High‐throughput screening of optimal solution conditions for structural biological studies by fluorescence correlation spectroscopy

Protein aggregation is an essential molecular event in a wide variety of biological situations, and is a causal factor in several degenerative diseases. The aggregation of proteins also frequently hampers structural biological analyses, such as solution NMR studies. Therefore, precise detection and characterization of protein aggregation are of crucial importance for various research fields. In this study, we demonstrate that fluorescence correlation spectroscopy (FCS) using a single‐molecule fluorescence detection system enables the detection of otherwise invisible aggregation of proteins at higher protein concentrations, which are suitable for structural biological experiments, and consumes relatively small amounts of protein over a short measurement time. Furthermore, utilizing FCS, we established a method for high‐throughput screening of protein aggregation and optimal solution conditions for structural biological experiments.     

Accumulation of multiacetylated forms of histones by trichostatin A and its developmental consequences in early starfish embryos

Summary External application of 10 rig/ml (R)-trichostatin A (TSA), a potent and specific inhibitor of mammalian histone deacetylase, to the embryo of the starfish Asterina pectinifera inhibited development during the early gastrula stage before formation of mesenchyme cells. The TSA-sensitive period was limited to the mid-blastula stage before hatching. The pulse-chase experiment clearly demonstrated that TSA induced an accumulation of acetylated histone species in blastulae through inhibition of historic deacetylation. Similar blockage of development at the early gastrula stage was observed with n-butyrate, which has been known as a weak inhibitor of historic deacetylase. These results suggest an intimate role for historic acetylation-deacetylation equilibria in starfish development. Correspondence to: S. Ikegami     

Utilization of Escherichia coli outer-membrane endoprotease OmpT variants as processing enzymes for production of peptides from designer fusion proteins

Escherichia coli outer-membrane endoprotease OmpT has suitable properties for processing fusion proteins to produce peptides and proteins. However, utilization of this protease for such production has been restricted due to its generally low cleavage efficiency at Arg (or Lys)-Xaa, where Xaa is a nonbasic N-terminal amino acid of a target polypeptide. The objective of this study was to generate a specific and efficient OmpT protease and to utilize it as a processing enzyme for producing various peptides and proteins by converting its substrate specificity. Since OmpT Asp(97) is proposed to interact with the P1' amino acid of its substrates, OmpT variants with variations at Asp(97) were constructed by replacing this amino acid with 19 natural amino acids to alter the cleavage specificity at Arg (P1)-Xaa (P1'). The variant OmpT that had a methionine at this position, but not the wild-type OmpT, efficiently cleaved a fusion protein containing the amino acid sequence -Arg-Arg-Arg-Ala-Arg downward arrow motilin, in which motilin is a model peptide with a phenylalanine at the N terminus. The OmpT variants with leucine and histidine at position 97 were useful in releasing human adrenocorticotropic hormone (1-24) (serine at the N terminus) and human calcitonin precursor (cysteine at the N terminus), respectively, from fusion proteins. Motilin was produced by this method and was purified up to 99.0% by two chromatographic steps; the yield was 160 mg/liter of culture. Our novel method in which the OmpT variants are used could be employed for production of various peptides and proteins.     

Anti-allodynic effects of intrathecally and intracerebroventricularly administered 26RFa, an intrinsic agonist for GRP103, in the rat partial sciatic nerve ligation model

26RFa and QRFP are endogenous ligands of GPR103. 26RFa binding sites are widely distributed in the brain and the spinal cord where they are involved in processing pain. In the present study, the effects of intrathecal and intracerebroventricular applications of 26RFa on the level of mechanical allodynia induced by partial sciatic nerve ligation were examined in rats. The level of mechanical allodynia was measured using von Frey filaments. Intrathecal and intracerebroventricular injection of 26RFa attenuated the level of mechanical allodynia. 26RFa has been reported to activate not only GPR103 but also neuropeptide FF2 receptor and the effect of intrathecally and intracerebroventricularly administered 26RFa was not antagonized by BIBP3226, an antagonist of neuropeptide FF receptor. Immunohistochemical examination revealed that QRFP-like immunoreactivity (QRFP-LI) was expressed mainly in the small to medium sized neurons in the L5 dorsal root ganglion (DRG) and that partial sciatic nerve injury increased the percentage of QRFP-LI positive neurons. 7 days after the nerve injury, QRFP-LI positive neurons in the L5 DRG ipsilateral to the partial sciatic nerve injury were larger than those in the L5 DRG ipsilateral to the sham operation. These data suggest that (1) exogenously applied 26RFa modulates nociceptive transmission at the spinal and the supraspinal brain in the neuropathic pain model, (2) the mechanism 26RFa uses to produce an anti-allodynic effect may be mediated by the activation of GPR103, and (3) partial sciatic nerve ligation affects the expression of QRFP-LI in the dorsal root ganglion.     

