Impact of the Australian litter re-use practice on Salmonella in the broiler farming environment

This study has examined the dynamics (in terms of levels and serovar diversity) of Salmonella in the "dual litter environment" that occurs within a single shed as a result of a management practice common in Australia. The study also looked at the physical parameters of the litter (pH, moisture content, water activity and litter temperature) as a means of understanding the Salmonella dynamics in these litter environments. The Australian practice results in the brooder end of the shed having new litter each cycle while the grow-out end has re-used litter (a "dual litter environment"). Two farms that adopted this partial litter re-use practice were studied over one full broiler cycle each. Litter was sampled weekly for the levels (and serovars) of Salmonella during a farming cycle. There was a trend for lower levels of Salmonella (and a lower Salmonella serovar) diversity in the re-used litter environment as compared with the new litter environment. Of the physical parameters examined, it would appear that the lower water activity associated with the re-used litter may contribute to the Salmonella dynamics in the dual environment.

What was behind the bark? : An assessment of decay among urban Tilia, Betula and Acer trees felled as hazardous in the Helsinki City area

Old trees growing in urban environments are often felled due to symptoms of mechanical defects that could be hazardous to people and property. The decisions concerning these removals are justified by risk assessments carried out by tree care professionals. The major motivation for this study was to determine the most common profiles of potential hazard characteristics for the three most common urban tree genera in Helsinki City: Tilia, Betula and Acer, and in this way improve management practices and protection of old amenity trees. For this research, material from approximately 250 urban trees was collected in cooperation with the City of Helsinki Public Works Department during 2001 - 2004. From the total number of trees sampled, approximately 70% were defined as hazardous. The tree species had characteristic features as potential hazard profiles. For Tilia trees, hollowed heartwood with low fungal activity and advanced decay caused by Ganoderma lipsiense were the two most common profiles. In Betula spp., the primary reason for tree removal was usually lowered amenity value in terms of decline of the crown. Internal cracks, most often due to weak fork formation, were common causes of potential failure in Acer spp. Decay caused by Rigidoporus populinus often increased the risk of stem breakage in these Acer trees. Of the decay fungi observed, G. lipsiense was most often the reason for the increased risk of stem collapse. Other fungi that also caused extensive decay were R. populinus, Inonotus obliquus, Kretzschmaria deusta and Phellinus igniarius. The most common decay fungi in terms of incidence were Pholiota spp., but decay caused by these species did not have a high potential for causing stem breakage, because it rarely extended to the cambium. The various evaluations used in the study suggested contradictions in felling decisions based on trees displaying different stages of decay. For protection of old urban trees, it is crucial to develop monitoring methods so that tree care professionals could better analyse the rate of decay progression towards the sapwood and separate those trees with decreasing amounts of sound wood from those with decay that is restricted to the heartwood area.

Sources of vase life variation in cut roses: A review

n determining vase life (VL), it is often not considered that the measured VL in a particular experiment may greatly depend on both the preharvest and evaluation environmental conditions. This makes the comparison between studies difficult and may lead to erroneous interpretation of results. In this review, we critically discuss the effect of the growth environment on the VL of cut roses. This effect is mainly related to changes in stomatal responsiveness, regulating water loss, whereas cut flower carbohydrate status appears less critical. When comparing cultivars, postharvest water loss and VL often show no correlation, indicating that components such as variation in the tissue resistance to cavitate and/or collapse at low water potential play an important role in the incidence of water stress symptoms. The effect of the growth environment on these components remains unknown. Botrytis cinerea sporulation and infection, as well as cut rose susceptibility to the pathogen are also affected by the growth environment, with the latter being largely unexplored. A huge variability in the choices made with respect to the experimental setup (harvest/conditioning methods, test room conditions and VL terminating symptoms) is reported. We highlight that these decisions, though frequently overlooked, influence the outcome of the study. Specifications for each of these factors are proposed as necessary to achieve a common VL protocol. Documentation of both preharvest conditions and a number of postharvest factors, including the test room conditions, is recommended not only for assisting comparisons between studies, but also to identify factors with major effects on VL.

