Chirally-Modifiedoligonucleotides and the Control of Gene Expression. The Case of L-DNAS And-RNAS

Abstract

The affinity of L-DNAs, L-RNAs and L/D-DNAs for homopurine homopyrimidine d.s. D-DNA and s.s. D-RNA was probed by gel electrophoresis and CD spectroscopy. It was found that the L-modified oligomers do not bind to d.s. DNA and to natural RNA that contains all four natural bases. Thus they cannot be used, in general, for the control of gene expression according to the antigene and antisense methodologies. Heterochiral complexes with 1:1 stoichiometry and low thermal stability are formed, instead, by homopurinic L-RNA or L/D-DNA and homopyrimidinic L-RNA with the W/C complementary natural RNA sequences.     

On the structure and dynamics of the complex of the nucleosome and the linker histone

Several different models of the linker histone (LH)–nucleosome complex have been proposed, but none of them has unambiguously revealed the position and binding sites of the LH on the nucleosome. Using Brownian dynamics-based docking together with normal mode analysis of the nucleosome to account for the flexibility of two flanking 10 bp long linker DNAs (L-DNA), we identified binding modes of the H5-LH globular domain (GH5) to the nucleosome. For a wide range of nucleosomal conformations with the L-DNA ends less than 65 Å apart, one dominant binding mode was identified for GH5 and found to be consistent with fluorescence recovery after photobleaching (FRAP) experiments. GH5 binds asymmetrically with respect to the nucleosomal dyad axis, fitting between the nucleosomal DNA and one of the L-DNAs. For greater distances between L-DNA ends, docking of GH5 to the L-DNA that is more restrained and less open becomes favored. These results suggest a selection mechanism by which GH5 preferentially binds one of the L-DNAs and thereby affects DNA dynamics and accessibility and contributes to formation of a particular chromatin fiber structure. The two binding modes identified would, respectively, favor a tight zigzag chromatin structure or a loose solenoid chromatin fiber.     

稻田节肢动物群落优势功能集团的垂直分布、数量动态及天敌作用估计

研究了稻田节肢动物群落中优势功能集团的垂直空间分布和数量动态规律。结果表明,狼蛛的分布范围不象过去认识的那样广,而是主要分布在稻株的中下部。蛸蛛也不仅仅限制在稻株叶冠层,其在受到农药干扰后,向下部转移。顶位物种与基位物种垂直空间分布的相关性不大。在稻田内影响天敌对褐飞虱种群动态控制作用大小的因素,除了天敌的数量之外,若有天敌与褐飞虱的空间分布特征,褐飞虱占天敌食谱中的比例等。提出了包含天敌、褐飞虱     

稻田节肢动物群落优势功能集团的垂直分布、数量动态及天敌作用估计

研究了稻田节肢动物群落中优势功能集团的垂直空间分布和数量动态规律.结果表明,狼蛛的分布范围不象过去认识的那样广,而是主要分布在稻株的中下部.蛸蛛也不仅仅限制在稻株叶冠层,其在受到农药干扰后,向下部转移.顶位物种与基位物种垂直空间分布的相关性不大.在稻田内影响天敌对褐飞虱种群动态控制作用大小的因素,除了天敌的数量之外,尚有天敌与褐飞虱的空间分布特征,褐飞虱占天敌食谱中的比例等.提出了包含天敌、褐飞虱、中性昆虫的数量动态、空间分布、取食特性等信息的评价天敌作用的模型.     

Cortical sensitivity to visual features in natural scenes

A central hypothesis concerning sensory processing is that the neuronal circuits are specifically adapted to represent natural stimuli efficiently. Here we show a novel effect in cortical coding of natural images. Using spike-triggered average or spike-triggered covariance analyses, we first identified the visual features selectively represented by each cortical neuron from its responses to natural images. We then measured the neuronal sensitivity to these features when they were present in either natural images or random stimuli. We found that in the responses of complex cells, but not of simple cells, the sensitivity was markedly higher for natural images than for random stimuli. Such elevated sensitivity leads to increased detectability of the visual features and thus an improved cortical representation of natural scenes. Interestingly, this effect is due not to the spatial power spectra of natural images, but to their phase regularities. These results point to a distinct visual-coding strategy that is mediated by contextual modulation of cortical responses tuned to the spatial-phase structure of natural scenes.     

