Extracellular hydrolytic enzyme screening of culturable heterotrophic bacteria from deep-sea sediments of the Southern Okinawa Trough

The Southern Okinawa Trough is an area of focused sedimentation due to particulate matter export from the shelf of the East China Sea and the island of Taiwan. In order to understand the geomicrobiological characteristics of this unique sedimentary environment, bacterial cultivations were carried out for an 8.61 m CASQ core sediment sample. A total of 98 heterotrophic bacterial isolates were characterized based on 16S rRNA gene phylogenetic analysis. These isolates can be grouped into four bacterial divisions, including 13 genera and more than 20 species. Bacteria of the gamma-Proteobacteria lineage, especially those from the Halomonas ( 27 isolates) and Psychrobacter ( 20 isolates) groups, dominate in the culturable bacteria assemblage. They also have the broadest distribution along the depth of the sediment. More than 72.4% of the isolates showed extracellular hydrolytic enzyme activities, such as amylases, proteases, lipases and Dnases, and nearly 59.2% were cold-adapted exoenzyme-producers. Several Halomonas strains show almost all the tested hydrolases activities. The wide distribution of exoenzyme activities in the isolates may indicate their important ecological role of element biogeochemical cycling in the studied deep-sea sedimentary environment.

胶州湾悬浮颗粒物中脂肪酸的时空分布及其在初级生产者到初级消费者食物传递中的作用

研究初级食物供给与初级消费之间数量与质量的关系在海洋浮游生态系统食物网研究中占有基础地位。悬浮颗粒物及浮游动物中脂肪酸的组成和含量可以很好地为食物关系研究提供信息。当悬浮颗粒物在时空上存在数量和质量差异时，这种差异就可能在浮游动物中体现出来，而且通过脂肪酸的信息可以追踪到这种差异。本研究旨在阐明脂肪酸在悬浮颗粒物组成中的生物标记作用和在悬浮颗粒物到浮游动物食物传递过程中的营养指示作用，同时应用这一标记物研究胶州湾海域悬浮颗粒物的大体分布及其与浮游动物间的食物关系。 文章首先依据2005年3月－2006年2月胶州湾颗粒有机碳及叶绿素a的数据估测碳生物量的转化系数，发现该系数受时空环境差异的影响，平均为56，从而推导出胶州湾浮游植物有机碳浓度，进而探讨浮游植物对颗粒有机碳的贡献。对各参数分析结果显示胶州湾颗粒有机碳、叶绿素a和浮游植物有机碳年平均浓度分别为为0.47 mg.L-1、4.16 μg.L-1及0.23 mg.L-1，三者表现出相似的时空变化动态，即湾内沿岸水域较高，湾外较低，夏季较高秋冬季较低。浮游植物对颗粒有机碳的贡献较高，年平均接近37%。 对悬浮颗粒物的脂肪酸组成分析后发现饱和脂肪酸（SSFA）16:0，14:0，18:0及单不饱和脂肪酸（MUFA）Σ16:1(ω7+ω5+ω9)所占比例较高，多不饱和脂肪酸（PUFA）中EPA和DHA也相对较高。总脂肪酸在水体中的绝对浓度及在颗粒有机碳中的相对含量均存在着时空变异，二者的平均变动范围分别在4.7－60.2 μg . L-1及20.1－86.7 μg . mg-1之间，夏季高于秋冬季，空间分布上二者均在湾东部相对较高，而在湾外较低。不同脂肪酸组合的时空变化可以反映出悬浮颗粒物组成的时空动态，其中16:1ω7/18:1ω9、Σ16:1/18:1ω9、Σ16:1/Σ18:1、Σ16/Σ18、Σ16/ΣFA及20:5ω3/22:6ω3等脂肪酸组合在研究海域可以较好的指示硅藻组成，而Σ18/ΣFA 及22:6ω3/ΣFA可以指示甲藻组成，BSFA/ΣFA、Σ(Br+St)/ΣFA 、Br/St (15:0)及 Br/St (15:0+17:0)可以较好的指示细菌，SSFA/ΣFA及(24:0+26:0)/ΣFA可以示踪碎屑组分及其中的陆源成份。ω3系列脂肪酸在有机碳中的含量及在总脂肪酸中的比例以及不饱和指数可以表征悬浮颗粒物的食物质量。通过标志脂肪酸对悬浮颗粒物组成的指示发现冬季2月悬浮颗粒物组成中硅藻所占比例较高，多数月份湾内近岸水域尤其是湾东部细菌组成相对较高，而湾口至湾外水域碎屑含量相对较高。 浮游动物总平均干重生物量为72.6 mg.m-3，平面分布表现为湾内北部及中心区域生物量普遍较高，湾东部水域较低，季节变化表现为总生物量在春季4月及冬季12月形成峰值，总体上在春季5月、夏季7月及秋冬大部分月份相对较低，但不同粒径组成其动态不尽相同。浮游动物的脂肪酸组成与悬浮颗粒物存在一定差别，表现为MUFA比例下降，PUFA比例升高；SSFA中14:0的比例下降，18:0及20:0比例提高，MUFA中20:1ω9比例升高，PUFA中，EPA及DHA所占比例也相对较高。8月份总脂肪酸含量较高，9月与10月相对较小，各粒级内差别不大。 利用主成份分析发现悬浮颗粒物的组分在浮游动物中能够用相应脂肪酸指标进行示踪，当食物数量充分满足需求时，浮游动物脂肪酸特征与悬浮颗粒物组成一致性较高，同时通过脂肪酸示踪发现当潜在食物数量较丰富时，浮游动物的摄食存在选择性，这种选择可能受食物质量的调控，而当食物数量较低时，其选择性也降低。 悬浮颗粒物中EPA含量及不饱和指数是相对重要的食物质量指示物，通过对其指示特征的分析发现胶州湾总体上浮游动物的摄食会影响其食物质量组成；但在8月，浮游动物的生物量受悬浮颗粒物质量的调控，而浮游动物生物量对食物数量的摄食压力较小，认为该时期是食物质量限制对浮游动物生物量影响相对重要的时期，可以用特征脂肪酸进行清晰的分析。

