Gradient and sensitivity enhancement of 2D TROSY with water flip-back, 3D NOESY-TROSY and TOCSY-TROSY experiments

Previously we demonstrated a sensitivity enhancement of the original TROSY experiment by a factor of by the use of the sensitivity enhanced TROSY (en-TROSY) scheme. Here, we develop a gradient and sensitivity enhanced TROSY experiment (gs-TROSY), which is designed to select magnetization transfer pathways that suppress spectral artifacts and reduce the number of required phase cycles while having minimal loss of sensitivity. Both of these experimental methods (en-TROSY and gs- TROSY) have been combined with a water flip-back scheme which provides a further increase in sensitivity for labile NH groups by avoiding water saturation. We also apply these TROSY schemes to 3D NOESY-TROSY and 3D TOCSY-TROSY experiments.     

Improved sensitivity and coherence selection for [15N,1H]-TROSY elements in triple resonance experiments

In experiments with proteins of molecular weights around 100 kDa the implementation of [¹⁵N,¹H]-TROSY-elements in [¹⁵N]-constant-time triple resonance experiments yields sensitivity enhancements of one to two orders of magnitude. An additional gain of 10 to 20% may be obtained with the use of sensitivity enhancement elements. This paper describes a novel sensitivity enhancement scheme which is based on concatenation of the ¹³ C ¹⁵N magnetization transfer with the ST2-PT element, and which enables proper TROSY selection of the ¹⁵N multiplet components.     

Gradient and sensitivity enhanced multiple-quantum coherence in heteronuclear multidimensional NMR experiments

Recent studies have indicated that the relaxation rate of the ¹H-¹³C multiple-quantum coherence is much slower than that of the ¹H-¹³C single-quantum coherence for non-aromatic methine sites in ¹³ C labeled proteins and in nucleic acids at the slow tumbling limit. Several heteronuclear experiments have been designed to use a multiple-quantum coherence transfer scheme instead of the single-quantum transfer method, thereby increasing the sensitivity and resolution of the spectra. Here, we report a constant time, gradient and sensitivity enhanced HMQC experiment (CT-g/s-HMQC) and demonstrate that it has a significant sensitivity enhancement over constant time HMQC and constant time gradient and sensitivity enhanced HSQC experiments (CT-g/s-HSQC) when applied to a ¹³C and ¹⁵ N labeled calmodulin sample in D₂O. We also apply this approach to 3D NOESY-HMQC and doubly sensitivity enhanced TOCSY-HMQC experiments, and demonstrate that they are more sensitive than their HSQC counterparts.     

A set of HNCO-based experiments for measurement of residual dipolar couplings in 15N, 13C, (2H)-labeled proteins

Several HNCO-based three-dimensional experiments are described for the measurement of ¹³C(i–1)-¹³C(i–1), ¹⁵N(i)-¹³C(i–1), ¹⁵N(i)-¹³C(i), ¹⁵N(i)-¹³C(i–1), ¹H^N(i)-¹³C(i), ¹H^N(i)-¹³C(i–1), and ¹³C(i–1)-¹³C(i–1) scalar and dipolar couplings in ¹⁵N, ¹³C, (²H)-labelled protein samples. These pulse sequences produce spin-state edited spectra superficially resembling an HNCO correlation spectrum, allowing accurate and simple measurement of couplings without introducing additional spectral crowding. Scalar and dipolar couplings are measured with good sensitivity from relatively large proteins, as demonstrated with three proteins: cardiac Troponin C, calerythrin and ubiquitin. Measurement of several dipolar couplings between spin-1/2 nuclei using spin-state selective 3D HNCO spectra provides a wealth of structural information.     

Detecting signatures of selection in nine distinct lines of broiler chickens

Modern commercial chickens have been bred for one of two specific purposes: meat production (broilers) or egg production (layers). This has led to large phenotypic changes, so that the genomic signatures of selection may be detectable using statistical techniques. Genetic differentiation between nine distinct broiler lines was calculated using Weir and Cockerham's pairwise F_ST estimator for 11 003 genome‐wide markers to identify regions showing evidence of differential selection across lines. Differentiation measures were averaged into overlapping sliding windows for each line, and a permutation approach was used to determine the significance of each window. A total of 51 regions were found to show significant differentiation between the lines. Several lines were consistently found to share significant regions, suggesting that the pattern of line divergence is related to selection for broiler traits. The majority of the 51 regions contain QTL relating to broiler traits, but only five of them were found to be significantly enriched for broiler QTL, including a region on chromosome 27 containing 39 broiler QTL and 114 genes. Additionally, a number of these regions have been identified by other selection mapping studies. This study has identified a large number of potential selection signatures, and further tests with higher‐density marker data may narrow these regions down to individual genes.     

