Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis.

5'-Phosphoramidites protected by 2-nitrophenylethyl (NPE) and 2-(4-nitrophenyl)ethoxy carbonyl (NPEOC) functions were employed for in situ synthesis of oligonucleotides in 5'-->3' direction on flat glass surfaces. By this inverse synthesis format, the oligonucleotides are attached to the solid support via their 5'-ends while the free 3'-hydroxyl groups are available as substrates for enzymatic reactions such as elongation by polymerases, thereby adding another feature to the portfolio of chip-based applications. Having a fluorescence dye present at the first base during synthesis, the quality of the oligonucleotides was analysed quantitatively by capillary electrophoresis after release from the solid support. With about 95% yield per condensation, it was found to be equivalent to synthesis results achieved on CPG support. The chip-bound oligonucleotides could be extended enzymatically upon hybridisation of a DNA-template. Surprisingly, however, only 63% of the oligonucleotides were elongated in polymerase reactions, while oligonucleotides that were released from the support behaved normally in standard PCR amplifications. This rate of 63% nevertheless compares favourably with an extension rate of only 50%, which was achieved under identical conditions, if pre-fabricated oligonucleotides of identical sequence had been spotted to the glass support.     

Use of methylphosphonic dichloride for the synthesis of oligonucleoside methylphosphonates.

Methylphosphonic dichloride was used to prepare protected deoxyribonucleoside 3'-methylphosphonate beta-cyanoethyl esters, d-[(MeO)2Tr]NpCNEt, and protected oligonucleoside methylphosphonates in solution. Reaction of d-[(MeO)2Tr]N with methylphosphonic dichloride gives d-[(MeO)2Tr]NpCl. The phosphonylation and subsequent esterification or condensation reactions are each complete within 60 min. The products are readily purified by "flash chromatography" on silica gel columns. d-[(MeO)2Tr]NpCl, or its tetrazole derivative, d-[(MeO)2Tr]Nptet, were tested as intermediates for the synthesis of oligothymidine methylphosphonates on a silica gel polymer support. The average yield per coupling step was 76% and did not increase with addition of more d-[(MeO)2Tr]TpCl. The formation of (5'-5') linked thymidine dimers indicated that the thymidine monomers are clustered closely together on the support. When N is ibuG, the yield for the coupling step on the support is very low. This may be due to steric hindrance of the 3'-phosphonate group by the N-2 isobutryl protecting group.     

Nucleoside analogue substitutions in the trinucleotide DNA template recognition sequence 3'-(CTG)-5' and their effects on the activity of bacteriophage T7 primase

Bacteriophage T7 primase catalyzes the synthesis of the oligoribonucleotides pppACC(C/A) and pppACAC from the single-stranded DNA template sites 3'-d[CTGG(G/T)]-5' and 3'-(CTGTG)-5', respectively. The 3'-terminal deoxycytidine residue is conserved but noncoding. A series of nucleoside analogues have been prepared and incorporated into the conserved 3'-d(CTG)-5' site, and the effects of these analogue templates on T7 primase activity have been examined. The nucleosides employed include a novel pyrimidine derivative, 2-amino-5-(beta-2-deoxy-D-erythro-pentofuranosyl)pyridine (d2APy), whose synthesis is described. Template sites containing d2APy in place of the cryptic dC support oligoribonucleotide synthesis whereas those containing 3-deaza-2'-deoxycytidine (dc(3)C) and 5-methyl-6-oxo-2'-deoxycytidine (dm(5ox)C) substitutions do not, suggesting that the N3 nitrogen of cytidine is used for a critical interaction by the enzyme. Recognition sites containing 4-amino-1-(beta-2-deoxy-D-erythro-pentofuranosyl)-5-methyl-2,6[1H, 3H]-pyrimidione (dm(3)2P) or 2'-deoxyuridine (dU) substitutions for dT support oligoribonucleotide synthesis whereas those containing 5-methyl-4-pyrimidinone 2'-deoxyriboside (d(2H)T) substitutions do not, suggesting the importance of Watson-Crick interactions at this template residue. Template sites containing 7-deaza-2'-deoxyguanosine (dc(7)G) or 2'-deoxyinosine (dI) in place of dG support oligoribonucleotide synthesis. The reduced extent to which dc(7)G is successful within the template suggests a primase-DNA interaction. Inhibition studies suggest that the primase enzyme binds "null" substrates but cannot initiate RNA synthesis.     

