Statistical and integrative approach for constructing biological network maps

A goal of systems biology is to build a concrete biochemical network map, which provides an important instruction to trace the pathways of interest or to understand the mechanism of a biological system. In the postgenomic era, not only the concrete biochemical maps, but also postgenomic maps (mRNA coexpression and protein-protein interaction networks) have been extensively produced. In the biochemical map, the individual reactions are reliable, but the number of the reactions is limited, because molecular biology requires extensive experiments to verify them. By contrast, postgenomic data provide much information regarding interactions, but are coarse-grained. To expand the biochemical network, an intuitional approach, which superposes postgenomic data on the map one by one, has been carried out, but it is not effective when a large amount of the coarse-grained data is handled. In order to effectively integrate such postgenomic interactions into a biochemical map, a statistical approach would be suitable rather than intuition. In this article, we proposed a novel statistical approach that integrates postgenomic interaction networks into the biochemical network, predicting novel pathways. A statistical correlation for such different types of networks identifies functional modules; subsequently the superposition of the different networks on the functional modules predicts inter-modular relations, which are the key pathways to construct a large-scale biochemical network.     

Protodioscin isolated from fenugreek (Trigonella foenumgraecum L.) induces cell death and morphological change indicative of apoptosis in leukemic cell line H-60, but not in gastric cancer cell line KATO III

Protodioscin (PD) was purified from fenugreek (Trigonella foenumgraecum L.) and identified by Mass, and 1H- and 13C-NMR. The effects of PD on cell viability in human leukemia HL-60 and human stomach cancer KATO III cells were investigated. PD displayed strong growth inhibitory effect against HL-60 cells, but weak growth inhibitory effect on KATO III cells. Morphological change showing apoptotic bodies was observed in the HL-60 cells treated with PD, but not in KATO III cells treated with PD. Flow cytometric analysis showed that the hypodiploid nuclei of HL-60 cells were increased to 75.2, 96.3, and 100% after a 3-day treatment with 2.5, 5, and 10 microM PD, respectively. The fragmentation by PD of DNA to oligonucleosomal-sized fragments, that is a characteristic of apoptosis, was observed to be both concentration- and time-dependent in the HL-60 cells. These findings suggest that growth inhibition by PD of HL-60 cells results from the induction of apoptosis by this compound in HL-60 cells.     

Modified Dynabeads method for enumerating CD4+ T-lymphocyte count for widespread use in resource-limited situations

The Dynabeads method showed the potential for enumerating CD4 T lymphocytes (CD4 count) in HIV-1-infected individuals. The large volume of Dynabeads required for 1 sample and complex procedure made the method expensive and not easy for use, however. To decrease the cost and simplify the procedure, we reduced the volume of the Dynabeads, added wash times, and skipped over the staining step so as to count the CD4 cells directly under an optical microscope. The CD4 count of 246 blood samples using our modified Dynabeads method (DynabeadsCD4) showed a significant correlation with that obtained by flow cytometry (FlowcytoCD4) (r = 0.91 [P < 0.0001]; slope = 1.03, intercept = -16). The sensitivity and specificity for a CD4 count less than 200 cells/microL were 79% and 94%, and for a CD4 count less than 350 cells/microL, the sensitivity and specificity were 95% and 88%, respectively. The positive and negative predictive values for a CD4 count less than 350 cells/microL were 97% and 83%, respectively. The systematic error was 8 cells/microL (95% confidence interval [CI]: 0.4-16). The cost of Dynabeads for 1 sample was less than $1.00; thus, the estimated cost per DynabeadsCD4 test is less than $3.00, including the cost of other disposable materials. Our modified method is simple, economic, and accurate enough to monitor antiretroviral therapy in resource-limited situations.     