Experimental study on the impact of dinoflagellate Alexandrium species on populations of the rotifer Brachionus plicatilis

To investigate harmful effects of the dinoflagellate Alexandrium species on microzooplankton, the rotifer Brachionus plicatilis was chosen as an assay species, and tested with 10 strains of Alexandrium including one known non-PSP-producer (Alexandrium tamarense, AT-6). HPLC analysis confirmed the PSP-content of the various strains: Alexandrium lusitanicum, Alexandrium minutum and Alexandrium tamarense (ATHK, AT5-1, AT5-3, ATC102, ATC103) used in the experiment were PSP-producers. No PSP toxins were detected in the strains Alexandrium sp1, Alexandrium sp2. Exposing rotifer populations to the densities of 2000 cells ml(-1) of each of these 10 Alexandrium strains revealed that the (non-PSP) A. tarnarense (AT-6) and two other PSP-producing algae: A. lusitanicum, A. minutum, did not appear to adversely impact rotifer populations. Rotifers exposed to these three strains were able to maintain their population numbers, and in some cases, increase them. Although some increases in rotifer population growth following exposures to these three algal species were noted, the rate was less than for the non-exposed control rotifer groups. In contrast, the remaining seven algal strains (A. tamarense ATHK, AT5-1, AT5-3, ATC102, ATC103; also Alexandrium sp1 and Alexandrium sp2) all have adverse effects on the rotifers. Dosing rotifers with respective algal cell densities of 2000 cells ml-1 each, for Alexandrium spl, Alexandrium sp2, and A. tamarense strains ATHK and ATC103 showed mean lethal time (LT50) on rotifer populations of 21, 28, 29, and 36h, respectively. The remaining three species (A. tamarense strains AT5-1, AT5-3, ATC102) caused respective mean rotifer LT50S of 56, 56, and 71 h, compared to 160 h for the unexposed "starved control" rotifers. Experiments to determine ingestion rates for the rotifers, based on changes in their Chlorophyll a content, showed that the rotifers could feed on A. lusitanicum, A. minutum and A. tamarense strain AT-6, but could graze to little or no extent upon algal cells of the other seven strains. The effects on rotifers exposed to different cell densities, fractions, and growth phases of A. tamarense algal culture were respectively compared. It was found that only the whole algal cells had lethal effects, with strongest impact being shown by the early exponential growth phase of A. tamarense. The results indicate that some toxic mechanism(s), other than PSP and present in whole algal cells, might be responsible for the adverse effects on the exposed rotifers. (C) 2004 Elsevier B.V. All rights reserved.

