On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

Ribosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.

A reference high-pressure CH4 adsorption isotherm for zeolite Y: results of an interlaboratory study

This paper reports the results of an international interlaboratory study led by the National Institute of Standards and Technology (NIST) on the measurement of high-pressure surface excess methane adsorption isotherms on NIST Reference Material RM 8850 (Zeolite Y), at 25 °C up to 7.5 MPa. Twenty laboratories participated in the study and contributed over one-hundred adsorption isotherms of methane on Zeolite Y. From these data, an empirical reference equation was determined, along with a 95% uncertainty interval (Uk=2). By requiring participants to replicate a high-pressure reference isotherm for carbon dioxide adsorption on NIST Reference Material RM 8852 (ZSM-5), this interlaboratory study also demonstrated the usefulness of reference isotherms in evaluating the performance of high-pressure adsorption experiments.

Diphtheria toxin-mediated transposon-driven poly (A)-trapping efficiently disrupts transcriptionally silent genes in embryonic stem cells

Random gene trapping is the application of insertional mutagenesis techniques that are conventionally used to inactivate protein-coding genes in mouse embryonic stem (ES) cells. Transcriptionally silent genes are not effectively targeted by conventional random gene trapping techniques, thus we herein developed an unbiased poly (A) trap (UPATrap) method using a Tol2 transposon, which preferentially integrated into active genes rather than silent genes in ES cells. To achieve efficient trapping at transcriptionally silent genes using random insertional mutagenesis in ES cells, we generated a new diphtheria toxin (DT)-mediated trapping vector, DTrap that removed cells, through the expression of DT that was induced by the promoter activity of the trapped genes, and selected trapped clones using the neomycin-resistance gene of the vector. We found that a double-DT, the dDT vector, dominantly induced the disruption of silent genes, but not active genes, and showed more stable integration in ES cells than the UPATrap vector. The dDT vector disrupted differentiated cell lineage genes, which were silent in ES cells, and labeled trapped clone cells by the expression of EGFP upon differentiation. Thus, the dDT vector provides a systematic approach to disrupt silent genes and examine the cellular functions of trapped genes in the differentiation of target cells and development.

Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons

Extrinsic cues trigger the local translation of specific mRNAs in growing axons via cell surface receptors. The coupling of ribosomes to receptors has been proposed as a mechanism linking signals to local translation but it is not known how broadly this mechanism operates, nor whether it can selectively regulate mRNA translation. We report that receptor-ribosome coupling is employed by multiple guidance cue receptors and this interaction is mRNA-dependent. We find that different receptors associate with distinct sets of mRNAs and RNA-binding proteins. Cue stimulation of growing Xenopus retinal ganglion cell axons induces rapid dissociation of ribosomes from receptors and the selective translation of receptor-specific mRNAs. Further, we show that receptor-ribosome dissociation and cue-induced selective translation are inhibited by co-exposure to translation-repressive cues, suggesting a novel mode of signal integration. Our findings reveal receptor-specific interactomes and suggest a generalizable model for cue-selective control of the local proteome.

Late Endosomes Act as mRNA Translation Platforms and Sustain Mitochondria in Axons

Local translation regulates the axonal proteome, playing an important role in neuronal wiring and axon maintenance. How axonal mRNAs are localized to specific subcellular sites for translation, however, is not understood. Here we report that RNA granules associate with endosomes along the axons of retinal ganglion cells. RNA-bearing Rab7a late endosomes also associate with ribosomes, and real-time translation imaging reveals that they are sites of local protein synthesis. We show that RNA-bearing late endosomes often pause on mitochondria and that mRNAs encoding proteins for mitochondrial function are translated on Rab7a endosomes. Disruption of Rab7a function with Rab7a mutants, including those associated with Charcot-Marie-Tooth type 2B neuropathy, markedly decreases axonal protein synthesis, impairs mitochondrial function, and compromises axonal viability. Our findings thus reveal that late endosomes interact with RNA granules, translation machinery, and mitochondria and suggest that they serve as sites for regulating the supply of nascent pro-survival proteins in axons.

