Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of information

To date, it has been problematic to accurately quantify multiple nucleic acid sequences, representing microbial targets, in multi-target mixtures using oligonucleotide microarrays, primarily due to nonspecific target binding (i.e., cross-hybridization). While some studies ignore the effects of nonspecific binding, other studies have developed approaches to minimize nonspecific binding, such as physical modeling to design highly specific probes, subtracting nonspecific signal using mismatch probes, and/or removing nonspecific duplexes by scanning through a range of wash stringencies. We have developed an alternative approach that, in contrast to previous approaches, uses nonspecific target binding as a source of information. Specifically, the new approach uses hybridization patterns (fingerprints) to quantify specific nucleic acid targets in complex target mixtures. We evaluated the approach by mixing together in vitro transcribed 28S rRNA targets at varying concentrations (up to 1.0 nM), and hybridizing the 24 mixtures to microarrays (n=3160 probes, in duplicate). Three independent Latin-square-designed experiments revealed accurate quantification of the targets. The regression between actual concentration of targets and those determined by the approach were highly positively correlated with high R(2) values (e.g., R(2)=0.90, n=6 targets; R(2)=0.84, n=8 targets; R(2)=0.82, n=10 targets).     

Two-component atomic force microscopy recognition imaging of complex samples

Biological complexes are typically multisubunit in nature and the processes in which they participate often involve protein compositional changes in themselves and/or their target substrates. Being able to identify more than one type of protein in complex samples and to track compositional changes during processes would thus be very useful. Toward this goal, we describe here a single-molecule technique that can simultaneously identify two types of proteins in compositionally complex samples. It is an adaptation of the recently developed atomic force microscopy (AFM) recognition imaging technique but involves the tethering of two different types of antibodies to the AFM tip and sequential blocking with appropriate antigenic peptides to distinguish the recognition from each antibody. The approach is shown to be capable of simultaneously identifying in a single AFM image two specific components, BRG1 and beta-actin, of the human Swi-Snf ATP-dependent nucleosome remodeling complex and two types of histones, H2A and H3, in chromatin samples.     

Ethidium and azidoethidium oligonucleotide derivatives: Synthesis,complementary complex formation and sequence-specific photomodification of the single-stranded and double-stranded target oligo- and polynucleotides

Oligodeoxyribonucleotide derivatives containing ethidium or azidoethidium residues attached to 3′ and/or 5′ end were prepared. These derivatives formed tight specific complexes with complementary oligodeoxyribonucleotides where each attached ethidium residue led to an increase of complex T_m by 20–30°C. Tandem complexes of two oligodeoxyribonucleotides containing ethidium residues with an oligodeoxyribonucleotide having two adjacent complementary sequences for these Oligonucleotide were investigated. Photoinduced reactions of a number of ethidium and azidoethidium oligodeoxyribonucleotide derivatives with target complementary single-stranded and double-stranded oligo- and polydeoxyribonucleotides were investigated. The irradiation led to direct photocleavage of the target oligo- or polynucleotide, to formation of hidden (piperidine cleavable) modifications of the target of formation of covalent adducts between ethidium oligodeoxyribonucleotide derivative and the target. In a number of experiments, azidoethidium dyes were demonstrated to be considerably stronger photosensitizers than ethidium ones. Depending on the nature of the target (single- or double-stranded DNA) and on the irradiation conditions, the total damages to the target oligo- or polydeoxyribonucleotides ranged from 10–70% (for ethidium dyes) to 30–80% (for azidoethidium dyes).     

