Miracle-dz/UniFAR-FTUs huggingface dataset:
Population genetics of Tuberolachnus salignus, an obligate parthenogenetic aphid

1 This study reports the results obtained in an investigation of the putatively parthenogenetic aphid species Tuberolachnus salignus Gmelin. Tuberolachnus salignus is one of the largest aphid species in the world but where and how it overwinters is not known. It has recently become noteworthy because it is increasingly found on commercially grown willows used in bioenergy production. 2 Seven newly‐developed polymorphic microsatellite markers were used to investigate the genetic diversity of the species, and also to confirm its reproduction strategy. 3 Tuberolachnus salignus shows very low clonal diversity; only 16 genotypes were found in 660 specimens from 27 populations in five countries. 4 There was limited geographical structuring in the samples, although the two most common genotypes, which comprised more than half of the specimens collected, had a very wide distribution. 5 Furthermore, we determined that these aphids, which live in very dense colonies, can consist of more than one genotype, suggesting aggregation of colonizing T. salignus. These results confirm the parthenogenetic nature of T. salignus and demonstrate the presence of common genotypes that are widespread in time and space.
Vegetative and reproductive anatomy of some Laurencia (Ceramiales, Rhodophyta) species with a description of L. maris-rubri sp. nov. from the Red Sea

Abstract The vegetative and reproductive anatomy of some species of Laurencia Lamouroux (Ceramiales, Rhodophyta) belonging to the subgenus Chondrophycus Tokida et Saito [L. tumida Saito et Womersley, L. intermedia Yamada, L. capituliformis Yamada and L. maris-rubri sp. nov.] have been investigated using type and additional material from Australia, Korea, Japan and the Red Sea. The species share several features: (1) vegetative axial segments with two pericentral cells, (2) procarp-bearing segments with four pericentral cells, the fourth of which becomes the supporting cell of the carpogonial branch, (3) tetrasporangia produced from the second pericentral cell of fertile axial segments and (4) the production of additional tetrasporangium-bearing pericentral cells. An assessment of these anatomical features suggests that the occurrence of two pericentral cells in vegetative axes provides a stable basis for delimiting the subgenus Chondrophycus from the subgenus Laurencia, in which four pericentral cells are.
A Cryoprotective Lectin Reduces the Solute Permeability and Lipid Fluidity of Thylakoid Membranes

Abstract It has recently been shown that some galactose-specific plant lectins protect thylakoid membranes from freeze–thaw damage [D. K. Hincha et al. Plant Physiol. 103, 59–65 (1993)]. In the present investigation, the Ricinus communis seed lectins RCA 60 and RCA 120 have been used to investigate further the effects of lectin binding on the physical properties of thylakoids. Both proteins bind to digalactolipids, but only RCA 60 is cryoprotective. We found that RCA 60 reduced the glucose permeability of the membranes. Fluorescence depolarization measurements with the probe trimethylammonium-diphenylhexatriene (TMA-DPH) showed a significant reduction of lipid fluidity in the presence of RCA 60 , but not with RCA 120 . The fluidity of the hydrocarbon core region of thylakoids, as probed with DPH, was not influenced. These results were corroborated by electron spin resonance spectroscopy using doxyl stearic acids (DSA) with the reporter group located in position 5, 12, or 16 of the fatty acyl chains. Clear effects of RCA 60 were only apparent with 5DSA. When we used the fluorescence probe merocyanine 540 to investigate the lipid packing density in the glycerol backbone region of the membrane, we found a decrease in fluorescence emission in the presence of RCA 60 . We conclude from these data that cryoprotective lectins lead to changes in the packing of the membrane lipids in the interfacial region which result in a lower solute permeability of the membranes.
Removal of mango inflorescence increases fruit set and does not affect yield (Mangifera indica cv. Cogshall)

