Spatial Variation among Lakes within Landscapes: Ecological Organization along Lake Chains

Although limnologists have long been interested in regional patterns in lake attributes, only recently have they considered lakes connected and organized across the landscape, rather than as spatially independent entities. Here we explore the spatial organization of lake districts through the concept of landscape position, a concept that considers lakes longitudinally along gradients of geomorphology and hydrology. We analyzed long-term chemical and biological data from nine lake chains (lakes in a series connected through surface or groundwater flow) from seven lake districts of diverse hydrologic and geomorphic settings across North America. Spatial patterns in lake variables driven by landscape position were surprisingly common across lake districts and across a wide range of variables. On the other hand, temporal patterns of lake variables, quantified using synchrony, the degree to which pairs of lakes exhibit similar dynamics through time, related to landscape position only for lake chains with lake water residence times that spanned a wide range and were generally long (close to or greater than 1 year). Highest synchrony of lakes within a lake chain occurred when lakes had short water residence times. Our results from both the spatial and temporal analyses suggest that certain features of the landscape position concept are robust enough to span a wide range of seemingly disparate lake types. The strong spatial patterns observed in this analysis, and some unexplained patterns, suggest the need to further study these scales and to continue to view lake ecosystems spatially, longitudinally, and broadly across the landscape.     

Drosophila Melanogaster Mitochondrial DNA: Gene Organization and Evolutionary Considerations

The sequence of a 8351-nucleotide mitochondrial DNA (mtDNA) fragment has been obtained extending the knowledge of the Drosophila melanogaster mitochondrial genome to 90% of its coding region. The sequence encodes seven polypeptides, 12 tRNAs and the 3' end of the 16S rRNA and CO III genes. The gene organization is strictly conserved with respect to the Drosophila yakuba mitochondrial genome, and different from that found in mammals and Xenopus. The high A + T content of D. melanogaster mitochondrial DNA is reflected in a reiterative codon usage, with more than 90% of the codons ending in T or A, G + C rich codons being practically absent. The average level of homology between the D. melanogaster and D. yakuba sequences is very high (roughly 94%), although insertion and deletions have been detected in protein, tRNA and large ribosomal genes. The analysis of nucleotide changes reveals a similar frequency for transitions and transversions, and reflects a strong bias against G + C on both strands. The predominant type of transition is strand specific.     

有效提取病毒诱导基因沉默植株中DNA的方法

根据PCR反应的要求,用改良的CTAB法,以番茄植株为材料,实现了微量番茄叶片基因组DNA的快速提取。提取基因组DNA所用的组织量少,所得的DNA经过电泳检测虽有降解,但足以用于PCR检测,以其作模板扩增中国番茄黄化曲叶病毒诱导的硫黄素酶（Su）基因沉默植株中病毒组分中的DNAmβ和1.7 A,片段大小分别为1 300、500 bp。测序结果证明是相应基因的部分片段。该方法的材料不需要使用液氮,可以单人大批量提取,并在基因沉默的番茄植株中能稳定而准确的规模化PCR检测。     

PEG-Protein Interaction Induced Contraction of NalD Chains

In a recent attempt to crystallize a regulator of MexAB-OprM multi-drug efflux systems in Pseudomonas aeruginosa (NalD), we found that adding polyethylene glycol (PEG3350, Mw = 3,350 g/mol) into the protein solution increases the speed of NalD migration in gel electrophoresis, signaling a smaller hydrodynamic size. At first we conjectured that NalD was degraded unexpectedly by PEG; however, we found that there was no change in its molar mass by MALDI-TOF characterization. Moreover, we found that adding polyacrylic acid (PAA) into the solution mixture returned the NalD migration to its normal speed. Furthermore, our analytic ultracentrifugation and dynamic laser light scattering results directly reveal that NalD interacts with PEG so that individual NalD chains gradually shrink as more PEG chains are added in the range of 10–50 mg/mL. Size exclusion chromatography also confirms that the NalD chain shrinks in the presence of PEG. A combination of these results indicates that PEG3350 chains can complex with NalD to induce an intra-protein chain contraction, presumably via the formation of hydrogen bond between –C-O-C– on PEG and –COOH on NalD, resulting in a smaller hydrodynamic size (faster migration) and a higher apparent molar mass. Note that because the presence of PEG affects osmotic pressure, it is considered to be a precipitator of protein crystallization. Our current finding reveals that the interaction of PEG/protein may play a significant role in protein crystallization. The complexation potentially makes the protein chain segments less flexible, and consequently makes crystallization easier. Hopefully, our current results will stimulate further studies in this direction.     

