Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of avian pathogenic E. coli (APEC) genes important for the colonization of the chicken lung and characterization of the novel ExPEC adhesin I

The extraintestinal pathogen, avian pathogenic E. coli (APEC), known to cause systemic infections in chickens, is responsible for large economic losses in the poultry industry worldwide. In order to identify genes, involved in the early essential stages of pathogenesis, namely adhesion and colonization, a lung colonization model of infection was established in 5-week old White leghorn specific-pathogen free (SPF) chickens, and Signature-tagged mutagenesis (STM) was applied to this model by generating and screening a total of 1,800 mutants of an APEC strain IMT5155 (O2:K1:H5; Sequence type complex 95). The study led to the identification of new genes of interest, including adhesins, genes involved in capsule and LPS formation, regulators, transporters, metabolic enzymes and genes of putative function. Among the many genes identified was one coding for a novel APEC fimbrial adhesin (Yqi) not described for its role in APEC pathogenesis to date. Its gene product was temporarily designated ExPEC Adhesin I (EA/I). Deletion of the ExPEC adhesin I gene resulted in reduced colonization ability by APEC strain IMT5155 both in vitro and in vivo. Furthermore, complementation of the adhesin gene restored its ability to colonize epithelial cells in vitro. The ExPEC adhesin I protein was expressed as a fusion protein in E. coli BL21 in vitro during the log phase as shown by SDS-PAGE and western blotting, to reveal a protein with a molecular mass of ~ 39 kDa. Electron microscopy of an afimbriate strain E. coli AAEC189 over-expressed with the putative EA/I gene cluster revealed short fimbrial like appendages protruding out of the bacterial outer membrane. We observed that this adhesin coding gene yqi is prevalent among extraintestinal pathogenic E. coli (ExPEC) isolates, including APEC (54.4%), uropathogenic E. coli (UPEC) (65.9%) and newborn meningitic E. coli (NMEC) (60.0%), and absent in all of the intestinal pathogenic E. coli strains tested, thereby validating the designation of the adhesin as ExPEC Adhesin I. In addition, prevalence of EA/I was most frequently associated with the E. coli phylogenetic group B2 and ST95 complex of the multi locus sequence typing (MLST) scheme, with evidence of a positive selection within this highly pathogenic complex. This is the first report of the newly identified and functionally characterized ExPEC adhesin I and its role during APEC infection in chickens.
GROWTH OF CAPTIVE JASUS EDWARDSII (HUTTON) (CRUSTACEA:PALINURIDAE) IN NORTH-EASTERN NEW ZEALAND

The relations between growth and mortality rates and water temperature are important in determining the economic success of spiny lobster aquaculture. Captive juvenile lobsters (Jasus edwardsii) were grown at a site in north-eastern New Zealand where ambient sea-water temperatures in the culture tanks ranged from 23.3°C in summer to 13.4°C in winter, with an annual mean of 17.2°C (s.d. = 2.8). The growth and mortality rates of three size classes of juvenile lobsters were examined over one year in captivity. All lobsters were fed cultured mussels. Lobsters in the smallest size class grew to an average of 39 mm carapace length (31 g) in their first year from settlement. Growth to 200 g was estimated to take three years. Total mortality of lobsters was 12.8% and was greatest in the 0+ size class, for which most mortality occurred in a single tank. Of the total mortality, 64% occurred during two summer months (January and February). The growth and mortality of J. edwardsii are compared with previously unpublished information.
Reproductive biology, age and growth in the chocolate hind, Cephalopholis boenak (Bloch, 1790), in Hong Kong

