The binding mechanism of eIF2β with its partner proteins, eIF5 and eIF2Bε

The eukaryotic translation initiation factor eIF2 delivers Met-tRNAiMet to the ribosomal small subunit in GTP-bound form associated with eIF1, eIF1A, eIF3 and eIF5, and dissociates together with eIF5 as eIF5-eIF2-GDP complex from the ribosomal small subunit after formation of start codon-anticodon base pairing between Met-tRNAiMet and mRNA. The inactive form eIF2-GDP is then exchanged for the active form eIF2-GTP by eIF2B for further initiation cycle. Previous studies showed that the C-terminal domains of eIF5 (eIF5-CTD) and eIF2Bε (eIF2Bε-CTD) have a common eIF2β-binding site for interacting with an N-terminal region of eIF2β (eIF2β-NTD). Here we have reconstructed the complexes of (eIF5-CTD)-(eIF2β-NTD) and (eIF2Bε-CTD)-(eIF2β-NTD) in vitro, and investigated binding mechanism by circular dichroism spectroscopy and small angle X-ray scattering in solution. The results showed the conformation of eIF2β-NTD was changed when bound to partner proteins, whereas the structures of eIF5-CTD and eIF2Bε-CTD were similar in both isolated and complex states. We propose that eIF2β-NTD works as an intrinsically disordered domain which is disorder in the isolated state, but folds into a definite structure when bound to its partner proteins. Such flexibility of eIF2β-NTD is expected to be responsible for its binding capability.     

Characterization and categorization of fluorescence activated cell sorted planarian stem cells by ultrastructural analysis

Planarians have regenerative ability made possible by pluripotent stem cells referred to as neoblasts. Classical ultrastructural studies have indicated that stem cells can be distinguished by a unique cytoplasmic structure known as the chromatoid body and their undifferentiated features, and they are specifically eliminated by X-ray irradiation. Recently, by using fluorescence activated cell sorting (FACS), planarian cells were separated into two X-ray-sensitive fractions (X1 and X2) and an X-ray-insensitive fraction (XIS) according to DNA content and cytoplasmic size. Here we analyzed the fractionated cells by transmission electron microscopy (TEM). First, we found that both undifferentiated cells (stem cells) and regenerative cells (differentiating cells) were concentrated in the X1 fraction containing the S/G2/M phase cells. The regenerative cells were considered to be committed stem cells or progenitor cells, suggesting that some stem cells may maintain proliferative ability even after cell fate-commitment. Second, we succeeded in identifying a new type of stem cells, which were small in size with few chromatoid bodies and a heterochromatin-rich nucleus. Interestingly, they were concentrated in the X2 fraction, containing G0/G1 phase cells. These results suggest that planarian stem cells are not homogeneous, but may consist of heterogeneous populations, like mammalian stem cells.     

Radiolarian faunal turnover across the Oligocene/Miocene boundary in the equatorial Pacific Ocean

The global warming trend of the latest Oligocene was interrupted by several cooling events associated with Antarctic glaciations. These cooling events affected surface water productivity and plankton assemblages. Well-preserved radiolarians were obtained from upper Oligocene to lower Miocene sediments at Ocean Drilling Program (ODP) Leg 199 Sites 1218 and 1219 in the equatorial Pacific, and 110 radiolarian species were identified.Four episodes of significant radiolarian faunal changes were identified: middle late Oligocene (27.5 to 27.3 Ma), latest Oligocene (24.4 Ma), earliest Miocene (23.3 Ma), and middle early Miocene (21.6 Ma). These four episodes approximately coincide with increases and decreases of biogenic silica accumulation rates and increases in δ¹⁸O values coded as “Oi” and “Mi” events. These data indicate that Antarctic glaciations were associated with change of siliceous sedimentation patterns and faunal changes in the equatorial Pacific.Radiolarian fauna was divided into three assemblages based on variations in radiolarian productivity, species richness and the composition of dominant species: a late Oligocene assemblage (27.6 to 24.4 Ma), a transitional assemblage (24.4 to 23.3 Ma) and an early Miocene assemblage (23.3 to 21.2 Ma). The late Oligocene assemblage is characterized by relatively high productivity, low species richness and four dominant species of Tholospyris anthophora, Stichocorys subligata, Lophocyrtis nomas and Lithelius spp. The transitional assemblage represents relatively low values of productivity and species richness, and consists of three dominant species of T. anthophora, S. subligata and L. nomas. The characteristics of the early Miocene assemblage are relatively low productivity, but high species richness. The two dominant species present in this assemblage are T. anthophora and Cyrtocapsella tetrapera. The most significant faunal turnover of radiolarians is marked at the boundary between the transitional/early Miocene assemblages.We also reviewed changes in other microfossil assemblages in the low latitudes during the late Oligocene through early Miocene. The microfossil assemblages of major groups show sequential changes near the Oligocene/Miocene (O/M) boundary (23.8 Ma). Many extinction events and some first occurrences of calcareous nannofossils and many occurrences of radiolarians are found from about 24.8 to 23.3 Ma, and first occurrences of planktic foraminifers and diatoms followed from 23.2 through 22 Ma. Hence, the O/M boundary is identified as a significant level for microfossil evolutions.     

