5-氟尿嘧啶-β-环糊精结肠靶向前体药物的研究

5-氟尿嘧啶(5-Fluorouracil， 5-FU)是一种抗代谢药物，广泛用于临床治疗结直肠癌、胃癌、乳腺癌等多种癌症，但其首过代谢显著、亲脂性较低，选择性差、毒副作用大。为克服这些缺点人们对5-FU进行了大量的修饰工作，包括小分子修饰以及与各种载体形成微球、微囊、纳米粒、共价前药等。 环糊精(Cyclodextrin，简称CD)，可被结肠中的糖苷酶特异性地降解成小分子糖，而胃和小肠中由于缺乏相应的酶而使环糊精不被降解，这一特性在结肠药物的靶向输送及释放中有重要应用价值。环糊精中含有丰富的羟基，易进行化学修饰，将药物与环糊精通过共价键结合制成前药，使其在胃和小肠中不降解，而在盲结肠中被特异性的酶降解释出药物，达到结肠靶向释药的目的。研究表明，环糊精作为一种前药载体为结肠靶向释药和缓释、控释系统提供了一种有效的手段。 本工作选择5-氟尿嘧啶为模型药物、β-环糊精作为载体，通过中间体5-FU羧酸衍生物的制备及其与β-环糊精的偶联，合成了系列5-FU-β-CD前体药物，并利用紫外、红外、质谱、核磁、元素分析、热分析等手段对其进行结构表征。同时，还研究了前体药物的体外释药性质。具体内容包括： 1. 含有羧基的5-FU衍生物中间体的合成：(5-氟尿嘧啶-1-基)-乙酸(FUAC)、3-(5-氟尿嘧啶-1-基)-丙酸(FUPC)、5-(5-氟尿嘧啶-1-基)-戊酸(FUVC)的合成。 2. 中间体5-FU的羧酸衍生物与β-CD的偶联：分别通过以6-OTs-β-CD为中间体的取代法和活化酯法，合成了第一面取代和第二面取代的5-FU-β-CD大分子前体药物。在二面取代的前体药物制备中，通过改变原料的比例，合成了系列不同取代度(DS)的2-[(5-氟尿嘧啶-1-基)-乙酰基] -β-环糊精结合物。 3. 对上述前体药物进行体外释放研究：分别考察了前体药物在不同pH缓冲溶液中的水解行为及其在小鼠胃肠道人工体液中的酶解行为，并通过UV-Vis及HPLC对前体药物释放情况进行检测分析。 5-Fluorouracil(5-Fu), commonly known as a broad-spectrum antineoplastic drug, has been widely used in the treatment of various kinds of cancer including colon cancer for 40 years. However, this antitumor agent exhibits serious adverse effects, such as their marrow toxicity, gastrointestinal reaction and low selectivity in their clinical use. In order to improve its antitumor activity and reduce its toxicity, the compound was modified in various ways, including the formation of conjugated prodrugs with kinds of carrier, microsphere and nanoparticles etc. Cyclodextrins(CDs) are known to be barely capable of being hydrolyzed and only slightly absorbed in passing through the stomach and small intestine; however they are fermented into small saccharides by colonic microflora and thus absorbed as small saccharides in the large intestine. This biodegradation property of CDs may be useful as a colon-targeting carrier, and thus CD prodrugs may serve as a source of site-specific delivery of drugs to colon. It was demonstrated that prodrugs of CDs can provide a versatile means for construction of not only colon targeted delivery systems, but also delayed release systems. 5-Fluorouracil was taken as a model drug and β-CD as the carrier in this study. Series prodrugs of 5-FU was prepared through the preparation of reactive 5-FU derivatives containing carboxyl group and coupling to hydroxyl groups of CD. The structures of the conjugates were charactered by using IR, UV–vis, ESI-MS, 1H, 13C-NMR spectra, elemental analyses, and thermal analysis. In vitro hydrolysis behavior in aqueous solution and in rat gastrointestinal tract contents of the conjugates were also investigated. The main content of this dissertation includes following aspects: 1. The preparation of 5-FU derivatives containing carboxyl group: 5-Fluorouracil- acetic acid(FUAC)、3-(5-FU-1)-propionic acid (FUPC)、and 5-(5-FU-1)-valeric acid(FUVC). 2. The coupling of 5-FU derivatives to β-CD: 5-FU was selectively conjugated onto the primary or secondary hydroxyl groups of β-CD through an ester linkage, by the substitution of 6-OTs-β-CD and the activated ester method respectively. For the secondary face conjugation, the degree of substitution(DS) can be controlled by changing the mole ratio of the starting materials(FUAC and β-CD). 3. In vitro release behavior of the conjugates in aqueous solution and in rat gastro- intestinal tract contents of the conjugates were investigated, and the reaction was monitored and analyzed by using UV-Vis and HPLC methods.