Divergent selection as revealed by P(ST) and QTL-based F(ST) in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient

Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P(ST) (a phenotypic alternative for Q(ST)) and neutral F(ST). However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F(ST) at only one of two QTL was detected as an outlier, although F(ST) at both loci correlated significantly with P(ST). No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P(ST) were observed.     

Selective PCR: a novel internal amplification control strategy for enhanced sensitivity in Salmonella diagnosis

Aims: The aim of this study was to develop a novel strategy that permits the independent amplification of internal amplification control (IAC) and target sequence using the same set of primers, to improve the sensitivity of diagnostic PCR assays. Methods and Results: The method described here is a Salmonella specific PCR test targeting the quorum sensing gene sdiA. It is based on a large size difference between the IAC and the target and consequently on their different extension time. The results indicate the enhanced sensitivity of this test when compared with the competitive IAC strategy. This is demonstrated through parallel testing of artificially contaminated human faecal samples. Conclusions: Utilizing this method, the concentration of the IAC, which often leads to false negative results if the target is present in extremely low concentration owing to competition, does not constitute a critical parameter for the detection limit of a PCR assay. Significance and Impact of the Study: To our knowledge, this is the first report of using extension time as a critical parameter for the sensitivity of a PCR test. A different approach for the construction of an IAC, based on inverse PCR, has also been introduced.     

Chemotypes sensitivity and predictivity of in vivo outcomes for cytotoxic assays in THLE and HepG2 cell lines

In the present study, we demonstrate the utility of in vitro ATP depletion assays in both THLE and HepG2 cells for predicting the toxicological outcome in Exploratory Toxicology Studies across 446 Pfizer proprietary compounds. Our results suggest a higher likelihood of selecting suitable compounds for in vivo safety studies by using cytotoxicity assays in multiple cell-lines over a single cell line. In addition, we demonstrate that different cell-lines have different sensitivities to compounds depending on their ionization state, that is, acid, base or neutral. HepG2 cells are more sensitive for basic compounds, whereas THLE cells have a relatively higher sensitivity for the acidic and neutral compounds. These in vitro cytotoxicity assays when combined with physicochemical properties (c Log P >3 and topological polar surface area (TPSA) <75 Å²), are the most effective means to prioritize compounds having a lower probability of causing adverse events in vivo.     

Cytogenetic characterization of 20 lymphoblastoid lines derived from human individuals differing in bleomycin sensitivity

Summary Forty lymphoblastoid (lymphoid) lines were established from 42 volunteer blood donors, including healthy individuals and patients with head and neck carcinomas. Each peripheral blood sample was split into two portions, one for the establishment of a lymphoid line and the other for short-term culture, which was used to estimate bleomycin sensitivity by cytogenetic procedures. Twenty lymphoid lines were selected at random to compare bleomycin sensitivity with data obtained from short-term lymphocyte cultures. In each set, bleomycin sensitivity of lymphoid cells was similar to that of the lymphocytes. The lymphoid lines, which can be propagated for an unlimited supply of relatively homogeneous cellular material, will be useful for a variety of future investigations. This investigation was supported by grants from the John S. Dunn Foundation, Houston, TX, the Esther Knispel Fund administered by The University of Texas M. D. Anderson Cancer Center, Houston, TX, and Department of Health and Human Services PHS grant DE 07007.     

New pulsed field gradient NMR experiments for the detection of bound water in proteins

Summary New H₂O-selective homonuclear and heteronuclear 2D NMR experiments have been designed for the observation of protein hydration (PHOGSY, Protein Hydration Observed by Gradient Spectroscop Y). These experiments utilize selective excitation of the H₂O resonance and pulsed field gradients for coherence selection and efficient H₂O suppression. The method allows for a rapid and sensitive detection of H₂O molecules in labelled and unlabelled proteins. In addition it opens a way to measure the residence time of water bound to proteins. Its application to uniformly ¹⁵N-labelled FKBP-12 (FK-506 binding protein) is demonstrated.     