The Structures of Corynecins; Chloramphenicol Analogues Produced by a n-Paraffin-grown Bacterium

Corynebacterium sp. produced antibacterial substances (corynecins) when a n-paraffin mixture was used as the sole carbon sourse. Structures of the substances were determined as acyl derivatives of d-(?)-threo-l-p-nitrophenyl-2-amino-l,3-propanediol (free base of chloramphenicol).     

PCR-Based Ribosomal DNA Detection Technique for Microalga (Heterosigma carterae) Causing Red Tide and Its Application to a Biosensor Using Labeled Probe

A technique for detecting Raphidophycean, a bloom-forming genus of algae, was developed using a specific DNA probe. The design of the probe was based on a sequence polymorphism within the small subunit (SSU) ribosomal RNA gene (rDNA) of this strain by using fluorescence polarization (FP) analysis and the BIAcore 2000 biosensor, which utilized surface plasmon resonance (SPR). The specific sequence in SSU rDNA for Heterosigma carterae was determined by sequence data analysis. One pair of polymerase chain reaction (PCR) probes was designed for use in making the identification. H. carterae SSU rDNA was amplified by PCR. Using a fluoroscein isothiocyanate–labeled or biotin-labeled oligonucleotide probe, the PCR-amplified rDNA was selectively detected as an FP-intensity change via FP analysis or as a resonance-unit change via SPR. Although total time for final detection after sampling was within 3 hours, specific rDNA could be detected within 10 minutes after PCR through these detection methods.     

Effect of Polyglycerol Esters of Fatty Acids on the Physicochemical Properties and Stability of β-Carotene Emulsions during Digestion in Simulated Gastric Fluid

The effects of six different polyglycerol esters of fatty acids (PGEs) and two different particle sizes produced using various processing parameters on the physicochemical properties and stability of the β-carotene emulsions during digestion in simulated gastric fluid (SGF) were investigated. β-Carotene emulsions were prepared by high-pressure homogenization using β-carotene (0.1% w/w) in soybean oil as the oil phase and 1% (w/w) PGE in Milli-Q water as the water phase. The particle size of β-carotene emulsions was measured by a laser diffraction technique, and the stability of emulsions was interpreted in terms of the increase in particle size and span value of emulsion droplets and the retention of β-carotene during digestion in SGF. The average particle size ranges of emulsions were 0.17 to 0.27 μm for fine emulsions and 1.16 to 1.59 μm for coarse emulsions. In the prepared β-carotene emulsions, the particle size decreased with increasing polymerization of the glycerol in PGEs, and the higher polymerization of the glycerol also increased the stability of emulsions during digestion in SGF. Although the β-carotene content in the emulsions significantly decreased with increasing digestion period, loss of β-carotene was more severe in unstable emulsions than in stable emulsions, suggesting that the particles incorporated into droplets could provide some protective barrier for decreasing the β-carotene degradation. Therefore, β-carotene emulsions stabilized by PGEs with high polymerization of the glycerol may be useful for further applications in food and drug formulations. Decaglycerol monooleate (MO750) was demonstrated to be the most effective emulsifier in stabilizing β-carotene emulsions in this study.