Singularity-free constraint on molecular dynamics beyond Lagrange multiplier

We propose a constraint algorithm of molecular dynamics (MD) in the case that the Lagrange multipliers would bring about singularity, such as the constraint of linear molecules. Present extension to allow for the singular constraints is readily implemented in MD programs, and demonstrates stable and efficient performance to treat various singular constraints during the MD simulation.     

Complete nucleotide sequence of the <Emphasis Type="Italic">Cryptomeria japonica</Emphasis>D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

Background  

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.     

Isolation of a novel platform bacterium for lignin valorization and its application in glucose-free cis,cis-muconate production

Journal of Industrial Microbiology & Biotechnology - Microbial production of cis,cis-muconate (ccMA) from phenolic compounds obtained by chemical depolymerization of lignin is a promising...     

The postnatal development of Masera's organ in the rat

Growth and fine-structural postnatal development of Masera'sorgan (MO) in the rat was studied. As with the olfactory epitheliumproper (OEP) on the nasal septum, the area covered by MO increasesduring the first 3 weeks of life. The rate of increase in areaof MO is the same as for the OEP on the nasal septum. Concomitantwith the increase in overall area of MO, the complexity of thefree neuroepithelial surface of MO increases. There is an increasein both the number of sensory cilia of receptor cells and microvilliof supporting cells. At 14 days and after sensory cilia arefurther characterized by the development of a thicker proximaland thinner distal part, and a parallel orientation at the freeepithelial surface. The transition zone between the respiratoryepithelium and the MO demonstrates additional developmentalfeatures during the first postnatal week. The results are suggestiveof incomplete development of MO at birth and ongoing morphologicalmaturation at least up to weaning. We conclude therefore thatMO is not vestigial but is functional beyond weaning.     

Structure and Methylation-Based Silencing of a Gene (DBCCR1) within a Candidate Bladder Cancer Tumor Suppressor Region at 9q32–q33

Loss of heterozygosity (LOH) on chromosome 9q is the most frequent genetic alteration in transitional cell carcinoma (TCC) of the bladder, indicating the presence of one or more relevant tumor suppressor genes. We previously mapped one of these putative tumor suppressor loci to 9q32–q33 and localized the candidate region within a single YAC 840 kb in size. This locus has been designatedDBC1(for deleted in bladder cancer gene 1). We have identified a novel gene,DBCCR1,in this candidate region by searching for expressed sequence tags (ESTs) that map to YACs spanning the region. Database searching using the entireDBCCR1cDNA sequence identified several human ESTs and a few homologous mouse ESTs. However, the predicted 761-amino-acid sequence had no significant homology to known protein sequences. Mutation analysis of the coding region and Southern blot analysis detected neither somatic mutations nor gross genetic alterations in primary TCCs. AlthoughDBCCR1was expressed in multiple normal human tissues including urothelium, mRNA expression was absent in 5 of 10 (50%) bladder cancer cell lines. Methylation analysis of the CpG island at the 5′ region of the gene and the induction ofde novoexpression by a demethylating agent indicated that this island might be a frequent target for hypermethylation and that hypermethylation-based silencing of the gene occurs in TCC. These findings makeDBCCR1a good candidate forDBC1.     

Enzymatic synthesis of β-D-Gal-(1→3)-[β-D-GlcNAc-(1→6)]-α-D-GalNAc-OC6H4NO2-p as a carbohydrate unit of mucin-type 2 core

We have established a synthetic method for obtaining β-D-Gal-(1→3)-[β-D-GlcNAc-(1→6)]-α-D-GalNAc-OC6H4NO2 -p (1), which is a carbohydrate unit of mucin-type 2 core. A β-N-acetyl-D-hexosaminidase from Nocardia orientalis catalyzed the synthesis of the desired compound 1 with its isomers β-D-GalNAc-(1→6)-β-D-Gal-(1→3)-α-D-GalNAc-OC6H4NO2-p (2) β-D-GlcNAc-(1→3)-β-D-Glc-(1→3)-α-D-GalNAc-OC6H4NO2-p (3) through N-acetylglucosaminyl transfer from N,N′-diacetylchitobiose and β-D-Gal-(1→3)-α-D-GalNAc-OC6H4NO2-p. The enzyme formed the trisaccharides 1, 2, and 3 in 14% overall yield based on β-D-Gal-(1→3)-α-D-GalNAc-OC6H4NO2-p as an acceptor substrate, and in the ratio of 44:32:24. In this way, N-acetylglucosaminyl transfer favored O-6 of the acceptor rather than O-6′, and occurred to a lesser extent at O-3′. This reaction was efficient enough to allow a one-pot preparation of the desired carbohydrate unit of mucin-type 2 core. When β-D-Gal-(1→3)-β-D-GalNAc-OC6H4NO2-p was used as an acceptor, the enzyme also synthesized three kinds of trisaccharides in the same regioselectivity with respect to O-6 and O-6′ versus O-3′ of the acceptor.     

Prehibernal insemination and short dispersal of Ceratina flavipes (Hymenoptera: Anthophidae) in northernmost Japan

Although females of Ceratina flavipes are believed to be inseminated in spring on Honshu Island, Japan, 100% of the females were inseminated before hibernation on Ishikari Coast, northernmost Japan. Because most, if not all, of the males also overwintered with the females, this prehibernal insemination may be a local event. In the hibernal season, females were more frequently alone in nests than males, whereas the sex ratio in their main habitat was almost 1:1, suggesting that prehibernal dispersal is more frequent in females, but that the dispersal distance is shorter than previously reported.     

Feeding of a benthic goby in a river where nektonic fishes are absent

The social structure and feeding behaviour of the benthic goby Rhinogobius sp. DA (dark type) were investigated in a small river in Shikoku, Japan, where nektonic fishes are absent. The gobies had overlapped home ranges but were often aggressive against conspecifics, especially of the same sex and similar body size. Their diet consisted mainly of aquatic invertebrates, but terrestrial invertebrates were also an important item. This contrasted with few terrestrial invertebrates in the diet of the conspecifics in an adjacent river harbouring a nektonic cyprinid fish. An increase in flow level greatly changed their feeding behaviour; on high flow days, a greater portion of the population appeared from the interstices of the bottom and more often rose into the water column to catch drift than on normal flow days. Plasticity of their feeding behaviour is discussed in terms of ecological release.