Collisionally activated dissociation and infrared multiphoton dissociation of oligonucleotides in a quadrupole ion trap

Infrared multiphoton dissociation (IRMPD) of deprotonated and protonated oligonucleotides ranging from 5 to 40 residues has been performed in a quadrupole ion trap mass spectrometer at normal operating pressure and temperature. Only moderate exposure times and laser powers were required to achieve efficient dissociation. In general, IRMPD and collisionally activated dissociation (CAD) produce comparable sequencing information, indicating that IRMPD is a viable alternative to CAD for oligonucleotide analysis in the quadrupole ion trap. Two major characteristics distinguish CAD and IRMPD spectra for a given parent ion. First, structurally uninformative M-B ions that dominate CAD spectra are generally only low-intensity species in IRMPD spectra because nonresonant activation causes these species to dissociate to backbone cleavage products. Second, phosphate and nucleobase ions can be observed directly in IRMPD experiments because the low-mass cutoff can be set to trap small fragment ions. For this reason IRMPD can sometimes facilitate analysis of sequences containing modified bases.     

A mutant impaired in SNARE complex dissociation identifies the plasma membrane as first target of synaptobrevin 2

Membrane fusion depends on the formation of a complex of four SNARE motifs, three that bear a central glutamine and are localized in the target membrane (t-SNARE) and one that bears an arginine and is localized in the donor vesicle (v-SNARE). We have characterized the arginine 56 to proline mutant (R56P) of synaptobrevin-2 (Sb). SbR56P was blocked at the plasma membrane in association with the endogenous plasma membrane t-SNARE due to an inhibition of SNARE complex dissociation, suggesting that the plasma membrane is its first target. Cell surface blockade of SbR56P could be rescued by coexpression of synaptophysin, a partner of Sb. Sb was blocked at the plasma membrane but SNARE complexes were unaffected in cells expressing defective dynamin, indicating that the phenotype of SbR56P was not due to an internalization defect. When expressed in neurons, SbR56P localized both to axonal and dendritic plasma membranes, showing that both domains are initial targets of Sb. The R56P mutation affects a highly conserved position in v-SNAREs, and might thus provide a general tool for identifying their first target membranes.     

Characterization of sodium and proton flows in sub-bacterial particles of Halobacterium halobium in terms of nonequilibrium thermodynamics

A thermodynamic characterization of the Na⁺-H⁺ exchange system in Halobacterium halobium was carried out by evaluating the relevant phenomenological parameters derived from potential-jump measurements. The experiments were performed with sub-bacterial particles devoid of the purple membrane, in 1 M NaCl, 2 M KCl, and at pH 6.5–7.0. Jumps in either pH or pNa were brought about in the external medium, at zero electric potential difference across the membrane, and the resulting relaxation kinetics of protons and sodium flows were measured. It was found that the relaxation kinetics of the proton flow caused by a pH-jump follow a single exponential decay, and that the relaxation kinetics of both the proton and the sodium flows caused by a pNa-jump also follow single exponential decay patterns. In addition, it was found that the decay constants for the proton flow caused by a pH-jump and a pNa-jump have the same numerical value. The physical meaning of the decay constants has been elucidated in terms of the phenomenological coefficients (mobilities) and the buffering capacities of the system. The phenomenological coefficients for the Na⁺-H⁺ flows were determined as differential quantities. The value obtained for the total proton permeability through the particle membrane via all available channels, $\text{L}{}_{\mathrm{<mtext>H</mtext>}}\text{= (}\text{?J}{}_{\mathrm{<mtext>H\; +</mtext>}}\text{?Δ}\text{pH}\text{)}{}_{\mathrm{<mtext>\Delta \psi ,\Delta </mtext><mtext>pNa</mtext>}}$, was in the range of 850–1150 nmol H⁺·(mg protein)^?1·h^?1·(pH unit)^?1 for four different preparations; for the total Na⁺ permeability, $\text{L}{}_{\mathrm{<mtext>Na</mtext>}}\text{= (}\text{?J}{}_{\mathrm{<mtext>Na</mtext>}}{}^{\mathrm{+}}\text{?Δ}\text{pNa}\text{)}{}_{\mathrm{<mtext>\Delta \psi ,\Delta </mtext><mtext>pH</mtext>}}$, it was 1620–2500 nmol Na⁺·(mg protein)^?1·h^?1·(pNa unit)^?1; and for the proton ‘cross-permeability’, $\text{L}{}_{\mathrm{<mtext>HNa</mtext>}}\text{= (}\text{?J}{}_{\mathrm{<mtext>H</mtext>}}{}^{\mathrm{+}}\text{?Δ}\text{pNa}\text{)}{}_{\mathrm{<mtext>\Delta \psi ,\Delta </mtext><mtext>pH</mtext>}}$, it was 220–580 nmol H⁺·(mg protein)^?1·h^?1·(pNa unit)^?1, for different preparations. From the above phenomenological parameters, the following quantities have been calculated: the degree of coupling (q), the maximal efficiency of Na⁺-H⁺ exchange (η_max), the flow and force efficacies (?) of the above exchange, and the admissible range for the values of the molecular stoichiometry parameter (r). We found q ? 0.4; η_max ? 5%; 0.36 ? r ? 2; ?_JNa⁺ ? 1.3 · 10⁵μmol · (RT unit)^?1 at J_Na = 1 μmolNa⁺ · (mgprotein)^?1 · h^?1; and ?_ΔpNa ? 5 · 10⁴ ΔpNa · (mg protein) · h · (RT unit)^?1 at ΔpNa = 1 unit, for different preparations.     

