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As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at ∼58% compared with a peak at ∼42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at ∼42%, relatively low compared with that of protein-coding cDNAs.

Nitrification, a microbial process, is a key component and integral part of the nitrogen (N) cycle. Soil N is in a constant state of flux, moving and changing chemical forms. During nitrification, a relatively immobile N-form (NH + 4) is converted into highly mobile nitrate-N (NO − 3). The nitrate formed is susceptible to losses via leaching and conversion to gaseous forms via denitrification. Often less than 30% of the applied N fertilizer is recovered in intensive agricultural systems, largely due to losses associated with and following nitrification. Nitrogen-use efficiency (NUE) is defined as the biomass produced per unit of assimilated N and is a conservative function in most biological systems. A better alternative is to define NUE as the dry matter produced per unit N applied and strive for improvements in agronomic yields through N recovery. Suppressing nitrification along with its associated N losses is potentially a key part in any strategy to improve N recovery and agronomic NUE. In many mature N-limited ecosystems, nitrification is reduced to a relatively minor flux. In such systems there is a high degree of internal N cycling with minimal loss of N. In contrast, in most highproduction agricultural systems nitrification is a major process in N cycling with the resulting N losses and inefficiencies. This review presents the current state of knowledge on nitrification and associated N losses, and discusses strategies for controlling nitrification in agricultural systems. Limitations of the currently available nitrification inhibitors are highlighted. The concept of biological nitrification inhibition (BNI) is proposed for controlling nitrification in agricultural systems utilizing traits found in natural ecosystems. It is emphasized that suppression of nitrification in agricultural systems is a critical step required for improving agronomic NUE and maintaining environmental quality.

OH and CH stretching vibrations of bare phenol, phenol-(H2O)n clusters (n=1–4), and partially deuterated clusters in the S0 state were observed by using IR–UV double resonance and stimulated Raman-UV double resonance spectroscopies. Characteristic spectral features of the OH stretching vibrations of the phenol as well as of the H2O sites were observed, which are directly related to their structures. The cluster structures were investigated by comparing the observed spectra with the calculated ones obtained by the ab initio molecular orbital calculation with (self-consistent field) SCF 6-31G and SCF 6-31G* basis sets given by Watanabe and Iwata. It was found that for the clusters with n≥2, the isomer of ring form hydrogen-bonded structure is most stable and the simulated IR spectra based on the calculated structure showed good agreements with the observed ones. For a particular cluster, which was assigned as an isomer of the n=4 cluster, an anomalous IR spectrum was observed. Two forms of the isomer are proposed with respect to the structure of water moiety: (1) an ‘‘ice’’ structure and (2) an ‘‘ion-pair’’ structure. The relative IR absorption cross sections of each bands were also investigated for the clusters with n=1 to 4. It was found that the IR absorption cross section of the phenolic OH stretching vibration of the n=1 cluster increases by a factor of 6 compared to that of bare phenol and it further increases with the cluster size.

A whole-genome radiation hybrid (RH) panel was used to construct a high-resolution map of the rat genome based on microsatellite and gene markers. These include 3,019 new microsatellite markers described here for the first time and 1,714 microsatellite markers with known genetic locations, allowing comparison and integration of maps from different sources. A robust RH framework map containing 1,030 positions ordered with odds of at least 1,000:1 has been defined as a tool for mapping these markers, and for future RH mapping in the rat. More than 500 genes which have been mapped in mouse and/or human were localized with respect to the rat RH framework, allowing the construction of detailed rat-mouse and rat-human comparative maps and illustrating the power of the RH approach for comparative mapping.

Helicobacter pylori infection induces various gastroduodenal diseases. We examined the role of two genes, vacA and cagE, in the gastric pathogenesis induced by H. pylori using a long-term (62 wk) animal model. Reportedly, both genes are associated with the virulence of H. pylori: vacA encodes vacuolating cytotoxin, and cagE, with other genes in the cag pathogenicity islands, encodes a type IV secretion system. Mongolian gerbils were challenged in this study by a wild-type TN2 strain and its isogenic mutants of cagE or vacA. The wild-type and vacA mutants induced severe gastritis, whereas cagE mutants induced far milder changes. Gastric ulcer was induced at the highest rate (22/23) by the wild-type TN2, followed by the vacA mutant (19/28). No ulcer was found in the gerbils infected with the cagE mutant (0/27) or in controls (0/27). Intestinal metaplasia was also found in the gerbils infected with the wild-type (14/23) or vacA mutant (15/28). Gastric cancer developed in one gerbil with wild-type infection and in one with vacA mutant infection. In conclusion, the knocking out of the cagE gene deprived wild-type H. pylori of the pathogenicity for gastritis and gastric ulcer, suggesting that the secretion system encoded by cag pathogenicity island genes plays an essential role.

