基于直接接触的微生物胞外电子传递

微生物电子传递在微生物的代谢繁殖和物质的生物地球化学循环中发挥着关键作用。其中基于直接接触的微生物胞外电子传递(Direct extracellular electron transfer,DEET)已成为微生物学、地球化学和生物物理学等学科共同关注的焦点,并在近几年取得了一系列重要发现和理论突破,包括微生物纳米导线、电缆细菌、微生物种间DEET等。伴随着这些新进展,更多的问题也需要研究者们在进一步的研究中解决,包括DEET的分子机制及其相关功能微生物种群等。不同学科理论和技术的交叉是进一步揭示DEET过程的关键。     

Comparison of three electron microscopy techniques for the detection of human rotaviruses

Rotavirus detection by direct electron microscopy was compared with direct and indirect immune electron microscopy techniques. The latter two approaches permitted the enumeration of 25 and 103 times more rotaviruses respectively, than direct electron microscopy. Also, 70% and 90% of the virus particles were aggregated by direct and indirect immune electron microscopy techniques respectively, thus facilitating their detection.     

The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7.

The frequency of genetic deletion between directly repeated DNA sequences in bacteriophage T7 was measured as a function of the length of the direct repeat. The non-essential ligase gene (gene 1.3) of bacteriophage T7 was interrupted with pieces of synthetic DNA bracketed by direct repeats of various lengths. Deletion of these 76 bp long inserts was too low to be measured when the direct repeats were less than 6 bp long. However, the frequency of deletion of inserts with longer direct repeats increased exponentially as the length of the repeats increased from 8 to 20 bp. When inverted repeats (palindromes) were designed in the midst of the insert there was essentially no increase in deletion frequency between 10 bp direct repeats. But, the same palindromic sequences increased the deletion frequency between 5 bp direct repeats by at least two orders of magnitude. Thus, in this system homology at the endpoints is a more important determinant of deletion frequency than is the presence of palindromes between the direct repeats.     

You get what you pay for: reward-specific trade-offs among direct and ant-mediated defences in plants

Plant defences against herbivores include direct defences such as secondary metabolites or physical structures (e.g. trichomes) as well as indirect defences mediated via mutualistic interactions with other organisms including ants. Production of both direct defences and rewards for mutualistic ants may be costly for a plant, and it has been suggested that trade-offs may exist between direct and ant-mediated defences. We have conducted a meta-analysis of 25 studies testing the above hypothesis and found a significant negative correlation between plant allocation to direct and ant-mediated defences. The strength of correlation was similar for across- and within-species comparisons, and for chemical and physical direct defences. However, trade-offs with direct defences were significant only in plants which offered to ants more costly rewards such as food bodies and/or domatia, but not in plants which attracted ants with relatively cheap extrafloral nectaries. Our results therefore support the hypothesis that plant investment in ant-mediated defences may reduce the requirement for direct chemical and physical defences, but only in plants which offer more costly rewards to their bodyguards.     

Environs: The Superniches of Ecosystems

Evolution proceeds by natural selection of heritable variationsof individual organisms based on direct influences of environment.However, indirect effects probably vastly outweigh direct onesin ecosystems. Therefore, why is evolution based on direct effectsonly? The ecological niche represents the point of direct contactbetween organisms and their environments. To encompass indirectinfluences, niches are extended to new structures, environs,which are units of organism-environment coevolution. The motiveforce for coevolution is closure of outputs back upon inputsof the organism members of ecosystems. Closure is achieved bybiogeochemical cycling and feedback interactions, direct andindirect, between organisms. To the extent that closure doesnot occur, there is no imperative for organism-environment coevolution.Coevolution at the system level based on indirect effects iscompatible with normal evolution at the individual organismlevel based on direct effects. The organism is the unit of thelatter, but environs are the unit of coevolution.     

Biosensors based on novel peroxidases with improved properties in direct and mediated electron transfer.

Native horseradish peroxidase (HRP) on graphite has revealed approximately 50% of the active enzyme molecules to be in direct electron transfer (ET) contact with the electrode surface. Some novel plant peroxidases from tobacco, peanut and sweet potato were kinetically characterised on graphite in order to find promising candidates for biosensor applications and to understand the nature of the direct ET in the case of plant peroxidases. From measurements of the mediated and mediatorless currents of hydrogen peroxide reduction at the peroxidase-modified rotating disk electrodes (RDE), it was concluded that the fraction of enzyme molecules in direct ET varies substantially for the different plant peroxidases. It was observed that the anionic peroxidases (from sweet potato and tobacco) demonstrated a higher percentage of molecules in direct ET than the cationic ones (HRP and peanut peroxidase). The peroxidases with a high degree of glycosylation demonstrated a lower percentage of molecules in direct ET. It could, thus, be concluded that glycosylation of the peroxidases hinders direct ET and that a net negative charge on the peroxidase (low pI value) is beneficial for direct ET. Especially noticeable are the values obtained for sweet potato peroxidase (SPP), revealing both a high percentage in direct ET and a high rate constant of direct ET. The peroxidase electrodes were used for determination of hydrogen peroxide in RDE mode (mediatorless). SPP gave the lowest detection limit (40 nM) followed by HRP and peanut peroxidase.     

