Adhesion,Presence and Antifouling of Deinococcus geothermalis in Paper Machine Environment

This thesis has two items: biofouling and antifouling in paper industry. Biofouling means unwanted microbial accumulation on surfaces causing e.g. disturbances in industrial processes, contamination of medical devices or of water distribution networks. Antifouling focuses on preventing accumulation of the biofilms in undesired places. Deinococcus geothermalis is a pink-pigmented, thermophilic bacterium, and extremely resistant towards radiation, UV-light and desiccation and known as a biofouler of paper machines forming firm and biocide resistant biofilms on the stainless steel surfaces. The compact structure of biofilm microcolonies of D. geothermalis E50051 and the adhesion into abiotic surfaces were investigated by confocal laser scanning microscope combined with carbohydrate specific fluorescently labelled lectins. The extracellular polymeric substance in D. geothermalis microcolonies was found to be a composite of at least five different glycoconjugates contributing to adhesion, functioning as structural elements, putative storages for water, gliding motility and likely also to protection. The adhesion threads that D. geothermalis seems to use to adhere on an abiotic surface and to anchor itself to the neighbouring cells were shown to be protein. Four protein components of type IV pilin were identified. In addition, the lectin staining showed that the adhesion threads were covered with galactose containing glycoconjugates. The threads were not exposed on planktic cells indicating their primary role in adhesion and in biofilm formation. I investigated by quantitative real-time PCR the presence of D. geothermalis in biofilms, deposits, process waters and paper end products from 24 paper and board mills. The primers designed for doing this were targeted to the 16S rRNA gene of D. geothermalis. We found D. geothermalis DNA from 9 machines, in total 16 samples of the 120 mill samples searched for. The total bacterial content varied in those samples between 107 to 3 ×1010 16S rRNA gene copies g-1. The proportion of D. geothermalis in those same samples was minor, 0.03 1.3 % of the total bacterial content. Nevertheless D. geothermalis may endanger paper quality as its DNA was shown in an end product. As an antifouling method towards biofilms we studied the electrochemical polarization. Two novel instruments were designed for this work. The double biofilm analyzer was designed for search for a polarization program that would eradicate D. geothermalis biofilm or from stainless steel under conditions simulating paper mill environment. The Radbox instrument was designed to study the generation of reactive oxygen species during the polarization that was effective in antifouling of D. geothermalis. We found that cathodic character and a pulsed mode of polarization were required to achieve detaching D. geothermalis biofilm from stainless steel. We also found that the efficiency of polarization was good on submerged, and poor on splash area biofilms. By adding oxidative biocides, bromochloro-5,5-dimethylhydantoin, 2,2-dibromo-2-cyanodiacetamide or peracetic acid gave additive value with polarization, being active on splash area biofilms. We showed that the cathodically weighted pulsed polarization that was active in removing D. geothermalis was also effective in generation of reactive oxygen species. It is possible that the antifouling effect relied on the generation of ROS on the polarized steel surfaces. Antifouling method successful towards D. geothermalis that is a tenacious biofouler and possesses a high tolerance to oxidative stressors could be functional also towards other biofoulers and applicable in wet industrial processes elsewhere.

Holographic optical element based single-mode hybrid fiber optic interferometer for realizing zero-order fringe

A holographic optical element (HOE) based single-mode hybrid fiber optic interferometer for realizing the zero-order fringe is described. The HOE proposed and used integrates the actions of a beam combiner and a lens, and endows the interferometer with high tolerance for repositioning errors. The proposed method is simple and offers advantages such as the elimination of in situ processing for the hologram.

Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

Background: Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis. Results: More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs. Conclusions: Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.

Acute toxicity of un-ionized ammonia to milkfish (Chanos chanos) fingerlings

The acute toxicity of un-ionized ammonia to milkfish (Chanos chanos) fingerlings was determined using a static bioassay system. Median lethal concentrations found show that milkfish fingerlings have a high tolerance to ammonia and it is unlikely that levels as high as those employed for the acute exposure would be found to occur under natural conditions. Although the threat of acute toxicological effects induced by ammonia are remote, such conditions might be encountered in stressed natural environments or in heavily loaded aquaculture systems.