The chocolate hind, Cephalopholis boenak, is a relatively small grouper, attaining a maximum standard length (SL) of 215 mm. The females mature at 80 mm SL and aged one year or less, if increments in sagittal otoliths form annually. Based on gonadal histology, this species was determined to be a diandric protogynous hermaphrodite with two possible pathways of male development, although all testes were similar in morphology. Crypts of spermatogenic cells may be present at all female developmental stages and sex change from female to male occurs at between 100 and 150 mm SL (ages one to four years). Spawning season for this species, around Hong Kong, is from April to October, as indicated both by the gonadosomatic index (GSI) and histological examination of gonads. Half of all specimens sampled from local municipal markets were small and young, between 112 mm and 142 mm SL (ages two to four years). Sectioned sagittal otoliths suggested that sampled fishes ranged from 0 to 11 years, although most fishes taken in the fishery are below age five years. The von Bertalanffy growth-curve parameters were, provisionally, L∞ = 147.66 mm SL, K = 0.49 and t0 = -1.52 years. Fisheries management should be applied to this last remaining commercially important local grouper in the Hong Kong market.
Oxidative stress and cigarette smoke alter chromatin remodeling but differentially regulate NF‐κB activation and proinflammatory cytokine release in alveolar epithelial cells

Oxidative stress is implicated in lung inflammation due to its effect on proinflammatory gene transcription. Changes in gene transcription depend on chromatin remodeling and the relative activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Alterations in the nuclear histone acetylation:deacetylation balance may result in uncontrolled transcription of specific proinflammatory genes. We studied the effect of hydrogen peroxide (H2O2) and cigarette smoke condensate (CSC) on histone acetylation:deacetylation in human alveolar epithelial cells (A549). H2O2 and CSC significantly increased acetylation of histone H4 proteins and were associated with decreased HDAC activity and HDAC2 levels in A549 cells. Also, the decreased HDAC2 activity was due to protein modification by aldehydes and nitric oxide products. Pretreatment of A549 cells with N‐acetyl‐L‐cysteine attenuated the oxidant‐mediated reduction in HDAC activity. Treatment of A549 cells with CSC did not cause nuclear factor‐κB (NF‐κB) activation or expression and release of either interleukin (IL)‐8 or IL‐6. However, H2O2, tumor necrosis factor‐α (TNF‐α), and IL‐1β significantly increased NF‐κB activation and expression of IL‐8 compared with control cells. Interestingly, CSC dose dependently inhibited TNF‐α‐ and IL‐ 1β‐mediated NF‐κB activation and IL‐8 expression. Thus, H2O2 and CSC enhance acetylation of histone proteins and decrease histone deacetylase activity but differentially regulate proinflammatory cytokine release in alveolar epithelial cells.
The differential role of mechanisms for drought resistance in a Mediterranean evergreen shrub: a simulation approach

Plants have the ability to dampen the effects of variability in water resources. Various mechanisms contribute to these properties: reduction of leaf area, increased rooting depth and stomatal conductance. To evaluate the differential roles and interactions of these mechanisms, we have built a model and simulated flows of water in Mediterranean evergreen scrub. The essential concept of this model is that the water status of the canopy is governed by the water lost by transpiration, the availability of soil water and the hydraulic resistances to water flow in soil and plant. The amount of water supplied by the roots is related to changes in water potential between the soil and the leaf. The amount of water lost to the atmosphere is regulated by an interaction between atmospheric demand and canopy water potential. Water uptake by plant is assumed equal to plant water loss. Leaf area appears to affect largely the annual water balance. The critical leaf water potential required to reduce the maximum stomatal conductance by half has a dominant effect on annual leaf water potential. Reducing rooting depth induces a new functional equilibrium for the plant. This new equilibrium is reached by decreasing leaf area and the critical leaf water potential. Our results show the complexity of interactions of these mechanisms and highlight the importance of the coordination between them. Finally, we suggest a reconsideration of these mechanisms in a context of the survival and long-term persistence of the plant.
Corinto bianco: A Seedless Mutant of Pedro Ximenes

The cultivated variety Pedro Ximenes is a seeded winegrape and Corinto bianco is a parthenocarpic seedless variety maintained in collection. To date, the two varieties have not been considered as related. In this study, identical DNA profiles were observed in both varieties for 25 microsatellite loci. Among morphological characteristics, they only differed in the presence or absence of seeds and in seed-related characteristics such as berry size, cluster density, and cluster size. These results suggest that both varieties arose from the same original embryo and one is a mutation of the other. Parentage analysis revealed the cultivar Gibi as a probable parent of Pedro Ximenes.
Germination, Emergence, and Seedling Growth of Tomato and Impatiens in Response to Seed Treatment with Paclobutrazol

