Miracle-dz/UniFAR-FTUs huggingface dataset:
MEDIA FOR THE CULTURE OF OCEANIC ULTRAPHYTOPLANKTON 1,2

A medium (K) developed for culturing fastidious oceanic phytoplankton has been tested using recently isolated ultraphytoplankton clones representing at least seven different algal classes. The medium was designed to satisfy as completely as possible the nutritional requirements of this diverse group of phytoplankters. Important aspects are the addition of selenium, the inclusion of both nitrate and ammonium, an increased level of chelation and a moderate level of pH buffering. The seawater‐based version of this medium has been tested on 200 clones of which 186 grew reliably. A synthetic counterpart (AK) was tested on 40 of the more difficult clones and 27 grew well; 13 grew not all. While neither medium meets the exacting nutritional needs of all the ultraphytoplankton forms tested, they are excellent for most oceanic clones and are very successful for the isolation and establishment in culture of new oceanic phytoplankton clones.
PLANT SEEDS: AN EXCITING MODEL SYSTEM FOR DISSECTING MOLECULAR AND CELLULAR REGULATION OF METABOLIC PROCESSES

Metabolic processes are regulated by complex networks of interacting mechanisms that utilize various cellular machineries. Such complex networks may be well exemplified by the synthesis, accumulation, and degradation of storage proteins in developing and germinating seeds. Our laboratories are using plant seeds as a model system for studying the regulation of production of the essential amino acid lysine, the control of synthesis of storage proteins and their transport to the storage vacu- oles, and the de novo formation of new forms of lytic vacuoles in germinating seeds which fuse with the storage vacuoles to enable degradation of the storage proteins and their mobilization into the germinating embryo. We show that: (i) production of lysine in developing seeds is regulated by complex pathways of synthesis and catabolism that involve the sensing of free lysine levels in the seeds, and (ii) analysis of the deposition of storage proteins in seed storage vacuoles and their subsequent degradation during germination provide novel insights into the biogenesis and function of vacuoles in plants.
Enhancement of the thermostability of β-1,3-1,4-glucanase by directed evolution

In order to improve the thermostability of β-1,3-1,4-glucanase, evolutionary molecular engineering was used to evolve the β-1,3-1,4-glucanase from Bacillus subtilis ZJF-1A5. The process involves random mutation by error-prone PCR and DNA shuffling followed by screening on the filter-based assay. Two mutants, EGs1 and EGs2, were found to have four and five amino acid substitutions, respectively. These substitutions resulted in an increase in melting temperature from Tm=62.5 °C for the wild-type enzyme to Tm=65.5 °C for the mutant EGs1 and 67.5 °C for the mutant EGs2. However, the two mutated enzymes had opposite approaches to produce reducing sugar from lichenin with either much higher (28%) for the former or much lower (21.6%) for the latter in comparison with their parental enzymes. The results demonstrate that directed evolution is an effective approach to improve the thermostability of a mesophilic enzyme.
Improved two‐grade delayed particle swarm optimisation (TGDPSO) for inventory facility location for perishable food distribution centres in Beijing

Abstract Resolving inventory and location problems is the most important and fundamental tactical decision in the initial stages of developing a distribution network design. This is especially true for a logistics system dealing with perishable food. To minimise both the total inventory transportation cost of fresh agri‐products and also waste in the supply chain, the evolution of the food supply chain structure is analysed and an inventory location allocation model is presented describing the real‐life problem. The key issues are to describe food demand distribution and to determine the balance of transportation and inventory cost. To improve the quality of the solution, a local search is embedded in the two‐grade delayed particle swarm optimisation. Experimental results demonstrate the algorithm can effectively resolve conflict between different costs and improve development decisions regarding Beijing's perishable food distribution centres.
Genetic analysis of M94 of murine cytomegalovirus

