Structure-activity Relationship for FR901464: A Versatile Method for the Conversion and Preparation of Biologically Active Biotinylated Probes

The structure-activity relationship for FR901464, a potent cell-cycle inhibitor, was examined by synthesizing its analogs. A versatile method for converting FR901464 was devised. This method made it possible to synthesize biologically active FR901464-biotin conjugates which could be used to isolate the binding proteins.     

Sudemycin E influences alternative splicing and changes chromatin modifications

Sudemycin E is an analog of the pre-messenger RNA splicing modulator {"type":"entrez-nucleotide","attrs":{"text":"FR901464","term_id":"525229801","term_text":"FR901464"}}FR901464 and its derivative spliceostatin A. Sudemycin E causes the death of cancer cells through an unknown mechanism. We found that similar to spliceostatin A, sudemycin E binds to the U2 small nuclear ribonucleoprotein (snRNP) component SF3B1. Native chromatin immunoprecipitations showed that U2 snRNPs physically interact with nucleosomes. Sudemycin E induces a dissociation of the U2 snRNPs and decreases their interaction with nucleosomes. To determine the effect on gene expression, we performed genome-wide array analysis. Sudemycin E first causes a rapid change in alternative pre-messenger RNA splicing, which is later followed by changes in overall gene expression and arrest in the G2 phase of the cell cycle. The changes in alternative exon usage correlate with a loss of the H3K36me3 modification in chromatin encoding these exons. We propose that sudemycin E interferes with the ability of U2 snRNP to maintain an H3K36me3 modification in actively transcribed genes. Thus, in addition to the reversible changes in alternative splicing, sudemycin E causes changes in chromatin modifications that result in chromatin condensation, which is a likely contributing factor to cancer cell death.     

Cytotoxic Spliceostatin Analogs from Pseudomonas sp.

Two new spliceostatin analogs, designed as spliceostatins J and K ( 1 and 2 ), were isolated and identified from the culture of Pseudomonas sp., along with two known ones, FR901464 ( 3 ) and spliceostatin E ( 4 ). Their structures were elucidated by detailed interpretation of their spectroscopic data, especially 2D‐NMR and HR‐ESI‐MS. Spliceostatin J ( 1 ) represented the first example of spliceostatins bearing an unusual hexahydrofuro[3,4‐b]furan moiety. Biological assay showed all the isolated compounds except 1 displayed potent cytotoxic activities against two cancer cell lines (MDA‐MB‐231 and A‐549). Structure‐activity‐relationship studies revealed that the tetrahydropyran ring in spliceostatin analogs was necessary for their bioactive retention.     

Inhibition of splicing and nuclear retention of pre-mRNA by spliceostatin A in fission yeast

Nuclear retention of pre-mRNAs is tightly regulated by several security mechanisms that prevent pre-mRNA export into the cytoplasm. Recently, spliceostatin A, a methylated derivative of a potent antitumor microbial metabolite FR901464, was found to cause pre-mRNA accumulation and translation in mammalian cells. Here we report that spliceostatin A also inhibits splicing and nuclear retention of pre-mRNA in a fission yeast strain that lacks the multidrug resistance protein Pmd1. As observed in mammalian cells, spliceostatin A is bound to components of the SF3b complex in the spliceosome. Furthermore, overexpression of nup211, a homolog of Saccharomyces cerevisiae MLP1, suppresses translation of pre-mRNAs accumulated by spliceostatin A. These results suggest that the SF3b complex has a conserved role in pre-mRNA retention, which is independent of the Mlp1 function.     

提高复合型产絮菌F2-F6产絮能力的驯化方法

为了提高复合型产絮菌F1-F6的产絮能力,采用贫富营养交替的方法,利用发酵法生物制氢反应器排放的废液连续驯化复合型产絮菌F1-R。试验结果表明,此驯化方法可以有效地促进复合型产絮菌F1-R利用生物制氢废液产絮,絮凝率由11.4％提高到92．4％。调节高岭土悬浊液pH值的顺序对絮凝率有较大影响,后调节pH值比先调可以获得更高的絮凝率。生物絮凝剂与无机絮凝剂AlCl3结合有更好的絮凝效果。     

Biosynthetic engineering and fermentation media development leads to gram-scale production of spliceostatin natural products in Burkholderia sp.