Response Specificity to Advertisement Vocalization in the Chinese Alligator (Alligator sinensis)

Stringency in the identification of conspecific call properties is essential among sympatric species to ensure conspecific mating, as the risk of improper recognition and heterospecific mating is high. In this study we investigated the basic signal structure required for intraspecies communication in the Chinese alligator (Alligator sinensis), a species that has no relatives living in sympatry, by playback of signals modified in the temporal (truncating original bellows with first 1/4, 1/2, 3/4 or last 1/4, 1/2, 3/4 portion) or frequency domain (with low- or high-pass filters at frequencies 100, 250, 500 and 1000 Hz), or by reversal of natural bellows. The playback experiments revealed that relatively large modifications in bellow temporal or frequency structure failed to impair Chinese alligators' bellowing behavior; even reversed bellows effectively evoked a positive response. In general, the first half of the bellow in temporal domain and frequencies below 500 Hz were critical for behavioral induction, while the last half of the bellow in temporal domain and frequencies above 500 Hz failed to produce a single positive response, implying a potential functional signal redundancy. The observed high tolerance to bellow variations in Chinese alligators may be an evolutionary adaptation to (1) the acoustic constraints of propagation imposed by dense vegetative habitats; or (2) a lack of selection pressure due to the low risk of incorrect conspecific recognition and heterospecific mating.

Physiological comparison between colonial and unicellular forms of Microcystis aeruginosa Kutz. (Cyanobacteria)

In order to gain insight into the bloom sustainment of colonial Microcystis aeruginosa Katz., physiological characterizations were undertaken in this study. Compared with unicellular Microcystis, colonial Microcystis phenotypes exhibited a higher maximum photosynthetic rate (Pm), a higher maximum electron transfer rate (ETRmax), higher phycocyanin content, and a higher affinity for inorganic carbon (K-0.5 DIC <= 8.4 +/- 0.7 mu M) during the growth period monitored in this study. This suggests that photosynthetic efficiency is a dominant physiological adaptation found in colonial Microcystis, thus promoting bloom sustainment. In addition, the high content of soluble and total carbohydrates in colonial Microcystis suggests that this phenotype may possess a higher ability to tolerate enhanced stress conditions when compared to unicellular (noncolonial) phenotypes. Therefore, high photosynthetic activities and high tolerance abilities may explain the bloom sustainment of colonial Microcystis in eutrophic lakes.

Sequential ultrastructural and biochemical changes induced in vivo by the hepatotoxic microcystins in liver of the phytoplanktivorous silver carp Hypophthalmichthys molitrix

Up to now, in vivo studies on the toxic effects of microcystins (MCs) on the ultrastructures of fish liver have been very limited. The phytoplanktivorous silver carp was injected i.p. with extracted hepatotoxic microcystins (mainly MC-RR and -LR) at a dose of 1000 mu g MC-LReq. kg(-1) body weight, showing a time-dependent ultrastructural change in liver as well as significant increases in enzyme activity of plasma alanine aminotransferase (ALT), aspartate aminotransferase (AST) and lactate dehydrogenase (LDH). We observed for the first time the occurrence of a large amount of activated secondary lysosomes, which might be an adaptive mechanism to eliminate or lessen cell damage caused by MCs through lysosome activation. Quantitative and qualitative determinations of MCs in the liver were conducted by HPLC and LC-MS2, respectively. MCs concentration in the liver reached the maximum (114.20 mu g g(-1) dry weight) after 3 h post-injection, and then rapidly dropped to 7.57 mu g g(-1) dry weight at 48 h, indicating a deputation of 99% accumulated MC-LReq. On the other hand, a decrease trend in glutathione (GSH) concentration was observed in the liver of silver carp while the activity of glutathione S-transferase (GST) increased significantly after injection. The high tolerance of silver carp to MCs might be due to the high basic GSH level in their liver, and/or an increased GSH synthesis. (C) 2007 Elsevier Inc. All rights reserved.