The Influence of Primary and Secondary DNA Structure in Deletion and Duplication between Direct Repeats in Escherichia Coli

We describe a system to measure the frequency of both deletions and duplications between direct repeats. Short 17- and 18-bp palindromic and nonpalindromic DNA sequences were cloned into the EcoRI site within the chloramphenicol acetyltransferase gene of plasmids pBR325 and pJT7. This creates an insert between direct repeated EcoRI sites and results in a chloramphenicol-sensitive phenotype. Selection for chloramphenicol resistance was utilized to select chloramphenicol resistant revertants that included those with precise deletion of the insert from plasmid pBR325 and duplication of the insert in plasmid pJT7. The frequency of deletion or duplication varied more than 500-fold depending on the sequence of the short sequence inserted into the EcoRI site. For the nonpalindromic inserts, multiple internal direct repeats and the length of the direct repeats appear to influence the frequency of deletion. Certain palindromic DNA sequences with the potential to form DNA hairpin structures that might stabilize the misalignment of direct repeats had a high frequency of deletion. Other DNA sequences with the potential to form structures that might destabilize misalignment of direct repeats had a very low frequency of deletion. Duplication mutations occurred at the highest frequency when the DNA between the direct repeats contained no direct or inverted repeats. The presence of inverted repeats dramatically reduced the frequency of duplications. The results support the slippage-misalignment model, suggesting that misalignment occurring during DNA replication leads to deletion and duplication mutations. The results also support the idea that the formation of DNA secondary structures during DNA replication can facilitate and direct specific mutagenic events.     

高产水稻品种及种植方式对稻田甲烷排放的影响

采用大田试验研究了不同水稻品种（早稻：超级稻“陆两优996”和常规稻“创丰1号”;晚稻：T优259）及不同种植方式（直播和移栽）对稻田甲烷排放通量的影响.结果表明：早稻晒田前甲烷排放量占排放总量的52%～73%,排水晒田减少了甲烷排放通量;晚稻生育前期甲烷排放量占生长期间甲烷排放总量的70%.早稻直播方式的甲烷排放通量均值低于移栽种植方式,但甲烷排放总量大于移栽种植方式;晚稻直播方式的甲烷排放通量均值与排放总量都大于移栽种植方式.早、晚稻直播方式的单位稻谷甲烷排放量与移栽种植方式间均存在显著差异,早稻中超级稻和常规稻直播方式的单位稻谷甲烷排放量分别比移栽方式高4.84和3.48 g·kg^-1稻谷,常规稻的甲烷排放量高于超级稻;晚稻直播方式的单位稻谷甲烷排放量比移栽方式高6.67 g·kg^-1稻谷.相同面积、相同时间不同种植方式的稻田甲烷排放量、单位经济产量甲烷排放量表现为：早稻：常规稻直播＞常规稻移栽＞超级稻直播＞超级稻移栽;晚稻：直播＞移栽.     

Terminal repeats of the Drosophila transposable element copia: nucleotide sequence and genomic organization

We have determined the nucleotide sequence of the terminal regions of two members of the copia sequence family of D. melanogaster. The first 276 bp at one end of a copia element are repeated in direct orientation at its other end. The direct repeats on a single copia element are identical to each other, but they differ by two nucleotide substitutions between the two elements which were examined; this suggests that during transposition only one direct repeat of the parent element is used as a template for both direct repeats of the transposed element. Each direct repeat itself contain a 17 bp imperfectly matched inveted terminal repetition. The ends of copia show significant sequence homology both to the yeast Ty1 element and to the integrated provirus of avian spleen necrosis virus, two other eucaryotic elements known to insert at many different chromosomal locations. Analysis of the genomic organization of the direct repeat sequence demonstrates that it seldom, if ever, occurs unlinked to an entire copia element.     

A study of direct moxibustion using mathematical methods

Direct moxibustion is an important and widely used treatment method in traditional medical science. The use of a mathematical method to analyse direct moxibustion treatment is necessary and helpful in exploring the new direct moxibustion instruments and their standardisation. Thus, this paper aims to use a mathematical method to study direct moxibustion in skin to demonstrate a direct relationship between direct moxibustion and skin stimuli. In this paper, the transient thermal response of skin layers is analysed to study direct moxibustion using the data got from standardised method to measure the temperature of a burning moxa cone. Numerical simulations based on an appropriate finite element model are developed to predict the heat transfer, thermal damage and thermal stress distribution of barley moxa cones and jujube moxa cones in the skin tissue. The results are verified by the ancient literatures of traditional Chinese medicine and clinical application, and showed that mathematical method can be a good interface between moxa cone and skin tissue providing the numerical value basis for moxibustion.     

