revolution. As our questions about distributions, abundances, structures and evolution grow in complexity with access to data, we need to stay aware of advances in tools for analysis and visualization. Here I review several advances in statistics and visualisation that might influence the future of limnology and freshwater ecology and evolution.
Etudes d'associations pan-génomiques chez la canne à sucre (Saccharum spp.) : Analyse de la résistance à l'échaudure des feuilles (Xanthomonas albilineans) et à la maladie de la feuille jaune (Sugarcane Yellow Leaf Virus)

Les cultivars modernes de canne a sucre ont un genome particulierement complexe, polyploide et aneuploide. Ils derivent de croisements impliquant un nombre reduit de clones ancestraux (Saccharum officinarum et S. spontaneum), ayant pour consequence un desequilibre de liaison (DL) appreciable chez ces cultivars. Ce travail vise a confirmer la faisabilite d'etudes d'associations exploitant le DL, afin d'identifier des alleles impliques dans le determinisme de la resistance a deux maladies : la feuille jaune (ac. Sugarcane Yellow Leaf Virus), et l'echaudure des feuilles (ac. X. albilineans). Deux populations de pres de 200 cultivars ont ete phenotypees pour la resistance a la feuille jaune, l'une a la Reunion et l'autre en Guadeloupe. Cette derniere a egalement ete phenotypee pour la resistance a l'echaudure des feuilles. Les analyses d'associations ont ete realisees avec pres de 4000 marqueurs (AFLP et DArT), avec differents modeles prenant en compte la structure de la population et les apparentements entre individus. Les marqueurs les plus robustes ont ete selectionnes a un risque d'erreur calcule sur l'ensemble du genome. Une etude de diversite a ete realisee sur un panel de clones ancestraux pour determiner l'origine specifique des marqueurs. Ces analyses ont permis d'identifier 23 marqueurs associes a la resistance a l'echaudure des feuilles, et 30 marqueurs associes a la resistance a la feuille jaune, presentant des R2 individuels de 2,2 a 4%. Des sous-ensembles de 6 a 10 marqueurs expliquent 36 a 51% de la variation phenotypique. La majorite des sources de resistance et de sensibilite est issue de l'espece sauvage S. spontaneum. (Resume d'auteur)
Linolenic acid content in soybean improved by X-ray irradiation.

Dry seeds of soybean [Glycine max (L.) Merr. cv. Bay] were irradiated with X-rays (21.4 kR) and the M2 progeny was evaluated for linolenic acid (18:3) content in the oil. A significant amount of genetic variability was observed for linolenic acid content in the oil of Bay cultivar after X-ray irradiation compared with the control. Out of 3,000 M2 plants, a mutant was identified, M923, in which the linolenic acid content accounted for 4.4 percent, about half the amount of the original variety. An inverse relationship between linoleic acid and linolenic acid contents was observed. The mutant M923 always had lower linolenic acid content in different environmental conditions in the M3 generation.
Deep-fat frying modifies high-fat fish lipid fraction

The lipid composition of three high-fat fishes (sardines, mackerel, and salmon) was analyzed to study the effect of deep-fat frying with sunflower oil and warmholding (65 °C, 3 h). Only sardines increased total fat content with cooking. Saturated fatty acids content decreased, especially in sardines and mackerel, mostly because of the palmitic acid reduction. Raw sardines and mackerel presented an important content of ω-3 polyunsaturated fatty acids (24.0 and 16.6 g/100 g of fat, respectively), but it decreased significantly during frying (6.6 and 5.4 g/100 g of fat, respectively). Salmon, despite having the lower amount of eicosapentaenoic acid and docosahexaenoic acid in raw samples, was the best source of these fatty acids after frying (1.7 g/100 g of food). The ratio of total ω-6 fatty acids to total ω-3 fatty acids increased with cooking from 0.12 to 1.07 in salmon, from 0.12 to 6.19 in mackerel, and from 0.07 to 5.98 in sardines. Cholesterol content was differently affected by frying: it increased .
Increasing Regional Temperatures Associated with Delays in Atlantic Salmon Sea-Run Timing at the Southern Edge of the European Distribution

Abstract Populations of Atlantic salmon Salmo salar at the edge of the species’ distribution are the most vulnerable to environmental changes. Those inhabiting southern European rivers are expected to be particularly affected by global warming. However, they are exploited as a very valuable resource for the region, attracting tourism and generating substantial income. In the central part of northern Spain (Asturias), there is a long tradition of sport fisheries (angling). The first salmon caught in a river each year is called the “campanu. ” Analysis of a 50-year time series demonstrates that the run timing of the Asturian Atlantic salmon has changed over this period, as inferred from significant delays in the date of capture of the campanu. Average campanu weight has experienced a parallel significant decrease but age has not changed, indicating diminution of salmon condition. These changes are statistically associated with an increase in regional temperature, there being a minor effect of the global clim.
Bacterial species selective toxicity of two isomeric α/β-peptides: Role of membrane lipids