镉、铅排异大白菜品种的筛选和鉴定及安全生产调控技术

随着工农业的快速发展，土壤重金属尤其Cd和Pb污染日益严重。筛选和培育具有重金属低积累特性的农作物排异品种被认为是当前应对土壤重金属污染最为合理和有效的途径之一。本文通过盆栽试验、大田试验和砂培试验，研究了大白菜品种对Cd和Pb的吸收和积累的品种差异、对Cd、Pb胁迫的响应以及大白菜安全生产的调控技术，得出以下结论： 1) 盆栽梯度试验中，80种大白菜地上部对Cd的吸收存在显著差异(p < 0.05)。在3种Cd处理下(1.0, 2.5和5.0 mg/kg)，80种大白菜Cd含量浓度范围分别为(mg/kg) 0.22–2.46, 0.90–14.10和2.03–18.01, 其平均值分别为 0.79, 3.76 和6.79 mg/kg DW。大白菜对Cd胁迫具有较强的耐性。大田试验中，15种大白菜的富集系数和转运系数与盆栽梯度试验的结果基本一致。排异植物的筛选和鉴定标准包括：(1)该植物的地上部和根部的Cd含量都很低或者可食部位低于有关标准；(2) 富集系数(BF) < 1.0；(3) 转运系数(TF) < 1.0；(4)该植物具有较高的Cd耐性，在较高的Cd污染下能够正常生长且生物量无显著下降。采用此标准，结合盆栽梯度试验和大田试验结果，北京新3号、绿星70和丰源新3号可鉴定为Cd排异品种。秋傲和赛新5号具有排异Cd特性，但其对Cd的耐性较差。 2) 盆栽梯度试验中，在Pb投加浓度为500和1500 mg/kg处理下，30种大白菜地上部对Pb的吸收存在显著差异 (p < 0.05)，其Pb浓度的范围分别为：0.52–8.68 和1.86–16.20 mg/kg, 其平均值分别为3.01 和6.87 mg/kg DW。并且，随着Pb浓度的增加，白菜地上部Pb含量有随之增加的趋势。大白菜对Pb具有较强的耐性。低浓度的Pb处理对大白菜的生物具有一定的促进作用。结合盆栽试验和大田试验的结果，秋傲、世博秋抗和福星80可鉴定为Pb排异大白菜品种。 3) 砂培试验中，在Cd和Pb胁迫下，大白菜地上部的丙二醛(MDA)含量增加，随着Cd处理浓度的增加，超氧化物歧化酶(SOD)活性呈现先下降后上升接着下降的趋势，酸菜王的SOD活性要高于北京新3号SOD的活性。随着Pb处理浓度的增加，福星80地上部的SOD活性随之增加，而绿星大棵菜地上部的SOD活性先下降后增加。在不同梯度的Cd处理下，大白菜地上部的可溶性蛋白(SP)含量未见显著降低，甚至有所增加，而在不同梯度的Pb处理下，大白菜地上部的SP含量有所降低。 4) 施用改良剂可升高土壤的pH值和降低土壤中的有效态Cd，从而对大白菜的生长具有促进作用。施用改良剂可显著降低大白菜对Cd和Pb的吸收和累积。

Enzymatic reaction of the immobilized enzyme on porous silicon studied by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry

Desorption/ionization on silicon mass spectrometry (DIOS-MS) is a matrix-free technique that allows for the direct desorption/ionization of low-molecular-weight compounds with little or no fragmentation of analytes. This technique has a relatively high tolerance for contaminants commonly found in biological samples. DIOS-MS has been applied to determine the activity of immobilized enzymes on the porous silicon surface. Enzyme activities were also monitored with the addition of a competitive inhibitor in the substrate solution. It is demonstrated that this method can be applied to the screening of enzyme inhibitors. Furthermore, a method for peptide mapping analysis by in situ digestion of proteins on the porous silicon surface modified by trypsin, combined with matrix-assisted laser desorption/ionization-time of flight-MS has been developed.