Proteomic analysis of tissue samples in translational breast cancer research

In the last decade, many proteomic technologies have been applied, with varying success, to the study of tissue samples of breast carcinoma for protein expression profiling in order to discover protein biomarkers/signatures suitable for: characterization and subtyping of tumors; early diagnosis, and both prognosis and prediction of outcome of chemotherapy. The purpose of this review is to critically appraise what has been achieved to date using proteomic technologies and to bring forward novel strategies – based on the analysis of clinically relevant samples – that promise to accelerate the translation of basic discoveries into the daily breast cancer clinical practice. In particular, we address major issues in experimental design by reviewing the strengths and weaknesses of current proteomic strategies in the context of the analysis of human breast tissue specimens.     

Current progress in protein profiling of complex samples

Accurate cancer biomarkers are needed for early detection, disease classification, prediction of therapeutic response and monitoring treatment. While there appears to be no shortage of candidate biomarker proteins, a major bottleneck in the biomarker pipeline continues to be their verification by enzyme linked immunosorbent assays. Multiple reaction monitoring (MRM), also known as selected reaction monitoring, is a targeted mass spectrometry approach to protein quantitation and is emerging to bridge the gap between biomarker discovery and clinical validation. Highly multiplexed MRM assays are readily configured and enable simultaneous verification of large numbers of candidates facilitating the development of biomarker panels which can increase specificity. This review focuses on recent applications of MRM to the analysis of plasma and serum from cancer patients for biomarker verification. The current status of this approach is discussed along with future directions for targeted mass spectrometry in clinical biomarker validation.     

Farnesylthiosalicylic acid inhibits mammalian target of rapamycin (mTOR) activity both in cells and in vitro by promoting dissociation of the mTOR-raptor complex

The mammalian target of rapamycin (mTOR) functions with raptor and mLST8 in a signaling complex that controls rates of cell growth and proliferation. Recent results indicate that an inhibitor of the Ras signaling pathway, farnesylthiosalicylic acid (FTS), decreased phosphorylation of the mTOR effectors, PHAS-I and S6K1, in breast cancer cells. Here we show that incubating 293T cells with FTS produced a stable change in mTOR activity that could be measured in immune complex kinase assays using purified PHAS-I as substrate. Similarly, FTS decreased the PHAS-I kinase activity of mTOR when added to cell extracts or to immune complexes containing mTOR. Incubating either cells or extracts with FTS also decreased the amount of raptor that coimmunoprecipitated with mTOR, although having relatively little effect on the amount of mLST8 that coimmunoprecipitated. The concentration effect curves of FTS for inhibition of mTOR activity and for dissociation of the raptor-mTOR complex were almost identical. Caffeine, wortmannin, LY294002, and rapamycin-FKBP12 also markedly inhibited mTOR activity in vitro, but unlike FTS, none of the other mTOR inhibitors appreciably changed the amount of raptor associated with mTOR. Thus, our findings indicate that FTS represents a new type of mTOR inhibitor, which acts by dissociating the functional mTOR-raptor signaling complex.     