A key challenge in natural products drug discovery is compound supply. Hundreds of grams of purified material are needed to advance a natural product lead through preclinical development. Spliceostatins are polyketide-nonribosomal peptide natural products that bind to the spliceosome, an emerging target in cancer therapy. The wild-type bacterium Burkholderia sp. FERM BP-3421 produces a suite of spliceostatin congeners with varying biological activities and physiological stabilities. Hemiketal compounds such as FR901464 were the first to be described. Due to its improved properties, we were particularly interested in a carboxylic acid precursor analog that was first reported from Burkholderia sp. MSMB 43 and termed thailanstatin A. Inactivation of the iron/α-ketoglutarate-dependent dioxygenase gene fr9P had been shown to block hemiketal biosynthesis. However, a 4-deoxy congener of thailanstatin A was the main product seen in the dioxygenase mutant. We show here that expression of the cytochrome P450 gene fr9R is a metabolic bottle neck, as use of an l-arabinose inducible system led to nearly complete conversion of the 4-deoxy analog to the target molecule. By integrating fermentation media development approaches with biosynthetic engineering, we were able to improve production titers of the target compound >40-fold, going from the starting ~60 mg/L to 2.5 g/L, and to achieve what is predominantly a single component production profile. These improvements were instrumental in enabling preclinical development of spliceostatin analogs as chemotherapy.     

Unexpected instability of family of repeats (FR), the critical cis-acting sequence required for EBV latent infection, in EBV-BAC systems

A group of repetitive sequences, known as the Family of Repeats (FR), is a critical cis-acting sequence required for EBV latent infection. The FR sequences are heterogeneous among EBV strains, and they are sometimes subject to partial deletion when subcloned in E. coli-based cloning vectors. However, the FR stability in EBV-BAC (bacterial artificial chromosome) system has never been investigated. We found that the full length FR of the Akata strain EBV was not stably maintained in a BAC vector. By contrast, newly obtained BAC clones of the B95-8 strain of EBV stably maintained the full length FR during recombinant virus production and B-cell transformation. Investigation of primary DNA sequences of Akata-derived EBV-BAC clones indicates that the FR instability is most likely due to a putative secondary structure of the FR region. We conclude that the FR instability in EBV-BAC clones can be a pitfall in E. coli-mediated EBV genetics.     

Clustering of GPI-Anchored Folate Receptor Independent of Both Cross-Linking and Association with Caveolin

The distribution of the glycosyl-phosphatidylinositol (GPI)-anchored folate receptor (FR) in a diffuse pattern vs. functional clusters associated with caveolae has been debated. The equivocal nature of direct localization studies is due to possible experimental artifacts such as cross-linking of the protein by the antibody probes prior to fixation and alternatively the use of a disruptive fixation method. Such studies have also been complicated by the use of cells that vastly overexpress FR. In this study a monovalent probe, i.e., a biotinylated folate affinity analogue was used to covalently label FR. Cells expressing moderate levels of FR, i.e., JAR epithelial cells expressing FR-α and recombinant CHO fibroblasts expressing FR-β, were used. The affinity label and either caveolin or antigenic sites on FR were localized by electron microscopy using colloidal gold conjugated antibody probes post-embedding in the relatively permeable LR White resin. The method avoided both receptor cross-linking and early fixation steps and also enabled the use of transport permissive conditions while labeling FR at the cell surface. The results indicate that in steady-state FR is not significantly colocalized with caveolin. However, the receptor molecules occur predominantly in clusters, independent of cross-linking, providing a physical basis for the observed kinetics of receptor internalization and recycling during folate transport. Evidence is also presented to suggest that early mild fixation will disrupt the clustering of FR. Received: 26 September 1996/Revised: 7 May 1997     

Diagnosis of B-cell lymphoma. Utility of the polymerase chain reaction for detecting clonality from archival cytologic smears