Quantitative analysis of correlations among flower traits in Gerbera hybrida,Compositae

Summary A Mean Correlation Response (MCR) model was developed to estimate the relative effectiveness of direct selection when other traits also respond to the selection. A measure of the relative effects of mean correlated response and direct response (R) and a measure of the relative efficiency of direct selection (IE) were applied to a genetic correlation matrix of 38 traits. These were measurements of inflorescence, receptacle and involucre, scape, disk florets, ray florets, and trans florets in the Davis population of Gerbera hybrida, Compositae. Generally, traits with high heritability had high direct and mean correlated response; these were often traits measuring disk and trans florets. Traits with low heritability had low direct and mean correlated response; these were often traits measuring the inflorescence. Traits of the inflorescence had the lowest efficiency of direct to mean correlated response.     

A study of direct moxibustion using mathematical methods

Direct moxibustion is an important and widely used treatment method in traditional medical science. The use of a mathematical method to analyse direct moxibustion treatment is necessary and helpful in exploring the new direct moxibustion instruments and their standardisation. Thus, this paper aims to use a mathematical method to study direct moxibustion in skin to demonstrate a direct relationship between direct moxibustion and skin stimuli. In this paper, the transient thermal response of skin layers is analysed to study direct moxibustion using the data got from standardised method to measure the temperature of a burning moxa cone. Numerical simulations based on an appropriate finite element model are developed to predict the heat transfer, thermal damage and thermal stress distribution of barley moxa cones and jujube moxa cones in the skin tissue. The results are verified by the ancient literatures of traditional Chinese medicine and clinical application, and showed that mathematical method can be a good interface between moxa cone and skin tissue providing the numerical value basis for moxibustion.     

Direct methylation from mouse plasma and from liver and brain homogenates

The analysis of fatty acid composition of plasma and tissue is important as a method for studying lipid nutrition. We investigated the possibility of direct methylation of fatty acids by BF(3)-methanol from plasma and from liver and brain homogenates without lipid extraction. There were no ghost peaks in the chromatogram produced by the direct methylation method. The 18:0 percentages were significantly higher in the direct methylation method than in the lipid extraction method. There were not remarkable differences in fatty acid composition in the direct methylation and methylation after lyophilization methods. Furthermore, the recovery ratio of the internal standard in the direct methylation method was higher than that in the lipid extraction method. The difference of fatty acid composition with lipid extraction may be caused by the change of lipid class extraction. Therefore, the direct methylation method without lipid extraction is the most suitable for determining fatty acid composition in plasma and tissue.     

Detection of Listeria monocytogenes using polyclonal antibody

Polyclonal antibody sensitive to Listeria was assayed for the detection of Listeria using two different methods, direct and sandwich enzyme linked immunosorbent assays (ELISAs). The direct ELISA uses anti-goat IgG antibody conjugated with horse-radish peroxidase, while the sandwich ELISA uses two antibodies both specific to Listeria antigens, one coated onto the microtitre plate and the other conjugated to horse-radish peroxidase. The results obtained show that the direct ELISA is superior to the sandwich ELISA in two distinct ways: (i) with direct ELISA the non- Listeria gave readings <0.2, whereas with sandwich ELISA it gave readings of 0.3–0.4; (ii) the direct ELISA is more cost-effective than the sandwich ELISA.     

Direct repeats surrounding the ribosomal RNA genes of Physarum polycephalum

Sequence homology was found between the external transcribed spacer and the terminal non-transcribed spacer of Physarum polycephalum rDNA. The homologous sequences were located 2kb upstream from the 19s rRNA gene and 0.3kb downstream from 26S rRNA gene, respectively, and were arranged in a direct repeat manner. Sequence analyses showed that the direct repeats consisted of two parts: one was sequences of about 130bp which showed over 90% sequence homology with each other. The other consisted mainly of many tandem repeats of a 50 to 52bp unit. The direct repeat-rRNA genes-direct repeat unit was found to be flanked by short direct repetitious sequences. Based on these findings, the significance of the direct repeat is discussed in terms of evolution of rDNA.     

Instability of large direct repeats in retrovirus vectors.

Retrovirus vectors were constructed with large (0.85- to 1.3-kilobase-pair) direct repeats in their genomes. Deletions involving the direct repeats occurred at a high frequency. Deletions occurred both when the direct repeats were in tandem and when they were separated by additional sequences. These deletions occurred during virus replication.     