The M94 gene of murine cytomegalovirus (MCMV) is one of the about 40 core genes of the subfamily of β-Herpesvirinae with unknown function. MCMV is utilised as an in vivo model for studying human cytomegalovirus (HCMV) due to the strict species specifity of HCMV and major homologies to MCMV. HCMV is an important human pathogen with worldwide distribution. Although infection of the immune competent host is usually clinically silent, infection of the foetus and the newborn causes severe organ damage and infection of immunocompromised patients induces life-threatening disease. M94 has not been studied intensely as a single gene before, but studies on its homologues in other Herpesviridae demonstrated expression as true late gene, presence in the virion, interaction of UL94 and UL99 in HCMV and capsid binding in α-Herpesvirinae. While UL94 in HCMV is essential, M94 homologues in α-Herpesvirinae are not essential, indicating an essential function of M94 conserved in β-Herpesvirinae but lost in α-Herpesvirinae. For the identification of this essential function, a library of random mutants was generated by a modified Tn7 transposon mutagenesis. The modifications in the transposon mutagenesis produced a library of high diversity and wide coverage containing 32,000 primary clones including stop and insertion mutants. The analysis of 613 clones by sequencing resulted in 399 unique mutants containing a correct 15 base pair (bp) insertion in M94. 116 stop and insertion mutants were individually reinserted into the viral genome and studied in the viral context. The primary analysis showed the ability of certain mutants to complement the M94 deletion, thereby identifying the essential regions in the M94 protein. Secondly, the M94 mutants were re-inserted as second gene and analysed for their inhibitory capacity of the M94 wild type (wt) functions to identify dominant negative (DN) mutants. The inhibitory mutants found were then verified as DN mutants by regulated expression in the virus context and by analysis of their specific phenotype induced by overexpression. Further analysis of the DN mutant in comparison to a M94 deletion mutant revealed no effect of M94 in viral cleavage-packaging, despite previous publications. Additional analysis showed a block in secondary envelopment for both the DN mutant and the deletion mutant and the determination of the spread deficient phenotype of the M94 deletion virus. Altogether these results constitute a new model for secondary envelopment in β-Herpesvirinae.
Potato Root Diffusate Production

Topfversuche werden beschrieben, in denen der Einfluss von Alter, Sorte und Nematodenbefall auf die Wurzeldiffusatproduktion von Kartoffeln untersucht wurde. Die Pflanzen wurden in 15 cm grosse mit grobem Sand gefullte Topfe angezogen und mit 250 ml Wasser bewassert. Die Diffusate wurden im Schlupfversuch mit je 100 Cysten in 5-facher Wiederholung gepruft. Das am starksten aktiv wirkende Diffusat bildete sich bis zu 4 Wochen nach dem Erscheinen der Triebe. Die Pflanzen fullten zu diesem Termin den Topf aus. Nach 6 Wochen nahm die Aktivitat des Wurzeldiffusats ab. Zehn im Handel befindliche Kartoffelsorten wurden gepruft und erbrachten Diffusate von annahernd gleicher Aktivitat. Die Sorten "Eclipse" und "Majestic" zeigten in zwei Jahren eine bessere, "Duke of York" und "King Edward" eine geringere Aktivitat ihres Wurzeldiffusats. Wenn die Kartoffeln in Sand heranwachsen, der mit 21, 45 und 102 Eiern und Larven je g Boden infiziert war, wurde eine erhohte Diffusatmenge aus den Pflanzen erhalten im Vergleich zu den Kontrollpflanzen. Obwohl die starkste Population das kraftigste Wurzelwachstum bis zu 6 Wochen nach dem Erscheinen der Triebe in beiden Jahren hervorrief, kam es zu keinem entsprechenden Ansteigen in der Diffusat-Produktion, im zweiten Jahr war sie sogar vermindert. Ein Vergleich zwischen Kartoffeln und Tomaten zeigte, dass Kartoffeln das meiste Diffusat je Wurzeleinheit bis zwei Wochen nach dem Erscheinen der Triebe produzierten. Es waren Anzeichen vorhanden, dass nach 9 Wochen das umgekehrte Bild eintrat.
The Relative Contributions of Chlorogenic Acid and Rutin to Antioxidant Activities of Two Endemic Prangos (Umbelliferae) Species (P. Heynia and P. Denticulata)