OBJECTIVE: To apply the polymerase chain reaction (PCR) to detect clonality for potentially helping to establish a definitive diagnosis of lymphoma in cytologic material. STUDY DESIGN: In this retrospective study, Papanicolaou-stained cytologic smears and formalin-fixed, paraffin-embedded tissues from 17 cases of B-cell lymphoma were examined to investigate their clonality by a PCR technique using three different approaches (FR3, FR3A and FR2) for amplification of immunoglobulin heavy chain genes. Cytologic smears from 10 cases of nonneoplastic lymphoid tissues and T-cell lymphomas served as negative controls. RESULTS: Monoclonality was detected in 9 of 17 cases (53%) of B-cell lymphoma in cytologic smears as compared with 8 of 16 cases (50%) in tissue sections. Semi-nested PCRs (FR3A/FR2) were superior to the single PCR (FR3) in the detection rate (41% vs. 18%). Five of seven cases (71%) of marginal zone B-cell lymphomas showed monoclonality, whereas only 4 of 10 cases (40%) of diffuse large B-cell lymphomas did so. Monoclonality was demonstrated in none of the negative controls. CONCLUSIONS: Clonality detection in B-cell lymphomas by PCR using cytologic smears is specific and equal in sensitivity to that using formalin-fixed, paraffin-embedded tissues. The detection rate is especially excellent in marginal zone B-cell lymphoma, in which the cytologic diagnosis is particularly challenging. Combined seminested PCRs for FR3A and FR2 are advocated for a reliable assessment of clonality.     

Light from below matters: Quantifying the consequences of responses to far‐red light reflected upwards for plant performance in heterogeneous canopies

In vegetation stands, plants receive red to far‐red ratio (R:FR) signals of varying strength from all directions. However, plant responses to variations in R:FR reflected from below have been largely ignored despite their potential consequences for plant performance. Using a heterogeneous rose canopy, which consists of bent shoots down in the canopy and vertically growing upright shoots, we quantified upward far‐red reflection by bent shoots and its consequences for upright shoot architecture. With a three‐dimensional plant model, we assessed consequences of responses to R:FR from below for plant photosynthesis. Bent shoots reflected substantially more far‐red than red light, causing reduced R:FR in light reflected upwards. Leaf inclination angles increased in upright shoots which received low R:FR reflected from below. The increased leaf angle led to an increase in simulated plant photosynthesis only when this low R:FR was reflected off their own bent shoots and not when it reflected off neighbour bent shoots. We conclude that plant response to R:FR from below is an under‐explored phenomenon which may have contrasting consequences for plant performance depending on the type of vegetation or crop system. The responses are beneficial for performance only when R:FR is reflected by lower foliage of the same plants.     

TG/DTG/DTA evaluation of flame retarded cotton fabrics and comparison to cone calorimeter data

Unbleached cotton fabrics (UCF) with 12.5% polypropylene scrim treated with two phosphate-urea based fire-retardant (FR) formulations were evaluated for FR properties using thermogravimetry/differential thermogravimetry/differential thermal analysis (TG/DTG/DTA) method. In addition to testing the two FR-treated unbleached cotton fabrics (CF-FR1 and CF-FR2), bleached cotton fabric (BCF) treated with the two FR formulations (BCF-FR1 and BCF-FR2) was evaluated. Both formulations were washable with add-on of FR chemicals at 18.7% (FR1) or 17.4% (FR2) for UCF and 22.5% (FR1) or 24.9% (FR2) for BCF. The decreasing order of sums at maximal rates of samples degradation in air environment according to DTG method was: BCF (21.40%/min)>UCF (12.91%/min)>BCF-FR2 (12.83%/min)>BCF-FR1 (11.68%/min)>CF-FR2 (10.20%/min)>CF-FR1 (9.73%/min). It indicates that both formulations cause the decrease of thermooxidation of the products at slower rates than the starting material. Several endo- and exothermic peaks observed by DTA in inert and oxidative environment gives additional information about the degradation process. The order of decreasing thermal responses of the studied samples based on sums of DTA peak values of endothermic and exothermic peaks in air environment is: UCF (0.597°C/mg)>BCF (0.120°C/mg)>CF-FR1 (0.089°C/mg)>BCF-FR1 (0.077°C/mg)>CF-FR2 (0.062°C/mg)>BCF-FR2 (0.053°C/mg). This is in agreement with the cone calorimeter results according to which the flammability properties are improving with the decreasing heat release rates or ignition time prolongation in order: UCF>CF-FR1>CF-FR2. The advantage of TG/DTG/DTA method is slower linear heating rate, which allows the more detailed evaluation of the light and flammable cotton fabric.     