Morphometric difference in the human maxillary nerve fibers between dentulous and edentulous jaw subjects

This study was conducted to quantify the change in the number and size of myelinated nerve fibers of the maxillary nerve with tooth loss in humans. We carried out a morphometric analysis to compare the number and size of myelinated nerve fibers in the human maxillary nerve between four dentulous and four edentulous jaw cases. Our results indicated that the number of axons decreased by approximately 13,000 with tooth loss. The average size of axons remained unchanged, but there was a change in the fiber size distribution, namely the loss of a large number of small-sized axons was accompanied by the total disappearance of small number of large-sized axons.     

Rapid and efficient generation of lentivirally gene-modified dendritic cells from DC progenitors with bone marrow stromal cells

Since dendritic cells (DC) play pivotal roles in both innate and adaptive immunity, DC can be a good target for immuno-gene therapy. However, the optimal generation method for gene-modified DC has not yet been well exploited. CD34+ cells from cord blood (CB), bone marrow (BM), or peripheral blood (PB) were expanded in a medium containing stem cell factor (SCF), flt 3 ligand (Flt3L) and thrombopoietin (TPO) with or without HESS-5, a murine BM stromal cell line, for 2 weeks (the first expansion step), then differentiated to DC in a medium containing granulocyte-macrophage colony-stimulating factor (GM-CSF), flt 3 ligand (Flt3L), stem cell factor (SCF), tumor necrosis factor-alpha (TNF-alpha), IL-4, and lipopolysaccharide (LPS) for 9 days (the second differentiation step). DC progenitors were transduced with human immunodeficiency virus (HIV) vectors at different time points during the second step. Use of HESS-5 during the first step resulted in more DC generation than without it (cell expansion: CB, 10,461 vs. 354-fold; BM, 962 vs. 225-fold; peripheral blood mononuclear cell (PBMC), 8,506 vs. 240-fold; %DC: CB, 83.4% vs. 76.9%; BM, 83.6 vs. 69.8%; PBMC, 85.9 vs. 60.5%). Gene transduction to the in vitro expanded DC progenitors at day 3 during the second step, resulted in better final yield of the gene-modified DC than that to those at day 0 or day 6 (as much as 44% of DC expressed green fluorescence protein (GFP) as a transgene) and the transduction efficiency correlated with endocytic ability and percent of S phase. DC transduced with an HIV vector encoding a melanoma antigen, MART-1, were adequately recognized by specific anti-MART-1 CTL. The two-step culture method with HESS-5 is useful for rapid expansion of DC progenitors and subsequent lentiviral gene transduction to DC.     

Seasonal variation in sweating responses of older and younger men

Eight older (60–65 years) and six younger (20–25 years) men were exposed to a standard heat stress for 60 min in summer, autumn, winter, and spring. The test consisted of placing the lower legs and feet in a 42°C water bath while sitting in constant environmental conditions (30°C and 45% relative humidity). The increase of rectal temperature (T _re) was significantly greater (P < 0.05) in autumn, winter, and spring than in summer for the older group, but significantly greater only in winter than in summer for the younger group (P < 0.05). The T _re was greater for the older group in all seasons, but of significance only in autumn and spring (P < 0.01). There were no significant season-related differences for metabolic heat production (m) and mean skin temperature ( _sk) during the heat test in the respective groups, although the m and _sk were lower for the older group in all seasons (P < 0.01). In the older group total body sweating rate (m_sw) divided by T _re (total m_sw/T _re) decreased from summer to winter (P < 0.02) and did not differ between winter and spring, whereas total m_sw/T _re in the younger group increased in spring after decreasing from autumn to winter (P < 0.03). The variations of the value, local sweating rate on the back and thigh divided by T _re (back m_sw/T _re and thigh m_sw/T _re), were similar to those of the total m_sw/T _re in each group, except for back m_sw/T _re in the younger group, which did not increase from winter to spring. The total m_sw/T _re, back m_sw/T _re and thigh m_sw/T _re were significantly less for the older group in summer, autumn and spring (P < 0.05). The range of seasonal variations was significantly less for the older group (P < 0.001). The results indicated that, compared with younger men in older men, the enhancement of sweating function toward summer occurred later and its reduction toward winter occurred earlier despite a smaller range of seasonal variation and that older men had a somewhat lesser capability to maintainT _re when challenged by heat stress in all seasons.     

