Sequence specific recognition and cleavage of DNA by synthetic molecules

DNA recognition is an essential biological process responsible for the regulation of cellular functions including protein synthesis and cell division and is implicated in the mechanism of action of some anticancer drugs. Studies directed towards defining the elements responsible for sequence specific DNA recognition through the study of the interactions of synthetic organic ligands with DNA are described.

DNA recognition by poly-N-methylpyrrolecarboxamides was studied by the synthesis and characterization of a series of molecules where the number of contiguous N-methylpyrrolecarboxamide units was increased from 2 to 9. The effect of this incremental change in structure on DNA recognition has been investigated at base pair resolution using affinity cleaving and MPE•Fe(II) footprinting techniques. These studies led to a quantitative relationship between the number of amides in the molecule and the DNA binding site size. This relationship is called the n + 1 rule and it states that a poly-N methylpyrrolecarboxamide molecule with n amides will bind n + 1 base pairs of DNA. This rule is consistent with a model where the carboxamides of these compounds form three center bridging hydrogen bonds between adjacent base pairs on opposite strands of the helix. The poly-N methylpyrrolecarboxamide recognition element was found to preferentially bind poly dA•poly dT stretches; however, both binding site selection and orientation were found to be affected by flanking sequences. Cleavage of large DNA is also described.

One approach towards the design of molecules that bind large sequences of double helical DNA sequence specifically is to couple DNA binding subunits of similar or diverse base pair specificity. Bis-EDTA-distamycin-fumaramide (BEDF) is an octaamide dimer of two tri-N methylpyrrolecarboxamide subunits linked by fumaramide. DNA recognition by BEDF was compared to P7E, an octaamide molecule containing seven consecutive pyrroles. These two compounds were found to recognize the same sites on pBR322 with approximately the same affinities demonstrating that fumaramide is an effective linking element for Nmethylpyrrolecarboxamide recognition subunits. Further studies involved the synthesis and characterization of a trimer of tetra-N-methylpyrrolecarboxamide subunits linked by β-alanine ((P4)_(3)E). This trimerization produced a molecule which is capable of recognizing 16 base pairs of A•T DNA, more than a turn and a half of the DNA helix.

DNA footprinting is a powerful direct method for determining the binding sites of proteins and small molecules on heterogeneous DNA. It was found that attachment of EDTA•Fe(II) to spermine creates a molecule, SE•Fe(II), which binds and cleaves DNA sequence neutrally. This lack of specificity provides evidence that at the nucleotide level polyamines recognize heterogeneous DNA independent of sequence and allows SE•Fe(II) to be used as a footprinting reagent. SE•Fe(II) was compared with two other small molecule footprinting reagents, EDTA•Fe(II) and MPE•Fe(II).

The variations and climatic significance of D/H ratios in the carbon-bound hydrogen of cellulose in trees

The σD values of nitrated cellulose from a variety of trees covering a wide geographic range have been measured. These measurements have been used to ascertain which factors are likely to cause σD variations in cellulose C-H hydrogen.

It is found that a primary source of tree σD variation is the σD variation of the environmental precipitation. Superimposed on this are isotopic variations caused by the transpiration of the leaf water incorporated by the tree. The magnitude of this transpiration effect appears to be related to relative humidity.

Within a single tree, it is found that the hydrogen isotope variations which occur for a ring sequence in one radial direction may not be exactly the same as those which occur in a different direction. Such heterogeneities appear most likely to occur in trees with asymmetric ring patterns that contain reaction wood. In the absence of reaction wood such heterogeneities do not seem to occur. Thus, hydrogen isotope analyses of tree ring sequences should be performed on trees which do not contain reaction wood.

Comparisons of tree σD variations with variations in local climate are performed on two levels: spatial and temporal. It is found that the σD values of 20 North American trees from a wide geographic range are reasonably well-correlated with the corresponding average annual temperature. The correlation is similar to that observed for a comparison of the σD values of annual precipitation of 11 North American sites with annual temperature. However, it appears that this correlation is significantly disrupted by trees which grew on poorly drained sites such as those in stagnant marshes. Therefore, site selection may be important in choosing trees for climatic interpretation of σD values, although proper sites do not seem to be uncommon.

