attB site disruption in marine Actinomyces sp M048 via DNA transformation of a site-specific integration vector

An efficient conjugation method has been developed for the marine Actinomyces sp. isolate M048 to facilitate the genetic manipulation of the chandrananimycin biosynthesis gene cluster. A phi C31-derived integration vector pIJ8600 containing oriT and attP fragments was introduced into strain M048 by bi-parental conjugation from Escherichia coli ET12567 to strain M048. Transformation efficiency was (6.38 +/- 0.41) x 10(-5) exconjugants per recipient spore. Analysis of eight exconjugants showed that the plasmid pIJ8600 was stably integrated at a single chromosomal site (attB) of the Actinomyces genome. The DNA sequence of the attB was cloned and shown to be conserved. The results of antimicrobial activity analysis indicated that the insertion of plasmid pIJ8600 seemed to affect the biosynthesis of antibiotics that could strongly inhibit the growth of E. coli and Mucor miehei (Tu284). HPLC-MS analysis of the extracts indicated that disruption of the attB site resulted in the complete abolition of chandrananimycin A-C production, proving the identity of the gene cluster. Instead of chandrananimycins, two bafilomycins were produced through disruption of the attB site from the chromosomal DNA of marine Actinomyces sp. M048.

卫星高度计资料在海洋潮汐研究中的应用

本文依据收集到的392个地面验潮站8个主要分潮（M2、S2、K1、O1、N2、K2、P1及Q1）的调和常数，对现有7个全球大洋潮汐模式的准确度进行了检验，结果显示各模式在深海区域均达到了比较高的准确度，相互之间差别也不大。经验模式GOT00和CSR4.0、同化模式NAO99、反演同化模式TPXO7.0、数值同化模式FES2002和FES2004的M2分潮均方根偏差在3 cm左右，其它分潮（S2、K1、O1、N2、K2、P1及Q1）大约在1～2 cm。本文还依据中国近海18个岛屿的调和常数对其中的5个大洋潮汐模式的准确度进行了检验，结果表明，M2分潮均方根偏差在6～14 cm，明显高于大洋部分的偏差，其中日本国家天文台的潮汐模式NAO99在中国近海的结果相对较准确。 我们利用1992年8月至2008年8月的TOPEX/POSEIDON和JASON-1(T/P-J)卫星高度计资料，对沿卫星轨道的302816个站点进行了14个分潮的潮汐调和分析，得到了全球大洋潮汐的8个主要分潮以及2个气象分潮Sa、Ssa的经验同潮图。主要结果有：（1）各分潮在卫星上升轨道与下降轨道的交叉点(约7000个)相关性分析表明：M2分潮的振幅和迟角的相关系数很高（分别为0.9965和0.9961）；S2，K1，O1和Sa分潮也有较好的相关性（相关系数为0.94～0.99）；（2）该结果与392地面个验潮站吻合较好，其中M2分潮的振幅、迟角和向量的均方根偏差分别为：1.73 cm，2.340和2.93 cm；S2，K1和O1分潮的振幅、迟角和向量的均方根偏差为1 cm左右，5.250～7.270和1.5～2.1 cm，该精度与最近几年国际上的主要大洋潮汐模式的准确度相近；（3）首次通过卫星资料获得了Sa、Ssa分潮的同潮图。周期为1年的Sa分潮与大洋105个地面站相比，振幅、迟角和向量的均方根偏差分别为1.50 cm、18.360和2.16 cm。在此基础上，进一步分析了构成Sa、Ssa气象分潮的两个主要因素（海水密度以及海面气压）在全球的分布。 在T/P-J等卫星资料无法覆盖到南大洋和北冰洋，本文利用Princeton Ocean Model（POM）进行了数值模拟，模拟结果与162个地面实测站（其中南大洋30个，北冰洋132个）的观测比较一致。基于卫星资料分析的结果和数值模拟结果合并得到了全球大洋的8个主要分潮同潮图。在此基础上通过全球潮汐能量耗散的计算得到潮能通量的分布，并得到全球M2、S2、K1和O1分潮的潮汐能量耗散率为2.431TW、0.401TW、0.336TW和0.176TW。 本文还利用卫星资料对南海潮汐进行了研究，在中国南海，获得了主要的半日潮、全日潮、四分日分潮和长周期分潮（M2，S2，N2，K2，K1，O1，P1，Q1，M4, MS4，Sa, Ssa）的经验同潮图。与南海沿岸94个地面验潮站的数据符合得比较好，M2，S2，K1及O1等4个主要分潮的平均振幅差为2～4 cm，均方根偏差分别是9～11 cm.其它4个主要分潮N2，K2，P1，Q1的平均振幅差为1～2 cm，均方根偏差为2～4 cm。此外，本文还利用卫星高度计资料潮汐分析结果沿卫星轨道进行高通滤波，分离得出中国近海的M2，S2，K1及O1分潮的内潮信息。

