Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Microbially Reducible Fe(III) on the Bacterial Community Structure of Estuarine Surface Sediments

We analyzed PCR-amplified 16S rRNA genes from native and Fe(III)-enriched surface sediments of a major tidal channel in the Tijuana River Estuary, California, USA. Clones from native sediments were most closely affiliated with photosynthetic taxa (Cyanobacteria, Chloroflexi, and Halochromatium) and microorganisms known to reduce (Desulfatibacillus, Desulfobacterium, and Desulfuromusa) or oxidize (Microcoleus, Phormidium, and Halochromatium) various sulfur species, reflective of the fluctuating redox conditions in the tidal zone. Fe(III) was rapidly reduced in anaerobic microcosms amended with 2-line ferrihydrite, with or without the sulfate reduction inhibitor sodium molybdate. The addition of ferrihydrite without molybdate caused a major shift in community structure to a dominance of the Fe(III)-reducing genus Shewanella, while at the same time the sulfate-reducing and sulfide-oxidizing populations were replaced by taxa known to cycle elemental sulfur. Sediments amended with both ferrihydrite and molybdate were again populated by Shewanella clones, but also numerically important were clones most similar to Marinobacterium, Pseudomonas, and Bacillus, suggesting a role for these taxa in Fe(III) reduction in marine habitats.
The Diet of Eurasian Otters in the Jajrood River System, Iran

Abstract The diet and feeding habits of Eurasian otters (Lutra lutra) were studied by spraint analysis over a one year period on the four sections of the Jajrood River, eastern Tehran. Two methods were used to estimate the proportions of different prey consumed: frequency of occurrence and score-bulk estimate. The number of prey categories in a spraint varied between one and four. Fish, crabs, birds and insects were found in the spraints. Fish is the main prey. Otters mainly eat fish, preferring three species: the chub (Leuciscus cephalus), riffle minnow (Alburnoides bipunctatus) and various barbel (Capoeta spp.) species. The otters' diet differed significantly across four sites positive for otter sign. Seasonal variation was also found: birds were taken more in the cold season and insects in the warm season. The proportion of crab in the diet was almost constant throughout the year. Leuciscus cephalus was the most taken fish species in the cold season and Capoeta spp. in the warm season. Only L. Cephalus appeared to be preferred. There was no significant correlation between the estimated proportion of fish in the diet and relative prey fish population at any of the four studies sites.
Plant mitochondrial F0F1 ATP synthase

Spinach leaf mitochondrial F0F1 ATPase has been purified and is shown to consist of twelve polypeptides. Five of the polypeptides constitute the F1 part of the enzyme. The remaining polypeptides, with molecular masses of 28 kDa, 23 kDa, 18.5 kDa, 15 kDa, 10.5 kDa, 9.5 kDa and 8.5 kDa, belong to the F0 part of the enzyme. This is the first report concerning identification of the subunits of the plant mitochondrial F0. The identification of the components is achieved on the basis of the N-terminal amino acid sequence analysis and Western blot technique using monospecific antibodies against proteins characterized in other sources. The 28-kDa protein crossreacts with antibodies against the subunit of bovine heart ATPase with N-terminal Pro-Val-Pro- which corresponds to subunit F0b of Escherichia coli F0F1. Sequence analysis of the N-terminal 32 amino acids of the 23-kDa protein reveals that this protein is similar to mammalian oligomycin-sensitivity-conferring protein and corresponds to the F1δ subunit of the chloroplast and E. coli ATPases. The 18.5-kDa protein crossreacts with antibodies against subunit 6 of the beef heart F0 and its N-terminal sequence of 14 amino acids shows a high degree of sequence similarity to the conserved regions at N-terminus of the ATPase subunits 6 from different sources. ATPase subunit 6 corresponds to subunit F0a of the E. coli enzyme. The 15-kDa protein and the 10.5-kDa protein crossreact with antibodies against F6 and the endogenous ATPase inhibitor protein of beef heart F0F1-ATPase, respectively. The 9.5-kDa protein is an N,N′-dicyclohexylcarbodiimide-binding protein corresponding to subunit F0c of the E. coli enzyme. The 8.5-kDa protein is of unknown identity. The isolated spinach mitochondrial F0F1 ATPase catalyzes oligomycin-sensitive ATPase activity of 3.5 μmol · mg−1· min−1. The enzyme catalyzes also hydrolysis of GTP (7.5 μmol · mg·1· min−1) and ITP (4.4 μmol · mg−1· min−1). Hydrolysis of ATP was stimulated fivefold in the presence of amphiphilic detergents, however the hydrolysis of other nucleotides could not be stimulated by these agents. These results show that the plant mitochondrial F0F1 ATPase complex differs in composition from the other mitochondrial, chloroplast and bacterial ATPases. The enzyme is, however, more closely related to the yeast mitochondrial ATPase and to the animal mitochondrial ATPase than to the chloroplast enzyme. The plant mitochondrial enzyme, however, exhibits catalytic properties which are characteristic for the chloroplast enzyme.
Colonisation-induced protection against Streptococcus pneumoniae disease