川西亚高山针叶林主要针叶树种年轮生态学研究

米亚罗地区是四川西部较为典型的亚高山针叶林区域之一。为建立该地区主要针叶树种岷江冷杉、云杉、紫果云杉和红杉的年轮宽度年表资料，了解不同海拔高度岷江冷杉原始林和不同恢复过程的人工针叶林及次生混交林树木径向生长规律，结合样地调查，用生长锥钻取了树木芯样做年轮生态学分析。芯样经过标准化程序固定和打磨抛光后，用WinDENDRO图像分析系统测量年轮宽度序列，用COFECHA程序交叉定年和控制测量数据质量，用ARSTAN程序建立了4个主要针叶树种的地区年表和不同海拔高度岷江冷杉林及人工针叶林和次生混交林针叶树的样地年表。 4个主要针叶树种年轮宽度年表的平均敏感度低于0.2，而其晚材宽度年表都具相对较高的平均敏感度。早材宽度与年轮总宽度标准化年表间的相关系数均在0.9以上；晚材宽度与年轮总宽度标准化年表间的相关系数则种间差异较大，红杉的最高，岷江冷杉的最低。岷江冷杉晚材宽度与年轮总宽度的相关性从1970年以后明显下降，而其他种的相关系数则随时间变化较小。树种之间标准化年表显著正相关，而云杉与紫果云杉和红杉与岷江冷杉之间相关系数明显较高。年表序列的第1主分量表达了4个树种树木共同径向生长变化格局；第2至第4主分量分别表达了云杉属和冷杉属、常绿针叶树种和落叶针叶树种以及云杉和紫果云杉树木径向生长变化差异。 不同海拔高度的8个岷江冷杉样地年轮宽度年表序列敏感度大体上随海拔高度升高而降低。各样地早材宽度与年轮总宽度年表之间的相关系数均在0.9以上，且随海拔高度变化不大；晚材宽度与年轮总宽度之间的相关系数随海拔高度的变化较大，并有随海拔升高而降低的趋势。样地年表序列之间相关系数差异很大，高海拔样地年表间多为显著正相关；低海拔样地年表间的相关系数变化不一；高海拔和低海拔样地年表之间相关性较差，且多不显著。样地年表的第1主分量能解释年表序列总方差的37.5%，反映了不同海拔高度岷江冷杉林木共同的径向生长变化格局；第2和第3主分量分别解释总方差的24.5%和18.2%，表现出明显的高海拔和低海拔样地树木间不同的径向生长变化，除一些样地例外，它们一般与低海拔样地年表有正相关，与高海拔样地年表有负相关。在那些另外的样地，海拔以外的其他因素可能也影响了树木径向生长变化。不同海拔高度样地林木的生长抑制和生长释放频率在不同时期表现出较大的差异，表明了不同的干扰历史和林木补充时间。 人工针叶林和次生混交林各样地林木早材宽度与其年轮总宽度年表之间相关系数均高达0.9以上；晚材宽度与年轮总宽度年表之间也都显著正相关，但人工针叶林样地的明显较高。样地年表序列之间的相关关系表现为，林分起源和经营管理相似的样地年表之间的相关系数明显较高，如人工针叶林与人工针叶林尽管树种不同，但样地年表之间显著正相关，而与次生混交林样地年表间关系不显著；反之亦然。综合比较各项生长参数及不同时期的树木径向生长速率，人工针叶林树木的胸径增长至少在40年以内是优于次生混交林的同种（或不同种）针叶树的。不同样地林木生长释放和生长抑制及人工针叶林树木胸高断面积增长分析表明，除严重的人为干扰外，林分郁闭后林木密度过大是造成高频率生长抑制的主要原因，在林分发育的适当时期通过抚育间伐等措施调控林分密度，是保证林木胸高断面积在一定时期内保持较高的连年增长的关键。日本落叶松作为引进的树种，在海拔3100 m左右种植表现良好，近30年来各项生长指标均高于林龄相近的云杉人工林，因此，适当用其作为川西亚高山针叶林采伐迹地快速恢复是合理的。 Miyaluo area is one of the typical regions covered by subalpine coniferous forests in western Sichuan province of southwestern China. To develop the regional tree-ring width chronology series for the dominant conifers such as Abies faxoniana, Picea asperata, P. purpurea and Larix potaninii, and to understand the radial growth patterns of conifers in Abies faxoniana natural forest stands at different altitudes, and in coniferous plantations and natural regenerated mixed stands in their different restoring processes as well, increment cores were sampled in the field together with conventional plots investigations for dendroecological analyses. After the increment cores being prepared according to standard procedures, the ring widths (total-ring and intra-ring widths) were measured with a WinDENDRO image-analysis system, and the measured tree-ring sequences were crossdated and quality-controlled with the software COFECHA. Using the software ARSTAN, we developed tree-ring width based chronology series of the four dominant conifers, eight site-specific Abies faxoniana chronologies, and seven site-specific chronologies of conifers in coniferous plantations and natural regenerated mixed stands. Mean sensitivities for total ring width chronologies of the four sampled dominant conifers were all below 0.2, while those for the latewood width chronologies of the same species were relatively much higher. Correlation coefficients between standard earlywood and total ring width chronologies of the four conifers were all above 0.9, but those between standard latewood and total ring width chronologies exhibited differences among species, with the coefficient of Larix potaninii the highest and that of Abies faxoniana the lowest. Correlation coefficients between latewood and total ring width of A. faxoniana obviously decreased from 1920-1970 for successive 50-year segments with 10-years lag analyses, though the same for the other three species changed unnoticeably with time. Tree-ring standard chronologies among species showed significant positive correlations, with the correlation coefficients between chronologies of Picea asperata and P. purpurea, and of Larix potaninii and Abies faxoniana relatively much higher. The first principal component of tree-ring chronologies represented the common radial growth patterns of the four conifers in Miyaluo area. The second, third and fourth PCs expressed the differences in radial growth responses for the genus Picea and Abies, for the evergreen and deciduous