We have studied how membrane interactions of two synthetic cationic antimicrobial peptides with alternating α- and β-amino acid residues (“α/β-peptides”) impact toxicity to different prokaryotes. Electron microscopic examination of thin sections of Escherichia coli and of Bacillus subtilis exposed to these two α/β-peptides reveals different structural changes in the membranes of these bacteria. These two peptides also have very different effects on the morphology of liposomes composed of phosphatidylethanolamine and phosphatidylglycerol in a 2:1 molar ratio. Freeze fracture electron microscopy indicates that with this lipid mixture, α/β-peptide I induces the formation of a sponge phase. 31P NMR and X-ray diffraction are consistent with this conclusion. In contrast, with α/β-peptide II and this same lipid mixture, a lamellar phase is maintained, but with a drastically reduced d-spacing. α/β-Peptide II is more lytic to liposomes composed of these lipids than is I. These findings are consistent with the greater toxicity of α/β-peptide II, relative to α/β-peptide I, to E. coli, a bacterium having a high content of phosphatidylethanolamine. In contrast, both α/β-peptides display similar toxicity toward B. subtilis, in accord with the greater anionic lipid composition in its membrane. This work shows that variations in the selectivity of these peptidic antimicrobial peptides toward different strains of bacteria can be partly determined by the lipid composition of the bacterial cell membrane.
Production of Interferon-γ by Chicken T Cells

In mammals, interferon (IFN)-α/β (type I) is typically resistant to exposure to heat and low pH, whereas IFN-γ (type II) is labile. Type I IFN has been described in birds; however, the existence of type II IFN has been questioned. We have generated cloned chicken T cell lines that produce high levels of IFN and have studied the physiochemical properties of this IFN activity to determine whether it represents the type I or type II IFN found in mammals. When incubated at 60°C, the IFN activity present in the supernatants from these chicken T cells was found to be labile, two-thirds of the activity being lost within 1–2 minutes. Consistent with IFN-γ activity, this heat-labile IFN was also sensitive to exposure to pH 2. The heat-resistant IFN lost activity at a much slower rate (half-life >2 h at 60°C) and was also resistant to exposure to pH 2, which is characteristic of IFN-α/β. To confirm further the presence of IFN-γ activity, these T cell supernatants were assayed for their ability to activate macrophag.
Circadian locomotor activity and response to different light conditions in the Volcano mouse, Neotomodon alstoni (Merriam, 1898)

The volcano mouse, Neotomodon alstoni, was studied in order to describe basic circadian behavior during free running and entrainment to parametric and non-parametric photoperiods. Responses to short and long days were also tested to ascertain any potential photoperiodic response. This species is endemic to the high grasslands of central Mexico. Its breeding peaks during summer, indicating a possible circannual regulation of reproduction. Our results indicate that locomotor activity in Neotomodon alstoni is typical of a nocturnal rodent when studied using running wheels, however, when activity was observed in freely moving recordings with no running wheel, locomotor activity shifts to a semidiurnal architecture when exposed to long day photoperiods. When gonadal activity was studied in males exposed to short and long days, significant differences were observed in testis size, nevertheless levels of testosterone and seminiferous tubuli indicated that day length does not inhibit sexual maturity in this species. The results indicated that N. alstoni may not be photoperiodic with regard to gonadal activity, however it does display photoperiodic differences with regard to behavior, body weight and testis size.
CD36 or αvβ3 and αvβ5 Integrins Are Not Essential for MHC Class I Cross-Presentation of Cell-Associated Antigen by CD8α+ Murine Dendritic Cells1

Cross-presentation of cell-associated Ag is thought to involve receptor-mediated uptake of apoptotic cells by dendritic cells (DC), and studies with human DC strongly implicate the endocytic receptor CD36 and the integrins αvβ3 and/or αvβ5 in this process. In the mouse, cross-presentation was recently shown to be a function of CD8α+ DC. Here we report that CD36 is expressed on CD8α+, but not on CD8α−, DC. To address the role of CD36 in cross-presentation we compared CD36−/− and CD36+/+ H-2b DC for their ability to stimulate naive OT-1 T cells specific for OVA plus H-2Kb in the presence of OVA-loaded MHC-mismatched splenocytes as a source of cell-associated Ag for cross-presentation. Surprisingly, no difference was seen between CD36−/− and CD36+/+ CD8α+ DC in their ability to cross-present cell-associated OVA or to capture OVA-bearing cells. Furthermore, the proliferation of CFSE-labeled OT-1 cells in response to OVA cross-presentation in vivo was normal in CD36−/− bone marrow chimeras, also arguing against a necessary role for CD36 in cross-presentation by DC or other APC. DC doubly deficient for β3 and β5 integrins were similarly unimpaired in their ability to cross-present OVA-bearing cells in vitro. These data demonstrate that in the mouse, receptors other than CD36 or β3 and β5 integrins can support the specialized cross-presenting function of CD8α+ DC.
Local adaptation to biotic factors: reciprocal transplants of four species associated with aromatic Thymus pulegioides and T. serpyllum