Metabolomics as a tool to evaluate exercise-induced improvements in insulin sensitivity

Exercise affects substrate utilisation and insulin sensitivity, which in turn improve blood glucose and lipid levels in subjects with type 2 diabetes (T2D). However, making long-lasting lifestyle-changes might be more realistic if the results were easier to record. Screening for biomarkers reflecting metabolic fitness could thus serve as a tool for maintained motivation. The aim of this study was to test the possibility that metabolomics can be used to identify individuals with improved insulin sensitivity as a result of increased physical activity. Healthy and diabetic subjects were investigated before and after 3 months of exercise to determine various metabolic parameters. Insulin sensitivity was determined by hyperinsulinemic euglycemic clamps and found to be improved in the diabetic men. Plasma was collected during the clamp and analyzed through GC/TOFMS. Healthy subjects could be distinguished from diabetics by means of low molecular-weight compounds (LMC) in plasma independently of gender or exercise, and exercise induced differences in LMC patterns both for healthy and T2D subjects. Forty-four significant metabolites were found to explain differences between LMC patterns obtained from trained and non-trained diabetics. Among these compounds, 17 could be annotated and 5 classified. Inositol-1-phosphate showed the highest correlation to insulin sensitivity in diabetic men, whereas an as yet unknown fatty acid correlated best with insulin sensitivity in women. Both metabolites were better correlated to insulin sensitivity than glucose. Finally, the finding that inostitol-1-phosphate negatively correlates with insulin sensitivity in diabetic men, was validated using samples obtained from a similar training study on diabetic men. Jeanette Kuhl and Thomas Moritz contributed equally to this study.     

Stomatal sensitivity to vapour pressure difference over a subambient to elevated CO2 gradient in a C3/C4 grassland

In the present study the response of stomatal conductance (g_s) to increasing leaf‐to‐air vapour pressure difference (D) in early season C₃ (Bromus japonicus) and late season C₄ (Bothriochloa ischaemum) grasses grown in the field across a range of CO₂ (200–550 µmol mol^?1) was examined. Stomatal sensitivity to D was calculated as the slope of the response of g_s to the natural log of externally manipulated D (dg_s/dlnD). Increasing D and CO₂ significantly reduced g_s in both species. Increasing CO₂ caused a significant decrease in stomatal sensitivity to D in Br. japonicus, but not in Bo. ischaemum. The decrease in stomatal sensitivity to D at high CO₂ for Br. japonicus fit theoretical expectations of a hydraulic model of stomatal regulation, in which g_s varies to maintain constant transpiration and leaf water potential. The weaker stomatal sensitivity to D in Bo. ischaemum suggested that stomatal regulation of leaf water potential was poor in this species, or that non‐hydraulic signals influenced guard cell behaviour. Photosynthesis (A) declined with increasing D in both species, but analyses of the ratio of intercellular to atmospheric CO₂ (C_i/C_a) suggested that stomatal limitation of A occurred only in Br. japonicus. Rising CO₂ had the greatest effect on g_s and A in Br. japonicus at low D. In contrast, the strength of stomatal and photosynthetic responses to CO₂ were not affected by D in Bo. ischaemum. Carbon and water dynamics in this grassland are dominated by a seasonal transition from C₃ to C₄ photosynthesis. Interspecific variation in the response of g_s to D therefore has implications for predicting seasonal ecosystem responses to CO₂.     

基于景观感知敏感度的生态旅游地观光线路自动选址

引入景观感知敏感度模型中的可视范围、最佳观赏距离、最佳观赏方位等视域感知影响因子,和景观类型、资源价值等生态感知影响因子,并增加地形坡度和起伏度因子,建立了生态旅游地观光线路选址综合权重计算模型,用于观光线路的自动选址。以武安国家地质公园奇峡谷景区为例,基于ArcGIS软件平台,实现了景区旅游观光最佳线路自动选址;通过景区野外考察,并综合考虑其它修正因子,对计算结果进行了专家修正,获得了一条旅游者景观感知较好且容易实施的观光线路。观光线路自动选址为微观尺度下的生态旅游地规划、景观设计提供了定量分析方法,为景区管理和生态保护提供了思路和参考。     