The inhibitory activity of natural products on plant p-hydroxyphenylpyruvate dioxygenase

The inhibitory activity of 34 natural products of various structural classes on hydroxyphenylpyruvate dioxygenase (HPPD), the target site for triketone herbicides, and the mode of interaction of selected natural products were investigated. Recombinant HPPD from arabidopsis is sensitive to several classes of natural compounds including, in decreasing order of sensitivity, triketones, benzoquinones, naphthoquinones and anthraquinones. The triketone natural products acted as competitive tight-binding inhibitors, whereas the benzoquinones and naphthoquinones did not appear to bind tightly to HPPD. While these natural products may not have optimal structural features required for in vivo herbicidal activity, the differences in their kinetic behavior suggest that novel classes of HPPD inhibitors may be developed based on their structural backbones.     

Natural cytolytic activity in mice with natural or induced cellular defects. I. Differential ability of in vitro interleukin-2 addition to augment natural cytolytic function

The ability of in vitro addition of recombinant interleukin 2 (rIL-2) to differentially enhance natural cytotoxicity was assessed using cells from mice with natural and induced cellular defects. In vivo treatment with most immunosuppressive or cytoreductive agents, anti-asialo-GM1 antibody, or gamma irradiation dramatically reduced in vitro cytotoxicity against natural killer (NK) sensitive targets by direct reduction in either percentage specific lysis or lytic units per spleen. In most cases, in vitro addition of rIL-2 (at concentrations causing augmented NK function in cells from naive Balb/C mice) enhanced cytotoxic activity of cells from treatment groups to a normal value but not within the rIL-2-enhanced range of nontreated animals. Additionally, cytotoxic activity of cells from animals treated with certain drugs or gamma irradiation could be augmented by rIL-2 when measured by percentage lysis but not lytic units per spleen. In vivo treatment with cyclosporin A did not affect natural cytotoxic activity and addition of rIL-2 augmented the NK activity in a similar fashion to the profile of naive cells. In experiments using cells from beige (C57Bl/6-bg) mice which have a natural defect in NK activity against YAC-1 targets, addition of rIL-2 (at concentrations causing augmented natural cytotoxic function in cells from C57Bl/6 mice) could not effectively enhance in vitro natural cytotoxic function.     

Glucocorticoid receptor mediated suppression of natural killer cell activity: identification of associated deacetylase and corepressor molecules

Physical and psychological stressors reduce natural killer cell function. This reduction in cellular function results from stress-induced release of glucocorticoids. Glucocorticoids act upon natural killer cells to deacetylate and transrepress immune response genes through epigenetic processes. However, other than the glucocorticoid receptor, the proteins that participate in this process are not well described in natural killer cells. The purpose of this study was to identify the proteins associated with the glucocorticoid receptor that are likely epigenetic participants in this process. Treatment of natural killer cells with the synthetic glucocorticoid, dexamethasone, produced a significant time dependent reduction in natural killer cell activity as early as 8h post treatment. This reduction in natural killer cell activity was preceded by nuclear localization of the glucocorticoid receptor with histone deacetylase 1 and the corepressor, SMRT. Other class I histone deacetylases were not associated with the glucocorticoid receptor nor was the corepressor NCoR. These results demonstrate histone deacetylase 1 and SMRT to associate with the ligand activated glucocorticoid receptor within the nuclei of natural killer cells and to be the likely participants in the histone deacetylation and transrepression that accompanies glucocorticoid mediated reductions in natural killer cell function.     