The aim of this study was to investigate the metal chelating, radical-scavenging and anti-lipid peroxidative properties and the chlorogenic acid/rutin contents of two endemic Prangos species; Prangos heyniae H. Duman & M. F. Watson and Prangos denticulata Fisch. & Mey. According to high-performance liquid chromatography analysis, the highest rutin and chlorogenic acid contents were found in P. denticulata leaf methanol extract (33.6 ± 2.8 μg/mg extract) and P. heyniae leaf methanol extract (24.8 ± 0.2 μg/mg extract), respectively. The water and methanol extracts of the species showed high scavenging abilities and significant capacities to suppress lipid peroxidation. These results demonstrated that chlorogenic acid may be an important component in the antioxidant activities of these Prangos species. Practical Applications Prangos Lindl. (Umbelliferae) species are known as “Caksir otu” in Turkey and used to make herbed cheese to give the desired aroma and taste. Young shoots of Prangos species are used as boiled vegetables and pickles. Prangos species have been used in folk medicine as emulient, carminative, to stop bleeding and heal the scars. The results demonstrated that the extracts of two Prangos species exhibited good antioxidant activity, which correlated with high polyphenol content. Therefore, they may be used as a potential source of natural antioxidants for food supplementation or development of nutraceuticals.
How landscape structure, land-use intensity and habitat diversity affect components of total arthropod diversity in agricultural landscapes

1. Agricultural intensification poses a serious threat to biodiversity as a consequence of increased land-use intensity, decreased landscape heterogeneity and reduced habitat diversity. Although there is interest in the preservation of total species richness of an agricultural landscape (γ diversity), the effects of intensification have been assessed primarily by species richness at a local scale (α diversity). This ignores species richness between local communities (β diversity), which is an important component of total species richness. 2. In this study, measures of land-use intensity, landscape structure and habitat diversity were related to γ, α and β diversity of wild bees (Apoidea), carabid beetles (Carabidae), hoverflies (Syrphidae), true bugs (Heteroptera) and spiders (Araneae) within 16 local communities in 24 temperate European agricultural landscapes. 3. The total landscape species richness of all groups was most strongly affected by increased proximity of semi-natural habitat patches. Bees also decreased in landscapes with a high intensity of farmland management, demonstrating additive effects of both factors. 4. Separating total species diversity into components, the decrease in total species richness could be attributed primarily to a decrease in species diversity between local communities. Species richness of the local communities of all investigated groups decreased with increasing land-use intensity and, in the case of spiders, decreasing proximity of the semi-natural habitat patches. 5. The effect of increased habitat diversity appeared to be of secondary importance to total species richness but caused a shift in the relative contribution of α and β diversity towards the latter.
Hollow occurrence and abundance varies with tree characteristics and among species in temperate woodland Eucalyptus

Tree hollows are a critical but diminishing resource for a wide range of fauna around the world. Conservation of these fauna depends on sustainable management of tree species that produce the hollows on which they depend. This study addressed the need for empirical data about intraspecific and interspecific variation in hollow occurrence and abundance in woodland trees in Australia. We measured and performed hollow surveys on 1817 trees of seven species of woodland Eucalyptus in central-western New South Wales, Australia. Trees were surveyed at 51 one-hectare sites and about 30% of trees surveyed had multiple stems. Generalized linear mixed models that accounted for nestedness of stems within trees and trees within sites detected a significant amount of variation in hollow occurrence and abundance. Models for individual tree stems of live trees showed hollow probability and abundance increased with diameter at breast height (DBH) and with increasing senescence (form). Stems of Eucalyptus microcarpa Maiden had a higher probability of having hollows than similar DBH stems of Eucalyptus camaldulensis Dehnh. , Eucalyptus melliodora A.Cunn. ex Schauer or Eucalyptus populnea ssp. bimbil L.A. S.Johnson & K.D. Hill. Dead stems in live trees were more likely to have hollows than live stems of similar DBH. Each stem in a multi-stemmed tree had a lower probability of hollow occurrence and lower abundance of hollows than single-stemmed trees of similar DBH. For stems of dead trees, hollow occurrence and abundance increased with DBH and differed depending on stage of senescence. A comparison of our data with other studies indicates regional variation of hollow abundances within tree species.
MOLECULAR CHARACTERIZATION AND GENETIC DIVERSITY IN FINE GRAIN AND AROMATIC LANDRACES OF RICE (Oryza sativa L.) USING MICROSATELLITE MARKERS