Mango is the fifth fruit in the world in regards to production volume. Although this has increased strongly in the past 15 years, yields are still low and irregular. The most frequent hypothesis found in the literature to explain this is that the availability of carbohydrate can limit the formation of reproductive organs and growth and that high carbon mobilization during flowering can limit sugar availability for fruit growth. Furthermore, a long fruit growth period could reduce the formation of flowering twigs. A one-year experiment was carried out at CIRAD research station in Reunion Island with the objective to reduce energy loss during flowering to optimize, at tree level, source/sink relationships during fruit growth. As compared to control trees (with no removal of inflorescence) and trees where the distal half of each inflorescence was removed, removing 50% of the inflorescences increased fruit set and maintained yield and fruit size.
How tissues tell time

A circadian clock in peripheral tissues regulates physiological functions through gene expression timing. However, despite the common and well studied core clock mechanism, understanding of tissue-specific regulation of circadian genes is marginal. Overrepresentation analysis is a tool to detect transcription factor binding sites that might play a role in the regulation of co-expressed genes. To apply it to circadian genes that do share a period of about 24 hours, but differ otherwise in peak phase timing and tissue-specificity of their oscillation, clear definition of co-expressed gene subgroups as well as the appropriate choice of background genes are important prerequisites. In this setting of multiple subgroup comparisons, a hierarchical method for false discovery control reveals significant findings. Based on two microarray time series in mouse macrophages and liver cells, tissuespecific regulation of circadian genes in these cell types is investigated by promoter analysis. Binding sites for CLOCK:BMAL1, NF-Y and CREB transcription factors are among the common top candidates of overrepresented motifs. Related transcription factors of BHLH and BZIP families with specific complexation domains bind to motif variants with differing strengths, thereby arranging interactions with more tissue-specific regulators (e.g. HOX, GATA, FORKHEAD, REL, IRF, ETS regulators and nuclear receptors). Presumably, this influences the timing of pre-initiation complexes and hence tissue-specific transcription patterns. In this respect, the content of guanine (G) and cytosine (C) bases as well as CpG dinucleotides are important promoter properties directing the interaction probability of regulators, because affinities with which transcription factors are attracted to promoters depend on these sequence characteristics.
Ornament and body size variation and their measurement in natural populations

Measurement of intrapopulation variation in secondary sexual traits is a priority in the testing of sexual selection models. However, it is important to take care in the choice of materials and delimitation of populations. The use of museum skins to study variation in male tail ornaments may substantially underrepresent the real degree of intrapopulation variation. Data from live animals in specific areas provide more realistic estimates, and should be used whenever possible. I use as an example field data on male ornament length and body size in Vidua macroura (Aves: Ploceidae), a promiscuous, parasitic African finch with elongated tail plumes. Individual males differ in the timing and rate of ornament growth, and females are therefore faced with a large degree of phenotypic variation in male ornament size, even though genetic variation may not be great. By correcting for seasonal variation in the ornament lengths of males caught at different times, I show that mid-season coefficients of variation in ornament length of breeding males in two populations are as high as 18% and 55%. By contrast, tarsus, wing and unornamented tail lengths of the same males vary from 2 to 4%.
Identification of Bacterial Pathogens in Biofilms of Recirculating Aquaculture Systems

Abstract Biofilms are capable of forming on all aquaculture system components, incorporating the various microflora present in the water. Pathogenic bacteria released from the biofilms are potentially capable of causing recurring diseases. Seven recirculating freshwater and two recirculating saltwater facilities were sampled, with eight different types of materials tested. Pathogenic bacteria were identified using standard bacteriological methods and commercial kits. The most significant human pathogens were Bacillus cereus, Shigella spp. and Vibrio spp. The major piscine pathogens of concern were Photobacterium damsela, Vibrio spp. , and Aeromonas hydrophila. The most significant variation in biofilm pathogen occurrence was observed between facilities and not between construction materials. This study implicates biofilms as another reservoir for pathogenic bacteria in recirculating aquaculture systems.
Comparative seed morphology of Thuja occidentalis (eastern white cedar) from upland and lowland sites