confers, and for the two species of the genus Picea, respectively. In general, mean sensitivities of the eight Abies faxoniana site-specific tree-ring width chronologies decreased with increasing altitude. The correlation coefficients between earlywood and total ring width chronologies for all sites reached 0.9, which did not change much with altitude; but those between latewood and total ring width chronologies diversified, with a decreasing tendency from lower altitudinal sites to higher altitudinal sites. Correlation coefficients among site chronologies varied considerably, with significant positive correlations among higher site chronologies, mixed results among lower site chronologies, and poor and insignificant correlations between chronologies of higher site and lower site. The first PC, which represents 37.5% of the total variance, reflected a common radial growth response at sites of different altitudes, and it showed a tendency of explaining more variance with increasing altitude. The second and the third PCs contributed to 24.5% and 18.2% of the total variance, respectively, exhibiting distinctive differences in radial growth responses between low- and high-altitudinal sites. With some exceptions, the radial growth represented by the second and third PCs had a positive correlation with that at the low-altitudinal sites and a negative correlation with that at the high-altitudinal sites. For those exceptional sites, factors other than altitude might also play a role in affecting tree-ring growth variations. Trees in stands of different altitudes showed great differences in frequencies of growth suppressions and releases through times, suggesting different disturbance histories and periods when trees recruiting to the canopy. Correlation coefficients between earlywood and total ring width chronologies for all sites of coniferous plantations and natural regenerated mixed stands were also above 0.9; and the same between latewood width and total ring width chronologies all positively correlated, too, with the coefficients of the coniferous plantations obviously much higher. Correlations among site chronologies showed that the coefficients among sites with similar stand origin and management regimes were much higher than those among sites with different stand origin and management regimes. For example, significant positive correlations were found for chronologies among different coniferous plantations, irrespective of species differences; while insignificant correlations between chronologies of the same conifer from a coniferous plantation and a natural regenerated mixed stand, and vise versa. Integrative comparisons of different tree growth parameters and radial growth rates at different stages indicated that the diameter at breast height (DBH) increments for trees in coniferous plantations were faster than those for trees of the same (or different) species in the natural regenerated mixed stands, at least within their first 40 years of stand development. Analyses of growth releases and suppressions, and basal area increments of trees in different stands demonstrated that over-dense individuals after canopy closure was the main factor resulting in high frequencies of radial growth suppressions, with some exceptions of severe man-made disturbances. Therefore, to ensure a continuous basal area current annual increment in certain periods, tree density controlling through thinning in due time during the stand development process are necessary. It should be mentioned that, as an introduced conifer to Miyaluo area, Larix kaempferi grew quite well at altitude of ca. 3100 m after planting in 1970s. In their near 30 years of stand development, Larix kaempferi trees exhibited faster growth in various parameters than Picea asperata trees of the similar stand age did. Thus we think it reasonable to use Larix kaempferi as a fast restoring species at appropriate sites of cutting blanks of subalpine coniferous forests in western Sichuan.