A novel approach and protocol for discovering extremely low-abundance proteins in serum

The proteomic analysis of serum (plasma) has been a major approach to determining biomarkers essential for early disease diagnoses and drug discoveries. The determination of these biomarkers, however, is analytically challenging since the dynamic concentration range of serum proteins/peptides is extremely wide (more than 10 orders of magnitude). Thus, the reduction in sample complexity prior to proteomic analyses is essential, particularly in analyzing low-abundance protein biomarkers. Here, we demonstrate a novel approach to the proteomic analyses of human serum that uses an originally developed serum protein separation device and a sequentially linked 3-D-LC-MS/MS system. Our hollow-fiber-membrane-based serum pretreatment device can efficiently deplete high-molecular weight proteins and concentrate low-molecular weight proteins/peptides automatically within 1 h. Four independent analyses of healthy human sera pretreated using this unique device, followed by the 3-D-LC-MS/MS successfully produced 12 000-13 000 MS/MS spectra and hit around 1800 proteins (>95% reliability) and 2300 proteins (>80% reliability). We believe that the unique serum pretreatment device and proteomic analysis protocol reported here could be a powerful tool for searching physiological biomarkers by its high throughput (3.7 days per one sample analysis) and high performance of finding low abundant proteins from serum or plasma samples.     

Update of mouse microsatellite database of Japan (MMDBJ).

We updated a database of microsatellite marker polymorphisms found in inbred strains of the mouse, most of which were derived from the wild stocks of four Mus musculus subspecies, M. m. domesticus, M. m. musculus, M. m.castaneus and M. m. molossinus. The major aim of constructing this database was to establish the genetic status of these inbred strains as resources for linkage analysis and positional cloning. The inbred strains incorporated in our database are A/J, C57BL/6J, CBA/J, DBA/2J, SM/J, SWR/J, 129Sv/J, MSM/Ms, JF1/Ms, CAST/Ei, NC/Nga, BLG2/Ms, NJL/Ms, PGN2/Ms, SK/CamEi and SWN/Ms, which have not or have only been poorly incorporated in the Whitehead Institute/MIT (WI/MIT) microsatellite database. The number of polymorphic microsatellite loci incorporated in our database is over 1,000 in all strains, and the URL site for our database is located at http:// www.shigen.nig.ac.jp /mouse/mmdbj/mouse.html.     

Improvement in spermatogenic function after subcutaneous implantation of a capsule containing an aromatase inhibitor in four oligozoospermic dogs and one azoospermic dog with high plasma estradiol-17beta concentrations

A capsule containing an aromatase inhibitor (4-androsten-4-ol-3,17-dione) was subcutaneously implanted in four oligozoospermic beagle dogs and one azoospermic beagle dog with high plasma estradiol-17beta (E2) concentrations (15-19 pg/ml) and low plasma testosterone (T) concentrations (0.6-0.8 ng/ml) for 8 weeks and the effect of the aromatase inhibitor on spermatogenic dysfunction was assessed. Plasma E2 and T concentrations and semen quality were examined at 1 week intervals from 3 weeks before to 12 weeks after the start of treatment. Testicular biopsies were done twice (capsule implantation and removal). Plasma E2 concentrations of all dogs decreased (9-14 pg/ml) and plasma T concentrations increased (2.0-2.6 ng/ml) from 3 weeks after capsule implantation to capsule removal. The mean number of spermatozoa ejaculated by all four oligozoospermic dogs between 4 and 9 weeks after implantation was higher (127 x 10(6) to 205 x 10(6)) than before implantation (20 x 10(6) to 38 x 10(6)) (P < 0.05 and 0.01). Very low numbers (2 x 10(4) to 4 x 10(4)) of immotile spermatozoa were observed between 7 and 8 weeks after implantation in the semen collected from the dog with azoospermia. Before implantation, a few spermatozoa were seen in only one-fifth of the seminiferous tubules in this dog; 8 weeks after implantation, the mean diameter and mean number of round spermatids in the seminiferous tubules in all five dogs were higher than before implantation (P < 0.05). Implantation of the capsule containing the aromatase inhibitor in infertile dogs with abnormally high plasma E2 concentrations improved their spermatogenic function, concurrent with decreased plasma E2 and increased plasma T.     

