A ternary complex model of Sirtuin4-NAD+-Glutamate dehydrogenase

Sirtuin4 (Sirt4) is one of the mammalian homologues of Silent information regulator 2 (Sir2), which promotes the longevity of yeast, C. elegans, fruit flies and mice. Sirt4 is localized in the mitochondria, where it contributes to preventing the development of cancers and ischemic heart disease through regulating energy metabolism. The ADP-ribosylation of glutamate dehydrogenase (GDH), which is catalyzed by Sirt4, downregulates the TCA cycle. However, this reaction mechanism is obscure, because the structure of Sirt4 is unknown. We here constructed structural models of Sirt4 by homology modeling and threading, and docked nicotinamide adenine dinucleotide+ (NAD+) to Sirt4. In addition, a partial GDH structure was docked to the Sirt4-NAD+ complex model. In the ternary complex model of Sirt4-NAD+-GDH, the acetylated lysine 171 of GDH is located close to NAD+. This suggests a possible mechanism underlying the ADP-ribosylation at cysteine 172, which may occur through a transient intermediate with ADP-ribosylation at the acetylated lysine 171. These results may be useful in designing drugs for the treatment of cancers and ischemic heart disease

Multi-Layer Distributed Storage of LHD Plasma Diagnostic Database

At the end of LHD experimental campaign in 2003, the amount of whole plasma diagnostics raw data had reached 3.16 GB in a long-pulse experiment. This is a new world record in fusion plasma experiments, far beyond the previous value of 1.5 GB/shot. The total size of the LHD diagnostic data is about 21.6 TB for the whole six years of experiments, and it continues to grow at an increasing rate. The LHD diagnostic database and storage system, i.e. the LABCOM system, has a completely distributed architecture to be sufficiently flexible and easily expandable to maintain integrity of the total amount of data. It has three categories of the storage layer: OODBMS volumes in data acquisition servers, RAID servers, and mass storage systems, such as MO jukeboxes and DVD-R changers. These are equally accessible through the network. By data migration between them, they can be considered a virtual OODB extension area. Their data contents have been listed in a “facilitator” PostgreSQL RDBMS, which now contains about 6.2 million entries, and informs the optimized priority to clients requesting data. Using the “glib” compression for all of the binary data and applying the three-tier application model for the OODB data transfer/retrieval, an optimized OODB read-out rate of 1.7 MB/s and effective client access speed of 3?25 MB/s have been achieved. As a result, the LABCOM data system has succeeded in combination of the use of RDBMS, OODBMS, RAID, and MSS to enable a virtual and always expandable storage volume, simultaneously with rapid data access

Transmembrane proteins of tight junctions

AbstractTight junctions contribute to the paracellular barrier, the fence dividing plasma membranes, and signal transduction, acting as a multifunctional complex in vertebrate epithelial and endothelial cells. The identification and characterization of the transmembrane proteins of tight junctions, claudins, junctional adhesion molecules (JAMs), occludin and tricellulin, have led to insights into the molecular nature of tight junctions. We provide an overview of recent progress in studies on these proteins and highlight their roles and regulation, as well as their functional significance in human diseases

Proton transfer pathway in anion channelrhodopsin-1

Anion channelrhodopsin from Guillardia theta (GtACR1) has Asp234 (3.2 angstrom) and Glu68 (5.3 angstrom) near the protonated Schiff base. Here, we investigate mutant GtACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths was also analyzed using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shorten and lengthen the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild-type GtACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients toward the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism

Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift

The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named 'schizorhodopsin (SzR)' has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, pK(a)=12.3) is stabilised by the deprotonated counterion (presumably Asp184, pK(a)=3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral 'blue-shift' due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift

Aquaporin 4 Expression in the mdx Mouse Diaphragm

Expression of aquaporin (AQP) 4 in the surface membranes of skeletal myofibers is well established; however, its functional significance is still unknown. The alterations of AQP4 expressions in dystrophic muscles at RNA and protein levels have been reported in various dystrophic muscles such as dystrophinopathy, dysferlinopathy, and sarcoglycanopathy. We are interested in the relationship between the severity of dystrophic muscle degeneration and the expression of AQP4. Here we compared the AQP4 expression of the limb muscles with that of diaphragms in both mdx and control mice. The dystrophic muscle degeneration, such as rounding profile of cross sectional myofiber shape, dense eosin staining, central nuclei, and endomysial fibrosis in mdx mice, were more marked in diaphragms than in limb muscles. The decrease of AQP4 expression at protein level was more marked in diaphragms than in the limb muscles of mdx mice. However, the expression of AQP4 mRNA in the diaphragms of mdx mice was not reduced in comparison with limb muscles of mdx mice. The present study revealed that AQP4 expression at protein level was correlated with the severity of dystrophic changes in muscle tissues of mdx mice

Sperm allocation in relation to female size in a semelparous salmonid

To maximize reproductive success, males have to adaptively tailor their sperm expenditure in relation to the quality of potential mates because they require time to replenish their sperm supply for subsequent mating opportunities. Therefore, in mating contexts where males must choose among females in a short period of time, as is the case with semelparous species (which die after one intensely competitive short duration breeding season), selection on sperm allocation can be expected to be a powerful selective agent that shapes the male reproductive success. We quantitatively investigated sperm allocation patterns in chum salmon in relation to perceived female quality by developing a novel method for determining the amount of sperm allocated per ejaculate during spawning bouts. We examined the relationship between sperm expenditure and the body size of paired females (a proxy of egg number and egg quality) in the absence of male–male competition in an experimental channel. The estimated amount of sperm released per spawning event was positively correlated with the size of paired females. However, the number of spawning events a female participated in, which reduces the number of eggs she spawns in each subsequent bout, did not affect this relationship. These results provide support for predictions arising from the sperm allocation hypothesis, male salmon do economize their sperm expenditure in accordance with paired female body size as predicted for their first spawning event, but males overestimate or are unable to assess the quality of females beyond size and provide more sperm than they should in theory when paired with a female that spawned previously. Overall, the observed sperm allocation pattern in chum salmon appears to be adapted to maximize reproductive success assuming female size is an honest indicator of quality, although temporal changes in a female\u27s quality during a reproductive season should be considered when examining sperm allocation strategies

Nonstop Lose-Less Data Acquisition and Storing Method for Plasma Motion Images

Plasma diagnostic data analysis often requires the original raw data as they are, in other words, at the same frame rate and resolution of the CCD camera sensor. As a non-interlace VGA camera typically generates over 70 MB/s video stream, usual frame grabber cards apply the lossy compression encoder, such as mpeg-1/-2 or mpeg-4, to drastically lessen the bit rate. In this study, a new approach, which makes it possible to acquire and store such the wideband video stream without any quality reduction, has been successfully achieved. Simultaneously, the real-time video streaming is even possible at the original frame rate. For minimising the exclusive access time in every data storing, it has adopted the directory structure to hold every frame files separately, instead of one long consecutive file. The popular ‘zip’ archive method improves the portability of data files, however, the JPEG-LS image compression is applied inside by replacing its intrinsic deflate/inflate algorithm that has less performances for image data