A total of thirty microsatellite molecular markers were used across 21 rice genotypes for their characterization and discrimination. The number of alleles per locus ranged from three (RM165, RM219, RM248, RM463, RM470 and RM517) to nine (RM223), with an average of 4.53 alleles across the 30 loci obtained in the study. The polymorphism information content (PIC) values ranged from 0.30 (RM219) to 0.84 (RM223) in all 30 loci. RM223 was found the best marker for the identification of 21 genotypes as revealed by PIC values. The frequency of the most common allele at each locus ranged from 24% (RM223 and RM334) to 81% (RM219). A two dimensional principal coordinate analysis (PCoA) with 21 genotypes showed that the genotypes Supper Basmoti, Basmati370, BasmatiD, Keora, Chinisakkora, Thakurbhog, Benaful, Kolgochi, Buchi, Awnedtapl and Kalijira-11 were found far away from centroid of the cluster than rest of the genotypes which placed around the centroid. The pair-wise genetic dissimilarity coefficients indicated that the highest genetic distance was obtained between Thakurbhog and Supper Basmoti (0.81) as well as between Benaful and Keora (0.81). Basmati (Basmoti D, Super Basmati, Basmati 370) and Kalijira (Kalijira 11, 12, 13, 14) genotypes had close similarity among them but showed wide dissimilarity with other local genotypes. Being grouped into distant clusters, SupperBasmoti, Thakurbhog, Keora, and Benaful could be utilized as potential parents for the improvement of fine grain aromatic rice varieties. Genotypes Kolgochi and Buchi (having zero dissimilairty) might be possessed same genetic background. The microsatellite marker based molecular fingerprinting could serve as a sound basis in the identification of genetically distant accessions as well as in the duplicate sorting of the morphologically close accessions.
Experimental brown spider bite in the guinea pig: Results of treatment with dapsone or hyperbaric oxygen

The brown recluse spider (Loxosceles reclusa) is a common inhabitant of the central United States. Loxoceles envenomation is a cause of significant medical problems, causing a necrotic skin lesion that often becomes a problem wound. Treatment of the skin lesion is controversial, with no current widely accepted therapy. The effects of treatment with hyperbaric oxygen or dapsone on brown spider bites were studied using guinea pigs. Progression and healing of experimental brown spider bites were measured in animals treated or pretreated with dapsone or hyperbaric oxygen and in controls. There was a significant decrease in lesion size in animals pretreated with hyperbaric oxygen at days 3,5, and 6 as compared to dapsone-pretreated animals or untreated controls. However, there were no differences noted between groups when treatment was begun 36 h after envenomation. There was a nonsignificant increase (p = 0.12) noted in myeloperoxidase levels from lesions of animals pretreated with hyperbaric oxygen. No other differences in levels of catalase, glutathione, or superoxide dismutase activity were noted between treatment groups. These results suggest that hyperbaric oxygen may have potential in the treatment of brown spider bites; however, further study is necessary to prove its efficacy.
Characterization and Modeling of Itchgrass (Rottboellia cochinchinensis) Biphasic Seedling Emergence Patterns in the Tropics