栽培稻杂种不育性的遗传研究：Ⅱ。F1花粉不育性的基因模式

Oka建立了台中65等基因F_1不育系,并把该试验的结果作为支持重复配子致死模式的证据。本研究利用台中65及其3个等基因F_1不育系分析了花粉育性的分离方式。试验结果符合单基因座孢子体-配子体互作模式,而不符合重复配子致死模式。假设在S-E2、S-E3和S-E5基因座上,台中65的基因型为,等基因F_1不育系E2的基因型为,等基因F_1不育系E4的基因型为,等基因F_1不育系E5的基因型为。在杂合株中,等位基因互作导致携带s~f基因的雄配子不完全败育。对采用与Oka不同的基因模式作了讨论。     

Supported synthesis and functionnalization of 2'-deoxyuridine by Suzuki-Miyaura cross-coupling

The synthesis and modification of 2'-deoxyuridine has been realized under Suzuki-Miyaura palladium-catalyzed cross-coupling conditions. Using Pd(PPh(3))(4) and Na(2)CO(3), 5-iodo-2'-deoxyuridine bound to solid support is coupled with various boronic acids to give 5-(hetero)aryl-2'-deoxyuridine. Pd(PPh(3))(4) palladium catalyzed was found to be superior to Pd(OAc)(2) and (NHC)Pd(allyl)Cl for Suzuki-Miyaura palladium-catalyzed reactions.     

Inexpensive purification of P450 reductase and other proteins using 2',5'-adenosine diphosphate agarose affinity columns

Two reductases, P450 oxidoreductase and P450Bm-3 reductase, were purified on a 2',5'-adenosine diphosphate solid support. Although the efficiency of these columns is well established, the cost of the resin and the eluting material 2'-adenosine can be prohibitive. Herein we show that the less costly 2',3'-adenosine monophosphate is an excellent eluting material.     

Conformational transmission in the glyceryl backbone of phospholipid model compounds, induced by a P(4-coordinated) into trigonal bipyramidal P(5-coord) transition

Triesterified phospholipid model compounds have been synthesized and extensively studied with 300-MHz 1H NMR in the monomer phase in order to get additional support for the effect of conformational transmission induced by a P(4-coord) into a trigonal bipyramidal P(5-coord) transition, as was suggested by Merkelbach and Buck. To elucidate any conformational preferences around the C2-C3 bond, the stereospecifically deuterated precursor 1,2-dihexanoyl-(3R)-sn-[3-2H]glycerol was synthesized. The results reveal that a coordinational change of phosphorus from four to five is transmitted in a significant increase in population of the conformer, in which the vicinally substituted oxygens O-2 and O-3 are trans located. The impact of this transmission seems not to be restricted to conformational changes in the adjacent C2-C3 bond, but is also present in specific rotations around the C1-C2 bond, thereby shifting the C1-C2 conformational equilibrium towards a decreased contribution of the trans arrangement of the acyl chains. As a consequence the interchain distance will be reduced and thus van der Waals interactions will be maximized. The results are interpreted in terms of increased electron density on O-3 when axially located in a P(5-coord) trigonal bipyramidal compound, thereby introducing enhanced electrostatic repulsions within the oxygen pairs O-3, O-2 and O-3, O-1. Relaxation of this energetically unfavourable geometry leads to the observed conformational shifts. Absence of conformational transmission, as found in P(5-coord) trigonal bipyramidal compounds with the 2-ester group substituted for an alkyl moiety, can be considered as additional support for the introduced concept. In the alkyl part of the model phospholipids, however, no conformational changes were observed by means of 13C NMR. Extrapolating this outcome to more condensed phases, a proposition could be made about the mechanism by which conformational changes in the head-group and/or glyceryl backbone will be compensated.     

New approaches towards automated oligoribonucleotide synthesis.

Several protecting group combinations have been investigated to achieve an automated oligoribonucleotide synthesis on a solid support. The use of 2'-O-tert-butyldimethylsilyl-5'-O-monomethoxytrityl-ribonucleoside -3'-(p-nitrophenylethyl, N,N-diethyl)-phosphoramidites in conjunction with beta-eliminating blocking groups at the aglycone gave satisfactory results. An inverse protecting group strategy based upon analogously substituted 5'-O-2-dansylethoxycarbonyl-2'-O-4- methoxytetrahydropyran-4-yl-phosphoramidites can be regarded as another promising approach.     

Association of 2''-5'' oligoribonucleotides.

Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imino proton NMR spectra and NOEs for (2'-5') CGGCGCCG are consistent with formation of an antiparallel duplex. The results suggest greater duplex stability was one factor favoring 3'-5' over 2'-5' linkages in evolution.     

Synthesis and properties of oligonucleotides containing aminodeoxythymidine units.

Procedures are described for synthesis via solid support methodology of oligonucleotide analogues derived in part from 3'-amino-3'-deoxythymidine or 5'-amino-5'-deoxythymidine. Oligothymidylate decamers terminated with a 3'-amino group or containing a 3'-NHP(O)(O-)O-5' internucleoside link are found to form unusually stable complexes with poly(dA), poly(A), and oligo(dA). For related derivatives of 5'-amino-5'-deoxythymidine enhancement is less or absent, and in the case of multiple substitution destabilization of the heteroduplex may be observed. That the effect of the 3'-amino group is general for oligonucleotide derivatives is indicated by enhanced Tm values for heteroduplex complexes of the mixed-base oligomer, d(TATTCAGTCAT(NH2)), and the methyl phosphonate derivatives, TmTmTmTmTmTmTmTmTmT(NH2) and d(TmAmTmTmCmAmGmTmCmAmT(NH2)).     

5-Hydroxytryptamine and (+)-lysergic acid diethylamide displace [3H]thyrotropin-releasing hormone at its binding sites in the rat limbic forebrain

Binding of [3H]thyrotropin-releasing hormone (TRH) to its receptors in the rat limbic forebrain was partially displaced by 5-hydroxytryptamine (5-HT, ligand for 5-HT1 receptors) and (+)-lysergic acid diethylamide ((+)-LSD, ligand for 5-HT1 and 5-HT2 receptors) at nanomolar concentrations. Spiperone (ligand for 5-HT2 receptors) displaced [3H]TRH in a dose-dependent manner at micromolar concentrations. These results suggest that some TRH receptors are related to 5-HT1 receptors, probably adjoining them on the membrane. This type of TRH receptor is shown to be among the high-affinity receptors which we reported previously. The significance of the receptor-coexistence is such that TRH facilitates serotonergic transmission by increasing the density of 5-HT1 receptors. This finding seems to support a pharmacological observation of other investigators that TRH potentiates 5-HT-induced hyperactivity in mice, probably by affecting postsynaptic 5-HT receptors.     

A general method for the synthesis of 3''-sulfhydryl and phosphate group containing oligonucleotides.

The syntheses are described of polymer supports useful for the synthesis of 3'-partially protected sulfhydryl, free sulfhydryl or phosphate group containing oligonucleotides. The supports are compatible with established phosphoramidite chemistry of oligonucleotide synthesis giving rise to oligonucleotides with terminal 3'-partially protected sulfhydryl, free sulfhydryl or phosphate function during final deprotection. Crosslinking of the thiol group containing oligonucleotide to sulfhydryl group specific fluorescent probes was carried out with high selectivity, in high yields under mild conditions. 3-Aminopropylated Controlled Pore Glass (CPG) was succinylated with succinic anhydride followed by the reaction with S-(2-thio-5-nitropyridyl)-2-mercaptoethanol in the presence of dicyclohexylcarbodiimide (DCC). The resultant polymer support was reacted with 4,4'-dimethoxytrityloxyalkanthiol 5(a - c) to yield the derivatized polymer supports 5(a - c). The support 5a directly leads to oligonucleotide-3'-phosphate on deprotection with ammonical DTT at 55 degrees C while the supports 5b and 5c lead to oligonucleotide-3'-thiols or partially protected 3'-sulfhydryl group containing oligonucleotides during final deprotection.     

Probing the sequence effects on NarI-induced -2 frameshift mutagenesis by dynamic 19F NMR, UV, and CD spectroscopy