Morphology and Molecular Phylogeny of Trimyema koreanum n. sp., a Ciliate from the Hypersaline Water of a Solar Saltern

A new ciliate, Trimyema koreanum n. sp., isolated from hypersaline water (salinity of 293 parts per thousand) from a solar saltern in Korea, was investigated using live observation, protargol impregnation, and gene sequencing. Trimyema koreanum is about 30 x 13 mu m in vivo, has usually 23 longitudinal ciliary rows forming two distinct ciliary girdles visible both in vivo and in protargol impregnation. A third indistinct ciliary girdle as well as a girdle of mucocysts is distinguishable only in impregnated cells. We suggest T. koreanum as a new species, differing from the most similar species, T. marinum, by the presence of two distinct ciliary girdles (T. marinum usually has six ciliary girdles clearly visible in living cells and three anterior spirals that encircle the cell completely). Although the number of known 18S rRNA sequences in the genus Trimyema was limited, the Trimyema group including T. koreanum forms a strong clade. The phylogenetic position confirms that the isolate belongs to the genus Trimyema and is different from previously sequenced species. Trimyema koreanum is able to consume both prokaryotes and small eukaryotes (specifically, the alga Dunaliella sp.).

H5N1 avian influenza re-emergence of Lake Communication Qinghai: phylogenetic and antigenic analyses of the newly isolated viruses and roles of migratory birds in virus circulation

Highly pathogenic avian influenza H5N1 virus has swept west across the globe and caused serious debates on the roles of migratory birds in virus circulation since the first large-scale outbreak in migratory birds of Lake Qinghai, 2005. In May 2006, another outbreak struck Lake Qinghai and six novel strains were isolated. To elucidate these QH06 viruses, the six isolates were subjected to whole-genome sequencing. Phylogenetic analyses show that QH06 viruses are derived from the lineages of Lake Qinghai, 2005. Five of the six novel isolates are adjacent to the strain A/Cygnus olor/Croatia/1/05, and the last one is related to the strain A/duck/Novosibirsk/ 02/05, an isolate of the flyway. Antigenic analyses suggest that QH06 and QH05 viruses are similar to each other. These findings implicate that QH06 viruses of Lake Qinghai may travel back via migratory birds, though not ruling out the possibility of local circulation of viruses of Lake Qinghai.

Jiangella gansuensis gen. nov., sp nov., a novel actinomycete from a desert soil in north-west China

A novel actinomycete strain, designated YIM 002(T), was isolated from a desert soil sample in Gansu Province, north-west China. This actinomycete isolate formed well-differentiated aerial and substrate mycelia. In the early stages of growth, the substrate mycelia fragmented into short or elongated rods. Chemotaxonomically, it contained LL-2,6-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose and glucose. Phospholipids present were phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol. MK-9(H-4) was the predominant menaquinone. The major fatty acids were anteiso C-15:0 (35.92%), anteiso C-17:0 (15.84%), iso C-15:0 (10.40%), iso C-16:0 (7.07%) and C(17:10)w8c (9.37%). The G+C content of the DNA was 70 mol%. Phylogenetic analysis and signature nucleotide data based on 16S rRNA gene sequences showed that strain YIM 002(T) is distinct from all recognized genera of the family Nocardioidaceae in the suborder Propionibacterineae. On the basis of the phenotypic and genotypic characteristics, it is proposed that isolate YIM 002(T) be classified as a novel species in a new genus, Jiangella gansuensis gen. nov., sp. nov. The type strain is YIM 002(T) (= DSM 44835(T) = CCTCC AA 204001(T) = KCTC 19044(T)).