Suppression of telomere-binding protein TPP1 resulted in telomere dysfunction and enhanced radiation sensitivity in telomerase-negative osteosarcoma cell line

Mammalian telomeres are protected by the shelterin complex that contains the six core proteins POT1, TPP1, TIN2, TRF1, TRF2 and RAP1. TPP1, formerly known as TINT1, PTOP, and PIP1, is a key factor that regulates telomerase recruitment and activity. In addition to this, TPP1 is required to mediate the shelterin assembly and stabilize telomere. Previous work has found that TPP1 expression was elevated in radioresistant cells and that overexpression of TPP1 led to radioresistance and telomere lengthening in telomerase-positive cells. However, the exact effects and mechanism of TPP1 on radiosensitivity are yet to be precisely defined in the ALT cells. Here we report on the phenotypes of the conditional deletion of TPP1 from the human osteosarcoma U2OS cells using ALT pathway to extend the telomeres.TPP1 deletion resulted in telomere shortening, increased apoptosis and radiation sensitivity enhancement. Together, our findings show that TPP1 plays a vital role in telomere maintenance and protection and establish an intimate relationship between TPP1, telomere and cellular response to ionizing radiation, but likely has the specific mechanism yet to be defined.     

PRP4K is a HER2-regulated modifier of taxane sensitivity

The taxanes are used alone or in combination with anthracyclines or platinum drugs to treat breast and ovarian cancer, respectively. Taxanes target microtubules in cancer cells and modifiers of taxane sensitivity have been identified in vitro, including drug efflux and mitotic checkpoint proteins. Human epidermal growth factor receptor 2 (HER2/ERBB2) gene amplification is associated with benefit from taxane therapy in breast cancer yet high HER2 expression also correlates with poor survival in both breast and ovarian cancer. The pre-mRNA splicing factor 4 kinase PRP4K (PRPF4B), which we identified as a component of the U5 snRNP also plays a role in regulating the spindle assembly checkpoint (SAC) in response to microtubule-targeting drugs. In this study, we found a positive correlation between PRP4K expression and HER2 status in breast and ovarian cancer patient tumors, which we determined was a direct result of PRP4K regulation by HER2 signaling. Knock-down of PRP4K expression reduced the sensitivity of breast and ovarian cancer cell lines to taxanes, and low PRP4K levels correlated with in vitro-derived and patient acquired taxane resistance in breast and ovarian cancer. Patients with high-grade serous ovarian cancer and high HER2 levels had poor overall survival; however, better survival in the low HER2 patient subgroup treated with platinum/taxane-based therapy correlated positively with PRP4K expression (HR = 0.37 [95% CI 0.15-0.88]; p = 0.03). Thus, PRP4K functions as a HER2-regulated modifier of taxane sensitivity that may have prognostic value as a marker of better overall survival in taxane-treated ovarian cancer patients.     

Solution Structure of RCL, a Novel 2′-Deoxyribonucleoside 5′-Monophosphate N-glycosidase

RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2′-deoxyribonucleoside 5′-monophosphates, a novel enzymatic reaction reported only recently. In this work, we determined the solution structure by multidimensional NMR and provide a structural framework to elucidate its mechanism with computational simulation. RCL is a symmetric homodimer, with each monomer consisting of a five-stranded parallel β-sheet sandwiched between five α-helices. Three of the helices form the dimer interface, allowing two monomers to pack side by side. The overall architecture featuring a Rossmann fold is topologically similar to that of deoxyribosyltransferases, with major differences observed in the putative substrate binding pocket and the C-terminal tail. The latter is seemingly flexible and projecting away from the core structure in RCL, but loops back and is positioned at the bottom of the neighboring active site in the transferases. This difference may bear functional implications in the context of nucleobase recognition involving the C-terminal carboxyl group, which is only required in the reverse reaction by the transferases. It was also noticed that residues around the putative active site show significant conformational variation, suggesting that protein dynamics may play an important role in the enzymatic function of apo-RCL. Overall, the work provides invaluable insight into the mechanism of a novel N-glycosidase from the structural point of view, which in turn will allow rational anti-tumor and anti-angiogenesis drug design.     