Microbial communities in Pb contaminated boreal forest soil

Lead contamination in the environment is of particular concern, as it is a known toxin. Until recently, however, much less attention has been given to the local contamination caused by activities at shooting ranges compared to large-scale industrial contamination. In Finland, more than 500 tons of Pb is produced each year for shotgun ammunition. The contaminant threatens various organisms, ground water and the health of human populations. However, the forest at shooting ranges usually shows no visible sign of stress compared to nearby clean environments. The aboveground biota normally reflects the belowground ecosystem. Thus, the soil microbial communities appear to bear strong resistance to contamination, despite the influence of lead. The studies forming this thesis investigated a shooting range site at Hälvälä in Southern Finland, which is heavily contaminated by lead pellets. Previously it was experimentally shown that the growth of grasses and degradation of litter are retarded. Measurements of acute toxicity of the contaminated soil or soil extracts gave conflicting results, as enchytraeid worms used as toxicity reporters were strongly affected, while reporter bacteria showed no or very minor decreases in viability. Measurements using sensitive inducible luminescent reporter bacteria suggested that the bioavailability of lead in the soil is indeed low, and this notion was supported by the very low water extractability of the lead. Nevertheless, the frequency of lead-resistant cultivable bacteria was elevated based on the isolation of cultivable strains. The bacterial and fungal diversity in heavily lead contaminated shooting sectors were compared with those of pristine sections of the shooting range area. The bacterial 16S rRNA gene and fungal ITS rRNA gene were amplified, cloned and sequenced using total DNA extracted from the soil humus layer as the template. Altogether, 917 sequenced bacterial clones and 649 sequenced fungal clones revealed a high soil microbial diversity. No effect of lead contamination was found on bacterial richness or diversity, while fungal richness and diversity significantly differed between lead contaminated and clean control areas. However, even in the case of fungi, genera that were deemed sensitive were not totally absent from the contaminated area: only their relative frequency was significantly reduced. Some operational taxonomic units (OTUs) assigned to Basidiomycota were clearly affected, and were much rarer in the lead contaminated areas. The studies of this thesis surveyed EcM sporocarps, analyzed morphotyped EcM root tips by direct sequencing, and 454-pyrosequenced fungal communities in in-growth bags. A total of 32 EcM fungi that formed conspicuous sporocarps, 27 EcM fungal OTUs from 294 root tips, and 116 EcM fungal OTUs from a total of 8 194 ITS2 454 sequences were recorded. The ordination analyses by non-parametric multidimensional scaling (NMS) indicated that Pb enrichment induced a shift in the EcM community composition. This was visible as indicative trends in the sporocarp and root tip datasets, but explicitly clear in the communities observed in the in-growth bags. The compositional shift in the EcM community was mainly attributable to an increase in the frequencies of OTUs assigned to the genus Thelephora, and to a decrease in the OTUs assigned to Pseudotomentella, Suillus and Tylospora in Pb-contaminated areas when compared to the control. The enrichment of Thelephora in contaminated areas was also observed when examining the total fungal communities in soil using DNA cloning and sequencing technology. While the compositional shifts are clear, their functional consequences for the dominant trees or soil ecosystem remain undetermined. The results indicate that at the Hälvälä shooting range, lead influences the fungal communities but not the bacterial communities. The forest ecosystem shows apparent functional redundancy, since no significant effects were seen on forest trees. Recently, by means of 454 pyrosequencing , the amount of sequences in a single analysis run can be up to one million. It has been applied in microbial ecology studies to characterize microbial communities. The handling of sequence data with traditional programs is becoming difficult and exceedingly time consuming, and novel tools are needed to handle the vast amounts of data being generated. The field of microbial ecology has recently benefited from the availability of a number of tools for describing and comparing microbial communities using robust statistical methods. However, although these programs provide methods for rapid calculation, it has become necessary to make them more amenable to larger datasets and numbers of samples from pyrosequencing. As part of this thesis, a new program was developed, MuSSA (Multi-Sample Sequence Analyser), to handle sequence data from novel high-throughput sequencing approaches in microbial community analyses. The greatest advantage of the program is that large volumes of sequence data can be manipulated, and general OTU series with a frequency value can be calculated among a large number of samples.