As part of an investigation of the extent of habitat-specific variation in Thuja occidentalis L. , cones were collected from cliff (dry upland) and swamp (wet lowland) sites in southern Ontario. The number of seeds per cone, number of fully developed seeds per cone, seed fresh weight, length, and width, length and width of embryo area, and length and width of right wing were determined. Seed yield on a per cone basis did not vary between habitat types or among sites within habitats. There was, however, significant variation among trees within sites. Individual seed characters did not vary between habitat types, but significant variation existed among sites within habitats, among trees within sites, and among cones within trees. Only the width of right wing failed to show cone to cone variation within individual trees. The majority of explainable variance for all characters could be apportioned to trees within sites. This and a relatively low degree of cone to cone variation suggest that the seed morphologi.
Energy allocation in response to reduced food intake in pregnant and lactating laboratory mice

An empirical and modeling approach was taken to the study of the mechanisms of energy allocation in small mammals. Feeding trials were conducted to provide data on the relationship between body weight, body composition, milk production, and food intake in white laboratory mice (Mus musculus). Pregnant and lactating females were fed ad libitum and at five levels of reduced intake during gestation only, gestation and lactation, and lactation only.
Efficacy of Selected Insecticides Against the South American Tomato Moth, Tuta absoluta Meyrick (Lepidoptera: Gelechiidae) on Tomato in the Central Rift Valley of Ethiopia

Occurrence of the tomato leaf miner, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) in Ethiopia was confirmed following heavy infestation of tomato, Solanum lycopersicum L. , in the Central Rift Valley (CRV) region of Ethiopia in February 2013. The pest wiped out tomato plantations, causing 100 % crop loss for some producers. This was despite the use of a variety of insecticides locally available to manage other vegetable insect pests. In this study, 10 insecticides from different insecticide classes including pyrethroids, organophosphates, spinosyns, insect growth regulators and diamides were screened for their efficacy against T. absoluta using a randomized complete block design with two different planting dates in 2013. The mean fruit infestation in the untreated control plot ranged between 54 and 76 %. In plots treated with diamide insecticides (chlorantraniliprole) fruit infestation was significantly lower with 2–6 % fruit damage followed by spinosyns (spinetoram and spinosad) with 30–35 % damage. A similar trend was observed in leaf damage severity. Mean marketable and total yield from the best performing treatment, Ampligo (a mixture of a diamide and a pyrethroid), were 18.4 and 31.9 t/ha, respectively. The corresponding marketable and total yields from the untreated plot were 3.2 and 13.5 t/ha. This corresponds to yield losses of 82.6 and 57.7 % in marketable and total yield, respectively. T. absoluta has the potential to develop pesticide resistance very quickly due to short generation time and high reproductive potential. Insecticides found effective need to be used judiciously including the rotation of effective insecticides from different classes. Future research on the management of this pest should focus on developing a biocontrol based integrated pest management system.
Influence of young poplar stands on floristic diversity in agricultural landscapes (Sweden)