1 A plant producing secondary compounds may affect the fitness of other plants in the vicinity, and, likewise, associated plants may evolve adaptation to the presence of their ‘chemical neighbour’. Species of the genus Thymus are aromatic plants, well known for their production of aromatic oils whose constitution is dominated by mono‐ or sesquiterpenes. A polymorphism for the production of the dominant terpene in the oil exists both within and between thyme species. 2 Here we examine the effects of two different terpenes produced by Thymus pulegioides and T. serpyllum on the performance of four associated plant species: Achillea millefolium, Agrostis capillaris, Galium verum and Plantago lanceolata. In a reciprocal transplant experiment we studied how plants naturally occurring together with thyme producing either carvacrol or b‐caryophyllene perform on soil treated with these compounds. 3 We found evidence of local adaptation to the ‘home’ terpene. Plants originating from sites where they grow together with carvacrol‐producing thyme plants also perform better on soil treated with carvacrol. One of the associated species (A. millefolium) also showed evidence of local adaptation to the sesquiterpene b‐caryophyllene . 4 Seed germination and root biomass showed an adaptive response to soil treatment. Vegetation analysis supported the results of the reciprocal transplant experiment. When the associated species performed best on ‘home’ soil, thyme and the associated species also showed a positive spatial association at natural sites of origin. Moreover, coefficients of variation in plant traits were significantly lower on ‘home’ soil compared to other soils for both A. capillaris and A. millefolium, but higher for G. verum. 5 Synthesis. Our results show that plant species can adapt to the presence of neighbour plants that produce specific chemical compounds. This supports the idea that local plant communities may be a lot more co‐evolved than was previously thought.
Analysis of the Amylolytic Enzyme System of Clostridium thermosulfurogenes EM1: Purification and Synergistic Action of Pullulanases and Maltohexaose Forming α-Amylase

During growth of C. thermosulfurogenes EM1 on starch, seven forms of pullulanase and one form of α-amylase were detected after gel electrophoretic separation of proteins. By determining the isoelectric points and N-terminal sequences of various pullulanase species it was evident that no structural differences exist between these proteins. These pullulanases hydrolyzed α-1,4- and α-1,6-linkages in various soluble sugar polymers causing their breakdown to maltose and maltotriose. Unlike these enzymes, the α-amylase produced by C. thermosulfurogenes EM1 preferentially attacked non-soluble starch. The main product of hydrolysis was maltohexaose. The combined action of pullulanases and α-amylase on native starch showed synergistic effect. This synergistic effect was not observed if soluble starch was used as substrate. Analyse des amylolytischen Enzymsystems von Clostridium thermosulfurogenes EM1: Reinigung und synergistische Wirkung von Pullulanase und Maltohexaose bildender α-Amylase. Bei Wachstum auf Starke wurden bei Clostridium thermosulfurogenes EM1 sieben Pullulanase-Formen sowie eine α-Amylase mit Hilfe von Polyacrylamid-Gelelektrophorese nachgewiesen. Der isoelektrische Punkt der Pullulanase-Formen war identisch wie auch die N-terminalen Aminosaure-Sequenzen der daraufhin untersuchten Pullulanase-Formen. Die Pullulanasen hydrolysierten α-1,6- und α-1,4-glykosidische Bindungen verschiedener loslicher Kohlenhydrate, so das Maltose und Maltotriose als Endprodukte entstanden. Die α-Amylase hydrolysierte bevorzugt native, unlosliche Starke wobei Maltohexaose das Hauptprodukt war. Mit nativer Starke als Substrat konnte ein synergistischer Effekt bei gemeinsamen Einsatz der Pullulanasen mit der α-Amylase nachgewiesen werden, der bei loslicher Starke als Substrat jedoch nicht beobachtet wurde.
APPLICATION OF UAV AERIAL PHOTOGRAPHY TO TEMPOROSPATIAL ASSESSMENT OF TIDAL

This study is aimed at developing a new technology, which uses an unmanned aerial vehicle (UAV) and digital photography, for the temporospatial geomorphology of intertidal flats. The UAV used in this study can be used for autonomous flights. Because of the tranquility of the water surface of the intertidal flats, the waterline (i.e., water edge) in the UAV aerial photographs corresponds to a very precise contour of the intertidal flats. High-resolution photographs are useful for studying the interrelations between geomorphology and bioactivity in the intertidal flats. The method developed is applicable to not only the geomorphology of natural intertidal flats but also artificial intertidal flats.