Direct patterning of rhodamine 6G molecules on mica by dip-pen nanolithography

Dip-pen nanolithography (DPN) has been developed to pattern monolayer film of various molecules on suitable substrate through the controlled movement of ink-coated atomic force microscopy (AFM) tip, which makes DPN a potentially powerful tool for making the functional nanoscale devices. In this paper, the direct patterning of rhodamine 6G on mica by dip-pen nanolithography was demonstrated. R6G features patterned on the mica was successfully achieved with different tip movement which can be programmed by Nanoscript(TM) language. From the AFM image of R6G patterns, we know that R6G molecule is flatly binding to the mica surface through electrostatic interaction, thus stable R6G nanostructures could be formed on mica. The influence of translation speed and contact time on DPN was discussed. The method can be extended to direct patterning of many other organic molecules, and should open many opportunities for miniaturized optical device and site-specific biological staining.

Responses of vegetative gametophytes of Undaria pinnatifida to high irradiance in the process of gametogenesis

The population of Undaria pinnatifida in its ecologic niche sustains itself in high temperature summer in the form of vegetative gametophytes, the haploid stage in its heteromorphic life cycle. Gametogenesis initiates when seawater temperature drops below the threshold levels in autumn in the northern hemisphere. Given that the temperature may fall into the appropriate range for gametogenesis, the level of irradiance determines the final destiny of a gametophytic cell, either undergoing vegetative cell division or initiating gametogenesis. In elucidating how vegetatively propagated gametophytes cope with changes of irradiance in gametogenesis, we carried out a series of culture experiments and found that a direct exposure to irradiance as high as 270 mu mol photons m(-2) s(-1) was lethal to dim-light (7-10 mu mol photons m(-2) s(-1)) adapted male and female gametophytes. This lethal effect was linearly corelated with the exposure time. However, dim-light adapted vegetative gametophytes were shown to be able tolerate as high as 420 mu mol photons m(-2) s(-1) if the irradiance was steadily increased from dim light levels (7-10 mu mol photons m(-2) s(-1)) to 90, 180 and finally 420 mu mol photons m(-2) s(-1), respectively, at a minimum of 1-3 h intervals. Percentage of female gametophytic cells that turned into oogonia and were eventually fertilized was significantly higher if cultured at higher but not lethal irradiances. Findings of this investigation help to understand the dynamic changes of population size of sporophytic plants under different light climates at different site-specific ecologic niches. It may help to establish specific technical details of manipulation of light during mass production of seedlings by use of vegetatively propagated gametophytes.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Arginine kinase from Litopenaeus vannamei: Cloning, expression and catalytic properties