which contains the catalytic site of the enzyme. In order to better define the roles of these chitinase domains in chitin degradation, modified chi4 genes encoding various deletions of chitinase Al were constructed. The modified chiA genes were expressed in Escherichia coli, and the gene products were analyzed after purification by high-performance liquid chromatography. Intact chitinase Al specifically bound to chitin, while it did not show significant binding activity towards partially acetylated chitosan and other insoluble polysaccharides. Chitinases lacking the C-terminal domain lost much of this binding activity to chitin as well as colloidal chitin-hydrolyzing activity. Deletion of the type III domains, on the other hand, did not affect chitin-binding activity but did result in significantly decreased colloidal chitin-hydrolyzing activity. Hydrolysis of low-molecular-weight substrates, soluble high-molecular-weight substrates, and insoluble high-molecular-weight substrates to which chitinase Al does not bind were not significantly afected by these deletions. Thus, it was concluded that the C-terminal domain is a chitin-binding domain required for the specific binding to chitin and that this chitin-binding activity is important for efficient hydrolysis of the sufficiently acetylated chitin. Type HI modules are not directly involved in the chitin binding but play an important functional role in the hydrolysis of chitin by the enzyme bound to chitin.Various organisms, including bacteria, fungi, plants, and some vertebrates, produce chitinases, enzymes which hydrolyze the ,-1,4 linkage of chitin. Bacterial chitinases are thought to be important in the digestion of chitin for utilization as a carbon and energy source, and, from the ecological point of view, such chitinases serve an important role in recycling chitin in nature.Bacillus circulans WL-12 is one of the bacteria which excrete chitinases into culture media (28). The chitinase system of the bacterium includes at least six different chitinase molecules: chitinases Al, A2, Bi, B2, C, and D. Chitinase A2 is a derivative of Al and is generated by proteolytic modification; likewise, B2 is thought to be a derivative of Bi. Chitinase Al is assumed to be the key enzyme in the chitinase system, as it (and A2) is the most abundantly produced form as well as the enzyme with the highest colloidal chitin-hydrolyzing activity and very high affinity toward chitin. The gene encoding chitinase Al (chiA) and the one encoding chitinase D (chiD), which is located immediately upstream of the chiA gene, have been cloned and sequenced (27,29). Amino acid sequence analysis suggests that chitinase Al comprises at least three discrete functional domains; namely, a C-terminal domain, a region consisting of two type III modules (domains), and a large N-terminal domain. In previous reports, we showed that the type III modules of chitinase Al were related to those of fibronectin, a multifunctional extracellular and plasma protein of higher eukaryotes (29), and that glutamic acid 2...

Streptozotocin (STZ), a glucose analogue known to induce diabetes in experimental animals, causes DNA strand breaks and subsequent activation of poly(ADPribose) polymerase (Parp). Because Parp uses NAD as a substrate, extensive DNA damage will result in reduction of cellular NAD level. In fact, STZ induces NAD depletion and cell death in isolated pancreatic islets in vitro. Activation of Parp therefore is thought to play an important role in STZ-induced diabetes. In the present study, we established Parp-deficient (Parp ؊/؊ ) mice by disrupting Parp exon 1 by using the homologous recombination technique. These mice were used to examine the possible involvement of Parp in STZ-induced ␤-cell damage in vivo. The wild-type (Parp ؉/؉ ) mice showed significant increases in blood glucose concentration from 129 mg͞dl to 218, 370, 477, and 452 mg͞dl on experimental days 1, 7, 21, and 60, respectively, after a single injection of 180 mg STZ͞kg body weight. In contrast, the concentration of blood glucose in Parp ؊/؊ mice remained normal up to day 7, slightly increased on day 21, but returned to normal levels on day 60. STZ injection caused extensive necrosis in the islets of Parp ؉/؉ mice on day 1, with subsequent progressive islet atrophy and loss of functional ␤ cells from day 7. In contrast, the extent of islet ␤-cell death and dysfunction was markedly less in Parp ؊/؊ mice. Our findings clearly implicate Parp activation in islet ␤-cell damage and glucose intolerance induced by STZ in vivo.Various types of DNA damage produced by many environmental chemicals or reactive oxygen species generated by inflammatory reactions contribute to insulin-dependent diabetes mellitus (IDDM) through the induction of ␤-cell death in pancreatic islets (1-3). Acute exposure to streptozotocin [2-deoxy-2-(3-methyl-3-nitrosourea)l-D-glucopyranose, STZ] induces massive ␤-cell death and diabetes mellitus in experimental animals (4, 5). STZ also causes a rapid depletion of cellular NAD in islets (6-9), but this depletion is prevented by injection of nicotinamide immediately before or soon after the administration of STZ (10). Okamoto and colleagues (2, 11) demonstrated that STZ induces DNA strand breaks and activation of poly(ADP-ribose) polymerase (Parp) with subsequent reduction of NAD levels in the isolated pancreatic islets in vitro. These findings suggest the involvement of Parp as a key molecule in STZ-induced ␤-cell death and diabetes through extensive poly(ADP-ribose) formation and NAD depletion, leading to reduction of ATP level and cell death. In agreement with this hypothesis, Parp inhibitors such as 3-aminobenzamide or nicotinamide prevent the depletion of NAD and induction of STZ-induced ␤-cell death (12, 13). However, because Parp inhibitors possess other effects, such as scavenging hydrogen peroxide (14), it is not clear whether and how Parp activity contributes to ␤-cell death and the development of diabetes in vivo. Thus, engineering of a Parp-deficient animal model would be useful for investigating the role of Parp in S...