Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functional characteristics, HFL22w was studied by generating expressed sequence tags (ESTs) and by analyzing the compiled expression profiles of liver at different developmental stages. A total of 13,077 ESTs were sequenced from a 3′-directed cDNA library of HFL22w, and classified as follows: 5819 (44.5%) matched to known genes; 5460 (41.8%) exhibited no significant homology to known genes; and the remaining 1798 (13.7%) were genomic sequences of unknown function, mitochondrial genomic sequences, or repetitive sequences. Integration of ESTs of known human genes generated a profile including 1660 genes that could be divided into 15 gene categories according to their functions. Genes related to general housekeeping, ESTs associated with hematopoiesis, and liver-specific genes were highly expressed. Genes for signal transduction and those associated with diseases, abnormalities, or transcription regulation were also noticeably active. By comparing the expression profiles, we identified six gene groups that were associated with different developmental stages of human fetal liver, tumorigenesis, different physiological functions of Itoh cells against the other types of hepatic cells, and fetal hematopoiesis. The gene expression profile therefore reflected the unique functional characteristics of HFL22w remarkably. Meanwhile, 110 full-length cDNAs of novel genes were cloned and sequenced. These novel genes might contribute to our understanding of the unique functional characteristics of the human fetal liver at 22 wk

High-throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale-free and high-degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small-world property with similar diameter at 4-5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of "systems biology".

Cytokines are of central importance in the regulation of hematopoiesis, immunity, inflammation, tissue remodeling, and embryonic development. Cytokine research is expected to provide the key to pharmacological manipulation of the immune response and commands the attention of a massive and highly focused biotechnology industry. Based upon the hypothetical secondary and tertiary structures, a superfamily of growth hormone (GH)-like cytokine was identified previously. Here, we report the phylogeny of this superfamily based upon 3D structural data from the Protein Data Bank. First, a retrieving program is designed to abstract their secondary structures and associated atomic coordinates. Helices, digitized as vectors in the Cartesian coordinate system, are collected from the retrieved atomic coordinates at the alpha carbons of the protein backbone. Then the scalar value and vector angle against the reference vector, usually the first vector, are calculated. Furthermore, cluster analysis among various cytokines is performed on their helical scales and helical angles. As a result, GH is close to the cluster formed by ciliary neurotrophic factor and granulocyte colony-stimulating factor (CSF); leptin and erythropoietin are in descending order close to the cluster formed by interleukin (IL)-6 and IL-10; the former seven members in the two subgroups above join together and form one group with leukemia inhibitory factor; granulocyte-macrophage CSF, IL-2, IL-4, and IL-5 are in descending order close to the cluster formed by IL-3 and macrophage CSF; and the latter six members form another group. Finally, it is demonstrated that the phylogeny of GH-like cytokines above is consistent with the evolutionary relationship of their gene organization, gene localization, receptor module composition, and receptor module compatibility.

ErrataProtein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustness Dong Li et al., vol. 6, issue 2,

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