Correlation of mRNA and protein in complex biological samples

The correlation between mRNA and protein abundances in the cell has been reported to be notoriously poor. Recent technological advances in the quantitative analysis of mRNA and protein species in complex samples allow the detailed analysis of this pathway at the center of biological systems. We give an overview of available methods for the identification and quantification of free and ribosome-bound mRNA, protein abundances and individual protein turnover rates. We review available literature on the correlation of mRNA and protein abundances and discuss biological and technical parameters influencing the correlation of these central biological molecules.     

Molecular dynamics study of the dissociation of an antigen-antibody complex in solution

Preliminary results are reported of a molecular dynamics calculation of free energy variations during the dissociation of an antigen-antibody complex, hen egg-white lysozyme — Fab D1.3, using atomic coordinates determined by the group of R. J. Poljak, and explicit handling of solvent molecules. After equilibration of the complex in solution at 300 K, a dissociation path was generated by a directed dynamics protocol. Then the thermodynamic perturbation method was used for computing the derivative of the free energy of the system with respect to dissociation coordinate, both for the undissociated complex and in two points along the path. 200-ps molecular dynamics simulations were carried out at each of these points. The results obtained are discussed, with special emphasis on the role of interstitial water in the appearance of a hydrophobic activation free energy.Université Paul Sabatier, and URA 505 of C.N.R.S.     

Improvements in the determination of radionuclide distribution in the analysis of irradiated samples using double-differentiation method

The spatial response of an 8x4 block detector made up of 5.6-mm-wide, 12.9-mm-high, 30-mm-thick individual detector crystals to a collimated line source of 511 keV annihilation photons was examined. The response of each crystal showed a spread around the average positioning values and distributions from adjacent crystals overlapped as the collimated source scanned the individual detectors. This leads to possible errors in the event assignment. The implementation of double differentiation or the second derivative method was proposed for the removal of scattered photons so as to reduce the overlap and, hence, avoid mispositioning. This method is a mathematical solution implemented when analysing the results. A curve in a spatial spectrum could be considered to be a function f(x), wherex is the position. When double differentiation of f(x) is carried out, then the normalized curve d²f(x) appears with some reduction in the wings. It was shown that a reduction of the scattering contribution in the tails without overestimating the contribution of scattered events could be achieved by implementing a double-differentiation process.     

The evolution of thermal performance curves in semi-aquatic newts: Thermal specialists on land and thermal generalists in water?

The position and shape of thermal performance curves (TPCs, the functions relating temperature to physiological performance) for ecologically relevant functions will directly affect the fitness of ectotherms and therefore should be under strong selection. However, thermodynamic considerations predict that relationships between the different components of the TPC will confound its evolutionary optimization. For instance, the “jack-of-all-temperatures” hypothesis predicts a trade-off between the breadth of the TPC and the maximal performance capacity; the “warmer is better” hypothesis suggests that low thermal optima will come with low absolute performances. Semi-aquatic organisms face the additional challenge of having to adjust their TPCs to two environments that are likely to differ in mean temperature and thermal variability. In this paper, we examine how parameters of the TPCs for maximal running and swimming speed have co-evolved in the semi-aquatic newt genus Triturus. We consider evolutionary relationships between the width and the height of the TPCs, the optimal temperatures and maximal performance. Phylogenetic comparative analyses reveal that in Triturus, swimming and running differ substantially in the (co-)variation of TPC parameters. Whereas evolutionary changes in the TPC for swimming primarily concern the shape of the curve (generalist versus specialist), most interspecific variation in running speed TPCs involves shifts in overall performance across temperatures.     