The NarI recognition sequence (5'-G1G2CG3CN-3') is the most vulnerable hot spot for frameshift mutagenesis induced by the carcinogen 2-aminofluorene and its analogues in Escherichia coli. Lesioning of the guanine in the G3 position induces an especially high frequency of -2 deletion mutations; vulnerability to these mutations is modulated by the nature of the nucleotide in the N position (C approximately A > G > T). The objective of the present study was to probe the structural basis of this N-mediated influence on the propensity of the G3 lesion to form a slipped mutagenic intermediate (SMI) during translesion synthesis. We studied NarI-based fully paired [(5'-CTCG1G2CG3*CNATC-3')(5'-GATNCGGCCGAG-3'), N = dC or dT] and -2 deletion [(5'-CTCG1G2CG3*CNATC-3')(5'-GATNGCCGAG-3'), N = dC or dT] duplexes, in which G* was either AF [N-(2'-deoxyguanosin-8-yl)-2-aminofluorene] or the 19F probe FAF [N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene]. The latter sequences mimic the bulged SMI for -2 deletion mutations. Dynamic 19F NMR, circular dichroism, and UV melting results indicated that the NarI-dC/-2 deletion duplex adopts exclusively an intercalated conformer, whereas the NarI-dT/-2 deletion duplex exists as multiple conformers. The data support the presence of a putative equilibrium between a carcinogen-intercalated and a carcinogen-exposed SMI for the dT/-2 duplex. A similar dT-induced conformational heterogeneity was observed for the fully paired duplexes in which all three guanines were individually modified by AF or FAF. The frequency of the carcinogen stacked S-conformation was found to be highest (69-75%) at the G3 hot spot in NarI-dC duplexes. Taken together, our results support the hypothesis that the conformational stability of the SMI is a critical determinant for the efficacy of -2 frameshift mutagenesis in the NarI sequence. We also provide evidence for AF/FAF conformational compatibility in the NarI sequences.     

The Influence of Social Support on Hematopoietic Stem Cell Transplantation Survival: A Systematic Review of Literature

Background

Hematopoietic Stem cell Transplantation (HSCT) can negatively impact the psychosocial well-being of the patient. Social support is a complex term that has been variably used to encompass perceived and objective support, including caregiver presence. Social support has been associated with superior psychosocial outcomes; however the influence of social support on HSCT survival remains unclear. We sought to summarize the literature on the influence of social support on HSCT survival.

Methods

Medline, EMBASE, Cochrane, CINAHL, and PsycINFO were searched using the following search categories/concepts: 1) HSCT, 2) Social support, 3) Caregiver, 4) Survival, and 5) Treatment outcomes.

Results

We identified 6 relevant studies: 4 publications, 1 dissertation, and 1 abstract. Three studies were retrospective and 3, prospective. Sample size ranged between 92–272 with a mean/median patient age between 30–55 yrs. The duration of follow-up ranged between 13.3–48 months. Social support was measured inconsistently: 2 by retrospective investigator assessment, 2 as patients’ perceived support, 1 as caregiver presence, and 1 included caregiver presence and retrospective investigator assessment. The 4 published studies and 1 abstract demonstrate an association between better social support and survival. However, the unpublished dissertation, with the largest sample size found no association.

Conclusions

There is a paucity of evidence examining social support with HSCT survival. Available studies are older, with the most recent publication in 2005. A heterogeneous group of HSCT patients were studied with variable follow-up times. Further, covariates were variably considered in HSCT survival analyses and we suggest that there may be publication bias, given the negative unpublished study with the largest sample size. Prospective studies using validated scales are necessary to better assess the influence of social support on HSCT mortality. Given the potential for improved HSCT survival with better social support, HSCT centres should routinely provide HSCT recipients and their caregivers with enhanced psychosocial services.     

Unidirectional waves on rings: Models for chiral preference of circumnutating plants

Twining plants exhibit a striking oscillation of their stems in their quest for a support. The oscillations, called circumnutation, have periods generally of 1–5 hr, and virtually all species have a preferred direction of twining. I seek to explain these chiral asymmetries in plant behavior by hypothesizing a chiral asymmetry in plant anatomy. Such asymmetries already exist, for example, in phyllotaxis. I explore wave phenomena on asymmetric but isotropic rings, and seek systems which will only support (stable) waves in one direction around the ring, and not in the other. Simulations indicate that (1) oscillatory reaction-diffusion systems do not support unidirectional waves on rings; (2) excitable reaction-diffusion systems do support unidirectional waves on rings; and (3) unidirectional phase-locking (discrete unidirectional waves) occurs in rings of coupled oscillators. Thus, chiral asymmetries of circumnutating plants cannot be explained by continuum oscillator phenomena, but can be explained by general discrete oscillators, or excitable phenomena on the continuum.     