Alcoholytic Cleavage of Polyhydroxyalkanoate Chains by Class IV Synthases Induced by Endogenous and Exogenous Ethanol

Polyhydroxyalkanoate (PHA)-producing Bacillus strains express class IV PHA synthase, which is composed of the subunits PhaR and PhaC. Recombinant Escherichia coli expressing PHA synthase from Bacillus cereus strain YB-4 (PhaRC_YB-4) showed an unusual reduction of the molecular weight of PHA produced during the stationary phase of growth. Nuclear magnetic resonance analysis of the low-molecular-weight PHA revealed that its carboxy end structure was capped by ethanol, suggesting that the molecular weight reduction was the result of alcoholytic cleavage of PHA chains by PhaRC_YB-4 induced by endogenous ethanol. This scission reaction was also induced by exogenous ethanol in both in vivo and in vitro assays. In addition, PhaRC_YB-4 was observed to have alcoholysis activity for PHA chains synthesized by other synthases. The PHA synthase from Bacillus megaterium (PhaRC_Bm) from another subgroup of class IV synthases was also assayed and was shown to have weak alcoholysis activity for PHA chains. These results suggest that class IV synthases may commonly share alcoholysis activity as an inherent feature.     

Coil-globule Coexistence and Compaction of DNA Chains

In this work we discuss different factors governing coil-globule coexistence in the compaction process of DNA. We initially analyse the role played by fluctuations in the degree of binding of an external compacting agent in the conformational behavior of the chain backbone. The analysis relies both on Monte Carlo simulation results and simple statistical approaches. Compacting agents of various binding characteristics are taken into consideration and the degree of charge neutralization upon the chain is related to conformational indicators. Selected model systems comprising stiff chains in the presence of multivalent ions are employed to assess intrinsic single-chain conformational fluctuation, in the presence of external agents but not resulting from differences in binding. It is shown that trends found for a variety of compacting agents, including the extension of the coil-globule coexistence regions, can be ratio-nalised on the basis of this analysis.     

Angular Optical Transparency Induced by Photonic Topological Transition in Hexagonal Boron Nitride

The transmission property of hexagonal boron nitride at its four photonic topological transitions has been studied. An interesting result is revealed that the angular optical transparency can be achieved at wavelength 12.0494 μm. The numerical results indicate that the transparency window has an angular full width at half maximum of 4° with an optical transmission higher than 0.9 at normal incidence. Besides, corresponding to an angular full width at half maximum narrower than 20°, the wavelength span is about 230 nm. These features may make the hexagonal boron nitride holds promise for applications in private screens and optical detectors.

     

Topological Comparison of Two Helix Destabilizing Proteins: Ribonuclease A and the Gene 5 DNA Binding Protein

Abstract

A topological comparison of the two helix destabilizing proteins, pancreatic ribonuclease A and the gene S DNA binding protein of bacteriophage fd has been completed utilizing the available high resolution tertiary structures of each protein. The results indicate these two proteins are structurally if not also evolutionarily related. Regions of closest topological equivalence occur between beta loops directly involved in nucleotide binding or are required for the maintenance of their respective oligonucleotide binding channels. In addition, there is a similar placement of critical amino acid side chains about the binding site. Further evidence for this structural relationship is obtained by comparison of structural data for the mode of complexation of polynucleotides to each protein. The results of topological comparison suggest the essential property shared by helix destabilizing proteins, whether specialized DNA binding proteins such as G5BP or proteins with other primary functional roles, like ribonuclease A, is the presence of an elongated oligonucleotide binding channel. Although ribonuclease A and G5BP are structurally related, it seems likely any protein with this structural feature will exhibit a helix destabilizing capacity. This conclusion is supported by the diversity of molecular characteristics shown by other proteins having this activity.     