The measurement of σD values in 5-year samples from the tree ring sequences of 13 trees from 11 North American sites reveals a variety of relationships with local climate. As it was for the spatial σD vs climate comparison, site selection is also apparently important for temporal tree σD vs climate comparisons. Again, it seems that poorly-drained sites are to be avoided. For nine trees from different "well-behaved" sites, it was found that the local climatic variable best related to the σD variations was not the same for all sites.

Two of these trees showed a strong negative correlation with the amount of local summer precipitation. Consideration of factors likely to influence the isotopic composition of summer rain suggests that rainfall intensity may be important. The higher the intensity, the lower the σD value. Such an effect might explain the negative correlation of σD vs summer precipitation amount for these two trees. A third tree also exhibited a strong correlation with summer climate, but in this instance it was a positive correlation of σD with summer temperature.

The remaining six trees exhibited the best correlation between σD values and local annual climate. However, in none of these six cases was it annual temperature that was the most important variable. In fact annual temperature commonly showed no relationship at all with tree σD values. Instead, it was found that a simple mass balance model incorporating two basic assumptions yielded parameters which produced the best relationships with tree σD values. First, it was assumed that the σD values of these six trees reflected the σD values of annual precipitation incorporated by these trees. Second, it was assumed that the σD value of the annual precipitation was a weighted average of two seasonal isotopic components: summer and winter. Mass balance equations derived from these assumptions yielded combinations of variables that commonly showed a relationship with tree σD values where none had previously been discerned.

It was found for these "well-behaved" trees that not all sample intervals in a σD vs local climate plot fell along a well-defined trend. These departures from the local σD VS climate norm were defined as "anomalous". Some of these anomalous intervals were common to trees from different locales. When such widespread commonalty of an anomalous interval occurred, it was observed that the interval corresponded to an interval in which drought had existed in the North American Great Plains.

Consequently, there appears to be a combination of both local and large scale climatic information in the σD variations of tree cellulose C-H hydrogen.

River Ure: fisheries drought report 1996

Yorkshire Water Services (YWS) are currently granted a Time Limited Licence (TLL) for abstraction at Kilgram Bridge which is due for renewal in 1999. The Environment. Agency requires information on fish populations with regards to drought conditions and any possible effects that abstraction may have when considering licence renewal. In' order to evaluate any effects of drought and abstraction a three year study was instigated to examine fish populations. Surveys were conducted at nine main River Ure sites and two tributaries in which the triennial rolling programme formed the basis of site selection. Multi-method sampling techniques were carried out at several sites in order to evaluate capture efficiency. High densities of brown trout juveniles were observed in the tributaries with an indication that fish had become crowded as a result of low flows. Recruitment of brown trout in the tributaries was not directly related to flow levels in the main R. Ure. However, it is concluded that salmonids are at risk during drought flows and high temperatures from increased susceptibility to disease, predation, poor water quality and the direct lethal effect of high temperatures in shallow water.

River Ouse: fisheries drought report 1996

The basis for undertaking this study was to examine factors and potential impacts affecting fish and fishing in relation to low flow drought conditions and what other impacts may arise as a result of further reduced flows resulting from abstraction. The study formed the basis of a three year project to concentrate on effects relating to potable water abstractions at Moor Monkton by YWS. To fully evaluate the possible effects on fisheries the study set out to encompass fish population surveys from fry to adult stock, analysis of angler catch data, reports from anglers and river reports from Environment Agency Fisheries staff. In order to evaluate any effects of drought and abstraction a three year study was instigated to examine fish populations. Fish population surveys were conducted at six sites in which the triennial rolling programme formed the basis of site selection. Multi-method sampling techniques were carried out at several sites in order to evaluate capture efficiency. Roach were prolific above the weir at Linton-on-Ouse, with gudgeon, perch and small bream also well represented. Roach dominated catches on the R.Ouse below Linton, with perch and bleak also relatively abundant. Low flows were not thought to be directly correlated to successful recruitment of coarse fish, rather the associated high temperatures during drought conditions showing a strong positive effect with most species exhibiting growth rates above their long-term average. At this stage in the study there are no clear indications that the drought has caused any deleterious effects to coarse fish populations or marked changes in species composition, with evidence of good recruitment by several species, indicating that the higher temperatures have generally been beneficial to recruitment. However, the indication that dace did not benefit as well as other coarse fish under these conditions may suggest some species are affected more than others. The successful strong recruitment of most coarse fish suggests that, in future, fisheries will be supported by the 1995 year-class.