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Ribonucleoprotein particles are associated with endosomes in axons

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Rab7a endosomes provide sites for axonal local translation

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Rab7a endosomes support axonal synthesis of survival factors

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CMT2B-Rab7a mutations affect axonal translation and mitochondrial integrity

Rapid Cue-Specific Remodeling of the Nascent Axonal Proteome

Axonal protein synthesis and degradation are rapidly regulated by extrinsic signals during neural wiring, but the full landscape of proteomic changes remains unknown due to limitations in axon sampling and sensitivity. By combining pulsed stable isotope labeling of amino acids in cell culture with single-pot solid-phase-enhanced sample preparation, we characterized the nascent proteome of isolated retinal axons on an unparalleled rapid timescale (5 min). Our analysis detects 350 basally translated axonal proteins on average, including several linked to neurological disease. Axons stimulated by different cues (Netrin-1, BDNF, Sema3A) show distinct signatures with more than 100 different nascent protein species up- or downregulated within the first 5 min followed by further dynamic remodeling. Switching repulsion to attraction triggers opposite regulation of a subset of common nascent proteins. Our findings thus reveal the rapid remodeling of the axonal proteomic landscape by extrinsic cues and uncover a logic underlying attraction versus repulsion.

Cell biology in neuroscience: RNA-based mechanisms underlying axon guidance

Axon guidance plays a key role in establishing neuronal circuitry. The motile tips of growing axons, the growth cones, navigate by responding directionally to guidance cues that pattern the embryonic neural pathways via receptor-mediated signaling. Evidence in vitro in the last decade supports the notion that RNA-based mechanisms contribute to cue-directed steering during axon guidance. Different cues trigger translation of distinct subsets of mRNAs and localized translation provides precise spatiotemporal control over the growth cone proteome in response to localized receptor activation. Recent evidence has now demonstrated a role for localized translational control in axon guidance decisions in vivo.

Evidence that the Upf1-related molecular motor scans the 3'-UTR to ensure mRNA integrity

Upf1 is a highly conserved RNA helicase essential for nonsense-mediated mRNA decay (NMD), an mRNA quality-control mechanism that degrades aberrant mRNAs harboring premature termination codons (PTCs). For the activation of NMD, UPF1 interacts first with a translation–terminating ribosome and then with a downstream exon–junction complex (EJC), which is deposited at exon–exon junctions during splicing. Although the helicase activity of Upf1 is indispensable for NMD, its roles and substrates have yet to be fully elucidated. Here we show that stable RNA secondary structures between a PTC and a downstream exon–exon junction increase the levels of potential NMD substrates. We also demonstrate that a stable secondary structure within the 3′-untranslated region (UTR) induces the binding of Upf1 to mRNA in a translation-dependent manner and that the Upf1-related molecules are accumulated at the 5′-side of such a structure. Furthermore, we present evidence that the helicase activity of Upf1 is used to bridge the spatial gap between a translation–termination codon and a downstream exon–exon junction for the activation of NMD. Based on these findings, we propose a model that the Upf1-related molecular motor scans the 3′-UTR in the 5′-to-3′ direction for the mRNA-binding factors including EJCs to ensure mRNA integrity.

Mixture of differentially tagged Tol2 transposons accelerates conditional disruption of a broad spectrum of genes in mouse embryonic stem cells

Among the insertional mutagenesis techniques used in the current international knockout mouse project (KOMP) on the inactivation of all mouse genes in embryonic stem (ES) cells, random gene trapping has been playing a major role. Gene-targeting experiments have also been performed to individually and conditionally knockout the remaining ‘difficult-to-trap’ genes. Here, we show that transcriptionally silent genes in ES cells are severely underrepresented among the randomly trapped genes in KOMP. Our conditional poly(A)-trapping vector with a common retroviral backbone also has a strong bias to be integrated into constitutively transcribed genome loci. Most importantly, conditional gene disruption could not be successfully accomplished by using the retrovirus vector because of the frequent development of intra-vector deletions/rearrangements. We found that one of the cut and paste-type DNA transposons, Tol2, can serve as an ideal platform for gene-trap vectors that ensures identification and conditional disruption of a broad spectrum of genes in ES cells. We also solved a long-standing problem associated with multiple vector integration into the genome of a single cell by incorporating a mixture of differentially tagged Tol2 transposons. We believe our strategy indicates a straightforward approach to mass-production of conditionally disrupted alleles for genes in the target cells.