Quantification of excitation energy distribution between photosystems based on a mechanistic model of photosynthetic electron transport

Absorbed light energy is converted into excitation energy. The excitation energy is distributed to photosystems depending on the wavelength and drives photochemical reactions. A non‐destructive, mechanistic and quantitative method for estimating the fraction of the excitation energy distributed to photosystem II (f) was developed. For the f values for two simultaneously provided actinic lights (ALs) with different spectral distributions to be estimated, photochemical yields of the photosystems were measured under the ALs and were then fitted to an electron transport model assuming the balance between the electron transport rates through the photosystems. For the method to be tested using leaves with different properties in terms of the long‐term and short‐term acclimation (adjustment of photosystem stoichiometry and state transition, respectively), the f values for red and far‐red light (R and FR) were estimated in leaves grown (~1 week) under white light without and with supplemental FR and adapted (~10 min) to R without and with supplemental FR. The f values for R were clearly greater than those for FR and those of leaves grown with and adapted to supplemental FR tended to be higher than the controls. These results are consistent with previous studies and therefore support the validity of the proposed method.     

Influence on adipocyte plasma membrane bound protein kinase by feedback regulator.

Protein kinase, phosphodiesterase and adenylate cyclase of plasma membrane of adipocytes and the effect of the feedback regulator (FR) on these three enzymes was measured and compared. The basal level ratio of adenylate cyclase to phosphodiesterase to protein kinase was 1:1.9:3.0. Epinephrine and/or FR alters this ratio. FR stimulated protein kinase activity up to 3 fold in the presence of a wide range of enzyme concentrations, 5-50 mug membrane protein/tube. The concentration of FR effective for stimulation of membrane protein kinase was much greater than that needed for inhibition of adenylate cyclase and phosphodiesterases. The inhibition by FR on adenylate cyclase was the most potent effect among the 3 enzymes. 1 U (or 2 U/ml) of FR inhibited 50% of the adenylate cyclase activity in a defined system. The maximum effective concentration of FR for stimulation of membrane protein kinase was greater than 10 U/ml. Histone type 11A was the best substrate for protein phosphorylation so far observed. The FR stimulatory effect was observed at all substrate concentrations used ranging from 1-5 mg/ml. A NaF concentration curve shows that 15 mM NaF gave maximum phosphorylation. The stimulatory effect of FR was observed both in the presence and absence of NaF. Protein kinase of adipocyte plasma membrane was mainly cAMP-independent. The effect of FR (20 U/ml) in stimulation of protein phosphorylation was much greater than that of cAMP (1 X 10(-6) M). The cAMP and FR effects seemed to be additive. Preincubation of plasma membrane with FR in the absence of ATP resulted in no decrease but slight increase in protein kinase activity. A shift in protein kinase, phosphodiesterase and adenylate cyclase ratios by FR suggests the regulatory role of FR in cAMP metabolism in adipocytes.     

The Gradient of Exciting Radiation within a Sample Affects the Relative Height of Steps in the Fast Chlorophyll a Fluorescence Rise

Measurement of the chlorophyll (Chl) a fluorescence rise (FR) under higher exciting irradiance (EI), the O-J-I-P transient, or under lower irradiance, the O-I-P transient, is a routinely used method to access photosystem 2 function in thylakoid membranes of chloroplasts. Our measurements with a suspension of pea thylakoid membranes showed that the relative heights of the J and I steps in the FR depended not only on EI but also on the concentration and thickness of the sample. We explain this effect as a consequence of the gradient of EI within the sample. We tested this suggestion by theoretical simulations of the FR based on the model that was previously used for simulation of the FR considering in addition the gradient of EI within the sample. Our theoretical results correspond well with the experiments. The irradiance gradient effect may influence measured FR significantly and this fact should be taken into consideration in the interpretation of measured FRs.     