Comparison of Solid-Phase Radioimmunoassays for Baculoviruses

The sensitivity and cross-reaction of four solid-phase radioimmunoassays (RIA) for Trichoplusia ni nuclear polyhedrosis virus containing singly enveloped virions were investigated. The detection limits of each assay were as follows: Indirect RIA, 5 ng of dissolved polyhedron antigen; direct RIA, 50 ng; indirect sandwich RIA, 200 ng; and direct sandwich RIA, 300 ng. The indirect and indirect sandwich RIAs showed considerable cross-reaction with other baculovirus antigens, but the direct and direct sandwich RIAs showed cross-reaction with only one closely related baculovirus. When microtiter plates used for the solid phase were pretreated with bovine serum albumin, nonspecific binding of labeled antibodies was reduced to a minimum. Antibodies prepared by an immunoadsorption procedure showed greater specific binding than antibodies prepared by ammonium sulfate precipitation of the immunoglobulin fraction. Highly contaminated antigen could not be detected by the indirect RIA, but the direct sandwich RIA was unaffected by antigen contamination. Antigen making up 0.0025% (wt/wt) of a sample of bird droppings could be detected by the direct sandwich RIA.     

Postsynaptic inhibition in the general cortex of the turtle forebrain

Postsynaptic inhibition in the general cortex of the turtle forebrain was investigated by recording unit activity intracellularly. Depending on the type of IPSPs recorded in response to electrical stimulation of the contralateral optic nerve and cortical surface the neurons were subdivided into three groups: 1) with long direct IPSPs, 2) with long and short direct, and also recurrent IPSPs, 3) with short direct and recurrent IPSPs. It is concluded that inhibitory pathways of the short direct and recurrent IPSPs have a common final component, a stellate interneuron. Compared with the recurrent collaterals of the principal neurons, the direct afferents make contact with more distal portions of the dendrites of this cell. Synapses formed on dendrites of the principal neurons by axons of the stellate cells are nearer to the soma than synapses responsible for generation of the long direct IPSP.M. V. Lomonosov Moscow State University. Translated from Neirofiziologiya, Vol. 5, No. 4, pp. 375–383, July–August, 1973.     

Natural Direct and Indirect Effects on the Exposed: Effect Decomposition under Weaker Assumptions

Summary We define natural direct and indirect effects on the exposed. We show that these allow for effect decomposition under weaker identification conditions than population natural direct and indirect effects. When no confounders of the mediator‐outcome association are affected by the exposure, identification is possible under essentially the same conditions as for controlled direct effects. Otherwise, identification is still possible with additional knowledge on a nonidentifiable selection‐bias function which measures the dependence of the mediator effect on the observed exposure within confounder levels, and which evaluates to zero in a large class of realistic data‐generating mechanisms. We argue that natural direct and indirect effects on the exposed are of intrinsic interest in various applications. We moreover show that they coincide with the corresponding population natural direct and indirect effects when the exposure is randomly assigned. In such settings, our results are thus also of relevance for assessing population natural direct and indirect effects in the presence of exposure‐induced mediator‐outcome confounding, which existing methodology has not been able to address.     

Calculation of the"Net Additions to Stock" Indicator for the Czech Republic Using a Direct Method

Abstract: Net additions to stock (NAS) are an indicator based on economy-wide material flow accounting and analysis. NAS, a measure of the physical growth rate of an economy, can be used for estimates of future waste flows. It is calculated using two methods: The indirect method of calculation is a simple difference between all input and output flows, whereas the direct method involves measuring the amounts of materials added to particular categories of physical stock and the amounts of waste flows from these stocks.
The study described in this article had one leading objective: to make available direct NAS data for the Czech Republic, which could later be used for predicting future waste flows. Two additional objectives emerged from the first: (1) to develop a method for direct NAS calculation from data availability in the Czech Republic; (2) to calculate NAS directly, compare the results with those achieved in indirect NAS calculation, and discuss the identified differences.
The NAS for the Czech Republic calculated by the direct method is equal to approximately 65 million tonnes on average in 2000–2002 and is approximately 27% lower than the NAS acquired by the indirect method of calculation. The actual values of directly calculated NAS and its uncertainties suggest that the indirect NAS is more likely to be an overestimation than an underestimation. Durables account for about 2% of the total direct NAS, whereas the rest is attributed to infrastructure and buildings. The direct NAS is dominated by nonmetal construction commodities such as building stone and bricks, which equal approximately 89% of the total direct NAS.
Calculation of NAS by the direct method has been proved to be feasible in the Czech Republic. Moreover, uncertainties related to direct NAS are lower than those related to indirectly acquired NAS.