克拉2异常高压气藏地质特征及开发技术研究

Kela-2 gas field in Tarim Basin is the main supply source for West-to-East Pipeline project, also the largest abnormally-pressured gas field discovered in China currently. The geological characterization, fine geological modeling and field development plan are all the world-class difficult problems. This work includes an integrated geological and gas reservoir engineering study using advanced technology and approaches, the scientific development plan of Kela-2 gas field as well as the optimizations of the drilling, production and surface schemes. Then, it's expected that the Kela-2 gas field can be developed high-efficiently.Kuche depression is one part of the thrust belt of the South Tianshan Mountains, Kela-2 field is located at the Kelasu structural zone in the north of Kuche depression. The field territory is heavily rugged with deeply cut gullies, complex geological underground structure, variable rock types, thrust structure development. Therefore, considerable efforts have been made to develop an integrated technique to acquire, process and interpret the seismic data in complicated mountain region. Consequently a set of seismic-related techniques in the complicated mountain region has been developed and successfully utilized to interpret the structure of Kela-2 gas field.The main reservoir depositional system of Kela 2 gas field is a platform - fan delta - braided river system. The reservoir rocks are medium-fine and extremely fine grained sandstones with high structure maturity and low composition maturity. The pore system structure is featured by medium-small pore, medium-fine throat and medium-low assortment. The reservoir of Kela-2 gas field is characteristic of medium porosity and medium permeability. The pay zone is very thick and its lateral distribution is stable with a good connection of sand body. The overpressure is caused mainly by the strongly tectonic squash activities, and other factors including the later rapid raise and compartment of the high-pressure fluid, the injection of high-pressure fluid into the reservoir.Based on the deliverability tests available, the average binomial deliverability equation is provided applicable for the overall field. The experimental results of rock stress-sensitive tests are employed to analyze the change trend of petrophysical properties against net confining stress, and establish the stress-based average deliverability equation. The results demonstrate the effect of rock deformation on the deliverability is limited to less than 5% in the early period of Kela-2 gas field, indicating the insignificant effect on deliverability of rock deformation.In terms of the well pattern comparisons and development planning optimizations, it is recommended that the producers should be located almost linearly along the structural axis. A total of 9 producers have a stable gas supply volume of 10.76 BCMPY for 17 years. For Kela-2 gas field the total construction investment is estimated at ￥7,697,690,000 RMB with the internal earning rate of 25.02% after taxation, the net present value of ￥7,420,160,000 RMB and the payback period of 5.66 years. The high profits of this field development project are much satisfactory.

Japonesinha: nova opção de mandioca de mesa para o Distrito Federal.

ABSTRACT: The cassava market within Distrito Federal (DF) presents potencial for expansion, for that reason, it is fundamental that the propagative material for planting (stem cuttings) presents genetic traits that confer high productivity to the crop, resistance against the main diseases and plagues and culinary qualities that fulfill the demands of the consumer market. In order to select varieties which combine the before mentioned interesting caracteristics for the producers and consumers of DF, we carried out experiments to evaluate table cassava type varieties at Núcleo Rural Jardim, DF (year 1999/2000), at an experimental area of Embrapa Cerrados located in the Municipy of Planaltina, DF (year 1999/2000), at Núcleo Rural Ponte Alta, DF (year 2002/2003) and at Brazlândia, DF (year 2003/2004). Among the evaluated varieties, if the parameters productivity, time necessary for cooking and colour of the pulp (which, in the case of DF, must be cream-colour or yellow due to market demands) are collectively considered, the variety Japonesinha / IAC 576-70 / BGMC 753 stands out as it combines high productivity of roots, moderate resistance to bacterial blight, good culinary quality (time necessary for cooking inferior to thirty minutes) and pulp of cream colour. Conclusively, this variety can be recommended to be cultivated at DF.