Kinetic study of dissociation of Eu(III) complex with H8dotp (H8dotp = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylphosphonic acid))

The dissociation kinetics of the europium(III) complex with H₈dotp ligand was studied by means of molecular absorption spectroscopy in UV region at ionic strength 3.0 mol dm⁻³ (Na,H)ClO₄ and in temperature region 25-60 °C. Time-resolved laser-induced fluorescence spectroscopy (TRLIFS) was employed in order to determine the number of water molecules in the first coordination sphere of the europium(III) reaction intermediates and the final products. This technique was also utilized to deduce the composition of reaction intermediates in course of dissociation reaction simultaneously with calculation of rate constants and it demonstrates the elucidation of intimate reaction mechanism. The thermodynamic parameters for the formation of kinetic intermediate (ΔH⁰ = 11 ± 3 kJ mol⁻¹, ΔS⁰ = 41 ± 11 J K⁻¹ mol⁻¹) and the activation parameters (E_a = 69 ± 8 kJ mol⁻¹, ΔH^≠ = 67 ± 8 kJ mol⁻¹, ΔS^≠ = −83 ± 24 J K⁻¹ mol⁻¹) for the rate-determining step describing the complex dissociation were determined. The mechanism of proton-assisted reaction was proposed on the basis of the experimental data.     

Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment

Chemical mutagenesis is routinely used to create large numbers of rare mutations in plant and animal populations, which can be subsequently subjected to selection for beneficial traits and phenotypes that enable the characterization of gene functions. Several next‐generation sequencing (NGS)‐based target enrichment methods have been developed for the detection of mutations in target DNA regions. However, most of these methods aim to sequence a large number of target regions from a small number of individuals. Here, we demonstrate an effective and affordable strategy for the discovery of rare mutations in a large sodium azide‐induced mutant rice population (F₂). The integration of multiplex, semi‐nested PCR combined with NGS library construction allowed for the amplification of multiple target DNA fragments for sequencing. The 8 × 8 × 8 tridimensional DNA sample pooling strategy enabled us to obtain DNA sequences of 512 individuals while only sequencing 24 samples. A stepwise filtering procedure was then elaborated to eliminate most of the false positives expected to arise through sequencing error, and the application of a simple Student's t‐test against position‐prone error allowed for the discovery of 16 mutations from 36 enriched targeted DNA fragments of 1024 mutagenized rice plants, all without any false calls.     

三氯化铝沉淀法浓缩水体中的病毒

近年来, 水源性病毒疾病的爆发在世界范围内被大量报道, 大量研究证实^[1], 外环境水体及淤泥是病毒存活循环的主要场所, 并因此频频引发传染病的流行。但在生活环境的各种水体中, 除生活污水外, 其所含有的病毒浓度往往很低, 以目前现有的检测方法, 仍然达不到不经浓缩而直接从水中检测病毒的目的。同时,食源性病毒的感染剂量非常低, 10?100 个病毒粒子即可引发感染。病毒在离体条件下存活力很强, 对各种理化因子有较强的抵抗力, 耐乙醚和弱酸, 用氯仿、反复冻融、超声波处理都不能使其失活。因此, 水环境中微量存在的病毒仍然对人类的健康带来很大的威胁。在我国, 虽然已经建立起了以PCR 为主导的病毒快速检测方法, 但是对于水样本的前处理技术至今没有找到十分理想的病毒浓缩方法, 无法有效去除样本中的抑制物, 这些因素都严重制约了针对水中食源性病毒的检测和预防。要掌握各种水体中病毒污染的基本状况, 样品中病毒的浓缩是能否得以成功检测的关键。另外, 目前世界上绝大多数国家所执行的标准中, 对病毒的检测标准及其指示生物都没有做出明确说明,归根结底的原因是由于至今没有建立起有效的方法。有鉴于此, 针对水中病毒研究的热点和存在问题, 本刊2009 年第1 期发表了寇晓霞、吴清平等^[2]针对自来水和污水两种不同水体中病毒的浓缩方法。在现有的检测和浓缩方法的基础上, 通过不断创新, 解决现有方法中存在的主要问题, 摸索制约水体中病毒浓缩方法的关键点, 评价不同方法的优劣和实用性。三氯化铝沉淀法最大的优点是可适用于绝大多数具有不同水质特性的水样, 特别是可以克服膜过滤法因易堵塞而对水体悬浮物浓度有严格限制的缺陷。另外, 就检测条件而言, 该方法无需过滤装置等, 也省去进口的阳电滤膜, 从应用推广的角度更为方便, 费用成本低, 对于系统研究我国水中常见食源性病毒检测和监测有一定的应用价值。目前, 该课题组对水体中病毒浓缩方法进行了多方面的应用。对广州河涌水的病毒污染情况进行了调研,初步了解和掌握了病毒的污染状况。广州市河涌水中食源性病毒污染的总阳性率为37.8％。其中有7 个点呈诺如病毒阳性, 8 个点呈轮状病毒阳性。文献[3?4]报道此类病毒的流行月份、季节性与环境水中调查的病毒污染情况基本吻合, 说明了临床发病与环境中此类病毒的污染有一定的相关性。另外还有些点呈甲肝病毒阳性和星状病毒阳性。调研结果表明三氯化铝沉淀法浓缩水体中病毒的方法具有实用性。     