Fuzzy waste load allocation model: a multiobjective approach

Fuzzy Waste Load Allocation Model (FWLAM), developed in an earlier study, derives the optimal fractional levels, for the base flow conditions, considering the goals of the Pollution Control Agency (PCA) and dischargers. The Modified Fuzzy Waste Load Allocation Model (MFWLAM) developed subsequently is a stochastic model and considers the moments (mean, variance and skewness) of water quality indicators, incorporating uncertainty due to randomness of input variables along with uncertainty due to imprecision. The risk of low water quality is reduced significantly by using this modified model, but inclusion of new constraints leads to a low value of acceptability level, A, interpreted as the maximized minimum satisfaction in the system. To improve this value, a new model, which is a combination Of FWLAM and MFWLAM, is presented, allowing for some violations in the constraints of MFWLAM. This combined model is a multiobjective optimization model having the objectives, maximization of acceptability level and minimization of violation of constraints. Fuzzy multiobjective programming, goal programming and fuzzy goal programming are used to find the solutions. For the optimization model, Probabilistic Global Search Lausanne (PGSL) is used as a nonlinear optimization tool. The methodology is applied to a case study of the Tunga-Bhadra river system in south India. The model results in a compromised solution of a higher value of acceptability level as compared to MFWLAM, with a satisfactory value of risk. Thus the goal of risk minimization is achieved with a comparatively better value of acceptability level.

Fish-scale bio-inspired multifunctional ZnO nanostructures

Scales provide optical disguise, low water drag and mechanical protection to fish, enabling them to survive catastrophic environmental disasters, predators and microorganisms. The unique structures and stacking sequences of fish scales inspired the fabrication of artificial nanostructures with salient optical, interfacial and mechanical properties. Herein, we describe fish-scale bio-inspired multifunctional ZnO nanostructures that have similar morphology and structure to the cycloid scales of the Asian Arowana. These nanostructured coatings feature tunable light refraction and reflection, modulated surface wettability and damage-tolerant mechanical properties. The salient properties of these multifunctional nanostructures are promising for applications in: - (i) optical coatings, sensing or lens arrays for use in reflective displays, packing, advertising and solar energy harvesting; - (ii) self-cleaning surfaces, including anti-smudge, anti-fouling and anti-fogging, and self-sterilizing surfaces, and; - (iii) mechanical/chemical barrier coatings. This study provides a low-cost and large-scale production method for the facile fabrication of these bio-inspired nanostructures and provides new insights for the development of novel functional materials for use in 'smart' structures and applications.

Developmental origins of physiological stress reactivity

The model of developmental origins of health and disease proposes that organisms during fetal period utilize cues that enable their adaptation in the postnatal environment they are likely to live, having short-term advantages when trying to survive in environment but simultaneously in the long run have costs for health. A large body of epidemiological research has found that low birth weight, a marker of intrauterine conditions, is associated with cardiovascular (CV) disease. Since the reported associations of birth weight with normal variation in the resting blood pressure (BP), a major predictor of CV disease risk, have been modest, a key candidate mediating the link has been CV and hypothalamus-pituitary-adrenal axes (HPAA) reactivity to stress. In addition, not only weight at birth but also gestational age and early postnatal growth may have independent associations to stress reactivity. The aim of this thesis was to investigate whether pre- and postnatal growth and gestational age are associated with CV and HPAA activity before, during and after stress in childhood and in late adulthood. Altogether 287 men and women aged 60-70 and 299 boys and girls aged 7-9 underwent Trier Social Stress Test. Several indices of HPAA and CV were measured and birth size and gestational age were obtained from birth records. Results showed that low birth weight was associated with low HPAA activity during psychosocial stress, and rapid gain in BMI during years 7-11 was related to heightened stress reactivity to psychosocial stress. Size at birth in children and gestational age and early postnatal (0-2 years) gain in height in adults were associated with CV stress responses; however, in a sex-specific manner. Given that CV stress responses and HPAA activity are markers of CV disease vulnerability, our results may partly explain the associations between early environment and later CV disease.

