Formalin-fixed archival samples are known to be poor materials for molecular biological applications. We conducted a series of experiments to understand the alterations in RNA in fixed tissue. We found that formalin-fixed tissue was resistant to solubilization by chaotropic agents. However, proteinase K completely solubilized the fixed tissue and enabled the extraction of almost the same amount of RNA as from a fresh sample. The extracted RNA did not show apparent degradation. However, as reported, successful PCR amplification was limited to short targets. The nature of such 'fixed' RNA was analyzed using synthetic homo-oligo RNAs. The heterogeneous increase in molecular weight of the RNAs, measured by MALDI-TOF mass spectrometry, showed that all four bases showed addition of mono-methylol (-CH(2)OH) groups at various rates. The modification rate varied from 40% for adenine to 4% for uracil. In addition, some adenines underwent dimerization through methylene bridging. The majority of the methylol groups, however, could be removed from bases by simply elevating the temperature in formalin-free buffer. This demodification proved effective in restoring the template activity of RNA from fixed tissue. The improvement in PCR results suggested that more than half of the modification was removed by this demodification.

BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a 3D whole-body model for an adult human male. It encompasses morphological and geometrical knowledge in anatomy and complements ontological representation. Moreover, BodyParts3D introduces a universal coordinate system in human anatomy, which may facilitate management of samples and data in biomedical research and clinical practice. As of today, 382 anatomical concepts, sufficient for mapping materials in most molecular medicine experiments, have been specified. Expansion of the dictionary by adding further segments and details to the whole-body model will continue in collaboration with clinical researchers until sufficient resolution and accuracy for most clinical application are achieved. BodyParts3D is accessible at: http://lifesciencedb.jp/ag/bp3d/.

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Olig family is a novel sub-family of basic helix-loop-helix transcription factors recently identified. Olig1 and Olig2 were first reported to promote oligodendrocyte differentiation, and later Olig2 was reported to be involved in motoneuron specification as well. Olig3 was isolated as a third member of Olig family, but its precise expression pattern is poorly understood. Here, we describe detailed Olig3 expression analyses in the neural tube of embryonic mice. Olig3 was first detected in the dorsal neural tube from the midbrain/hindbrain boundary to the spinal cord. In E11.5 spinal cord, Olig3 was transiently expressed in the lateral margin of the subventricular zone as three ventral clusters at the level of the p3, p2 and p0 domains, as well as in the dorsal neural tube. Olig3 was co-expressed with Nkx2.2 in the lateral margin of the p3 domain. In forebrain, Olig3 was expressed in the dorsal thalamus while Olig2 was complementarily expressed in the ventral thalamus with an adjacent boundary at E12.5. Olig3 is specifically and transiently expressed in different types of progenitors of embryonic central nervous system and then disappears in the course of development.

High endothelial venule (HEV) cells support lymphocyte migration from the peripheral blood into secondary lymphoid tissues. Using gene expression profiling of mucosal addressin cell adhesion molecule-1+ mesenteric lymph node HEV cells by quantitative 3′-cDNA collection, we have identified a leucine-rich protein, named leucine-rich HEV glycoprotein (LRHG) that is selectively expressed in these cells. Northern blot analysis revealed that LRHG mRNA is ∼1.3 kb and is expressed in lymph nodes, liver, and heart. In situ hybridization analysis demonstrated that the mRNA expression in lymph nodes is strictly restricted to the HEV cells, and immunofluorescence analysis with polyclonal Abs against LRHG indicated that the LRHG protein is localized mainly to HEV cells and possibly to some lymphoid cells surrounding the HEVs. LRHG cDNA encodes a 342-aa protein containing 8 tandem leucine-rich repeats of 24 aa each and has high homology to human leucine-rich α2-glycoprotein. Similar to some other leucine-rich repeat protein family members, LRHG can bind extracellular matrix proteins that are expressed on the basal lamina of HEVs, such as fibronectin, collagen IV, and laminin. In addition, LRHG binds TGF-β. These results suggest that LRHG is likely to be multifunctional in that it may capture TGF-β and/or other related humoral factors to modulate cell adhesion locally and may also be involved in the adhesion of HEV cells to the surrounding basal lamina.