cAMP inhibits mammalian target of rapamycin complex-1 and -2 (mTORC1 and 2) by promoting complex dissociation and inhibiting mTOR kinase activity

cAMP and mTOR signalling pathways control a number of critical cellular processes including metabolism, protein synthesis, proliferation and cell survival and therefore understanding the signalling events which integrate these two signalling pathways is of particular interest. In this study, we show that the pharmacological elevation of [cAMP]_i in mouse embryonic fibroblasts (MEFs) and human embryonic kidney 293 (HEK293) cells inhibits mTORC1 activation via a PKA-dependent mechanism. Although the inhibitory effect of cAMP on mTOR could be mediated by impinging on signalling cascades (i.e. PKB, MAPK and AMPK) that inhibit TSC1/2, an upstream negative regulator of mTORC1, we show that cAMP inhibits mTORC1 in TSC2 knockout (TSC2^−/−) MEFs. We also show that cAMP inhibits insulin and amino acid-stimulated mTORC1 activation independently of Rheb, Rag GTPases, TSC2, PKB, MAPK and AMPK, indicating that cAMP may act independently of known regulatory inputs into mTOR. Moreover, we show that the prolonged elevation in [cAMP]_i can also inhibit mTORC2. We provide evidence that this cAMP-dependent inhibition of mTORC1/2 is caused by the dissociation of mTORC1 and 2 and a reduction in mTOR catalytic activity, as determined by its auto-phosphorylation on Ser2481. Taken together, these results provide an important insight into how cAMP signals to mTOR and down-regulates its activity, which may lead to the identification of novel drug targets to inhibit mTOR that could be used for the treatment and prevention of human diseases such as cancer.     

The complex drivers of thermal acclimation and breadth in ectotherms

Thermal acclimation capacity, the degree to which organisms can alter their optimal performance temperature and critical thermal limits with changing temperatures, reflects their ability to respond to temperature variability and thus might be important for coping with global climate change. Here, we combine simulation modelling with analysis of published data on thermal acclimation and breadth (range of temperatures over which organisms perform well) to develop a framework for predicting thermal plasticity across taxa, latitudes, body sizes, traits, habitats and methodological factors. Our synthesis includes > 2000 measures of acclimation capacities from > 500 species of ectotherms spanning fungi, invertebrates, and vertebrates from freshwater, marine and terrestrial habitats. We find that body size, latitude, and methodological factors often interact to shape acclimation responses and that acclimation rate scales negatively with body size, contributing to a general negative association between body size and thermal breadth across species. Additionally, we reveal that acclimation capacity increases with body size, increases with latitude (to mid‐latitudinal zones) and seasonality for smaller but not larger organisms, decreases with thermal safety margin (upper lethal temperature minus maximum environmental temperatures), and is regularly underestimated because of experimental artefacts. We then demonstrate that our framework can predict the contribution of acclimation plasticity to the IUCN threat status of amphibians globally, suggesting that phenotypic plasticity is already buffering some species from climate change.