Seed treatments with paclobutrazol (PB), a triazole growth retardant, were examined for seedling growth suppression without exerting a deleterious effect on germination or emergence. Seeds of 'Salmon Picotee' impatiens (Impatiens wallerana Hook f.) and 'Marglobe' tomato (Lycopersicon esculentum Mill.) were soaked for 24 or 48 hours at 22 °C in 0, 50, 500, or 1000 mg.L -1 PB or were primed in polyethylene glycol 8000 or grade 5 exfoliated vermiculite (both at -1.0 MPa for 7 days at 22 °C) containing these PB solutions. Any PB seed treatment of impatiens (including a series of lower concentrations up to 50 mg.L -1 PB) that elicited seedling growth suppression also reduced germination and emergence. For tomato, soaking seeds for 24 hours in up to 1000 mg.L -1 PB had little or no effect on germination or emergence, and yet shoot height or dry weight was not decreased further by exceeding 50 mg.L -1 PB. At any PB concentration, soaking seeds for 48 hours or priming seeds resulted in lower percentage of germination or emergence than soaking seeds for 24 hours. Soaking tomato seeds in 50 mg.L -1 PB for 24 hours resulted in similar shoot growth suppression until at least 31 days after planting as a growth medium drench (1 mg.L -1 PB) or as a shoot spray (10 mg.L -1 PB), both applied at 14 days after planting. Beyond 31 days after planting, however, the latter two treatments gave greater shoot growth suppression than the PB seed soak treatment, which had lost its growth suppressive effect. Chemical name used: (±)-(R*,R*)-[(4-chlorophenyl)methyl]--(1,1,-dimethyl)-1H-1,2,4-triazole-1-ethanol (paclobutrazol).
Grow Tubes Change Microclimate and Bush Architecture but Have Little Effect on Bush Biomass Allocation at the End of the Establishment Year in Blueberry

Additional index words. mulch, radiation, temperature, tree shelter, Vaccinium corymbosum Abstract. Microclimate variables were integrated over a 6-month period during which blueberry (Vaccinium corymbosum cv. Liberty) bushes were grown in 51-cm high, 20-cm diameter round grow tubes (opaque or translucent) on a sawdust mulch-covered raised bed with the mulch incorporated into tilled soil. Grow tubes were installed around plants in the spring of 2006, 5 months after planting. Total photosynthetic photon flux (PPF) density was 55% and 21% of ambient in translucent and opaque tubes, respectively. Daily maximum vapor pressure deficit consistently was highest in translucent tubes. Air (Ta) and stem (Tstem) temperatures in both grow tube types exceeded Ta and Tstem in non- tubed plants (ambient). Maximum mulch surface temperature (Tm) was lowest in opaque tubes,whereastherewasnodifference inTmbetween ambientandtranslucenttubes.The soil-mulch interface temperature (Tsm) was warmer outside tubes than Tsm inside tubes. Soil temperatures directly under the tubes differed very little between tube types and ambient, generally less than 1 8C. Root and crown dry mass (DM) did not differ between tubed plants and ambient at the end of the establishment year. Leaf area, leaf DM, and fruit bud number were suppressed inside tubes. All plants were greater than 51 cm tall at the end of the growing season. Substantial compensatory growth occurred above tubes: tubed plants were more upright and had more leaf area, leaf DM, and shoot growth than ambient plants above 51 cm. However, there was no difference between tubed and ambient plants in fruit bud number, total plant leaf area, shoot:root, or DM of 1- and 2- year-old wood. Grow tubes can alter microclimate and architecture of young blueberry bushes but have no significant influence on size and distribution of total DM after one growing season in the field.
Bio-optical characteristics of diatom and prymnesiophyte populations in the Labrador Sea