Spatial Organization of DNA in the Nucleus May Determine Positions of Recombination Hot Spots

A hypothesis has been proposed that the regions of DNA loop anchorage to the nuclear matrix are the preferential sites (hot spots) of illegitimate recombination mediated or triggered by topoisomerase II of the nuclear matrix. Recombination between the regions of DNA loop anchorage to the nuclear matrix may result in deletion or repositioning of DNA loops or their groups. The proposed hypothesis is confirmed by the results of original experiments and published data obtained by other researchers.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 633–638.Original Russian Text Copyright © 2005 by Razin, Iarovaia.     

Topological Organization of Ventral Tegmental Area Connectivity Revealed by Viral-Genetic Dissection of Input-Output Relations

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Analysis of DNA Diversity by Spatial Autocorrelation

Two statistics are proposed for summarizing spatial patterns of DNA diversity. These autocorrelation indices for DNA analysis, or AIDAs, can be applied to RFLP and sequence data; the resulting set of autocorrelation coefficients, or correlogram, measures whether, and to what extent, individual DNA sequences or haplotypes resemble the haplotypes sampled at arbitrarily chosen spatial distances. Analyses of computer-generated sets of data, and of RFLP data from two natural populations, show that AIDAs allow one to objectively and simply identify basic patterns in the spatial distribution of haplotypes. These statistics, therefore, seem to be a useful tool both to explore the genetic structure of a population and to suggest hypotheses on the evolutionary processes that shaped the observed patterns.     

脱落酸（ABA）诱导基因表达的调控元件

本文详细介绍了脱落酸（ABA）诱导诱导基因表达的各种调控元件及各调控元件间的相经作用和关系,综述了近年来对ABA诱导基因表达的调控元件的研究进展。     

壳寡糖诱导的烟草SKP1基因表达

壳寡糖是一种高效的植物抗性诱导剂,应用mRNA差异显示技术从经过壳寡糖诱导的枯斑三生烟草叶片中分离到了编号为5、31、37和46的4个基因片段.4个基因片段与本塞姆氏烟草(Nicotiana benthamiana)SKP1基因的mRNA同源性都达到82%,据此推断这4个片段是感病烟草品种枯斑三生烟草的SKP1基因.质粒双酶切及反向Northern分析结果表明,该基因表达在壳寡糖诱导下增强.由于SKP1基因与植物的抗病毒病相关,从而在mRNA水平上验证了壳寡糖的诱导抗性效应.     

Spatial Organization of Microbial Biofilm Communities

Abstract The application of advanced microscopy and molecular and electrochemical high-resolution methods has provided insights into the structural organization and function of biofilm communities. It appears that cellular properties such as growth differentiation, chemotaxis, and cell-to-cell signaling enable biofilm communities to organize structurally in response to the external conditions and the activities of the different biofilm members. Thereby resource utilization becomes optimized, and processes which require syntrophic relationships or special micro-environments become facilitated. Received: 23 February 2000; Accepted: 8 June 2000; Online Publication: 28 August 2000     

Preparation of Effective and Safe Gene Carriers by Grafting Alkyl Chains to Generation 5 Polypropyleneimine