Attitudes to the importance of retaining natural teeth in an adult Swedish population

Objectives . To evaluate the attitudes to retaining natural teeth in an adult Swedish population, and to correlate the attitude to retaining natural teeth with some presumed influencing background factors. Design : Cross-sectional study using a newly developed questionnaire. Subjects : From the national census register of four municipalities in the southern part of the province of Halland, Sweden, with a total population of 126,878 adult (≥20 years) inhabitants, 4,200 persons were selected at random. The sample was randomised by age and sex, and 300 men and 300 women from the age groups 20, 30, 40, 50, 60, 70, and 80 years were included. Intervention and main outcome measures : The questionnaire aimed to evaluate the number of remaining natural teeth, the dental care habits, the self-estimated quality of natural teeth, and the attitude t o retaining natural teeth In the studied population, and also to evaluate the possible correlation between those factors, in particular, the attitude to retaining natural teeth versus the other factors. Results : It was found that the attitude to the importance of retaining natural teeth was strongly correlated with the number of remaining natural teeth, the dental care habits, and the self-estimated quality of natural teeth. Also sex had an influence on this attitude but not age. Conclusions : The attitude to the importance of retaining natural teeth in an adult Swedish population is correlated with the number of remaining natural teeth, the dental care habits, the self-estimated quality of natural teeth, and sex, but not with age.     

Bayesian natural selection and the evolution of perceptual systems

In recent years, there has been much interest in characterizing statistical properties of natural stimuli in order to better understand the design of perceptual systems. A fruitful approach has been to compare the processing of natural stimuli in real perceptual systems with that of ideal observers derived within the framework of Bayesian statistical decision theory. While this form of optimization theory has provided a deeper understanding of the information contained in natural stimuli as well as of the computational principles employed in perceptual systems, it does not directly consider the process of natural selection, which is ultimately responsible for design. Here we propose a formal framework for analysing how the statistics of natural stimuli and the process of natural selection interact to determine the design of perceptual systems. The framework consists of two complementary components. The first is a maximum fitness ideal observer, a standard Bayesian ideal observer with a utility function appropriate for natural selection. The second component is a formal version of natural selection based upon Bayesian statistical decision theory. Maximum fitness ideal observers and Bayesian natural selection are demonstrated in several examples. We suggest that the Bayesian approach is appropriate not only for the study of perceptual systems but also for the study of many other systems in biology.     

Naturally occurring anti-alpha-galactosyl antibodies: relationship to xenoreactive anti-alpha-galactosyl antibodies.

Antibodies produced by an individual without a known history of sensitization to the relevant antigen are called "natural" antibodies. Some natural antibodies, called xenoreactive antibodies, react with the cells of foreign species. Most xenoreactive antibodies in humans and higher primates bind to a nonreducing terminal galactose expressed by pigs and other lower mammals. Although human natural antibodies which bind to one or more of a variety of terminal alpha-galactosyl structures have been identified previously, the antigen recognized by anti-alpha-galactosyl antibodies on the cells of foreign species is thought to be exclusively Galalpha1-3Gal. Thus, anti-alpha-galactosyl antibodies which do not react with Galalpha1-3Gal are thought to be nonxenoreactive. Here, we identify natural antibodies in human serum which bind to Galalpha1-6Hexosepyrranosides but not Galalpha1-3Gal, indicating that these antibodies are not xenoreactive. Various lower mammals were found to have natural anti-Galalpha1-2Gal antibodies in their sera, suggesting that at least some anti-Galalpha1-2Gal antibodies might not be xenoreactive and indicating, surprisingly, that anti-alpha-galactosyl antibodies are much more phylogenetically disperse than previously known. Also surprising was the finding that some natural antibodies which bind to Galalpha1-3Gal in vitro do not bind to porcine xenografts. These studies show that naturally occurring anti-alpha-galactosyl antibodies in mammalian serum include antibodies with a greater variety of reactivities than previously thought, only some of which would bind to a porcine xenograft. Further, these studies show that the methods used to detect anti-alpha-galactosyl antibodies of relevance in xenotransplantation must be carefully evaluated to avoid detection of anti-alpha-galactosyl antibodies which would not bind to a porcine organ and which therefore are not involved in xenograft rejection.     