A educação como campo de batalha e local de seleção

Este trabalho é o resultado das reflexões relativas às leituras que venho realizando desde a minha graduação. A partir do entendimento de que a educação escolar, ao contrário de alguns de seus pressupostos, serviria especialmente à ordem social capitalista; sendo uma das maneiras mais eficientes de domesticar o ser humano. Não se trata de afirmar que toda educação escolar será sempre domesticadora, mas, que grande parte do seu trabalho acaba por contribuir para a diminuição da capacidade criativa do indivíduo. Entendo que a imposição da busca pela verdade e a tentativa de igualar a todos os indivíduos são julgamentos morais. Esses julgamentos representariam a interpretação da vida a partir de um ser enfraquecido, ou seja, teriam como função a preservação do decadente. Esses valores morais acabam por diminuir, também, a energia dos indivíduos que poderiam expandir-se. A escola pode ser um local onde o estudante poderá ter experiências capazes de levá-lo ao crescimento, ou não. Concordamos com Nietzsche, ao entender que há uma oposição entre a vontade de moral e a vontade de potência. O ser vivo quer crescer, ou preservar-se. A criação de novas formas de viver, de desejar uma vida com outra intensidade depende, dos instintos. A moral impõe ao indivíduo uma constante vigilância e coerção contra a expressão desses instintos. A energia que poderia gerar novas formas de viver, agora será utilizada contra o próprio indivíduo, atormentando-o. A escola ainda é uma fonte de experiências. Resta-nos saber como utilizá-la em seus potenciais criadores

A surveillance strategy for invasive species of concern in deepwater habitats of the Northwestern Hawaiian Islands

This report describes a surveillance strategy to detect deepwater invasive species in the Northwestern Hawaiian Islands. A need for this strategy was identified in the Papahānaumokuākea Marine National Monument Management Plan and the Monument’s Draft Natural Resources Science Plan. This strategy focuses on detecting two species of concern, the octocoral Carijoa riisei and the red alga Hypnea musciformis. Most research on invasive species in the Hawaiian archipelago has focused on shallow water habitats within the limits of conventional SCUBA (0-30 m). Deeper habitats such as mesophotic reefs are much more difficult to access and consequently little is known about the distribution of deepwater invasive species or their impacts. Recent deepwater (>30 m) sightings of H. musciformis and C. riisei, in and near NWHI, respectively, have prompted a call for further research and surveillance of invasive species in deepwater habitats. This report compiles the most up to date information about these two species of concern in deepwater habitats. A literature search and conversations with subject matter experts was used to identify their current distribution, preferred habitat types, optimal detection methods and ways to efficiently sample the vast extent of NWHI. The proposed sampling strategy prioritizes survey effort where C. riisei and H. musciformis are most likely to be found. At coarse spatial scales (tens to hundreds of kilometers), opportunistic observations and distance from the Main Hawaiian Islands, a principal propagule source, are used to identify high-risk islands and banks. At fine spatial scales (meters to tens of kilometers) a habitat suitability model was developed to identify high-risk habitats. The habitat suitability model focused on habitat preferences of C. riisei, since the species is well studied and adequate data exists to map habitats. There was insufficient information to identify suitable habitat for H. muscifomis. Habitat preferences for the algae are poorly understood and there is a lack of data at relevant spatial scales to map those preferences which are known. The principal habitats identified by the habitat suitability model were ledges and the edges of rugose coral reefs, where the shade loving octocoral would likely be found. Habitat suitability maps were developed for seven atolls and banks to aid in survey site selection. The protocol relied on technical divers to conduct visual surveys of benthic habitats. It was developed to increase the efficiency of surveys, maximize the probability of detection, identify important information relevant to future surveys and standardize results. The strategy, model and protocol were tested during a field mission in 2009 at several atolls and islands in NWHI. The field mission did not detect any invasive species among deepwater habitats and much was learned to improve future surveys. Data gaps and improvements are discussed.