Abstract Itchgrass is an aggressive weed species in tropical agroecosystems. Because of phytosanitary restrictions to exports, pineapple producers must use a zero tolerance level for this species. An understanding of itchgrass seedling emergence would help producers to better time POST control. The objective of the present study was to characterize itchgrass seedling emergence patterns and develop a predictive model. Multiple field experiments were conducted in four agricultural fields in Costa Rica between 2010 and 2011 for a total of 9 site-years. Itchgrass consistently showed a biphasic emergence pattern, with a first emergence phase that was faster and more consistent across site-years than the second one. Weibull + logistic models based on chronological time (R2adj = 0.92) and thermal time with Tbase = 20 C (R2adj = 0.92) provided the best fit for the combined emergence data for two experimental locations in 2010. Both models predicted itchgrass seedling emergence adequately for most site-years, but the thermal-time model was more accurate (R2adj = 0.64 to 0.86) than the chronological model (R2adj = 0.31 to 0.74), especially when temperatures were high. Both models showed high accuracy in the first emergence phase but tended to underestimate emergence rate during the second phase. The models predicted 50% emergence at 14 d or 80 growing degree days and the stabilization of the first emergence phase at approximately 25 d or 200 growing degree days. Thus, these models can be used to properly time itchgrass POST control. More research is needed to understand the regulatory mechanisms responsible for the variability of the second emergence phase. Nomenclature: Itchgrass, Rottboellia cochinchinensis (Lour.) W.D. Clayton, pineapple, Ananas comosus (L.) Merr.
Mode of resistance to respiration inhibitors at the cytochrome bc1 enzyme complex of Mycosphaerella fijiensis field isolates

Field isolates of Mycosphaerella fijiensis, causing black Sigatoka of banana, were characterised for their sensitivity to different inhibitors of the cytochrome bc1 enzyme complex (Qo respiration inhibitors, strobilurin fungicides), using physiological, biochemical and molecular genetic methods. Strobilurin-resistant isolates exhibited very high resistance factors both in mycelial growth inhibition and NADH consumption assays. Cross-resistance was observed among all Qo inhibitors, including trifloxystrobin, azoxystrobin, famoxadone, strobilurin B and myxothiazol. However, the Qi and the cytochrome aa3 inhibitors, antimycin A and potassium cyanide, respectively, were not cross-resistant to Qo inhibitors. In sensitive but not in resistant isolates, mixtures of Qo inhibitors and SHAM, an inhibitor of the alternative oxidase (AOX), were more active than the components alone, indicating that the alternative pathway is essential in metabolism, but not causal for resistance. In the cell-free NADH-consumption assay, the Qo inhibitors affected the sensitive but not the resistant isolates, suggesting that AOX was not active in sub-mitochondrial particles. In whole cells, however, the AOX has a basic expression level and is probably not inducible by trifloxystrobin. Sequencing of the cytochrome b gene of sensitive and resistant M fijiensis isolates revealed a difference in the nucleotide sequence leading to a single amino acid change from glycine to alanine at position 143 in the resistant isolate. This change is known to occur also in the naturally tolerant basidiomycete Mycena galopoda. It is suggested that the field isolates of M fijiensis can acquire resistance to Qo inhibitors due to a target site alteration with a single base pair change. Resistant isolates do not seem to contain a mixture of mutated and non-mutated DNA, indicating a complete selection of resistant mitochondria and a maternally donated mode of resistance. © 2000 Society of Chemical Industry
Chemical Composition and Antimicrobial Variability of Satureja montana L. Essential Oils Produced During Ontogenesis

Abstract The essential oils obtained from Satureja montana L. harvested in central part of Dalmatia (Croatia) at three ontogenical stages were evaluated for their chemical composition and antimicrobial activity. GC/MS analyses revealed the presence of 33 compounds in the oils. Carvacrol (52.4>26.2>16.1%) was found to be the main constituent especially before flowering while p-cymene (3.8<15.2<25.6%) increased through flowering. The antimicrobial activity of S. montana oils against five Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella typhi), four Gram-positive bacteria (Bacillus subtilis, Bacillus cereus, Staphylococcus aureus, Streptococcus faecalis) and five pathogenic fungi (Aspergillus fumigatus, Aspergillus niger, Candida albicans, Candida rugosa and Saccharomyces cerevisiae) was evaluated using the agar-plate dilution assay. The oil showed the strongest activity against all tests strains, with the exception of Pseudomonas aeruginosa. The maximum activity was observed against E. coli, S. aureus and fungal organisms. Escherichia coli had the lowest MIC of 0.06% with oils produced before and during the flowering period. These results support the notion that S. montana oil has a role as both a pharmaceutical and a preservative.