Evaluation of resources to support production of high quality health information for patients and the public. Final report for NHS Research Outputs Programme

Durbin, J., Urquhart, C. & Yeoman, A. (2003). Evaluation of resources to support production of high quality health information for patients and the public. Final report for NHS Research Outputs Programme. Aberystwyth: Department of Information Studies, University of Wales Aberystwyth. Sponsorship: Department of Health

An Imperial Legacy? An Exploration of the environmental impact of ancient metal mining and smelting in southern Jordan

Pyatt, B. Gilmore, G. Grattan, J. Hunt, C. McLaren, S. An imperial legacy? An exploration of the environmental impact of ancient metal mining and smelting in southern Jordan. Journal of Archaeological Science. 2000. 27 pp 771-778

Pink Worlds and Blue Worlds: A Portrait of Intimate Polarity

Griffiths, Merris, 'Pink Worlds and Blue Worlds: A Portrait of Intimate Polarity', In: 'Small Screens: television for children', D. Buckingham (Ed.), (London: Leicester University Press), pp. 159-184, 2002 RAE2008

Disseminação horizontal de genes que codificam para β-lactamases de espectro alargado em isolados de enterobacteriaceae de origem hospitalar

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Microbiological and physicochemical aspects of “salpicão”, a traditional dry sausage produced in the northeast of Portugal

Counts of total viable mesophilic bacteria (TVC), lactic acid bacteria (LAB), Microccocaceae, Enterobacteriaceae, Salmonella spp. and Listeria monocytogenes, in traditional Portuguese dry sausages from two industrial producers, were compared in batter and final product. During the production process, the TVC increased significantly, most likely due to the multiplication of fermentative flora. Enterobacteriaceae decreased from batter to final product while the S. aureus increased. Great variability was verified in detection of L. monocytogenes both between batches and industrial producers

The Challenges of Pluralism: Locating Religion in a World of Diversity

This is a postprint (author's final draft) version of an article published in the journal Social Compass in 2010. The final version of this article may be found at http://dx.doi.org/10.1177/0037768610362406 (login may be required). The version made available in OpenBU was supplied by the author.

Investigation of polyhydroxyalkanoate production by an activated sludge microbial consortium treating artificial dairy wastewater