During the spring of 1996, phytoplankton samples were collected along a transect from South Wolf Island (Labrador) to Cape Desolation (Greenland). Dense blooms of diatoms were found over the shelf near the coast of Labrador, whereas high concentrations of the colony-forming prymnesiophyte Phaeocystis pouchetii were found close to Greenland. Phytoplankton samples were separated into 2 major groups (diatoms or prymnesiophytes) on the basis of chlorophyll (chl) chl c 3 /chl a ratios (determined by HPLC analysis), and the effects of species composition on the absorption and photosynthetic characteristics of these 2 high-latitude phytoplankton populations were studied. At all pigment concentrations and all wavelengths examined (apart from 623 nm), the diatom population had a much lower absorption coefficient than the prymnesiophyte population; this was attributed to an increased pigment-packaging effect in the larger diatom cells. Varying proportions of photo-protective pigments also influenced the absorption characteristics of these populations. The low specific-absorption coefficient of the diatom population resulted in a higher maximum photosynthetic quantum yield relative to that of the prymnesiophyte population. The initial slope of the photosynthesis-irradiance (P-E) curve (α B ) also appeared to be taxon-specific, with higher α B values being recorded for the smaller prymnesiophytes than for the larger diatom cells. The implications of species-dependent variations in phytoplankton absorption coefficients for the retrieval of remotely-sensed chl a are discussed.
PCR‐based detection of Xanthomonas campestris pv. phaseoli var. fuscans in plant material and its differentiation from X. c. pv. phaseoli

A PCR‐based method was developed for the specific detection of Xanthomonas campestris pv. phaseoli var. fuscans from plant material. Primers Xf1 and Xf2, based on a sequence conserved amplified region (SCAR) derived from RAPD PCR analysis of X. c. pv. phaseoli var. fuscans, amplified a DNA fragment of 450 bp from all such isolates. In contrast, no amplification product was obtained from any X. c. pv. phaseoli isolates, or from any other DNAs tested. As few as 10 cells of X. c. pv. phaseoli var. fuscans (equivalent to about 100 fg DNA) could be detected in vitro. In planta, following an initial inoculation of as little as one cell, an amplification product was generated after only 2 d of incubation, allowing highly sensitive detection 10 d before disease symptoms were observed. Moreover, the failure to amplify DNA from X. c. pv. phaseoli isolates shows that these primers provide a rapid, improved method to differentiate these two varieties using PCR.
Effect of high-oleic sunflower oil and other pro-health ingredients on physical and sensory properties of biscuits

The purpose of this work was to determine the possibility of using high-oleic sunflower oil for the production of biscuits. Additives (inulin, β-glucan, lecithin) were introduced into the formulation to improve the quality and nutritional properties of products. Additives had a positive impact on the volume growth of products with oil, although the effect was lower than of biscuits with shortening. The breaking strength of biscuits with oil was greater than that of the ones with shortening, except products with the addition of lecithin. Inulin affected lightness of color, whereas replacement of shortening with oil darkened the color and caused the total color difference (ΔE) to be significantly different from that of the control sample. The fat migration was maximum from products in which oil was used without additives. Based on sensory evaluation, biscuits with oil – inulin and lecithin – which in the evaluation of overall quality scored 8/10 and 7.9/10, respectively, proved closest to the control sample. It was observed that the sensory quality of cookies significantly improved with the inclusion of lecithin.
Gonad maturity in female Chinese mitten crab Eriocheir sinensis from the southern Baltic Sea – the first description of ovigerous females and the embryo developmental stage

Abstract This paper describes for the first time the gonad maturity stage of Eriocheir sinensis females (carapace width 55.20–78.10 mm) collected in the autumns and winters of 2005–2012 in the Gulf of Gdansk and Vistula Lagoon (southern Baltic Sea). Seventeen females had gonads in the penultimate stage, which indicates that spawning would shortly take place. Four other females had gonads in the last stage, which means they were already carrying eggs. These accounted, on average, for 17.9 ± 2.9% of female weight and were in the 3rd and 4th embryo developmental stage. The results show that the low salinity of southern Baltic Sea (≤ 7 PSU) permits mating and fertilization as well as embryo development in E. sinensis. It is still not clear, whether such a salinity level will enable hatching and the complete larval cycle.
The application of palaeolimnology to evidence-based lake management and conservation : examples from UK lakes