Streptococus pneumoniae is an important human pathogen, yet in most individuals it establishes only transient nasopharyngeal colonisation without causing disease. Using murine models, this thesis explores the hypothesis that colonisation induces acquired immune responses which protect against subsequent pneumonia. Colonisation models with wild-type (WT) and mutant S. pneumoniae were established in outbred CD1 mice. Mutants lacked either capsule or lipoproteins, or were auxotrophs unable to replicate in vivo. WT colonisation protected against subsequent pneumonia. Mutants were cleared more rapidly than WT, were not immunogenic and did not protect. When the auxotroph was supplemented, colonisation, immunogenicity and protection were improved, suggesting duration of a colonisation event is an important factor in determining immunogenicity. This may be one factor explaining the poor immunogenicity of the other mutants. The mechanism by which previous colonisation protected against subsequent lethal pneumonia was then defined in a series of studies in inbred CBA/Ca mice. Colonisation induced both mucosal and systemic antibody responses to bacterial surface antigens but not capsule. There was also evidence of more robust cytokine production during subsequent pneumonia, including systemic and mucosal IL-17 responses dependant on the presence of CD4-cells. Protection was primarily against systemic invasion following pneumonia. Passive transfer studies and experiments using genetically modified mice demonstrated that systemic antibody was both necessary and sufficient to protect, and in vitro and in vivo models showed this to be via opsonophagocytosis and bloodstream clearance of bacteria. Antigenic protein targets of protective serum were defined using Western blotting and multiplex bead immunoassay techniques. Overall this thesis demonstrates that nasopharyngeal colonisation can protect against lethal pneumonia in mice via opsonophagocytic antibody against surface proteins thus preventing bacteraemia.
Indicadores de sustentabilidad para la producción lechera familiar en Uruguay: análisis de tres casos

Este artículo revisa los avances en la construcción de un sistema de indicadores que evalúa los procesos de in/sustentabilidad de los sistemas de producción lecheros familiares en Uruguay. Se presenta brevemente el concepto de sustentabilidad del cual se parte, para luego avanzar sobre la propuesta que se ha venido desarrollando. Se revisan tres casos concretos de su aplicación hasta el presente en distintos momentos y territorios en el departamento de San José. Por último, se identifican las potencialidades y restricciones que hasta ahora han emergido de dicho proceso de trabajo y se da cuenta de algunos resultados obtenidos con la aplicación de la metodología propuesta.
Visitor Responses to an Ethnic Garden Display in a Botanical Garden

S UMMARY . Program developers and administrators in settings such as botanical gardens are increasingly in need of information on the needs and interests of various groups. A need also exists for information on how to broaden interests in garden displays (exhibits including both plants and signs centered on a theme or topic) and increase the diversity of visitors. This article reports on research that explored visitor perceptions of an ethnic garden display highlighting African-American contributions to horticulture. The research also examined overall attitudes toward a botanic garden in Florida where the display was constructed. The results suggested that race did not affect visitors’ overall attitudes toward a botanic garden. Younger visitors, those who visit gardens more, and weekend visitors had a more positive attitude toward botanic gardens. Race was, however, related to visitor attitude toward the ethnic display. African-Americans liked the African-American horticulture display more than any other ethnic group. Sociodemographic characteristics, frequency of botanic garden visits, and time of year for visits all shaped visitor attitudes and opinions.
Greenhouse Disease Screen Facilitates Breeding Resistance to Tomato Early Blight

