Seasonal and site-specific variability in terrigenous particulate organic carbon concentration in near-shore waters of Lake Biwa, Japan

Identifying sources of particulate organic matter (POM) is important for clarifying fundamental mechanisms by which lake food webs are sustained. We determined carbon and nitrogen stable isotope ratios of POM in near-shore waters of Lake Biwa, a large, meso-eutrophic lake in Japan, to estimate relative contributions of terrigenous particulate organic carbon (T-POC), plankton-derived POC (P-POC) and epilithon-derived POC (E-POC) to POC in near-shore waters. Samples were collected during different months (November, February, May and July) at 29 sites located near the mouth of tributary rivers with different discharge and catchment land use. The data revealed that POC mainly consisted of P-POC and T-POC, with relative contributions varying widely over season and among locations. E-POC generally contributed little to the near-shore POC. Path analyses revealed that the concentration of riverine POC whose isotopic signatures were similar to those of rice straws increased with a larger %paddy field area in the catchment of tributary rivers, which subsequently enhanced T-POC inputs to near-shore waters through riverine transportation. Furthermore, our results suggested that T-POC contribution was influenced, with a time lag, by wave-driven turbulence and shore topography, which appear to affect sedimentation and resuspension of T-POC

A suitable stereoisomer of vibrioferrin probes for iron uptake of Vibrio parahaemolyticus

Suitable Stereostructures of vibrioferrin probes for iron uptake of Vibrio parahaemolyticus was revealed. Stereoisomers of dansyl labeled vibrioferrin at the 2′′-position were synthesized and their uptake activities were evaluated. Vibrio parahaemolyticus take in both isomers at the 2′′-position. In addition to Vibrio parahaemolyticus, several bacteria have also taken up the (R)-isomer

An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.

SACLAのX線自由電子レーザーを用いた新規タンパク質立体構造決定に世界で初めて成功. 京都大学プレスリリース. 2015-09-14.Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection

Persistence of the topological surface states in Bi2Se3 against Ag intercalation at room temperature

The electronic and atomic structures of topological insulator Bi2Se3, upon Ag atom deposition, have been investigated by combined experimental methods of scanning tunneling microscopy (STM), photoelectron spectroscopy, and first-principles calculations. We show from the results of STM that the deposited Ag atoms are stabilized beneath the surface instead of being adsorbed on the topmost surface. We further reveal from the angle-resolved photoemission spectroscopy that the Bi2Se3(0001) topological surface states stay uninterrupted after a large amount of absorption of Ag atoms. Our analysis of the photoelectron intensity of Ag core states excited by soft X-ray suggests that a large amount of deposited Ag atoms diffused into a deeper place, which is beyond the probing depth of X-ray photoelectron spectroscopy. The first-principles calculations identify the octahedral site in the van der Waals gaps between quintuple layers to be the most favorable locations of Ag atoms beneath the surface, which yields good agreement between the simulated and experimental STM images. These findings pave an efficient way to tailor the local lattice structures of topological insulators without disturbing the topologically nontrivial surface states

Plastid signalling under multiple conditions is accompanied by a common defect in RNA editing in plastids

Retrograde signalling from the plastid to the nucleus, also known as plastid signalling, plays a key role in coordinating nuclear gene expression with the functional state of plastids. Inhibitors that cause plastid dysfunction have been suggested to generate specific plastid signals related to their modes of action. However, the molecules involved in plastid signalling remain to be identified. Genetic studies indicate that the plastid-localized pentatricopeptide repeat protein GUN1 mediates signalling under several plastid signalling-related conditions. To elucidate further the nature of plastid signals, investigations were carried out to determine whether different plastid signal-inducing treatments had similar effects on plastids and on nuclear gene expression. It is demonstrated that norflurazon and lincomycin treatments and the plastid protein import2-2 (ppi2-2) mutation, which causes a defect in plastid protein import, all resulted in similar changes at the gene expression level. Furthermore, it was observed that these three treatments resulted in defective RNA editing in plastids. This defect in RNA editing was not a secondary effect of down-regulation of pentatricopeptide repeat protein gene expression in the nucleus. The results indicate that these three treatments, which are known to induce plastid signals, affect RNA editing in plastids, suggesting an unprecedented link between plastid signalling and RNA editing