A larval medaka (Oryzias latipes) acute toxicity assay combined with solid-phase extraction to efficiently determine the toxicity of organic contaminants in river water

Using a larval medaka (Oryzias latipes) acute toxicity assay combined with solid-phase extraction, we proposed a method for efficiently determining the fish toxicity of organic contaminants in river water. Organic toxicants were 10, 20, 50 and 100-fold concentrated from 4 L of the sample with adsorption cartridges. The lethal effect was observed by exposing every ten individuals of 48-72 h old larval medaka to 20 mL of each solution for 48h. The median lethal concentration rate (LCR50) was used as an indicator for the toxicity. With the developed toxicity test method, more than seven times difference was found in the LCR50 of the river water samples. LCR50 distribution profiles were compared with 125 samples in two typical rivers. The result revealed a lower toxicity level in the mainstream than in the confluences, and a lower toxicity level in Sagami River than in Ayase River. LCR50 proved unique as a toxicity indicator, which was impossible to speculate from the conventional water quality indicator of the dissolved organic carbon concentration. As an effective screening test for priority settings, the method can help us with an efficient planning for the environmental investigation and management.

Suppression of nonsense-mediated mRNA decay permits unbiased gene trapping in mouse embryonic stem cells

An international collaborative project has been proposed to inactivate all mouse genes in embryonic stem (ES) cells using a combination of random and targeted insertional mutagenesis techniques. Random gene trapping will be the first choice in the initial phase, and gene-targeting experiments will then be carried out to individually knockout the remaining ‘difficult-to-trap’ genes. One of the most favored techniques of random insertional mutagenesis is promoter trapping, which only disrupts actively transcribed genes. Polyadenylation (poly-A) trapping, on the other hand, can capture a broader spectrum of genes including those not expressed in the target cells, but we noticed that it inevitably selects for the vector integration into the last introns of the trapped genes. Here, we present evidence that this remarkable skewing is caused by the degradation of a selectable-marker mRNA used for poly-A trapping via an mRNA-surveillance mechanism, nonsense-mediated mRNA decay (NMD). We also report the development of a novel poly-A-trap strategy, UPATrap, which suppresses NMD of the selectable-marker mRNA and permits the trapping of transcriptionally silent genes without a bias in the vector-integration site. We believe the UPATrap technology enables a simple and straightforward approach to the unbiased inactivation of all mouse genes in ES cells.

Expression profiling with arrays of randomly disrupted genes in mouse embryonic stem cells leads to in vivo functional analysis

DNA arrays are capable of profiling the expression patterns of many genes in a single experiment. After finding a gene of interest in a DNA array, however, labor-intensive gene-targeting experiments sometimes must be performed for the in vivo analysis of the gene function. With random gene trapping, on the other hand, it is relatively easy to disrupt and retrieve hundreds of genes/gene candidates in mouse embryonic stem (ES) cells, but one could overlook potentially important gene-disruption events if only the nucleotide sequences and not the expression patterns of the trapped DNA segments are analyzed. To combine the benefits of the above two experimental systems, we first created approximately 900 genetrapped mouse ES cell clones and then constructed arrays of cDNAs derived from the disrupted genes. By using these arrays, we identified a novel gene predominantly expressed in the mouse brain, and the corresponding ES cell clone was used to produced mice homozygous for the disrupted allele of the gene. Detailed analysis of the knockout mice revealed that the gene trap vector completely abolished gene expression downstream of its integration site. Therefore, identification of a gene or novel gene candidate with an interesting expression pattern by using this type of DNA array immediately allows the production of knockout mice from an ES cell clone with a disrupted allele of the sequence of interest.

Embryonic development assay with Daphnia magna: application to toxicity of aniline derivatives