Gene therapy is a novel method to treat a variety of diseases including genetic disorders and cancer. Nonviral gene carriers have now gained considerable attention as gene carrier systems. Polyamidoamine (PAMAM) and polypropyleneimine (PPI) are the two most widely used denderimers in gene delivery studies. The aim of the current study was to investigate the effects of modification of generation 5 polypropyleneimine (G5 PPI) dendrimers with alkanoate groups as hydrophobic moieties on DNA transfection and cytotoxicity. Six, 10, and 16 carbon derivatives of bromoalkanoic acids were conjugated onto PPI with 10%, 30%, and 50% of surface amine grafting. Ethidium bromide exclusion assay results proved the ability of modified carriers to condense DNA. Transfection assay showed higher DNA delivery potential for 30% and 50% grafting with decanoate moieties compared to native G5 PPI and Superfect^TM. 3-(4,5-Dimethylthiazol-2-yl)-2,5-di phenyltetrazolium bromide (MTT) and apoptosis experiments showed lower toxicity for modified carriers compared to unmodified PPI. The hemolytic effect of grafted carriers was not significantly different from G5 PPI. Size and zeta potential measurements revealed that polyplex size was less than 200 nm and electrical charges were in the range 14–25 mV. The hydrophobic modifications improved transfection activity and toxicity of G5 PPI without negatively affecting hemocompatibility. These modified carriers are therefore promising candidates for further in vivo investigations.KEY WORDS: gene delivery, hydrophobic modification, nonviral vector, polypropyleneimine, transfection     

Developmental Modifications Induced by DNA Base Analogs

Pulse treatment of Drosophita melanogasler larvae with thymidineanalogs in the presence of inhibitors of thymidylate synthetaseactivity induces a variety of growth lesions in the adult flies.We determined the frequency of the developmental lesions inducedfor a variety of treatment conditions and examined the incorporationof the analogs into DNA of larvae treated in a similar mannerfor each of these conditions. Lesion induction is correlatedwith bromodeoxyundine incorporation into DNA. The distributionof incorporated bromodeoxyuridine in the pyrimidine oligonucleotidesreleased from DNA by formic acid-diphenylamine hydrolysis wascompared with the incorporation pattern of exogenous thymidine.This comparison shows that bromodeoxyuridine is not randomlyaccepted at all thymine sites for incorporation into DNA underthe feeding conditions used in these experiments. There werealso differences between the patterns of bromodeoxyuridine-incorporated DNAs from larvae receiving the analog under conditionsslightly effective and highly effective for morphogenic lesions.Examination of the size and frequency of lesions as a functionof larval age at the time of treatment indicates there is aclonal pattern of propagation of the analog-affected cells.Since several cell generations separate the analog pulse andthe time of eventual differentiation of the imaginal discs,we conclude that following the incorporation of bromodeoxyuridineinto morphogenically critical base sequences of DNA, a cellundergoes an informational change that is transmitted to itsprogeny cells which differentiate during metamorphosis as acluster of phenotypically altered cells. The presence of bromodeoxyuridineper se in each cell of a clone is not necessary for expressionof the altered patterns of differentiation.     

水稻R基因同源序列与遗传学上已知抗病基因的共定位(英文)

植物抗病（R）基因结构上的高度保守性,为利用基于PCR的方法快速分离R基因同源序列提供了基础。采用这种方法,我们曾从水稻中分离到8个R基因候选同源序列（Rgenecandidates,RGCs）。为了研究RGCs与遗传学上已知的R基因的关系,对它们进行了限制性片段长度多态性（RFLP）分析和染色体定位。DNA杂交结果显示RGCs都属于多基因家族（Fig．1）。6个RGCs（Osh359－1、Osh359－2、Osh359－3、Osh359－5、Os8558－3、Os8558－14）在两个籼稻品种H359和Acc8558中检测出多态性,并定位在水稻染色体上（Fig．2）。它们分别检测出了1、1、4、1、2和1个座位,共10个座位,其中9个定位在第11号染色体的3个区域上,即RFLP标记G181和C82之间（由Osh359－2、Osh359－3、Osh359－5和Os8558－3检测的6个座位）,G1465与C50之间（Osh359－3检测出的一个座位）,和C496附近（由Osh359－1和Os8558－14检测出的两个紧密连锁的座位）另有一个由Os8558－3检测出的座位定位到第8号染色体上,位于L457和G1082B之间。这些染色体区域包含近一半的遗传学上已知的抗病基因,如Xa-3、Xa－10、Pi－a和xa－13。这一结果表明RGCs与已知的抗病基因位于相同的染色体区域。此外,RGCs定位的结果表明,它们在水稻基因组中呈簇状分布,表现出