The basics of cage and pen culture

The article discusses the basics of cage and pen aquaculture. Factors to consider are: site selection; choice of nets, floats, frames, and anchors; and the choice of culture method.

Sleeping sites, sleeping trees, and sleep-related behaviors of black crested gibbons (Nomascus concolor jingdongensis) at Mt. Wuliang, central Yunnan, China

Data on sleep-related behaviors were collected for a group of central Yunnan black crested gibbons (Nomascus concolor jingdongensis) at Mt. Wuliang, Yunnan, China from March 2005 to April 2006. Members of the group usually formed four sleeping units (adult male and juvenile, adult female with one semi-dependent black infant, adult female with one dependent yellow infant, and subadult male) spread over different sleeping trees. Individuals or units preferred specific areas to sleep; all sleeping sites were situated in primary forest, mostly (77%) between 2,200 and 2,400 m in elevation. They tended to sleep in the tallest and thickest trees with large crowns on steep slopes and near important food patches. Factors influencing sleeping site selection were (1) tree characteristics, (2) accessibility, and (3) easy escape. Few sleeping trees were used repeatedly by the same or other members of the group. The gibbons entered the sleeping trees on average 128 min before sunset and left the sleeping trees on average 33 min after sunrise. The lag between the first and last individual entering the trees was on average 17.8 min. We suggest that sleep-related behaviors are primarily adaptations to minimize the risk of being detected by predators. Sleeping trees may be chosen to make approach and attack difficult for the predator, and to provide an easy escape route in the dark. In response to cold temperatures in a higher habitat, gibbons usually sit and huddle together during the night, and in the cold season they tend to sleep on ferns and/or orchids.

Seawater irrigation systems for intensive marine shrimp farming in Thailand

The aim of the seawater irrigation system (SIS) is to clean up shrimp pond effluent and provide high quality seawater for shrimp farming. The system has 3 components: water intake; treatment reservoir and discharge system. There are criteria for site selection because shrimp farmers are required to form associations so they can work closely together. The construction site must be on the coastal area outside a mangrove forest and located away from a production agricultural area. All construction sites must have undergone an environmental impact assessment, and should be located on the area listed in Thailand's Coastal Zone Management Plan. Five SIS projects, which cover a culture area of 6,500 ha with 1,300 farmers (families), were completed and operated. The Department of Fisheries has planned for another 28 projects, that will cover almost 44,000 ha of culture area.

The technology of milkfish hatchery in Indonesia

The culture of milkfish (Chanos chanos), which is the oldest fish cultured in Indonesia, has spread to almost all the provinces in the country. In order to answer the demand of milkfish fry, without decreasing production and wild fry supply, artificial fry production in big and small-scale hatcheries is being practiced. Details are given of the milkfish hatchery system, listing also the major criteria to be taken into account for site selection. Operation of the hatchery is described, outlining the following activities: broodstock rearing; hormone implantation; broodstock maintenance; egg production and harvest; and, larval rearing.

Sleeping sites of Rhinopithecus bieti at Mt. Fuhe, Yunnan

Data on sleeping site selection were collected for a group of black-and-white snub-nosed monkeys (Rhinopithecus bieti; around 80) at Mt. Fuhe, Yunnan, China (99degrees20'E, 26degrees25'N, about 3,000 m asl) from November 2000 to January 2002. At the site mainly three vegetation types were present in an elevation-ascending order: deciduous broad leaf forest, mixed coniferous and broad leaf forest, and dark coniferous forest. In addition, bamboo forest presented in areas burned in 1958. Sleeping sites (n = 10) were located in the coniferous forest, where trees were the tallest, bottommost branches were the highest, the diameter of crowns was the second largest, and the gradient of the ground was the steepest. Monkeys usually kept quiet during entering and staying at a sleeping site. The site choice and the quietness may be tactics to avoid potential predators. In the coniferous forest, however, monkeys did not sleep in the valley bottom where trees were the largest, but frequently slept in the middle of the slope towards the east/southeast, in the shadow of ridges in three other directions, to avoid strong wind and to access sunshine; in winter-spring, they ranged in a more southern and lower area than in summer-autumn. These may be behavioral strategies to minimize energy stress in the cold habitat. Monkeys often slept in the same sleeping site on consecutive nights, which reflected a reduced pressure of predation probably due to either the effectiveness of anti-predation through sleeping site selection, or the population decline of predators with increasing human activities in the habitat. The group's behavioral responses to interactive and sometimes conflicting traits of the habitat are site-specific and conform to expectations for a temperate zone primate.