Arginine kinase (AK) is a phosphotransferase that plays a critical role in energy metabolism in invertebrates. in this paper, the full-length cDNA of AI( was cloned from shrimp, Litopenaeus vannamei by using RT-PCR and RACE PCR. It was 1446 bp encoding 356 amino acids, and belongs to the conserved phosphagen kinase family. The quantitative real-time reverse transcription PCR analysis revealed a broad expression of AK with the highest expression in the muscle and the lowest in the skin. The expression of AK after challenge with LIPS was tested in hemocytes and muscle, which indicated that the two peak values were 6.2 times (at 3 h) and 10.14 times (at 24 h) in the hemocytes compared with the control values, respectively (P < 0.05), while the highest expression of AK was 41 times (at 24 h) in the muscle compared with the control (P < 0.05). In addition, AK was expressed in Eschetichia coli by prokaryotic expression plasmid pGEX-4T-2. The recombinant protein was expressed as glutathione s-transferase (GST) arginine kinase (GST-AK) fusion protein, which was purified by affinity chromatography using Glutathione Sepharose 4B. After cleavage from GST by using a site-specific protease, the recombinant protein was identified by ESI-MS and showed AK activity. After treatment with 10 mM ATP, the enzyme activity significantly increased. However, the enzyme activity was inhibited by 10 mM alpha-ketoglutarate, 50 mM glucose and 200 mM ATP. This research suggested that AK might play an important role in the coupling of energy production and utilization and the immune response in shrimps. (C) 2009 Elsevier Ltd. All rights reserved.

Intergeneric conjugation in holomycin-producing marine Streptomyces sp strain M095

Marine Streptomyces are potential candidates for novel natural products and industrial catalysts. In order to set up biosynthesis approach for a holomycin-producing strain M095 isotated from Jiaozhou Bay, China, a genetic transformation system was established using intergeneric conjugation. The plasmid pIJ8600 consists of an origin of replication for Escherichia coli, a phage integrase directing efficient site-specific integration in bacterial chromosome, thiostrepton-induced promoter and an attP sequence. Using E. coli ET12567 (pUZ8002) carrying pIJ8600 as a conjugal donor, while it was mated with strain M095, pIJ8600 was mobilized to the recipient and the transferred DNA was also integrated into the recipient chromosome. The frequency of exconjugants was 1.9 +/- 0.13 x 10(-4) per recipient cell. Analysis of eight exconjugants showed pIJ8600 was stable integrated at a single chromosomal site (attB) of the Streptomyces genome. The DNA sequence of the attB was cloned and shown to be conserved. The results of growth and antimicrobial activity analysis indicated that the integration of pIJ8600 did not seem to affect the biosynthesis of antibiotics or other essential amino acids. To demonstrate the feasibility of above gene transfer system, the allophycocyanin gene (apc) from cyanobacterium Anacystis nidulans UTEX625 was expressed in strain M095, and the results indicated heterologous allophycocyanin could be expressed and folded effectively. (c) 2006 Elsevier GmbH. All rights reserved.