Refractoriness to short and long days determines the end and onset of the breeding season in subtropical goats

The objective was to determine whether refractoriness to short and long days were involved in the end and onset of the breeding season, respectively, in goats adapted to subtropical latitudes. Ovariectomized does given a subcutaneous implant constantly releasing estradiol-l7 β (OVX+E) were used in two experiments. Plasma LH concentrations were determined twice weekly. In Experiment 1, the control group remained in an open-shed pen (natural day length and ambient temperature). Two experimental groups were placed in light-proof buildings (with natural temperature variations). One group was exposed to natural simulated increasing days (winter to spring), whereas the other was exposed to a winter solstice photoperiod (10 h of light) from December 21 to April 28. In Experiment 2, the control group remained under natural day length and ambient temperature. One experimental group was exposed to natural simulated decreasing days (summer to autumn), whereas the other group was exposed to a summer solstice photoperiod (14 h of light) from June 21 to October 20. In Experiment 1, the breeding season was not prolonged in does maintained in the winter solstice day length. Mean dates of decrease in LH secretion (end of the breeding season) did not differ significantly between does exposed to natural (February 3 ± 5 d) or natural simulated photoperiod (January 26 ± 14 d) and those exposed to constant short days of winter solstice (February 4 ± 10 d). In Experiment 2, the onset of the breeding season was not delayed in does maintained in the summer solstice day length. Mean dates of increase in LH secretion (onset of the breeding season) did not differ significantly between does exposed to natural (September 7 ± 8 d) or natural simulated photoperiod (September 18 ± 10 d) and those exposed to constant long days photoperiod of summer solstice (September 24 ± 4 d). In goats adapted to a subtropical environment, we concluded that: 1) the end of breeding season was due to refractoriness to short days, and not the inhibitory effect of increasing day length; and 2) the onset of the breeding season was due to refractoriness to long days, and not a stimulatory effect of decreasing day length.     

Intrinsic aging-related mortality in birds

Actuarial senescence in captive populations of 28 species of bird was quantified by estimating the parameters of Weibull models fitted to survival curves constructed from data obtained from zoos. Samples of natural and captive populations were compared using phylogenetically independent contrasts, which revealed that extrinsic mortality rates in captive populations are, on average, less than 30% of those of natural populations but that the component of mortality related to aging does not differ significantly between natural and captive birds. This result supports the hypothesis that aging-related mortality is associated with intrinsic causes of death that kill independently of the external environment. A logical implication of this result is that birds in natural populations maintain a high level of physical fitness into old age and do not become more vulnerable to extrinsic mortality factors with increasing age. Additional comparisons showed that the rate of aging in this sample of birds is correlated with body mass, but not with embryonic or postnatal growth rate. These analyses suggest that studies of aging in captive populations can provide powerful tools to help us understand senescence in natural populations.     

The selective growth of murine newborn-derived suppressor cells and their probable mode of action

Naturally occurring suppressor cells residing in the spleens of newborn mice of less than 5 days old are known to suppress various lymphocyte activities. A population of these suppressor cells can be maintained and expanded in the supernatants derived from Wehi-3 cells. These suppressor cells, designated as Wehi-3-expanded neonatal splenocytes (WENS), can suppress mixed lymphocyte reactions (MLR) and T and B cell mitogen responses without any genetic restrictions. The WENS bear the Ly-5, J11d, and class I molecules. WENS suppression is not mediated through an interleukin 1 or interleukin 2 absorptive mechanism. To achieve maximum suppression of MLR, WENS must be present for at least 24 hr. WENS inhibited the proliferation of Wehi-164 cells but not other tumor cells. The inhibition of Wehi-164 growth was due to the action of natural cytotoxic cells, because WENS lysed Wehi-164 cells but not the natural killer target cell YAC-1. Maximum lysis of Wehi-164 by WENS required 18 to 24 hr. Five WENS cell lines were cultured for more than 6 mo; three of the cell lines lost their capacity to lyse Wehi-164 targets (natural cytotoxicity) and simultaneously lost their natural suppressor activity. The two WENS lines that retained natural cytotoxicity also retained natural suppressor activity. Thus, natural suppressor cells may manifest their suppression through a natural cytotoxicity mechanism.     