(.) Selected F 3 lines derived from F 2 plants with resistant, intermediate, and susceptible stem lesion were grown in a replicated field trial and evaluated for foliar early blight resistance. Stem lesion and foliar resistance were closely associated, making the greenhouse screen for stem lesion resistance useful in identifying plants with foliar resistance
Predator sound playbacks reveal strong avoidance responses in a fight strategist baleen whale

Anti-predator strategies are often defined as ‘flight’ or ‘fight’, based upon prey anatomical adaptations for size, morphology and weapons, as well as observed behaviours in the presence of predators. The humpback whale Megaptera nova eangliae is considered a ‘fight’ specialist based upon anatomy and observations of grouping behaviour and active defence when attacked by killer whales. However, the early stage of humpback whale anti-predator strategy, when the prey detects the presence of a distant potential predator that may not have perceived it, has never been described. Our aim was to experimentally examine this initial stage of anti-predator responses. Humpbacks are likely to hear well at the frequencies of killer whale vocalisations, thus the perception of killer whale sounds could trigger anti-predator responses. To address this hypo thesis, we played mammal-eating killer whale sounds to 8 solitary or paired humpback whales in North Atlantic feeding grounds and monitored their behavioural responses. We found that predator sound playbacks induced a cessation of feeding, a change in the diving pattern and a clear directional and rapid horizontal avoidance away from the speaker. Interestingly, in mothercalf pairs with young calves, the directional horizontal avoidance was atypically alternated by 90 degree turns, which may serve as a mechanism to better track the pre dator or a stealth tactic when more vulnerable animals are present. These results provide experimental evidence that humpback whales can exhibit a strong horizontal avoidance as an initial stage of anti-predator defence, indicating that anti-predator responses may be more graded and mixed than previously recognized.
A new 'great-appendage' arthropod from the Lower Cambrian of China and homology of chelicerate chelicerae and raptorial antero-ventral appendages

The uniramous ‘great appendages’ of several arthropods from the Early to Middle Cambrian are a characteristic pair of pre-oral limbs, which served for prey capture. It has been assumed that the morphological differences between the ‘great-appendage’ arthropods indicate that raptorial antero-ventral and anteriorly pointing appendages evolved more than once in arthropod phylogeny. One set of Cambrian ‘great-appendage’ arthropods has, however, very similar short antero-ventral appendages with a peduncle of two segments angled against each other (elbowed) and with stout distally or medio-distally directed spines or long flexible flagellate spines on each of the four distal segments. Moreover, the head appendages of all these forms comprise the ‘great appendages’ and three pairs of biramous limbs. To this set of taxa we can add a new form from the Lower Cambrian Maotianshan Shale of southern China, Haikoucaris ercaiensis n. gen. and n. sp. It is known from three specimens, possibly being little abundant in the faunal community. It can be distinguished from all other taxa by the prominence of the proximal claw segment of its ‘great appendages’ and by only three distal spines (one on each of the distal segments). The similarity of the short, spiky ‘great appendages’ of Haikoucaris with the chelicera of the Chelicerata leads us to hypothesize that this particular type of ‘great appendages’ was the actual precursor of the chelicera. Homeobox gene and developmental data recently demonstrated the homology between the antenna of ateloceratans and the antennula of crustaceans on one side and the chelicera of chelicerates on the other. To this we add palaeontological evidence for the homology between the chelicerae of chelicerates and the ‘short great appendages’ of certain Cambrian arthropods, which leads us to hypothesize that the evolutionary path went from the ‘short great appendages’, by progressive compaction, toward the chelicera with only a two-spined chela. The new form from China is regarded as the possible latest offshoot, whereas the other ‘great appendages’ arthropods with similar short grasping limbs were derivatives of the stem lineage of the crown-group Chelicerata. Consequently, the chelicera with a chela with one fixed and one mobile finger is an autapomorphy of the crown group of Chelicerata, whereas a raptorial, but more limb-like antenna, with more distal spine-bearing segments, characterized the ground pattern of Chelicerata. Further taxa having ‘great appendages’, including the large Anomalocarididae, are also discussed in the light of their possible affinities to the Chelicerata and possible monophyly of all of these arthropods with raptorial anterior appendages.
Model-Based Cell Tracking and Analysis in Fluorescence Microscopy