Effect of alkyl groups on the rate constants of propagation and termination in the radical polymerization of dialkyl itaconates

Polymerization of dialkyl itaconates with dimethyl azoisobutyrate ( 5 ) was studied in benzene at 50°C by means of electron spin resonance (ESR). The monomers used are dimethyl ( 1 ), diethyl ( 2 ), dibutyl ( 3 ) and di-2-ethylhexyl ( 4 ) itaconates. All the polymerization systems involve ESR-observable propagating polymer radicals under the actual polymerization conditions. The polymerization rate (R_p) and degree of polymerization of the resulting polymer increase in going from shorter to longer alkyl groups. The ESR-determined rate constants of propagation (k_p) and termination (k_t) decrease as the alkyl chain becomes longer. k_p of 1 is 3,3 times higher than that of 4 , while k_t of 1 is 590 times higher than that of 4 . Thus, the steric effect due to the alkyl group suppresses much more termination than propagation, leading to the fact that R_p increases as the alkyl group becomes larger.     

Identification of a large novel imprinted gene cluster on mouse proximal chromosome 6

Mice with maternal duplication of proximal chromosome 6 die in utero at an early embryonic stage. Recently, two imprinted genes, paternally expressed Sgce and maternally expressed Asb4, were identified in this region. This report analyzes the imprinting status of genes within a 1-Mb region containing these two genes. Peg10, which is next to Sgce, shows complete paternal expression, like Sgce. Conversely, Neurabin, Pon2, and Pon3 show preferential maternal expression at embryonic stages, although they all show biallelic expression in neonatal tissues. These results demonstrate that there is a large novel imprinted gene cluster in this region. 5'-RACE (Rapid Amplification of cDNA Ends) analysis of Peg10 revealed the existence of a novel first exon separate from the second exon, which encoded two putative ORFs similar to the viral Gag and Pol proteins. A differentially methylated region established in sperm and eggs is located just within the region containing the two first exons of Peg10 and Sgce, and may play an important role in regulating the two paternally expressed genes: Peg10 and Sgce.     

Pulmonary metastases from a low-grade endometrial stromal sarcoma confirmed by chromosome aberration and fluorescence in-situ hybridization approaches: a case of recurrence 13 years after hysterectomy

Pulmonary metastasis from low-grade endometrial stromal sarcomas (ESSs) occasionally are found after long, disease-free periods, mostly as incidental histological or radiological discoveries. We describe a case of low-grade ESS presenting as nodular pulmonary metastases finally diagnosed by estrogen-receptor staining, cytogenetic and fluorescence in situ hybridization (FISH) analyses, and perusal of the histology of hysterectomy material. An abnormal nodule in the lung field was discovered by means of chest X-ray of a 47-year-old woman. She had been disease free for 13 years after hysterectomy for an alleged leiomyoma. A computed tomographic scan revealed nodules, with fluctuation in size over the 2-year period, in both lungs. Finally the lesion in the left lung was resected, and pulmonary endometriosis was suspected because of the lack of stromal cell nuclear atypia and positive immunohistochemical reactions for estrogen and progesterone receptors. However, a characteristic karyotype was identified cytogenetically: 46, XX, t(7;17)(p15;q11), the translocation of which, specific to ESS, was confirmed by FISH analysis. A final diagnosis of pulmonary metastases from an ESS could be made by reviewing the histology of the previous uterine tumor. In this case, metastatic lesions from an ESS showed a decrease as well as an increase in size, despite the malignant potential. Immunostaining for estrogen and progesterone receptors and cytogenetic and FISH analyses, together with clinical information on the past gynecological history, are valuable diagnostic keys.