Spartina alternifloramarshes on dredged material: a critical review of the ongoing debate over success

After three decades ofexperience, environmental managers continue toquestion the use of dredged material for creation andrestoration of Spartina alternifloramarshes. Different uses of the term `success' have led to someconfusion, and poor recognition of the limitations ofresearch design have contributed to confusion instudies comparing dredged material and naturalmarshes. This paper uses data from a number ofsources to compare dredged material and naturalmarshes. Quantitative analyses based on dataavailable in the scientific literature suggest thatmean values for aboveground and belowground biomass,organic carbon in sediments, polychaete densities, andcrustacean densities may differ in dredged materialand natural marshes. There is not sufficient evidenceto conclude that differences are present for othervariables, such as densities of stems, oligochaetes,or fish. Cumulative quantitative data do not supportthe contention that dredged material sites becomeincreasingly similar to nearby natural marshes overtime as a general rule, although some attributes ofindividual dredged material marshes may becomeincreasingly similar to some natural marshes. Although it is clear that dredged material marshesprovide habitat for birds, limited data suggest thatdredged material marshes may provide habitat for adifferent community of birds than natural marshes. Similarly, limited data suggest that geomorphologicalfeatures found in natural marshes are not duplicatedin dredged material marshes. In short, datasummarized from the literature suggest that dredgedmaterial marshes provide some of the functions ofnatural marshes but probably do not replace all of thefunctions of lost natural marshes.     

Fish assemblages on sunken vessels and natural reefs in southeast Florida,USA

Derelict ships are commonly deployed as artificial reefs in the United States, mainly for recreational fishers and divers. Despite their popularity, few studies have rigorously examined fish assemblages on these structures and compared them to natural reefs. Six vessel-reefs off the coast of southeast Florida were censused quarterly (two ships per month) to characterize their associated fish assemblages. SCUBA divers used a non-destructive point-count method to visually assess the fish assemblages over 13- and 12-month intervals (March 2000 to March 2001 and March 2002 to February 2003). During the same intervals, fish assemblages at neighboring natural reefs were also censused. A total of 114,252 fishes of 177 species was counted on natural and vessel-reefs combined. Mean fish abundance and biomass were significantly greater on vessel-reefs in comparison to surrounding natural reef areas. Haemulidae was the most abundant family on vessel-reefs, where it represented 46% of total fish abundance. The most abundant family on natural reefs was Labridae, where it accounted for 24% of total fish abundance. Mean species richness was significantly greater on vessel-reefs than neighboring natural reefs and also differed among vessel-reefs. Both mean fish abundance and mean species richness were not significantly different between natural reefs neighboring vessel-reefs and natural reefs with no artificial structures nearby. This suggests the vessel-reefs are not, in general, attracting fish away from neighboring natural reefs in our area. Additionally, economically important fish species seem to prefer vessel-reefs, as there was a greater abundance of these species on vessel-reefs than surrounding natural reef areas. Fish assemblage structure on natural versus artificial reefs exhibited a low similarity (25.8%). Although no one species was responsible for more than 6% of the total dissimilarity, fish assemblage trophic structure differed strikingly between the two reef types. Planktivores dominated on vessel-reefs, accounting for 54% of the total abundance. Conversely, planktivores only made up 27% of total abundance on natural reefs. The results of this study indicate vessel-reef fish assemblages are unique and that these fishes may be utilizing food resources and habitat characteristics not accessible from or found at natural reefs in our area. Production may also be occurring at vessel-reefs as the attraction of fish species from nearby natural reefs seems to be minimal. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users     

Natural killing in estrogen-treated mice responds poorly to poly I.C despite normal stimulation of circulating interferon.