textabstractBiological research is impossible to imagine without a microscope. Latest genera- tions of microscopes, able to produce huge arrays of multidimensional data, only distantly resemble Leeuwenhoek’s first microscope. Every advance in visualization techniques and hardware brings us one step closer to understanding life, e.g., how genome information gives identity to cells, how cells constitute organisms and how errant cells cause disease. Discovery of the green fluorescent protein (GFP) in the nineties of the previous century was definitely one of the most impor- tant milestones on that path, giving new strong impulse to the field of fluorescence microscopy.
The effect of undernutrition on circadian genes and rhythmic induction in NIH3T3 cells

Nutrition is essential for health, and it has been widely studied and demonstrated to be related with circadian rhythm. To verify the effect of nutrient deficiency on the in vitro cultured cells, we had NIH3T3 cells cultured in diluted medium for 5 days, and detected the expression levels of Bmal1, Clock and Cry1 on each day. Phorbol 12-myristate 13-acetate (1PMA) was also applied to induce the circadian expression of Period genes, and the temporal expression levels before and after undernutrition treatment were analyzed by cosinor method. Our study showed that the expressions of circadian genes would be affected as soon as a nutritional deficiency occurred. This influence was not only on the expression level of Bmal1, Clock, and Cry1 genes but also on the PMA induction of circadian expression of Per1 and Per2 in the NIH3T3 cells.
ACTIoN oF dwArF MUCUNA, PIGeoN PeA ANd sTyLosANTHes oN weed UNder FIeLd ANd LABorATory CoNdITIoNs

SUMMARY The quality and allelopathy properties of dwarf mucuna, dwarf pigeon pea and stylosanthes as cover crops on corn and weed species were evaluated. Seeds were sown in October 2007, with a control treatment, in 20 plots of 4×5m, with five replicates. Weed population was determined 30 and 60 days after sowing. At 90 days, plants were mowed and the residues left to remain on the plot. Fresh and dry mass of the cover crops were determined and the allelopathic potential of aqueous extract of their aerial part was tested. The extract was chemically characterized and applied on seeds of weeds and corn. The experimental design was completely randomized and averages compared by the Scott-Knott test at 5% signifi cance. The cover crops showed to be effective in the control of weeds. The highest values in fresh and dry mass were obtained for dwarf pigeon pea, followed by dwarf mucuna; fresh mass increased 72 and 34%, respectively, compared to the control. The extract with dwarf mucuna affected arrowleaf sida germination. The use of green manure in the summer or between harvests ensures that crop rotation is carried out properly and warrants its benefits.
Companion Crop and Planting Configuration Effect on Onion

Field trials were conducted to evaluate the effect of planting configurations (raised bed and no bed) and reservoir tillage on onion (Allium cepa) yield and grade when a cereal grass or cool-season broadleaf species was used as a companion crop. Total onion yield, the number of plants harvested, percentage of single centers, and cull-sized bulb yields did not differ among planting confi gurations. However, planting onion seed in raised beds with reservoir tillage resulted in more large-diameter bulbs compared to planting without a bed confi guration. Raised beds also had fewer small-sized bulbs than the non-bed confi guration. Companion crop infl uence on onion yield and grade varied among environments (location plus year). In general, canola (Brassica napus) as a companion crop increased the yield of small-sized bulbs and decreased total yield and the yield of large-sized bulbs. These results were attributed to poor canola control from the initial bromoxynil plus oxyfl uorfen application because each label restricts application until onions have reached the two true-leaf stage. Onion yield and grade with barley (Hordeum vulgare) as a companion crop was similar to that of onion with no companion crop except during 2002 (Carrington) when rain delayed the postemergence grass herbicide application and lowered onion yield.
A Review of the European Pond Turtle, Emys orbicularis (Testudines: Emydidae), as a Subject for Integrative Population Studies