Abstract Floristic diversity in 21 small short-rotation poplar plantations, 0.1 to 13 ha in size and aged 6 to 14 yr, was compared with adjacent agricultural fields of various crop types. The poplars were grown on former agricultural land and most of the study sites were located in southern and central Sweden. Surveys of ground vegetation were carried out by using nested quadrats (plots of 0.25 and 0.016 m 2 size) located along normally five transects running perpendicular to the habitat boundaries. Mean cumulative species number across all sites (all transects and plots included) was around 20 and similar in poplar stands and arable fields. However, the two habitat types shared only 3 to 12 species (mean: 8 species). Mean species number per survey plot was 4.5 in poplar stands compared to 5.3 in arable fields. Classification (TWINSPAN) and Detrended Correspondence Analysis (DCA) showed some floristic separation of the two habitat types. The results were interpreted in a landscape context. Mainly based on the low quantity of species shared by poplar stands and adjacent arable fields, the results support the hypothesis that small-scale poplar plantations increase floristic diversity in landscapes dominated by agriculture. Compared to old-growth mixed deciduous forests in different regions of Sweden, species richness of poplar plantations was similar or lower. Die floristische Artenvielfalt in 21 kleinflachigen Pappelbestanden (0,1–13 ha) im Kurzumtrieb wurde mit derjenigen benachbarter cker verglichen. Die Pappeln waren 6–14 Jahre alt und wuchsen auf ehemaligen Ackerflachen, vorwiegend in Sud- und Mittelschweden (ein Standort in Nordschweden). Die Bodenvegetation wurde mit Hilfe ineinander geschachtelter Aufnahmequadrate erfasst (Aufnahmeflachen 0,25 und 0,016 m 2 ). In jedem Bestand und Feld wurden funf parallel zueinander liegende Transekte angelegt, die senkrecht vom Bestandesrand ins Bestandesinnere verliefen. In jedem Transekt lagen in definierten Abstanden zum Bestandesrand funf Aufnahmeflachen. Die mittlere Gesamtartenzahl uber alle Bestande war 20 und etwa gleich in Pappelbestanden und ckern. Allerdings waren nur zwischen 3 und 12 (Mittelwert: 8) Arten gemeinsam in Pappelbestanden und benachbarten ckern. Die Artenanzahl pro Aufnahmeflache war kleiner in Pappelbestanden als in ckern. Klassifikation (TWINSPAN) und Ordination (DCA) zeigte eine gewisse Trennung der beiden Vegetationstypen. Die Ergebnisse wurden auf Landschaftsebene interpretiert und stutzen die Hypothese, dass kleinflachige Pappelplantagen die floristische Artenvielfalt v.a. in intensiv genutzter Agrarlandschaft erhohen kann. Im Vergleich zu naturlichen Laubmischwaldern verschiedener Regionen Schwedens war die Artenvielfalt in den Pappelplantagen entweder ahnlich (ostliches Mittelschweden) oder niedriger (Sudostschweden).
Desempenho agronômico e econômico do milho em diferentes níveis de manejo e épocas de semeadura

The objective of this work was to evaluate agronomic and economic performance of maize in five management levels and three sowing times. The experiment was conducted in 2001/2002 and 2002/2003, in Eldorado do Sul, RS, Brazil. Treatments consisted of three sowing times (August, October and December) and five management levels (low, average, high, potential I and II) which varied in relation to the soil winter cover, cultivar, plant arrangement and the level of chemical fertilizer, water supply and weed, insect and disease control. A randomized block design was used with split-plots and four replications. Sowing times were located in the main plots and the management level in the split-plots. The increments in maize yield in response to investments in management and cultivar were higher in August and October, and resulted in higher economic return, mainly in October. In December sowing, there was no economic return for the highest investment in management level. In August and October, it was possible to associate maximal economic and technical efficiencies through the management level increase and the choice of the greater potential yield cultivar. Index terms: Zea mays, agronomic and economic efficiency, cultivars, water regime, grain yield, gross margin.
Sugar brews and the chorleywood bread process

The use of sugar brews in a mechanical development process for the production of English-type bread was examined. In the absence of ascorbic acid as dough improver, the great improvement given to bread volume and softness by a strong brew with high yeast content was somewhat diminished when the yeast content was decreased to a normal level, and marginally further diminished when its starting sugar content was also reduced. These reductions overcame some disadvantages of the original brew and the brew effect was still appreciable, the bread being quite good provided that the flour had received normal bleaching and oxidising treatment at the mill. With untreated flour, other process modifications were necessary for the production of acceptable brew bread without a chemical improver. Even a strong brew only partly replaced flour treatment and oxidising improver simultaneously. With normally treated flour, the strongest brew had a favourable effect on the work input requirement at dough mixing and reduced the need for intermediate proof. The former advantage was lost when the strength of the brew was decreased, and the latter was diminished when the yeast content of the dough was decreased.
EFFECT OF PHOSPHORYLATION ON THE RETENTION BEHAVIOR OF PEPTIDES IN ION PAIRING REVERSED-PHASE HPLC BASED ON A PREDICTION MODEL