Petrochemical plastics/polymers are a common feature of day to day living as they occur in packaging, furniture, mobile phones, computers, construction equipment etc. However, these materials are produced from non-renewable materials and are resistant to microbial degradation in the environment. Considerable research has therefore been carried out into the production of sustainable, biodegradable polymers, amenable to microbial catabolism to CO2 and H2O. A key group of microbial polyesters, widely considered as optimal replacement polymers, are the Polyhydroxyalkaonates (PHAs). Primary research in this area has focused on using recombinant pure cultures to optimise PHA yields, however, despite considerable success, the high costs of pure culture fermentation have thus far hindered the commercial viability of PHAs thus produced. In more recent years work has begun to focus on mixed cultures for the optimisation of PHA production, with waste incorporations offering optimal production cost reductions. The scale of dairy processing in Ireland, and the high organic load wastewaters generated, represent an excellent potential substrate for bioconversion to PHAs in a mixed culture system. The current study sought to investigate the potential for such bioconversion in a laboratory scale biological system and to establish key operational and microbial characteristics of same. Two sequencing batch reactors were set up and operated along the lines of an enhanced biological phosphate removal (EBPR) system, which has PHA accumulation as a key step within repeated rounds of anaerobic/aerobic cycling. Influents to the reactors varied only in the carbon sources provided. Reactor 1 received artificial wastewater with acetate alone, which is known to be readily converted to PHA in the anaerobic step of EBPR. Reactor 2 wastewater influent contained acetate and skim milk to imitate a dairy processing effluent. Chemical monitoring of nutrient remediation within the reactors as continuously applied and EBPR consistent performances observed. Qualitative analysis of the sludge was carried out using fluorescence microscopy with Nile Blue A lipophillic stain and PHA production was confirmed in both reactors. Quantitative analysis via HPLC detection of crotonic acid derivatives revealed the fluorescence to be short chain length Polyhydroxybutyrate, with biomass dry weight accumulations of 11% and 13% being observed in reactors 1 and 2, respectively. Gas Chromatography-Mass Spectrometry for medium chain length methyl ester derivatives revealed the presence of hydroxyoctanoic, -decanoic and -dodecanoic acids in reactor 1. Similar analyses in reactor 2 revealed monomers of 3-hydroxydodecenoic and 3-hydroxytetradecanoic acids. Investigation of the microbial ecology of both reactors as conducted in an attempt to identify key species potentially contributing to reactor performance. Culture dependent investigations indicated that quite different communities were present in both reactors. Reactor 1 isolates demonstrated the following species distributions Pseudomonas (82%), Delftia acidovorans (3%), Acinetobacter sp. (5%) Aminobacter sp., (3%) Bacillus sp. (3%), Thauera sp., (3%) and Cytophaga sp. (3%). Relative species distributions among reactor 2 profiled isolates were more evenly distributed between Pseudoxanthomonas (32%), Thauera sp (24%), Acinetobacter (24%), Citrobacter sp (8%), Lactococcus lactis (5%), Lysinibacillus (5%) and Elizabethkingia (2%). In both reactors Gammaproteobacteria dominated the cultured isolates. Culture independent 16S rRNA gene analyses revealed differing profiles for both reactors. Reactor 1 clone distribution was as follows; Zooglea resiniphila (83%), Zooglea oryzae (2%), Pedobacter composti (5%), Neissericeae sp. (2%) Rhodobacter sp. (2%), Runella defluvii (3%) and Streptococcus sp. (3%). RFLP based species distribution among the reactor 2 clones was as follows; Runella defluvii (50%), Zoogloea oryzae (20%), Flavobacterium sp. (9%), Simplicispira sp. (6%), Uncultured Sphingobacteria sp. (6%), Arcicella (6%) and Leadbetterella bysophila (3%). Betaproteobacteria dominated the 16S rRNA gene clones identified in both reactors. FISH analysis with Nile Blue dual staining resolved these divergent findings, identifying the Betaproteobacteria as dominant PHA accumulators within the reactor sludges, although species/strain specific allocations could not be made. GC analysis of the sludge had indicated the presence of both medium chain length as well short chain length PHAs accumulating in both reactors. In addition the cultured isolates from the reactors had been identified previously as mcl and scl PHA producers, respectively. Characterisations of the PHA monomer profiles of the individual isolates were therefore performed to screen for potential novel scl-mcl PHAs. Nitrogen limitation driven PHA accumulation in E2 minimal media revealed a greater propensity among isoates for mcl-pHA production. HPLC analysis indicated that PHB production was not a major feature of the reactor isolates and this was supported by the low presence of scl phaC1 genes among PCR screened isolates. A high percentage distribution of phaC2 mcl-PHA synthase genes was recorded, with the majority sharing high percentage homology with class II synthases from Pseudomonas sp. The common presence of a phaC2 homologue was not reflected in the production of a common polymer. Considerable variation was noted in both the monomer composition and ratios following GC analysis. While co-polymer production could not be demonstrated, potentially novel synthase substrate specificities were noted which could be exploited further in the future.

Assessment of the immunomodulatory effects of raw/farm milk and probiotic bacteria

The overall aims of this study were to investigate the differences between raw/farm milk and pasteurised milk with respect to potential immune modifying effects following consumption and investigate the bacterial composition of raw milk compared to pasteurised milk. Furthermore, in this thesis, panels of potential probiotic bacteria from the Bifidobacterium and Lactobacillus genera were investigated. The overall bacterial composition of raw milk was compared with pasteurised milk using samples obtained from commercial milk producers around Ireland using next generation sequencing technology (454 pyrosequencing). Here the presence of previously unrecognised and diverse bacterial populations in unpasteurised cow’s milk was identified. Futhermore the bacterial content of pasteurised milk was found to be more diverse than previously thought. The global response of the adenocarcinoma cell line HT-29 to raw milk and pasteurised milk exposures were also characterised using whole genome microarray technology. Over one thousand differentially expressed genes were identified which were found to be involved in a plethora of cellular functions. Interestingly a reduction in immune related activity (e.g. Major histocompatability complex class II signalling and T and B cell proliferation) was identified in cells exposed to pasteurised milk compared with raw milk exposures. Further studies comparing human cell response to raw versus pasteurised milk was performed using peripheral blood mononuclear cells (PBMC) from healthy donors. A reduction in CD14 was identified following raw milk exposures compared with pasteurised milk and the pattern of cytokine production may indicate that gram positive bacteria in the raw milk were contributing to the differences in the cellular response to raw versus pasteurised milk. Panels of potentially probiotic bacteria (comprising of lactobacilli and bifidobacteria) were further assessed for immunomodulatory capabilities using cell culture based models. Gene expression and cytokine production were used to evaluate stimulated and unstimulated (LPS) cellular responses as well as interaction mechanisms