Immune condition of Chlamys farreri in response to acute temperature challenge

The effects of acute temperature challenge on some immune parameters of haemocyte in Zhikong scallop, Chlamys farreri, recognised as a temperature sensitive bivalve species, were evaluated over a short period of time. Scallops were suddenly transferred from 17 degrees C to 11 degrees C, 23 degrees C and 28 degrees C for a period of 72 h. Total haemocyte count (THC), percentage of phagocytic haemocytes, reactive oxygen species (ROS) production, acid phosphatase (ACP) and superoxide dismutase (SOD) activities (in both haemocyte lysate and cell-free haemolymph) were chosen as biomarkers of temperature stress. Results demonstrated that the percentage of phagocytic haemocytes and ACP activity in cell-free haemolymph of scallops challenged at 28 degrees C for 72 h significantly decreased. By contrast, reactive oxygen species production by haemocytes increased when compared to the initial values. It is concluded that haemocyte activities of C. farreri appear to be compromised when scallops were transferred from 17 degrees C to 28 degrees C. Meanwhile, no obvious negative effect of acute temperature stress was detected on haemocyte activities of C. farreri challenged at 11 degrees C, which highlighted the high tolerance of scallops to acute decrease of seawater temperatures. (C) 2007 Elsevier B.V. All rights reserved.

Blood-gas properties of plateau zokor (Myospalax baileyi)

Plateau zokor (Myospalax baileyi) is one of the blind subterranean mole rats that spend their life solely underground in scaled burrows. It is one of the special species of the Qinghai-Tibet plateau. In their burrows, oxygen is low and carbon dioxide is high and their contents fluctuate with the change of seasons, soil types, rain and depth of burrows. However, plateau zokors show successful adaptation to that extreme environment. In this study, their adapting mechanisms to the hypoxic hypercapnic environment were analyzed through the comparison of their blood-gas properties with that of pikas (Ochotona curzniae) and Sprague-Dawley rats. The results indicated that plateau zokors had higher red blood corpuscle counts (8.11 +/- 0.59 (10(12)/L)) and hemoglobin concentrations (147 +/- 9.85 g/L), but hematocrit (45.9 +/- 3.29%) and mean corpuscular volume (56.67 +/- 2.57 fL) were lower than the other rodents. Their arterial blood and venous blood pH were 7.46 +/- 0.07 and 7.27 +/- 0.07. Oxygen pressure in arterial blood of plateau zokors was about 1.5 times higher than that of pikas and rats, and it was 0.36 and 0.26 times in their venous blood. Partial pressure for carbon dioxide in arterial and venous blood of plateau zokors was 1.5-fold and 2.0-fold higher, respectively, than in rats and pikas. Oxygen saturation of plateau zokors was 5.7 and 9.3 times lower in venous blood than that of pikas and rats, respectively. As result, the difference of oxygen saturation in arterial blood to venous blood was 2- and 4.5-fold higher in plateau zokors as that of pikas and rats, respectively. In conclusion, plateau zokors had a high tolerance to pH changes in tissues, together with strong capabilities to obtain oxygen from their hypoxic-hypercapnic environment. (c) 2006 Published by Elsevier Inc.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with a matrix of carbon nanotubes for the analysis of low-mass compounds in environmental samples