An assay system using Daphnia magna embryos was applied to investigate the adverse effects of aniline derivatives. The data were compared with our previous data for chlorophenols. This new assay provides useful information to evaluate the toxicity of chemicals and the differences in sensitivity between the life stages. The effects of 15 aniline derivatives on embryonic development of D. magna embryos were determined. At the start of exposure, 2-6-h old eggs (between stages 1 and 2, round in shape, diameter approx. 400 microm), were used. In control and solvent control groups, embryonic development from an egg to a free-swimming animal proceeded completely within 3 days with more than 90% hatchability. Median effective concentrations (EC50s) to reduce the numbers hatched were determined and gross morphological abnormalities of hatched animals recorded. Anilines induced no obvious morphological abnormalities and no developmental delay although premature deaths occurred. However, they affected the number of embryos hatching in a dose-dependent manner. In addition, this embryo assay was more sensitive to aniline derivatives (except for aniline) than acute juveniles immobilization assay. Ratios of 48-h EC50 (juvenile)/3-day EC50 (embryo) for eight anilines were greater than 5.0. Particularly, the ratios of 4-methyl-, 4-ethyl- and 3-methylaniline were 77, 23 and 11, respectively. EC50s for embryos and juveniles were poorly correlated (r = 0.41). This indicated that the sensitivities of the two life stages were different to the effects of anilines. EC50s were poorly correlated (r = -0.097) with the log Kow (1-octanol/water partition coefficient). These results were compared with previous results for phenols.

Synthesis of fluorine analogs of protoporphyrin potentially useful for diagnosis and therapy of cancer. IV. Synthesis of (trifluorovinyl)vinyl- and (1-chloro-2,2-difluorovinyl)vinyldeuteroporphyrins

Trifluoro or chlorodifluoro analogs of protoporphyrin, the compounds in the title, were synthesized for use in the diagnosis and therapy of cancer. 3- Or 8-acetyldeuteroporphyrin dimethyl esters (2 and 3) were iodinated with iodine in the presence of potassium carbonate to the corresponding iodo compounds (5 and 6). The iodo compounds (5 and 6) were treated with bis(trifluorovinyl)zinc in the presence of tetrakis(triphenylphosphine)-palladium to give trifluorovinyl derivatives (7 and 8) in good yields. Reduction of the acetyl group of 7 and 8 with sodium borohydride afforded the corresponding hydroxyethyl derivatives (9 and 10). Compounds (9 and 10) were dehydrated with methanesulfonyl chloride and triethylamine to give (trifluorovinyl)vinyldeuteroporphyrin dimethyl esters (11 and 12). Treatment of 5 and 6 with bis(1-chloro-2,2-difluorovinyl)zinc in the presence of tetrakis(triphenylphosphine)palladium, followed by similar reactions as above gave (1-chloro-2,2-difluorovinyl)-vinyldeuteroporphyrin dimethyl esters (17 and 18).

Metabolism of 14C-labelled sucrose esters of stearic acid in rats

Rats were dosed by oral gavage (250 mg/kg) with compounds containing sucrose esterified in four, six or eight positions with stearic acid. For each compound, rats excreted greater than 95% of the dose in the faeces. The extent of absorption and metabolism of radioactivity was inversely related to the degree of esterification. For rats dosed with sucrose esters labelled in the fatty acid moieties, the degree of absorption of radioactivity was highest for the tetraesterified compound (5.9% of the dose). At 120 hr after dosing with this derivative, the highest concentrations of radioactivity, aside from tissues of the gastrointestinal tract, were found in fat (183 micrograms-equivalents/g tissue), lymph nodes (117 micrograms-equivalents/g tissue) and the liver (88 micrograms-equivalents/g tissue); appreciable radioactivity appeared in the blood (3.9 micrograms-equivalents/g tissue) and collected lymph (5.0-7.6% of the dose). For rats dosed with esters labelled in the sucrose moiety, the amounts of radioactivity absorbed were lower than after dosing with the corresponding sucrose derivatives labelled in the fatty acid moieties; the absorbed radioactivity was greatest following administration of the tetraesterified compound (3.0%). Relatively little radioactivity was found in tissue samples collected from these rats. These results are consistent with limited hydrolysis of the sucrose esters, presumably to sucrose and fatty acids, prior to intestinal absorption.

Mass propagation of shoots of Stevia rebaudiana using a large scale bioreactor

A procedure for the mass propagation of multiple shoots of Stevia rebaudiana is described. Isolated shoot primordia were used as the inoculum to obtain clusters of shoot primordia. Such clusters were grown in a 500 liter bioreactor to obtain shoots. A total of 64.6 Kg of shoots were propagated from 460 g of the inoculated shoot primordia. These shoots were easily acclimatized in soil.