Natural killing by mouse spleen cells can be stimulated in vivo by interferon or by agents that stimulate interferon, such as poly I.C. Natural killing can be suppressed in vivo by the sustained administration of 17 beta-estradiol. In BALB/c mice that had been treated with 17 beta-estradiol for 10 weeks, natural killing did not respond to intravenous poly I.C, although stimulation of circulating interferon was equal to controls. Estradiol, then, does not block interferon production but does suppress the response of natural killer cells to interferon. It is suggested that estrogens either block the maturation of natural killer cells or reduce the number of natural killer cell precursors.     

The area requirements of an ecosystem service: crop pollination by native bee communities in California

Managing ecosystem services is critical to human survival, yet we do not know how large natural areas must be to support these services. We investigated how crop pollination services provided by native, unmanaged, bee communities varied on organic and conventional farms situated along a gradient of isolation from natural habitat. Pollination services from native bees were significantly, positively related to the proportion of upland natural habitat in the vicinity of farm sites, but not to any other factor studied, including farm type, insecticide usage, field size and honeybee abundance. The scale of this relationship matched bee foraging ranges. Stability and predictability of pollination services also increased with increasing natural habitat area. This strong relationship between natural habitat area and pollination services was robust over space and time, allowing prediction of the area needed to produce a given level of pollination services by wild bees within this landscape.     

Neural representation of the acoustic biotope

Cats were stimulated with tones and with natural sounds selected from the normal acoustic environment of the animal. Neural activity evoked by the natural sounds and tones was recorded in the cochlear nucleus and in the medial geniculate body. The set of biological sounds proved to be effective in influencing neural activity of single cells at both levels in the auditory system. At the level of the cochlear nucleus the response of a neuron evoked by a natural sound stimulus could be understood reasonably well on the basis of the structure of the spectrograms of the natural sounds and the unit's responses to tones. At the level of the medial geniculate body analysis with tones did not provide sufficient information to explain the responses to natural sounds. At this level the use of an ensemble of natural sound stimuli allows the investigation of neural properties, which are not seen by analysis with simple artificial stimuli. Guidelines for the construction of an ensemble of complex natural sound stimuli, based on the ecology and ethology of the animal under investigation are discussed. This stimulus ensemble is defined as the Acoustic Biotope.     

Natural ceramide reverses Fas resistance of acid sphingomyelinase(-/-) hepatocytes

The role of the second messenger ceramide in Fas-mediated death requires clarification. To address this issue, we generated hepatocytes from paired acid sphingomyelinase (ASMase; asmase)(+/+) and asmase(-/-) mice. asmase(-/-) hepatocytes, derived from 8-week-old mice, manifested normal sphingomyelin content and normal morphological, biochemical, and biologic features. Nonetheless, ASMase-deficient hepatocytes did not display rapid ceramide elevation or apoptosis in response to Jo2 anti-Fas antibody. asmase(-/-) hepatocytes were not inherently resistant to apoptosis because staurosporine, which did not induce early ceramide elevation, stimulated a normal apoptotic response. The addition of low nanomolar quantities of natural C16-ceramide, which by itself did not induce apoptosis, completely restored the apoptotic response to anti-Fas in asmase(-/-) hepatocytes. Other sphingolipids did not replace natural ceramide and restore Fas sensitivity. Overcoming resistance to Fas in asmase(-/-) hepatocytes by natural ceramide is evidence that it is the lack of ceramide and not ASMase which determines the apoptotic phenotype. The ability of natural ceramide to rescue the phenotype without reversing the genotype provides evidence that ceramide is obligate for Fas induction of apoptosis in hepatocytes.