Sleeping sites of black-and-white snub-nosed monkeys (Rhinopithecus bieti) at Baima Snow Mountain, China

Data on sleeping sites of a group of black-and-white snub-nosed monkeys Rhinopithecus bieti (Colobinae, Primates) were collected between April-July and September-December 2001 to try to determine the factors affecting site selection at Nanren (99 degrees

PURIFICATION AND CHARACTERIZATION OF A KINASE SPECIFIC FOR THE SERINE-RICH AND ARGININE-RICH PRE-MESSENGER-RNA SPLICING FACTORS

Members of the SR family of pre-mRNA splicing factors are phosphoproteins that share a phosphoepitope specifically recognized by monoclonal antibody (mAb) 104. Recent studies have indicated that phosphorylation may regulate the activity and the intracellular localization of these splicing factors. Here, we report the purification and kinetic properties of SR protein kinase 1 (SRPK1), a kinase specific for SR family members. We demonstrate that the kinase specifically recognizes the SR domain, which contains serine/arginine repeats. Previous studies have shown that dephosphorylated SR proteins did not react with mAb 104 and migrated faster in SDS gels than SR proteins from mammalian cells. We show that SRPK1 restores both mobility and mAB 104 reactivity to a SR protein SF2/ASF (splicing factor 2/alternative splicing factor) produced in bacteria, suggesting that SRPK1 is responsible for the generation of the mAb 104-specific phosphoepitope in vivo. Finally, we have correlated the effects of mutagenesis in the SR domain of SF2/ASF on splicing with those on phosphorylation of the protein by SRPK1, suggesting that phosphorylation of SR proteins is required for splicing.