Method-MS, final report 2010

Radiometric determination methods, such as alpha spectrometry require long counting times when low activities are to be determined. Mass spectrometric techniques as Inductively Coupled Plasma Mass Spectrometry (ICP-MS), Thermal Ionisation Mass Spectrometry (TIMS) and Accelerator Mass Spectrometry (AMS) have shown several advantages compared to traditional methods when measuring long-lived radionuclides. Mass spectrometric methods for determination of very low concentrations of elemental isotopes, and thereby isotopic ratios, have been developed using a variety of ion sources. Although primarily applied to the determination of the lighter stable element isotopes and radioactive isotopes in geological studies, the techniques can equally well be applied to the measurement of activity concentrations of long-lived low-level radionuclides in various samples using “isotope dilution” methods such as those applied in inductively coupled plasma mass spectrometry (ICP-MS). Due to the low specific activity of long-lived radionuclides, many of these are more conveniently detected using mass spectrometric techniques. Mass spectrometry also enables the individual determination of Pu-239 and Pu-240, which cannot be obtained by alpha spectrometry. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) are rapidly growing techniques for the ultra-trace analytical determination of stable and long-lived isotopes and have a wide potential within environmental science, including ecosystem tracers and radio ecological studies. Such instrumentation, of course needs good radiochemical separation, to give best performance. The objectives of the project is to identify current needs and problems within low-level determination of long-lived radioisotopes by ICP-MS, to perform intercalibration and development and improvement of ICP-MS methods for the measurement of radionuclides and isotope ratios and to develop new methods based on modified separation chemistry applied to new auxiliary equipment.

Unique Utilization of a Phosphoprotein Phosphatase Fold by a Mammalian Phosphodiesterase Associated with WAGR Syndrome

Metallophosphoesterase-domain-containing protein 2 (MPPED2) is a highly evolutionarily conserved protein with orthologs found from worms to humans. The human MPPED2 gene is found in a region of chromosome 11 that is deleted in patients with WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome, and MPPED2 may function as a tumor suppressor. However, the precise cellular roles of MPPED2 are unknown, and its low phosphodiesterase activity suggests that substrate hydrolysis may not be its prime function. We present here the structures of MPPED2 and two mutants, which show that the poor activity of MPPED2 is not only a consequence of the substitution of an active-site histidine residue by glycine but also due to binding of AMP or GMP to the active site. This feature, enhanced by structural elements of the protein, allows MPPED2 to utilize the conserved phosphoprotein-phosphatase-like fold in a unique manner, ensuring that its enzymatic activity can be combined with a possible role as a scaffolding or adaptor protein. (C) 2011 Elsevier Ltd. All rights reserved.

Synconset Waves and Chains: Spiking Onsets in Synchronous Populations Predict and Are Predicted by Network Structure

Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define `synconset wave' as a cascade of first spikes within a synchronisation event. Synconset waves would occur in `synconset chains', which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of our framework to several aspects of network physiology including cell assemblies, population codes, and oscillatory synchrony.

Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme

Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacteriumsmegmatis (MsASL) and Mycobacteriumtuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16 angstrom. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. Structured digital abstract andby()

Bacterias halófilas extremas deteriorantes en anchoíta salada

En anchoita ( Engraulis anchoita) salada-maduradas, que poseen una actividad de agua (aw) de 0,75 a 0,80 se han encontrado bacterias halófilas . E l objetivo de este trabajo fue determinar la potencial capacidad deteriorante de los grupos bacterianos encontrados. Se realizaron estudios microbiológicos en 100 muestras de anchoíta salada-madurada. E l 71 % de las colonias halladas fueron halófilas extremas y el 29 % estrictas. De acuerdo a sus características bioquímicas se ha reconocido un 31% de Halococcus sp.; 15% de Haloferax spp. 5% de Halobacterium spp. y 7% de Haloarcula spp., el resto se encuentra aún sin identificar. De las bacterias halladas un 30% tienen actividad proteolítica, 30% lipolítica y 15% proteolítica y lipolítica. La presencia de estas bacterias podría llevar a modificaciones irreversibles y no deseables en distintas características sensoriales como olor, color y textura, que limitarían la vida útil de estos productos. La importancia de esta limitación estará dada por el número, las características de las mismas y las condiciones de almacenamiento del producto.