白垩纪超静磁带地球磁场古强度测定

The long-term variations in the strength of the geomagnetic field provide important constraints on the chemical-physical processes of the Earth’s interior. Especially, the intensity of the geomagnetic field during the Cretaceous normal superchron (CNS) is crucial to understand the geodynamo. But a paucity of paleointensity further limits to obtain essential knowledge interior process in the deep earth. In order to improve the experimental efficiency, this study tried to apply two new rock magnetic methods (FORC diagram and low-temperature demagnetization technique) to determine the paleointensity. First, some problems in the theory and technique in paleointensity experiments were introduced. A combined palaeomagnetic and geochronologic study was further conducted on a basaltic lava sequence at Jianchang in Liaoning Province, northeastern China. Radiometric 40Ar/39Ar dating indicates that the volcanism occurred at about 119 Ma within the marine anomaly C34n in Cretaceous normal superchron (CNS). Rock magnetic investigations show that pseudo-single domain (PSD) titanium-poor titanomagnetite is dominant in the studied lava flows. Both stepwise thermal and alternating field demagnetizations isolate the well-defined normal characteristic remanent magnetization (ChRM) in three independent lava flows with a mean direction of D/I = 6.0/51.9 degree(a95 = 12.3degree). Palaeointensity was determined using the modified Thellier method with systematic partial thermoremanent magnetization (pTRM) checks on total 72 samples, but only 10 samples exhibit ideal linear behavior on the Arai-plot in the temperature interval of 300-560 C and yield an average paleointensity of (25.8+/-1.4)uT. In addition, slopes of the line defined by the initial and the final points on the Arai-plot for the other 18 samples with characteristic PSD features give an average paleointensity estimation value of (24.8+/-1.9)uT. The consistency of these two approaches confidently demonstrates the fidelity of our results. The overall mean field strength determined using both approaches are thus estimated to be (25.2+/-0.7 )uT. This value corresponds to the virtual dipole magnetic moments (VDM) of (4.5+/-0.1)E22 Am^2, which is about half of the value of present field. This finding suggests that palaeointensity just at the onset of the CNS is characterized by a weak magnetic field.

Repairing Learned Knowledge Using Experience

Explanation-based learning occurs when something useful is retained from an explanation, usually an account of how some particular problem can be solved given a sound theory. Many real-world explanations are not based on sound theory, however, and wrong things may be learned accidentally, as subsequent failures will likely demonstrate. In this paper, we describe ways to isolate the facts that cause failures, ways to explain why those facts cause problems, and ways to repair learning mistakes. In particular, our program learns to distinguish pails from cups after making a few mistakes.

Hypothesizing Device Mechanisms: Opening Up the Black Box

I describe an approach to forming hypotheses about hidden mechanism configurations within devices given external observations and a vocabulary of primitive mechanisms. An implemented causal modelling system called JACK constructs explanations for why a second piece of toast comes out lighter, why the slide in a tire gauge does not slip back inside when the gauge is removed from the tire, and how in a refrigerator a single substance can serve as a heat sink for the interior and a heat source for the exterior. I report the number of hypotheses admitted for each device example, and provide empirical results which isolate the pruning power due to different constraint sources.

Qualitative Knowledge, Casual Reasoning and the Localization of Failures

This report investigates some techinques appropriate to representing the knowledge necessary for understanding a class of electronic machines -- radio receivers. A computational performance model - WATSON - is presented. WATSONs task is to isolate failures in radio receivers whose principles of operation have been appropriately described in his knowledge base. The thesis of the report is that hierarchically organized representational structures are essential to the understanding of complex mechanisms. Such structures lead not only to descriptions of machine operation at many levels of detail, but also offer a powerful means of organizing "specialist" knowledge for the repair of machines when they are broken.