环渤海花岗岩体地下油库建设的工程地质力学研究

As a kind of strategic resource，petroleum play an very important role in current social stability, economic development and state safety. Since 1993 China has turned from a net oil exporter into a net oil importer, the figure of imported oil increased from then on. In 2004 China's total energy consumption exceeded Japan’s, and ranked in the second place, just inferior to America. Today China is the world’s third-largest importing nation, accounting for 6% of world imports and 8% of world consumption. Comparing with other strategic petroleum reserve schemes, underground oil storage possess many advantages, such as security, economy, less pollution, save land, suited for strategic reserve and so on, so it is the most ideal form for strategic petroleum reserve. In the background of China Strategic Petroleum Reserve Program started just now, this paper choose Circum-Bo sea region as a study area, and do some system study on the underground oil storage caverns constructed in inter-large granite rock masses in Circum-Bo sea region. On the foundation of a great amount of information come from both home and abroad, firstly this paper analysed the principle, economy, cavern shape, profile dimension, and gain some cognizances and logos, as follows: ①Hard rock mass such as granite is the major rock, in which underground oil storage are constructed; ②Unlined underground oil storage caverns had been wide spread used as a sort of oil storage form abroad, there already exist a suit of skilled experience and technologies to prevent oil product from leaking; ③Compared with surface tanks, underground oil storage cavern possess predominance in economy clearly. In general, it will be more economical when the storage capacity exceed 50000m3. The quality of rock mass is the most important factor for underground storage cost, however such as hydrogeology, storage capacity, the number of storage galleries, the length, storage product, mechanical equipments, geographic location also influent the cost. In designed depth of the underground storage, the rock mass of Jinzhou mainly belong to class Ⅱ, but parts with dykes, clayization alteration, and dense joints are Ⅲ, Ⅳ; ④Now, there are few underground oil storages span more than 25m in both abroad and home. The examples of some ancient underground works and modern underground excavation with wide span surely give us many precious elicitations to construct more great unlined storage caverns, when the rock mass quality is good, cavern shape and construction method also are proper, it is quite possible to construct underground oil storage cavern with span more than 30m . The main axis orientation of Jinzhou underground oil storage cavern is NW direction, the cavern's elevation locate between -53msl and -76msl. The storage's total volume is about 3×106m3, composed of 8 parallel galleries with 950m length, the pillars between them are 45m, and every two of galleries form one unit, which can deposit 75×104m3 for each unit. The product will be stored are Saudi light and Saudi medium crude oil, the main cavern's section is 411.5m2, with 23m height and 19m width. According to the principle and technique of engineering geomechanics, this study supply a sort of system scientific thinking and method for sitting location of underground oil storage in granite region: ① On the foundation of the earth crust stability sub-zone appraise of Circum-Bo sea region, farther research concerning granite distribution, genesis, geological period and fault structure are conducted in stable areas, generally, this paper select Liaoxi, east shore of Liaotung peninsula and Jiaotung peninsula as target areas for underground oil storage regions, where Mesozoic granite is magnitude; ②After roundly comparison in facts of geologic structure, engineering geology, hydrogeology, topography, transportation and so on of three granite distributed areas, at last, selecting Jingzhou granite zone in Liaoxi out as an ideal construction area; ③ Detailed investigation is conducted in the southeast of Baimashi in Jingzhou development district, the final field. Ultrasonic Borehole Television, as a major way to collect original information of borehole rock mass were used, which is very effective to appraise the quality of deep rock mass; ④ According to the field data of tectonic stress, rock mass quality, the spatial distribution of fracture water, some optimum designs in cross section, axial direction and cavern span have been designed for the underground oil storage cavern layout in Jinzhou. To understand the characteristics of swelling alteration rock in Jinzhou granite mass, collected abundant swelling alteration rock engineering examples in granite, which study them in detail, concluded the swelling alteration rock distribute nearly everywhere in China, intruded medium-basic dykes alteration, along discontinuities and mineral hydrothermal alteration with genesis of granite are three main forms clayization alteration rock in granite rock mass. In Jinzhou field, from macro to micro studied the swelling rock which induced by mid-basic dyke intrusion, with weak swelling. In conclusion, this paper conclude the distribution rule and features of expansion alteration rock in filed, and advise some technical suggestions for excavation at swelling alteration rock part. The main features of this paper: ①In the process of site selection, investigation and design, a suit of technique and method of engineering geomechanics metasynthesis were formed, which is significative to guide the large scale underground oil storage cavern sitting location, investigation and design in granite rock mass; ②The detailed discussion on the engineering geology problems in granite mass, such as weathering crust, faults, dykes and clayization alteration rock, are useful for other projects in aspects of site selection, engineering geology evaluation and stability estimation; ③The summary and integration of the genesis, type, countermeasure relate to swelling alteration rock, also is likely to be used for other underground oil storage caverns constructed in swelling alteration granite. In conclusion, this study is meaningful for guiding the large scale underground oil storage for site selection, investigation and design in granite rock mass.

Inference and Labeling of Metric-Induced Network Topologies

The development and deployment of distributed network-aware applications and services over the Internet require the ability to compile and maintain a model of the underlying network resources with respect to (one or more) characteristic properties of interest. To be manageable, such models must be compact, and must enable a representation of properties along temporal, spatial, and measurement resolution dimensions. In this paper, we propose a general framework for the construction of such metric-induced models using end-to-end measurements. We instantiate our approach using one such property, packet loss rates, and present an analytical framework for the characterization of Internet loss topologies. From the perspective of a server the loss topology is a logical tree rooted at the server with clients at its leaves, in which edges represent lossy paths between a pair of internal network nodes. We show how end-to-end unicast packet probing techniques could b e used to (1) infer a loss topology and (2) identify the loss rates of links in an existing loss topology. Correct, efficient inference of loss topology information enables new techniques for aggregate congestion control, QoS admission control, connection scheduling and mirror site selection. We report on simulation, implementation, and Internet deployment results that show the effectiveness of our approach and its robustness in terms of its accuracy and convergence over a wide range of network conditions.