Influence of Foliar Exposure, Adjuvants, and Rain-free Period on the Efficacy of Glyphosate for Torpedograss Control

The proportion of torpedograss tissue exposed to glyphosate at application rates of 0.28, 0.56, 1.12, 2.24, and 4.48 kg/ha affected control as measured by regrowth. The effect of tissue exposure was more pronounced as application rate decreased. This study suggests that higher rates of glyphosate need to be used during higher water levels, when less torpedograss tissue is exposed to herbicide spray and lower rates may be used during periods of low water levels. Addition of the water conditioning agent Quest (R) (0.25% v/v) to glyphosate spray mixtures diminished the influence of simulated rain events following glyphosate application. Twelve other adjuvants did not influence the effect of simulated rain events.

Comments on hydrographic and topographic LIDAR acquisition and merging with multibeam sounding data acquired in the Olympic Coast National Marine Sanctuary

In April 2005, a SHOALS 1000T LIDAR system was used as an efficient alternative for safely acquiring data to describe the existing conditions of nearshore bathymetry and the intertidal zone over an approximately 40.7 km2 (11.8 nm2) portion of hazardous coastline within the Olympic Coast National Marine Sanctuary (OCNMS). Data were logged from 1,593 km (860 nm) of track lines in just over 21 hours of flight time. Several islands and offshore rocks were also surveyed, and over 24,000 geo-referenced digital still photos were captured to assist with data cleaning and QA/QC. The 1 kHz bathymetry laser obtained a maximum water depth of 22.2 meters. Floating kelp beds, breaking surf lines and turbid water were all challenges to the survey. Although sea state was favorable for this time of the year, recent heavy rainfall and a persistent low-lying layer of fog reduced acquisition productivity. The existence of a completed VDatum model covering this same geographic region permitted the LIDAR data to be vertically transformed and merged with existing shallow water multibeam data and referenced to the mean lower low water (MLLW) tidal datum. Analysis of a multibeam bathymetry-LIDAR difference surface containing over 44,000 samples indicated surface deviations from –24.3 to 8.48 meters, with a mean difference of –0.967 meters, and standard deviation of 1.762 meters. Errors in data cleaning and false detections due to interference from surf, kelp, and turbidity likely account for the larger surface separations, while the remaining general surface difference trend could partially be attributed to a more dense data set, and shoal-biased cleaning, binning and gridding associated with the multibeam data for maintaining conservative least depths important for charting dangers to navigation. (PDF contains 27 pages.)

A quantitative analysis of the phytoplankton of the Gulf of Panama II. On the relationship between C14 assimilation and the diatom standing crop

ENGLISH: The Inter-American Tropical Tuna Commission has maintained a hydro-biological station in the Gulf of Panama located at 8°45'N, 79°23'W in connection with their ecological investigation of the anchoveta (Cetengraulis mysticetus), a tuna baitfish (see Peterson, 1961, for references) . The depth is approximately 42 meters at mean low water at this station. Routine hydrographic and biological observations have been made (Schaefer, Bishop and Howard, 1958; Schaefer and Bishop, 1958; Forsbergh, 1963), including the collection of quantitative phytoplankton samples from November 1954 through May 1957 (Smayda, 1959; unpublished). The seasonal and regional variations in phytoplankton growth in the Gulf of Panama have also been investigated (Smayda, 1963). The relationships existing between C1 4 assimilation as determined by 24 hour in situ experiments and diatom standing crop at 10 meters when expressed as cell numbers, cell volume, cell surface area and cell plasma volume have been assessed for 30 observations made between November 1954 and May 1957 at 8°45'N, 79°23'W. The average cell volume and cell surface area characteristics for 110 diatom species and varieties are presented. SPANISH: Las relaciones existentes entre la asimilación del C14 , determinadas después de 24 horas de experimentos in situ, y la cosecha estable de las diatomeas a 10 metros, expresando el número de células, volumen celular, área de la superficie celular y volumen del plasma celular, han sido determinadas por medio de 30 observaciones hechas entre noviembre de 1954 y mayo de 1957, a los 8°45'N, 79°23'W. Se presenta, para 110 especies y variedades de diatomeas, el promedio de las características del volumen celular y del área de la superficie celular. (PDF contains 67 pages.)