Construction of a Festuca pratensis BAC library for map-based cloning in IFestulolium substitution lines

Iain S. Donnison, Donal M. O Sullivan, Ann Thomas, Peter Canter, Beverley Moore, Ian Armstead, Howard Thomas, Keith J. Edwards and Ian P. King (2005). Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines. Theoretical and Applied Genetics, 110 (5) pp.846-851 Sponsorship: BBSRC;BBSRC RAE2008

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome

Matthew J. Nicholson, Michael K. Theodorou and Jayne L. Brookman. (2005). Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome. Microbiology, 151 (1), 121-133. Sponsorship: BBSRC RAE2008

Selección de un aislado del nucleopoliedrovirus de Helicoverpa armigera (HearNPV) para su uso como base de un bioinsecticida

Helicoverpa armigera (Lepidoptera; Noctuidae), conocida como el taladro del tomate, es una especie polífaga y de amplia distribución, responsable de grandes pérdidas económicas en más de 60 cultivos a lo largo de las regiones tropicales y subtropicales del mundo. Estas plagas se controlan mayoritariamente con plaguicidas químicos, aunque existe un gran interés por desarrollar otros agentes de control biológico. Entre estos, se encuentra el nucleopoliedrovirus de Helicoverpa armigera (HearNPV, Baculoviridae), que por sus características de seguridad y eficacia, sería útil para impulsar los programas de gestión integrada de plagas que se fomentan desde la Directiva 2009/128/CEE. El objetivo de este trabajo fue realizar una caracterización bioquímica y biológica de varios aislados de HearNPV : un aislado silvestre español (Badajoz) HearNPV-SP1, un aislado chino HearSNPV-G4, tres aislados sudafricanos (HearNPV-Whl, HearNPV-Kzn, HearNPV-Alb) y la materia activa de un producto comercial en uso en Europa (HearNPV-Hx). El análisis con las enzimas de restricción determinó que la enzima BglII generaba perfiles similares pero con fragmentos característicos en todos los casos a excepción de los aislados HearNPV-Kzn y HearNPVAlb, que no pudieron ser diferenciados entre sí con ninguna de las enzimas probadas. El análisis filogenético, basado en las secuencias parciales de los genes poliedrina (polh), lef-8 y lef-9, donde se incluyeron las secuencias correspondientes a 18 genomas mostró que el aislado HearNPV-Whl es filogenéticamente próximo a las cepas de origen ibérico, mientras que los aislados HearNPV-Hx y HearNPV-Alb comparten la misma rama que los aislados asiáticos y australiano. La caracterización insecticida de los aislados HearNPV-SP1, HearNPV-Hx y HearNPV-G4 reveló que la virulencia (TMM) del aislado HearNPV-SP1 (104 h) fue significativamente menor que la de los aislados HearNPV-G4 (109 h) y HearNPV-Hx (111 h). En este trabajo, se determinó que el tiempo de acción del HearNPV-SP1 es menor al de otros bioinsecticidas en uso en Europa, por lo que se confirma la posibilidad de mejorar los productos activos en uno de los aspectos más sensibles de cara a su comercialización como es su tiempo de actuación.

On the Effectiveness of Genetic Search in Combinatorial Optimization

In this paper, we study the efficacy of genetic algorithms in the context of combinatorial optimization. In particular, we isolate the effects of cross-over, treated as the central component of genetic search. We show that for problems of nontrivial size and difficulty, the contribution of cross-over search is marginal, both synergistically when run in conjunction with mutation and selection, or when run with selection alone, the reference point being the search procedure consisting of just mutation and selection. The latter can be viewed as another manifestation of the Metropolis process. Considering the high computational cost of maintaining a population to facilitate cross-over search, its marginal benefit renders genetic search inferior to its singleton-population counterpart, the Metropolis process, and by extension, simulated annealing. This is further compounded by the fact that many problems arising in practice may inherently require a large number of state transitions for a near-optimal solution to be found, making genetic search infeasible given the high cost of computing a single iteration in the enlarged state-space.

Forensic analysis of analgesics by TLC

An introductory laboratory on the identification of analgesics in an unknown sample. Ideal for the first week of an organic chemistry sequence to get students familiar with their surroundings. Students extract, isolate, and perform thin layer chromatography on aspirin, acetominophen, or ibuprofen.

Borohydride Reduction of Fluorenone

A simple experiment to demonstrate nucleophilic addition to a carbonyl. Sodium borohydride-mediated reduction of fluorenone is a fast and high-yielding reaction that is suitable for beginning students. Students isolate their fluorenol product by recrystallization and characterize it by NMR and IR.