Oxygen radical scavenging capacity of phenolic and non-phenolic compounds in red and white wines

The aim of the present study was the evaluation of the antioxidant content in phenolic and non-phenolic extracts of ten wine samples, trying to elucidate the potential role of unusual antioxidant compounds. Samples of wines processed from red and white grapes (Vitis vinifera L.), deprived of the volatile fraction at low temperature and buffered at physiological pH, were fractionated by C₁₈ into two fractions: FR1 and FR2. Non-phenolics, such as tartaric, malic, lactic, and succinic acids; glucose; fructose; and glycerin were mainly found in FR1, while polyphenols were present exclusively in FR2. Peroxyl radical quenching was assayed by the ORAC method, while superoxide and hydroxyl radical scavenging activity were assayed by electron paramagnetic resonance. In the ORAC and superoxide assays, most of the activity was found in FR2, while in hydroxyl radical assay, the activity was found in FR1. Model solutions were used to attribute a role to the single compounds in the evaluation of wine’s ROS scavenging capacity: the ORAC and superoxide anion scavenging effects were mainly attributed to the polyphenols, averaging 94.8%, with some contribution from glycerin, particularly in white wines. Unexpectedly, the main chemical responsible for hydroxyl radical scavenging activity was glycerin (56.1%), with the polyphenols scavenging at 18.1%.     

Floral initiation in strawberry: Spectral evidence for the regulation of flowering by long-day inhibition

Summary Floral initiation in strawberry cv. Cambridge Favourite, a facultative short-day plant, was inhibited by a daylength extension with red light (R) during the second half of a 16-hour night but not during the first half, and by far-red light (FR) in the first half but not during the second. Mixed R plus FR light was inhibitory to flowering at both times. This change in sensitivity to R and FR light in the evening and morning resembles the pattern for flower induction in long-day plants but differs from the pattern for flower inhibition in several other short-day plants, examples of which are given. These experiments afford further support for the hypothesis that the control of flower initiation in strawberry depends on the production of a flower inhibitor by leaves exposed to long photoperiods.Abbreviations R red - FR far-red - SD short day - LD long day - SDP short-day plant - LDP long-day plant     

A general model for ontogenetic growth under food restriction

Food restriction (FR) retards animals' growth. Understanding the underlying mechanisms of this phenomenon is important to conceptual problems in life-history theory, as well as to applied problems in animal husbandry and biomedicine. Despite a considerable amount of empirical data published since the 1930s, there is no relevant general theoretical framework that predicts how animals vary their energy budgets and life-history traits under FR. In this paper, we develop such a general quantitative model based on fundamental principles of metabolic energy allocation during ontogeny. This model predicts growth curves under varying conditions of FR, such as the compensatory growth, different age at which FR begins, its degree and its duration. Our model gives a quantitative explanation for the counterintuitive phenomenon that under FR, lower body temperature and lower metabolism lead to faster growth and larger adult size. This model also predicts that the animals experiencing FR reach the same fraction of their adult mass at the same age as their ad libitum counterparts. All predictions are well supported by empirical data from mammals and birds of varying body size, under different conditions of FR.     

A functional antibody mutant with an insertion in the framework region 3 loop of the VH domain: implications for antibody engineering.

We have studied the effects of a four residue insertion into the FR3 loop of the heavy chain variable region from the anti-NP antibody B1-8. The insertion mutant is obtained as secreted antibody without major defects in biosynthesis, indicating that antibody variable domains can accommodate length variation not only in complementarity determining regions (CDRs), but also in framework region (FR) loops. The B1-8 antigen binding site is not affected by the change in a neighbouring loop. FR3 insertions represent a new method of antibody engineering with a potential to obtain strong antigen binding by designing additional antigen contacting residues.