Improved sensitivity in indirect monitoring of chemical shifts of proton-heteronuclear spin pairs (1H-13C and 1H-15N) in 3D and 4D NMR spectroscopy

In three-dimensional and four-dimensional experiments on doubly labelled proteins not only heteronuclear (¹³C or ¹⁵N) but also proton (¹H) frequencies are often indirectly monitored, rather than being directly observed. In this communication we show how in these experiments by overlaying ¹H and heteronuclear evolutions one can obtain decreased apparent relaxation rates of ¹H signals, yielding improved sensitivity. The new method applies to spin pairs like ¹H-¹⁵N, as in amide groups, or ¹H-¹³C, as in methine groups of alpha or aromatic systems.     

Exercise-induced enhancement of insulin sensitivity is associated with accumulation of M2-polarized macrophages in mouse skeletal muscle

Exercise enhances insulin sensitivity in skeletal muscle, but the underlying mechanism remains obscure. Recent data suggest that alternatively activated M2 macrophages enhance insulin sensitivity in insulin target organs such as adipose tissue and liver. Therefore, the aim of this study was to determine the role of anti-inflammatory M2 macrophages in exercise-induced enhancement of insulin sensitivity in skeletal muscle. C57BL6J mice underwent a single bout of treadmill running (20 m/min, 90 min). Twenty-four hours later, ex vivo insulin-stimulated 2-deoxy glucose uptake was found to be increased in plantaris muscle. This change was associated with increased number of CD163-expressing macrophages (i.e. M2-polarized macrophages) in skeletal muscle. Systemic depletion of macrophages by pretreatment of mice with clodronate-containing liposome abrogated both CD163-positive macrophage accumulation in skeletal muscle as well as the enhancement of insulin sensitivity after exercise, without affecting insulin-induced phosphorylation of Akt and AS160 or exercise-induced GLUT4 expression. These results suggest that accumulation of M2-polarized macrophages is involved in exercise-induced enhancement of insulin sensitivity in mouse skeletal muscle, independently of the phosphorylation of Akt and AS160 and expression of GLUT4.     

The adaptive role of Phosphoglucomutase and other allozymes in a marine snail across the vertical rocky-shore gradient

Natural selection can play an important role in the maintenance of genetic polymorphisms, despite ongoing gene flow. In the present study, we use previously analysed allozymic loci and perform an F _ST outlier-based analysis to detect the signatures of divergent selection between sympatric ecotypes of the marine snail Littorina saxatilis at different localities. The results obtained show that different allozyme polymorphisms are affected (directly or indirectly) by selection at distinct geographical regions. The Phosmogluco mutase-2 locus was the best candidate for adaptation and further biochemical analyses were performed. The kinetic properties of the three more common genotypes of Pgm-2 were studied. The results obtained are concordant with two alternative hypotheses: (1) natural selection is acting directly on this locus or, more probably, (2) selection is affecting a genomic region tightly linked to the enzyme locus. In both cases, the known existence of a parallel and partially independent origin of these ecotypes would explain why different candidate loci were detected in different localities.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 225–233.     

An increase in ethylene sensitivity following pollination is the initial event triggering an increase in ethylene production and enhanced senescence of Phalaenopsis orchid flowers

Cut Phalaenopsis (Phalaenopsis hybrid, cv. Herbert Hager) flowers usually last about 2 weeks. Following pollination however, there is a rapid acceleration of the wilting process, which is completed within 2 days. The first event detected following pollination was an increase in ethylene sensitivity. This increased sensitivity began about 4 h after pollination and peaked 6 h later. A subsequent increase in ethylene production could only be detected 12 to 14 h after pollination. Treatment of the flowers with silver thiosulfate or 1-methylcyclopropene, both inhibitors of ethylene action, completely inhibited the pollination-induced increase in ethylene production and the enhanced senescence of the flowers. This indicates that the pollination-induced increase in ethylene production is a response to the existing ethylene. Treatment of flowers with calcium and its ionophore A23187, which increased ethylene sensitivity and protein phosphorylation, also promoted ethylene production and senescence of unpollinated flowers, EGTA, a calcium chelator, decreased the sensitivity of pollinated flowers to ethylene and delayed and decreased the pollination-induced increase in ethylene production. We suggest that the pollination-induced increase in ethylene sensitivity is the initial pollination-induced event triggering the enhancement of ethylene production, which leads to enhanced senescence of Phalaenopsis flowers.