The Proceedings of the EMYS Symposium, held at Dresden in 1996, were published in 1998 as the 10th issue of Mertensiella. This volume, consisting of 28 articles and seven notes all devoted to the systematics, ecology, physiology, and conservation of the European pond turtle (Emys orbicularis) populations, is reviewed in the light of its significance as a first step toward the international exchange of information/experiences for the comprehensive understanding of this widely distributed, but locally differentiated and threatened species. All the articles and notes, though arranged in a rather curious way, contribute much to our knowledges of this systematically interesting and conservationally important turtle, which, until recently, had been poorly studied from the viewpoint of population biology. Reading of this book, one can realize the importance of integrative approaches for the designation of effective conservation measures, especially for a wide-ranging polymorphic organism like this species. This volume is thus recommended for the bookshelves of all students interested in this and relevant fields of biology. Applications of a few other methods/techniques, such as the multivariate analysis of morphological characters and allozyme electrophoresis, are recommended to further improve the evaluation of taxonomic status and conservation priority for local populations of this turtle. Establishment of the criteria and guidelines for international translocation-based conservation procedures seems to be an urgent necessity.
Permeability of the urban matrix to arboreal gliding mammals: Sugar gliders in Melbourne, Australia

Habitat corridors that facilitate functional connectivity are a fundamental component of wildlife conservation in fragmented landscapes. However, the landscape matrix separating suitable habitat is not uniformly impermeable to movement and management to increase matrix permeability could be an alternative means to maintain connectivity. Gliding mammals are particularly sensitive to fragmentation because their movements are constrained by glide distance thresholds. Populations of gliders in cities are at risk of being isolated by increasing habitat loss and urban development, yet little is known about how the urban matrix affects glider movement. Here we investigate how the level of urbanization and tree cover in the matrix influence matrix permeability to sugar gliders (Petaurus breviceps) within suburban forest reserves. Twenty-two sugar gliders were radio-tracked over winter and summer at four reserves. Boundary crossing behaviour was measured as the number of times each glider crossed into the matrix, and matrix permeability was determined as the maximum distance travelled by gliders into the matrix. The majority of gliders (81%) were located in the matrix at least once, and rates of boundary crossing were consistent across urbanization and tree cover levels. Matrix permeability was negatively affected by matrix urbanization, but not by matrix tree cover, and no interaction effects were found. Although distances travelled by gliders into the matrix did not exceed 180 m, they were comparable with typical movement distances by gliders in reserves. Our results demonstrate that the urban matrix can provide suitable habitat for gliding mammals to move and forage, but that increased urbanization may inhibit glider use of the matrix irrespective of tree cover. This finding has implications for conservation planning and suggests that structurally connected areas may not be used if movement behaviour is inhibited. Conversely, management of matrix permeability could be used to maintain connectivity without needing to construct physical corridors.
Impact of Various Canopy Manipulation Techniques on Growth, Yield, Fruit Composition, and Wine Quality of Gewürztraminer

Gewurztraminer vines were subjected over three seasons to seven canopy manipulation practices: Control (C); cluster thin (CT); hedge (H); hedge + paclobutrazol (H + P); basal leaf removal (LR); lateral shoot removal (LSR), and; CT/H + P/LR (REM-ALL). Hedging, LSR, and LR reduced °Brix and some parameters of juice color in two of three years, while leaf removal treatments also reduced titratable acidity in 1985 and pH in 1986. Free volatile terpene (FVT) concentration was improved in 1987 by LR, and in 1986 in CT, H, H + P, and REM-ALL vines. Potential volatile terpene (PVT) concentration was also increased over the C treatment in CT, H, LR, LSR, and REM-ALL vines in 1986 and in LR and REM-ALL vines in 1987. Treatments in which leaf area was removed (H, H + P, LR, LSR, and REM-ALL) tended to exhibit lower pruning weights than C and CT vines. Yield and periderm development was not strongly affected by any treatment. Paclobutrazol successfully reduced the length of lateral shoots on H + P and REM-ALL vines. This phenomenon was confined to the upper portion of the canopy only.