1. To help meet the requirements of water legislation, palaeolimnology has been widely used to establish ‘reference conditions’ and restoration targets for lakes. However, its potential for assessing the necessity and appropriateness of different lake management activities has been less publicized. 2. With reference to selected case studies covering consultancy projects commissioned by UK conservation agencies, this study highlights the important applied role of palaeolimnology. Using varying combinations of diatom, plant macrofossil and cladoceran analysis, the degree, timing and in many cases the likely drivers of ecological change were inferred for several lake sites. 3. From this basis advice was given on a range of lake management issues, including the need for sediment removal to combat eutrophication and/or the necessity of other nutrient reduction measures (Case study 1), the depth of sediment to be removed to maximize restoration potential through exposure of dormant banks of characean oospores (Case study 2), the requirement for fish management (Case study 3), and advice regarding fish farm expansion and licensing (Case study 4). Where possible management responses to the recommendations are outlined including any major outcomes. 4. All case studies illustrate the advantages, for lake management and conservation decision-making, of placing current lake ecological conditions in the context of long-term change. (Less)
Host-pathogen interactions in the innate immune response of the nematode Caenorhabditis elegans

The nematode Caenorhabditis elegans has been a powerful experimental organism for almost half a century. Over the past ten years, researchers have begun to exploit the power of C. elegans to investigate the biology of a number of human pathogens. This work continues to uncover mechanisms of host immunity and pathogen virulence that are either analogous to those involved during pathogenesis in alternative animal hosts or mechanisms which are, thus far, unique to the worm. In this thesis, we present data that describes an immunological balance in C. elegans, whereby heightened tolerance to one pathogen, the enteric bacteria Salmonella Typhimurium, comes at the cost of increased susceptibility to another, the fatal fungal human pathogen Cryptococcus neoformans. We find that this susceptibility trade-off is mediated by the reciprocal activity of two immune genes: the lysozyme lys-7 and the tyrosine kinase abl-1. We suggest that ABL-1 controls two different DAF-16-dependent pathways to regulate this balance. Both pathways are necessary for wild type resistance to C. neoformans, whilst the activity of only one pathway is a requirement for the tolerance phenotype to S. Typhimurium. We infer from sequence data that LYS-7 has an atypical mode of action in C. elegans, which we hypothesise to be detrimental to the worm during S. Typhimurium pathogenesis and thus a contributing factor to the tolerance phenotype. Furthermore, we find that this tolerance has a Salmonella-dependency which we propose to be under the control of the alternative sigma factor, RpoS. Taken together, we describe an immunological balance in C. elegans for the first time, one that is mediated by both host and pathogen factors. We therefore suggest that the innate immune response of C. elegans has a higher level of immune complexity than previously believed, and that such trade-offs are evolutionarily ancient mechanisms.
Poor Performance of Corals Transplanted onto Substrates of Short Durability

Worldwide, coral reefs are degrading due to increasing anthropogenic pressures. Yet, management of reefs still falls short of effectively addressing these threats, and active restoration methods are increasingly being called for. Coral transplantation is frequently advocated as a possible means of coral reef rehabilitation. Fragments produced in coral nurseries or farms have been proposed as a potential source for transplantation, and culture media (inexpensive but non‐durable materials such as wood or bamboo) may serve as transplantation substrate if placed directly in the reef. However, the performance of coral transplants attached to such substrates has not been examined yet. Here, the long‐term survival of transplants attached to bamboo substrates is reported. A total of 6,164 fragments of 4 coral species (Acroporids and Pocilloporids) were monitored for up to 20 months at three sites in North Sulawesi/Indonesia. Bamboo failed as a suitable inexpensive substrate in at least two of the three sites examined. Mortality of transplants 2 years after transplantation was high in three of the four species (67–95%) and was partially linked to substrate disintegration. The results show that, in places were currents or waves threaten to dislocate transplants, a higher effort needs to be directed at a strong and durable attachment of transplanted corals.