Intra-habitat heterogeneity of microbial food web structure under the regime of eutrophication and sediment resuspension in the large subtropical shallow Lake Taihu, China

Planktonic microbial community structure and classical food web were investigated in the large shallow eutrophic Lake Taihu (2338 km(2), mean depth 1.9 m) located in subtropical Southeast China. The water column of the lake was sampled biweekly at two sites located 22 km apart over a period of twelve month. Site 1 is under the regime of heavy eutrophication while Site 2 is governed by wind-driven sediment resuspension. Within-lake comparison indicates that phosphorus enrichment resulted in increased abundance of microbial components. However, the coupling between total phosphorus and abundance of microbial components was different between the two sites. Much stronger coupling was observed at Site 1 than at Site 2. The weak coupling at Site 2 was mainly caused by strong sediment resuspension, which limited growth of phytoplankton and, consequently, growth of bacterioplankton and other microbial components. High percentages of attached bacteria, which were strongly correlated with the biomass of phytoplankton, especially Microcystis spp., were found at Site 1 during summer and early autumn, but no such correlation was observed at Site 2. This potentially leads to differences in carbon flow through microbial food web at different locations. Overall, significant heterogeneity of microbial food web structure between the two sites was observed. Site-specific differences in nutrient enrichment (i.e. nitrogen and phosphorus) and sediment resuspension were identified as driving forces of the observed intra-habitat differences in food web structure.

In Comes I: Performance, Memory and Landscape

Pearson, Mike, In Comes I: Performance, Memory and Landscape (Exeter: University of Exeter Press, 2007) RAE2008

INVESTIGATION OF OCEAN ACOUSTICS USING AUTONOMOUS INSTRUMENTATION TO QUANTIFY THE WATER-SEDIMENT BOUNDARY PROPERTIES

Sound propagation in shallow water is characterized by interaction with the oceans surface, volume, and bottom. In many coastal margin regions, including the Eastern U.S. continental shelf and the coastal seas of China, the bottom is composed of a depositional sandy-silty top layer. Previous measurements of narrow and broadband sound transmission at frequencies from 100 Hz to 1 kHz in these regions are consistent with waveguide calculations based on depth and frequency dependent sound speed, attenuation and density profiles. Theoretical predictions for the frequency dependence of attenuation vary from quadratic for the porous media model of M.A. Biot to linear for various competing models. Results from experiments performed under known conditions with sandy bottoms, however, have agreed with attenuation proportional to f1.84, which is slightly less than the theoretical value of f2 [Zhou and Zhang, J. Acoust. Soc. Am. 117, 2494]. This dissertation presents a reexamination of the fundamental considerations in the Biot derivation and leads to a simplification of the theory that can be coupled with site-specific, depth dependent attenuation and sound speed profiles to explain the observed frequency dependence. Long-range sound transmission measurements in a known waveguide can be used to estimate the site-specific sediment attenuation properties, but the costs and time associated with such at-sea experiments using traditional measurement techniques can be prohibitive. Here a new measurement tool consisting of an autonomous underwater vehicle and a small, low noise, towed hydrophone array was developed and used to obtain accurate long-range sound transmission measurements efficiently and cost effectively. To demonstrate this capability and to determine the modal and intrinsic attenuation characteristics, experiments were conducted in a carefully surveyed area in Nantucket Sound. A best-fit comparison between measured results and calculated results, while varying attenuation parameters, revealed the estimated power law exponent to be 1.87 between 220.5 and 1228 Hz. These results demonstrate the utility of this new cost effective and accurate measurement system. The sound transmission results, when compared with calculations based on the modified Biot theory, are shown to explain the observed frequency dependence.

Optical micro- and nanofibres: Higher mode generation and particle manipulation studies