Transport and Fixation of Inorganic Carbon during Photosynthesis of Anabaena Grown under Ordinary Air. I. Active Species of Inorganic Carbon Utilized for Photosynthesis

Inorganic carbon transport during photosynthesis of cyanobacteriumAnabaena variabilis grown under ordinary air was investigatedby supplying ¹⁴CO₂ or H¹⁴CO₃^– solution to three differentstrains. Both CO₂ and HCO₃^– were accumulated within thealgal cells. In the cell suspension from which dissolved inorganiccarbon had been depleted by pre-illumination, CO₂ was transportedand accumulated faster than HCO₃^–. When the concentrationof HCO₃^– injected into the cell suspension of A. variabilisM3 was 25 times as high as that of CO2 (the expected ratio atequilibrium at pH 7.8), the initial rates of fixation of bothinorganic carbon species were practically the same. On the otherhand, when ¹⁴CO₂ or H¹⁴CO₃^– was added under steady statephotosynthetic conditions, both carbon species were transportedat similar rates. The ratio of fixed to transported carbon measuredafter the initial 5 s was only 23–27% regardless of thecarbon species supplied. This percentage is much lower thanthat reported for Chlorella cells. ¹ To whom reprint requests should be addressed (Received June 30, 1986; Accepted December 16, 1986)     

Regeneration processes of a boreal forest in Kamchatka with special reference to the contribution of sprouting to population maintenance

We studied regeneration patterns of three tree species Picea ajanensis, Betula platyphylla and Populus tremula from 1998 to 2000 in the Central Depression of the Kamchatka Peninsula. We paid special attention to the contribution of sprouting to their regeneration. P. ajanensis was the only species that regenerated by seedling. In a 40 × 40 m study plot, the density of P. ajanensis saplings < 2.0 cm in diameter at basal area (DBH) was 1132, and this was the highest among the three species studied. The number of saplings 2 cm in DBH declined sharply with size class. The spatial distribution of P. ajanensis saplings (< 2 cm in DBH) showed a significant positive correlation with that of adult trees and a negative correlation with that of gaps. These trends were not changed after re-measurement in 2000, although nearly half of the juveniles had died or been injured during the two years. These results suggest that small Picea saplings prefer habitats under the canopy of adult trees rather than in gaps for establishment. Most small individuals of B. platyphylla were produced from sprouts. The number of saplings in the smallest size class (< 2 cm in DBH) was much less than that of P. ajanensis, although the number of larger individuals did not decrease remarkably. The spatial distribution of B. platyphylla saplings showed a positive correlation with that of adult trunks and a negative correlation with that of canopy trees of P. ajanensis. These results suggest an effective contribution of sprouts to the regeneration of B. platyphylla. P. tremula was the only species that could invade big gaps and produce many root suckers efficiently. There were 181 suckers of P. tremula in the smallest size class (< 2 cm in DBH) in the study plot, although the number of saplings 2 cm in DBH declined abruptly. The spatial distribution of saplings of this species showed a slight positive correlation with that of gaps, and negative correlation with that of adult trees of B. platyphylla, P. ajanensis, and P. tremula. The root suckering strategy of P. tremula might be adaptive under severe conditions in high-latitude regions. Our data suggest, however, that it does not necessarily contribute to regeneration in mature forests. The three component species in this forest did not seem to utilize canopy gaps for regeneration; we suggest that gap dynamics do not work in this forest. The sparse canopy, which is a typical character of forests in high-latitude regions, might be a consequence of high mortalities of seedlings and root suckers inside gaps.     

Salinities, not diets, affect strontium/calcium ratios in otoliths of Anguilla japonica

Although otolith Strontium (Sr)/calcium (Ca) ratios have been widely used to reconstruct the past salinity environmental history of anguillid eels, factors affecting the Sr/Ca ratios in otoliths are incompletely understood. Japanese Eel (Anguilla japonica) elvers (mean length 54.7 ± 2.1 mm) were collected in the estuary during their upstream migration and reared at 5 different salinities (0, 5, 15, 25, and 35 psu) and 3 types of feeding conditions (formulated feed, tubifex, and starvation) for 30 days to evaluate the effects of salinity and diets on otolith Sr/Ca ratios. Ca and Sr concentrations in the ambient water significantly increased with salinity (SAL) as [Ca] _water = 15.50SAL − 5.56, and [Sr] _water = 0.21SAL + 0.03, respectively. Sr/Ca ratios in otoliths increased with salinity (SAL) of the rearing water as [(Sr/Ca) × 1000] _otolith = 0.091SAL + 3.790. In diets, Sr/Ca ratios were 4 times higher in tubifex than in formulated feed. However, in otoliths, ANOVA indicated that Sr/Ca ratios did not differ significantly between groups fed on tubifex or formulated feed (p = 0.118). Otolith Sr/Ca ratios were negatively correlated with fish growth rates while the growth rates differed significantly among rearing conditions with different salinities and diets. Partition coefficients of the Sr/Ca ratios from ambient water to fish tissues and otoliths significantly increased with salinity. The Sr/Ca ratios of Japanese Eel otoliths thus were positively correlated with the ambient salinity and decreased with increasing fish growth rate, but was not affected by fish diet.