Immunological properties of the primer-independent glucosyltransferase of Streptococcus mutans serotypes d and g

Streptococcus mutans serotype g secretes at least three kinds of glucosyltransferase with different enzymological and immunological properties. One of them is a primer-independent enzyme and seems to be the source of primer for the others, both of which are primer-dependent enzymes. Recently, we purified the primer-independent enzyme, the third glucosyltransferase in this group from S. mutans strain AHT-k serotype g. In the present study, we examined the specificity of the antiserum against the primer-independent glucosyltransferase using extracellular culture-conditioned fluids of many strains of the various serotypes of S. mutans. The antiserum cross-reacted with the extracellular culture fluids from strains of serotypes d and a, in addition to serotype g, but not with those of other serotypes, indicating that the primer-independent glucosyltransferase is secreted by the S. sobrinus and S. cricetus, but not by S. mutans and S. rattus. The antiserum did not completely inhibit the activity of the enzyme, even at more than twofold antibody excess, determined by indirect precipitation with immobilized staphylococcal protein A.

Studies on the metabolic fate of sucrose esters in rats

The metabolism in rats of sucrose esters of stearic acid and palmitic acid was studied in vivo and in vitro using esters labelled with 14C at the sucrose of fatty-acid moiety. In excretion studies, the ratio of expired radioactivity to absorbed radioactivity after oral administration of the sucrose esters labelled at the sucrose moiety was similar to that after the administration of [14C]sucrose. A similar correlation between the ester labelled at the fatty-acid moiety and the free [14C]fatty acid was also observed. No intact sucrose ester was detected in the urine. Studies in vitro using everted intestinal sacs showed that there was virtually no transport of 14C-labelled sucrose esters from the mucosal to the serosal solution through the intestinal tissues, and that the enzymes in the intestinal mucosa played a more important role in the hydrolysis of sucrose esters than did those in the digestive fluid. In studies of intestinal absorption through the mesenteric lymphatic system, during the 24 hr after ingestion 1.8% of the administered radioactivity was recovered in the lymph after dosing with [U-14C]sucrose monostearate whereas 20% was recovered in the lymph after dosing with sucrose [1-14C]monostearate. This difference in levels of recovery of administered radioactivity indicated that sucrose monostearate was absorbed only after hydrolysis. No intact ester was detected in the lymph or in the portal or femoral blood. The results of all of these experiments show that the sucrose esters are hydrolysed to sucrose and fatty acids prior to intestinal absorption.

Relationship between molar refraction and n-octanol/water partition coefficient

The n-octanol/water partition coefficient (Pow) for organic chemicals which do not form the hydrogen bond was considered on the basis of London's dispersion force, because the dispersion force is the main component of van der Waals-type attractive forces between solute and solvent molecules. The dispersion force is a function of both the ionization potential and the molar refraction. As the variation of the ionization potential is small in comparison with that of the molar refraction, the latter is the most important factor to determine the value of Pow. Thus the relationship between Pow and the molar refraction can be established. The relationship was confirmed for some halogenated alkanes, alkenes and aromatics, and polycyclic aromatic hydrocarbons by analysis of observed values of Pow and calculated values of the molar refraction. Estimation of Pow from the molar refraction is advantageous for the preliminary hazard assessment of new chemicals, because direct measurement of Pow is laborious and time consuming for lack of information about analytical methods.

Non-steady-state equilibrium model for the preliminary prediction of the fate of chemicals in the environment

Prediction of the fate of chemicals in the environment is essential to the assessment of the potential hazard of chemicals. The fate of a chemical in the environment depends mainly upon (1) transfer processes between environmental compartments due to physicochemical properties, (2) transformation processes in each compartment, and (3) characteristics of the environment. Many equilibrium or kinetic models have been proposed to predict the fate of chemicals in the environment. Though kinetic models are useful in predicting the concentration-time profile of a chemical at the non-steady state, they are rather complicated. In this work is proposed a simple and useful equilibrium model for prediction of the mass and concentration distribution fraction, mean residence time, and concentration-time profile of a chemical released into the environment, an advantage of our model. For the validation of this model, the results were compared with data from Neely's pond experiment and field data monitored by the Japanese Environment Agency. The results show that the equilibrium model is valuable for preliminary prediction of the fate of chemicals that are priority chemicals for hazard assessment in the environment.