This thesis is centred on two experimental fields of optical micro- and nanofibre research; higher mode generation/excitation and evanescent field optical manipulation. Standard, commercial, single-mode silica fibre is used throughout most of the experiments; this generally produces high-quality, single-mode, micro- or nanofibres when tapered in a flame-heated, pulling rig in the laboratory. Single mode fibre can also support higher transverse modes, when transmitting wavelengths below that of their defined single-mode regime cut-off. To investigate this, a first-order Laguerre-Gaussian beam, LG01 of 1064 nm wavelength and doughnut-shaped intensity profile is generated free space via spatial light modulation. This technique facilitates coupling to the LP11 fibre mode in two-mode fibre, and convenient, fast switching to the fundamental mode via computer-generated hologram modulation. Following LP11 mode loss when exponentially tapering 125μm diameter fibre, two mode fibre with a cladding diameter of 80μm is selected fir testing since it is more suitable for satisfying the adiabatic criteria for fibre tapering. Proving a fruitful endeavour, experiments show a transmission of 55% of the original LP11 mode set (comprising TE01, TM01, HE21e,o true modes) in submicron fibres. Furthermore, by observing pulling dynamics and progressive mode-lass behaviour, it is possible to produce a nanofibre which supports only the TE01 and TM01 modes, while suppressing the HE21e,o elements of the LP11 group. This result provides a basis for experimental studies of atom trapping via mode-interference, and offers a new set of evanescent field geometries for sensing and particle manipulation applications. The thesis highlights the experimental results of the research unit’s Cold Atom subgroup, who successfully integrated one such higher-mode nanofibre into a cloud of cold Rubidium atoms. This led to the detection of stronger signals of resonance fluorescence coupling into the nanofibre and for light absorption by the atoms due to the presence of higher guided modes within the fibre. Theoretical work on the impact of the curved nanofibre surface on the atomic-surface van der Waals interaction is also presented, showing a clear deviation of the potential from the commonly-used flat-surface approximation. Optical micro- and nanofibres are also useful tools for evanescent-field mediated optical manipulation – this includes propulsion, defect-induced trapping, mass migration and size-sorting of micron-scale particles in dispersion. Similar early trapping experiments are described in this thesis, and resulting motivations for developing a targeted, site-specific particle induction method are given. The integration of optical nanofibres into an optical tweezers is presented, facilitating individual and group isolation of selected particles, and their controlled positioning and conveyance in the evanescent field. The effects of particle size and nanofibre diameter on pronounced scattering is experimentally investigated in this systems, as are optical binding effects between adjacent particles in the evanescent field. Such inter-particle interactions lead to regulated self-positioning and particle-chain speed enhancements.

Analysis of memory B cell responses and isolation of novel monoclonal antibodies with neutralizing breadth from HIV-1-infected individuals.

BACKGROUND: The isolation of human monoclonal antibodies (mAbs) that neutralize a broad spectrum of primary HIV-1 isolates and the characterization of the human neutralizing antibody B cell response to HIV-1 infection are important goals that are central to the design of an effective antibody-based vaccine. METHODS AND FINDINGS: We immortalized IgG(+) memory B cells from individuals infected with diverse clades of HIV-1 and selected on the basis of plasma neutralization profiles that were cross-clade and relatively potent. Culture supernatants were screened using various recombinant forms of the envelope glycoproteins (Env) in multiple parallel assays. We isolated 58 mAbs that were mapped to different Env surfaces, most of which showed neutralizing activity. One mAb in particular (HJ16) specific for a novel epitope proximal to the CD4 binding site on gp120 selectively neutralized a multi-clade panel of Tier-2 HIV-1 pseudoviruses, and demonstrated reactivity that was comparable in breadth, but distinct in neutralization specificity, to that of the other CD4 binding site-specific neutralizing mAb b12. A second mAb (HGN194) bound a conserved epitope in the V3 crown and neutralized all Tier-1 and a proportion of Tier-2 pseudoviruses tested, irrespective of clade. A third mAb (HK20) with broad neutralizing activity, particularly as a Fab fragment, recognized a highly conserved epitope in the HR-1 region of gp41, but showed striking assay-dependent selectivity in its activity. CONCLUSIONS: This study reveals that by using appropriate screening methods, a large proportion of memory B cells can be isolated that produce mAbs with HIV-1 neutralizing activity. Three of these mAbs show unusual breadth of neutralization and therefore add to the current panel of HIV-1 neutralizing antibodies with potential for passive protection and template-based vaccine design.

Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles.