Interleukin 2-driven T lymphocyte proliferation is dependent upon a surface antigen distinct from the interleukin 2 receptor: requirements for inhibition of T-cell proliferation by monoclonal antibody 5C3

A monoclonal antibody (5C3) to an antigen expressed on activated guinea pig T lymphocytes that did not react with the interleukin 2 (IL-2) receptor, but inhibited IL-2-driven proliferative responses has been previously characterized. The present study provides further analysis of the inhibitory capacity of 5C3 for T-cell proliferation and of the relationship between the expression of the antigen defined by 5C3 and the capacity of cells to respond to IL-2. 5C3 inhibited proliferation of T-cell blasts to IL-2-containing fluids when added as late as 8 hr prior to termination of a 26-hr culture. 5C3 pretreatment of the IL-2-responsive blast cells was also sufficient to detect significant inhibition of proliferation. FACS analysis of these blasts indicated that maximal 5C3 binding was required for pretreatment to result in inhibition of IL-2-driven proliferation. Delayed addition of 5C3 to culture or pretreatment with 5C3 of responding cells also resulted in inhibition of proliferation of immune T lymphocytes to antigen-pulsed-presenting cells. Lastly, although modulated 5C3- blasts failed to proliferate to IL-2, induction of the 5C3-bearing molecule on these 5C3- blasts correlated with restoration of the ability of these cells to proliferate to IL-2. Collectively, these results further support the hypothesis that monoclonal antibody 5C3 interferes with a critical signal in the IL-2 growth pathway.     

Use of A Uridine Nucleotide as an Affinity Handle and 5′ Phosphorylating Agent for Synthetic DNA

Abstract

The 5′-(O-cyanoethyl N, N-diisopropyl phosphoramidite) of 2′,3′-O-bis(4,4′-dimethoxytrityl)uridine can be used to attach a uridine residue through a 5′-5′ phosphodiester linkage to a synthetic oligodeoxyribonucleotide. This 5′-terminal structure allows the oligomer to be selectively retarded on a chromatographic support containing dihydroxyboryl substituents, and to be converted upon periodate oxidation and p-elimination to the form possessing a 5′ phosphate group.     

Natural enemy diversity and biological control: Making sense of the context-dependency

Numerous studies have demonstrated that diverse predator assemblages can be more effective at controlling prey populations. Yet, other studies have shown no effect of predator diversity on prey mortality, or even negative effects (for example due to intraguild predation or interference). Much research emphasis has been placed on the traits of predators that maximise functional complementarity. However, comparatively less attention has been paid to the traits of the prey or habitat that may maximise predator diversity effects, even though there must be a variety of prey niches available to be partitioned in order for niche complementarity to occur. Following this logic, we review six hypotheses for when diverse enemy assemblages should be most effective: when 1) prey communities are diverse; 2) prey have complex life cycles; 3) prey are patchily distributed in space or time; 4) studies are conducted at larger spatial and temporal scales; 5) plant structures are complex; 6) prey are abundant. Many of these hypotheses lack direct tests, particularly in agricultural systems, but we find little or no direct or indirect support for hypotheses 1, 4, 5 and 6. However, previous work does provide some support for hypotheses 2 and 3. We discuss methods to test these hypotheses directly, and suggest that natural enemy diversity may only benefit the biological control of arthropods in heterogeneous systems.     

Molecular basis for differential elongation of omega-3 docosapentaenoic acid by the rat Elovl5 and Elovl2

Functional characterization of the rat elongases, Elovl5 and Elovl2, has identified that Elovl2 is crucial for omega-3 docosahexaenoic acid (DHA) (22:6n-3) synthesis. While the substrate specificities of the rat elongases had some overlap, only Elovl2 can convert the C₂₂ omega-3 PUFA docosapentaenoic acid (DPA) (22:5n-3) to 24:5n-3, which is the penultimate precursor of DHA. In order to better understand the potential for these elongases to be involved in DHA synthesis, we have examined the molecular reasons for the differences between Elovl5 and Elovl2 in their ability to elongate DPA to 24:5n-3. We identified a region of heterogeneity between Elovl5 and Elovl2 spanning transmembrane domains 6 and 7. Using a yeast expression system, we examined a series of Elovl2/Elovl5 chimeras and point mutations to identify Elovl2 residues within this region which are responsible for DPA substrate specificity. The results indicate that the cysteine at position 217 in Elovl2 and a tryptophan at the equivalent position in Elovl5 explain their differing abilities to elongate DPA to 24:5n-3. Further studies confirmed that Elovl2 C217 is a critical residue for elongation of DPA at the level observed in the native protein. Understanding the ability of elongases to synthesize 24:5n-3 may provide a basis for using sequence data to predict their ability to ultimately support DHA synthesis.