Food preservation using antifungal lactic acid bacteria

Fungal spoilage of food and feed prevails as a major problem for the food industry. The use antifungal-producing lactic acid bacteria (LAB) may represent a safer, natural alternative to the use of chemical preservatives in foods. A large scale screen was undertaken to identify a variety of LAB with antifungal properties from plant, animal and human sources. A total of 6,720 LAB colonies were isolated and screened for antifungal activity against the indicator Penicillium expansum. 94 broad-spectrum producers were identified through 16S rRNA sequencing with the majority of the population comprising Lactobacillus plantarum isolates. Six broad-spectrum isolates were consequently characterised. Pedicococcus pentosaceous 54 displayed potent anti-mould capabilities in pear, plum and grape models and may represent an ideal candidate for use in the beverage industry. Two antifungal Lb. plantarum isolates were assessed for their technological robustness and potential as biopreservatives in refrigerated foods. Lb. plantarum 16 and 62 displayed high levels of tolerance to freeze-drying, low temperature exposure and high salt concentrations. Both lactobacilli were introduced as supplements into orange juice to retard the growth of the spoilage yeast Rhodotorula mucilaginosa. Furthermore the isolates were applied as adjuncts in yoghurt production to successfully reduce yeast growth. Lb. plantarum 16 proved to be the optimal inhibitor of yeast growth in both food matrices. To date there is limited information available describing the mechanisms behind fungal inhibition by LAB. The effects of concentrated cell-free supernatant (cCFS), derived from Lb. plantarum 16, on the growth of two food-associated moulds was assessed microscopically. cCFS completely inhibited spore, germ tube and hyphal development. A transcriptomic approach was undertaken to determine the impact of antifungal activity on Aspergillus fumigatus Af293. A variety of genes, most notably those involved in cellular metabolism, were found to have their transcription modulated in response to cCFS which is indicative of global cellular shutdown. This study provides the first insights into the molecular targets of antifungal compounds produced by LAB. The genome sequence of the steep water isolate Lb. plantarum 16 was determined. The complete genome of Lb. plantarum16 consists of a single circular chromosome of 3,044,738 base pairs with an average G+C content of 44.74 % in addition to eight plasmids. The genome represents the smallest of this species to date while harbouring the largest plasmid complement. Some features of particular interest include the presence of two prophages, an interrupted plantaricin cluster and a chromosomal and plasmid encoded polysaccharide cluster. The sequence presented here provides a suitable platform for future studies elucidating the mechanisms governing antifungal production.

The defining characteristics of alternative food initiatives in Ireland: a social movement battling for an alternative food future?

Alternative food initiatives (AFIs) have been described as an attempt to change and improve aspects of how the food system operates. They are focused around more traditional, local and sustainable food production and circulation. AFIs such as farmers’ markets, allotments and community gardens, share a desire to reduce the number of steps food goes through from production to plate. The role of these initiatives in the food system, and their potential to impact real change, has however been questioned. Working to better understand this issue is a central concern of this research. To do this a two tier analysis has been deployed. The first tier involves identifying the characteristics and general dynamics of AFIs. Bourdieu’s theory of practice, and the theories of field and capital, are the concepts applied. The research then uses these findings in the second tier of analysis concerned with relating AFI characteristics and dynamics back to their key traits, positive and negative, as well as arguments made about AFI’s role identified from previous research. Another part of this second tier of analysis is exploring if AFIs, the producers, consumers, organisations and groups that make up this phenomenon, can be considered a social movement. AFIs can be referred to collectively as a social movement, but are not often explored theoretically from this perspective. AFIs in Ireland provide the empirical context for this research. A series of qualitative interviews in four areas of Ireland, as well as evidence from primary and secondary sources are analysed. The research finds that AFIs can be understood as the potential beginnings of a lifestyle social movement. Leaders are of central importance to its development. It is also found that an important role of AFIs is revitalising, supporting and contributing to food culture.