A prediction model of the peptide retention time was developed on the basis of 358 non-phosphorylated peptides, which had various amino acid residues in the C-terminal from the casein pancreatic hydrolysates. This model was applied to predict the retention times (RT) of another 43 peptides on C4 reversed phase columns with trifluoroacetic acid (TFA) as the ion-pairing reagent, with a relatively high R2 value (0.969). Furthermore, the experimental RTs of 32 phosphopeptides were compared with the predictive RTs of their non-phosphorylated cognates. Mono- and poly-phosphopeptides seemed to elute after or before the non-phosphorylated predictive cognates, respectively. The positive charges of peptides were partly masked by the ion-pairing reagent TFA. Single and multiple phosphorylation might generally lead to an increase or reduction in the overall hydrophobicity of peptides, respectively.
Genome size as a determinant of growth and life-history traits in crustaceans

Genome size varies tremendously both within and among taxa, and strong correlations between genome size and various physiological and ecological attributes suggest that genome size is a key trait of organisms, yet the causalities remains vague. In the present study, we tested how genome size is related to key physiological and ecological properties in five large orders of crustaceans: Decapoda, Cladocera, Amphipoda, Calanoida, and Cyclopoida. These span a wide range in sizes, habitats and life-history traits. To some extent, genome size reflected phylogenetic footprints but, generally, a very wide range in genome size was found within all orders. Genome size was positively correlated with body size in Amphipoda, Cladocera, and Copepoda, but not for Decapoda in general. This could indicate that the evolution of body size occurs mainly by changing cell size for the three first orders, whereas it is more attributed to cell numbers for Decapoda. Cladocera, with direct development and a high growth rate, have minute genomes compared to copepods that possess a more complex life history, whereas, within Decapoda and Amphipoda, developmental complexity is not related to genome size. The present study suggests that, within the crustaceans, selection for a wide variety of life-history strategies has led to widely different genome sizes. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 393–399.
Antibiotic Resistance and Slime Production in Coagulase-Negative Staphylococcus Strains from Retail Meat Samples

In this study, a total of 100 retail meat samples were analysed for the presence of coagulase negative Staphylococcus (CoNS). A total of 208 CoNS strains were isolated from these samples. Staphylococcus saprophyticus was the most prevalent species. Resistance to methicillin was detected in 63.4% of CoNS isolates. Methicillin-resistant CoNS (MRCoNS) strains were determined to be more resistant to antibiotics than methicillin-susceptible CoNS strains. Resistance of methicillin was found in 76.1% of slime positive and in 57.4% of slime negative strains. Most of isolated slime producing CoNS were methicillin resistant, which makes the detection of these microorganisms necessary to prevent their dissemination in the environment, veterinary medicine and public health.
Predicting performance and survival across topographically heterogeneous landscapes: the global pest insect Helicoverpa armigera (Hübner, 1808) (Lepidoptera: Noctuidae)

Species distribution models provide a means of better understanding how climate constrains the survival of organisms. Although effective in predicting the presence or absence of species across the landscape, model outputs are not necessarily relevant to, or easily interpreted for, local management and conservation programs. An alternative approach, however, would be to use species distribution models as a tool for applied ecological projects. Integrative pest management programs, for example, which aim to control the abundance and distribution of agricultural insect pests may benefit from a model that predicts the relative performance and survival of the target pest on its host plant. We present a microclimate model to predict ambient, and thus the equilibrium body, temperature of the globally significant agricultural pest the bollworm, Helicoverpa armigera. We allow the different life‐history stages of H. armigera to select specific microclimates within a host apple tree, thus developing a realistic framework for predicting core‐body temperatures, and proxies for physiological performance and fitness, of this species. Subsequently, we incorporate the predicted body temperature with established data for developmental rates and critical‐temperature thresholds to predict how fluctuations in temperature and variation in topography may affect phenology and survival. Although the model requires further validation against empirical data, the current outputs allow insights into how variation in local topography, farming practices and climate change will affect the relative phenology and survival of H. armigera. Moreover, the biophysical nature of the model means that with some modifications to parameter inputs, the fitness and survival of a range of pest insects on their host plants can be explored more readily.