In the event of a terrorist-mediated attack in the United States using radiological or improvised nuclear weapons, it is expected that hundreds of thousands of people could be exposed to life-threatening levels of ionizing radiation. We have recently shown that genome-wide expression analysis of the peripheral blood (PB) can generate gene expression profiles that can predict radiation exposure and distinguish the dose level of exposure following total body irradiation (TBI). However, in the event a radiation-mass casualty scenario, many victims will have heterogeneous exposure due to partial shielding and it is unknown whether PB gene expression profiles would be useful in predicting the status of partially irradiated individuals. Here, we identified gene expression profiles in the PB that were characteristic of anterior hemibody-, posterior hemibody- and single limb-irradiation at 0.5 Gy, 2 Gy and 10 Gy in C57Bl6 mice. These PB signatures predicted the radiation status of partially irradiated mice with a high level of accuracy (range 79-100%) compared to non-irradiated mice. Interestingly, PB signatures of partial body irradiation were poorly predictive of radiation status by site of injury (range 16-43%), suggesting that the PB molecular response to partial body irradiation was anatomic site specific. Importantly, PB gene signatures generated from TBI-treated mice failed completely to predict the radiation status of partially irradiated animals or non-irradiated controls. These data demonstrate that partial body irradiation, even to a single limb, generates a characteristic PB signature of radiation injury and thus may necessitate the use of multiple signatures, both partial body and total body, to accurately assess the status of an individual exposed to radiation.

Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein Determined by Nuclear Magnetic Resonance-Based Histidine pKa Measurements.

The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. We measured histidine pKa values (H3, H22, and H105) in the unfolded (U), intermediate (I), and sulfate-bound folded (F) states of RNase P protein, using an efficient and accurate nuclear magnetic resonance-monitored titration approach that utilizes internal reference compounds and a parametric fitting method. The three histidines in the sulfate-bound folded protein have pKa values depressed by 0.21 ± 0.01, 0.49 ± 0.01, and 1.00 ± 0.01 units, respectively, relative to that of the model compound N-acetyl-l-histidine methylamide. In the unliganded and unfolded protein, the pKa values are depressed relative to that of the model compound by 0.73 ± 0.02, 0.45 ± 0.02, and 0.68 ± 0.02 units, respectively. Above pH 5.5, H22 displays a separate resonance, which we have assigned to I, whose apparent pKa value is depressed by 1.03 ± 0.25 units, which is ∼0.5 units more than in either U or F. The depressed pKa values we observe are consistent with repulsive interactions between protonated histidine side chains and the net positive charge of the protein. However, the pKa differences between F and U are small for all three histidines, and they have little ionic strength dependence in F. Taken together, these observations suggest that unfavorable electrostatics alone do not account for the fact that RNase P protein is intrinsically unfolded in the absence of ligand. Multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

Modeling marine ecosystem responses to global climate change: Where are we now and where should we be going?

Modeling of global climate change is moving from global circulation model (GCM)-type projections with coupled biogeochemical models to projections of ecological responses, including food web and upper trophic levels. Marine and coastal ecosystems are highly susceptible to the impacts of global climate change and also produce significant ecosystem services. The effects of global climate change on coastal and marine ecosystems involve a much wider array of effects than the usual temperature, sea level rise, and precipitation. This paper is an overview for a collection of 12 papers that examined various aspects of global climate change on marine ecosystems and comprise this special issue. We summarized the major features of the models and analyses in the papers to determine general patterns. A wide range of ecosystems were simulated using a diverse set of modeling approaches. Models were either 3-dimensional or used a few spatial boxes, and responses to global climate change were mostly expressed as changes from a baseline condition. Three issues were identified from the across-model comparison: (a) lack of standardization of climate change scenarios, (b) the prevalence of site-specific and even unique models for upper trophic levels, and (c) emphasis on hypothesis evaluation versus forecasting. We discuss why these issues are important as global climate change assessment continues to progress up the food chain, and, when possible, offer some initial steps for going forward.