The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for environmental analysis has been mainly focused on qualitative analysis of high-mass molecules, such as toxins, humic acid, and microorganisms. Herein,we describe a novel MALDI-TOF-MS method with a matrix of oxidized carbon nanotubes for analysis of low-mass compounds in environmental samples. A number of chemicals in the environment were qualitatively analyzed by the present method, and it was found that most of them, especially the highly polar chemicals, were measurable with high sensitivity. With the intrinsic ability to measure high-mass chemicals, this method can compensate for the current shortage of methods for environmental analysis for the measurement of highly polar or high-mass chemicals. For sample analysis, arsenic speciation in Chinese traditional medicines was qualified and diphenylolpropane in water samples was quantified. With the relatively high tolerance of the method to interfering molecules, a simple pretreatment or even no pretreatment could be employed before MS detection. Furthermore, this method can be employed in a high-throughput format.

A robust approach to subsequence matching

In terms of a general time theory which addresses time-elements as typed point-based intervals, a formal characterization of time-series and state-sequences is introduced. Based on this framework, the subsequence matching problem is specially tackled by means of being transferred into bipartite graph matching problem. Then a hybrid similarity model with high tolerance of inversion, crossover and noise is proposed for matching the corresponding bipartite graphs involving both temporal and non-temporal measurements. Experimental results on reconstructed time-series data from UCI KDD Archive demonstrate that such an approach is more effective comparing with the traditional similarity model based algorithms, promising robust techniques for lager time-series databases and real-life applications such as Content-based Video Retrieval (CBVR), etc.

How crucial is back gate misalignment/oversize in double gate MOSFETs for ultra-low-voltage analog/rf applications?

In the present work, by investigating the influence of source/drain (S/D) extension region engineering (also known as gate-underlap architecture) in planar Double Gate (DG) SOI MOSFETs, we offer new design insights to achieve high tolerance to gate misalignment/oversize in nanoscale devices for ultra-low-voltage (ULV) analog/rf applications. Our results show that (i) misaligned gate-underlap devices perform significantly better than DC devices with abrupt source/drain junctions with identical misalignment, (ii) misaligned gate underlap performance (with S/D optimization) exceeds perfectly aligned DG devices with abrupt S/D regions and (iii) 25% back gate misalignment can be tolerated without any significant degradation in cut-off frequency (f(T)) and intrinsic voltage gain (A(VO)). Gate-underlap DG devices designed with spacer-to-straggle ratio lying within the range 2.5 to 3.0 show best tolerance to misaligned/oversize back gate and indeed are better than self-aligned DG MOSFETs with non-underlap (abrupt) S/D regions. Impact of gate length and silicon film thickness scaling is also discussed. These results are very significant as the tolerable limit of misaligned/oversized back gate is considerably extended and the stringent process control requirements to achieve self-alignment can be relaxed for nanoscale planar ULV DG MOSFETs operating in weak-inversion region. The present work provides new opportunities for realizing future ULV analog/rf design with nanoscale gate-underlap DG MOSFETs. (C) 2008 Elsevier Ltd. All rights reserved.

Isolation and Characterisation of 1-Alkyl-3- Methylimidazolium Chloride Ionic Liquid-Tolerant and Biodegrading Marine Bacteria

The aim of this study was to isolate and identify marine-derived bacteria which exhibited high tolerance to, and an ability to biodegrade, 1-alkyl-3-methylimidazolium chloride ionic liquids. The salinity and hydrocarbon load of some marine environments may induce selective pressures which enhance the ability of microbes to grow in the presence of these liquid salts. The isolates obtained in this study generally showed a greater ability to grow in the presence of the selected ionic liquids compared to microorganisms described previously, with two marine-derived bacteria, Rhodococcus erythropolis and Brevibacterium sanguinis growing in concentrations exceeding 1 M 1-ethyl-3-methylimidazolium chloride. The ability of these bacteria to degrade the selected ionic liquids was assessed using High Performance Liquid Chromatography (HPLC), and three were shown to degrade the selected ionic liquids by up to 59% over a 63-day test period. These bacterial isolates represent excellent candidates for further potential applications in the bioremediation of ionic liquid-containing waste or following accidental environmental exposure.