Multi-organ, multi-lineage engraftment by a single bone marrow-derived stem cell

Purification of rare hematopoietic stem cell(s) (HSC) to homogeneity is required to study their self-renewal, differentiation, phenotype, and homing. Long-term repopulation (LTR) of irradiated hosts and serial transplantation to secondary hosts represent the gold standard for demonstrating self-renewal and differentiation, the defining properties of HSC. We show that rare cells that home to bone marrow can LTR primary and secondary recipients. During the homing, CD34 and SCA-1 expression increases uniquely on cells that home to marrow. These adult bone marrow cells have tremendous differentiative capacity as they can also differentiate into epithelial cells of the liver, lung, GI tract, and skin. This finding may contribute to clinical treatment of genetic disease or tissue repair.     

Allometry and biomass of Korean pine (Pinus koraiensis) in central Korea

Aboveground tree biomass of Korean pine (Pinus koraiensis Sieb. et Zucc.) was determined for a natural forest of Korean pine and mixed deciduous trees and seven age classes of plantation forests in central Korea. Regression analyses of the dry weights of stem wood, stem bark, branches, and needles versus diameter at breast height were used to calculate regression equations of the form of log Y = a + b log X. Biomass of Korean pine in the mixed forest was 118 Mg ha(-1), and biomass in the plantations was linearly related to stand age, ranging from 52.3 Mg ha(-1) in 11 to 20-year-old stands to 317.9 Mg ha(-1) in 71 to 80-year-old stands. The proportions of stem wood and stem bark in the total aboveground biomass decreased with stand age while those of branch and needle increased. Specific leaf area of Korean pine ranging from 35.2 to 52.1 cm2 g(-1) was significantly different among crown positions and needle ages; in general, lower crown position and current needles had the greatest surface area per unit dry weight.     

Suppression of ceramide-induced cell death by hepatitis C virus core protein

The hepatitis C virus (HCV) core protein is believed to be one of viral proteins that are capable of preventing virus-infected cell death upon various stimuli. But, the effect of the HCV core protein on apoptosis that is induced by various stimuli is contradictory. We examined the possibility that the HCV core protein affects the ceramide-induced cell death in cells expressing the HCV core protein through the sphingomyelin pathway. Cell death that is induced by C(2)-ceramide and bacterial sphingomyelinase was analyzed in 293 cells that constitutively expressed the HCV core protein and compared with 293 cells that were stably transfected only with the expression vector. The HCV core protein inhibited the cell death that was induced by these reagents. The protective effects of the HCV core protein on ceramide-induced cell death were reflected by the reduced expression of p21(WAF1/Cip1/Sid1) and the sustained expression of the Bcl-2 protein in the HCV core-expressing cells with respect to the vector-transfected cells. These results suggest that the HCV core protein in 293 cells plays a role in the modulation of the apoptotic response that is induced by ceramide. Also, the ability of the HCV core protein to suppress apoptosis might have important implications in understanding the pathogenesis of the HCV infection.     

From proteomics toward systems biology: integration of different types of proteomics data into network models

Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.     

Reconstruction of methanol and formate metabolic pathway in non-native host for biosynthesis of chemicals and biofuels

One-carbon feedstock such as methanol and formate has attracted much attention as carbon substrate of industrial biotechnology for production of value-added chemicals and biofuels. Productivity improvement of natural one-carbon metabolic pathways in native hosts such as methanotrophs is somewhat difficult due to inefficient genetic tools and low specific growth rate. As an alternative, metabolic engineering can create new and efficient metabolic pathways of one-carbon substrate that can be readily transferred to non-native hosts. In this paper, recent progresses in protein and metabolic engineering for creation of methanol and formate-utilizing synthetic pathways based on RuMP cycle and formolase are reviewed. Perspectives on one-carbon metabolic pathway engineering in non-native host are also discussed.     

Crystal structure of CelM2, a bifunctional glucanase-xylanase protein from a metagenome library

Degradation of polysaccharides by cellulases and xylanases plays an important role in the carbon cycle, but only occurs in plant cell walls, a few bacteria and some animals. This process is also critical in processes such as biomass degradation and fuel production in the conversion cycles of cellulosic biomass. The enzyme CelM2 is bifunctional, because it is able to effectively hydrolyze barley glucan and xylan. Here, we show the crystal structure of the bifunctional enzyme CelM2, isolated from a metagenome library, and describe the sequence information and structure of its two domains. We believe that CelM2 is attractive as an industrial enzyme and that the structural results presented herein provide insights that are relevant to the genetic engineering of multifunctional enzymes.     

Decolorization of azo dye using PVA-immobilized microorganisms

A microbial consortium having a high capacity for rapid decolorization of azo dye (RED RBN) was immobilized by a phosphorylated polyvinyl alcohol (PVA) gel. The immobilized-cell beads exhibited a color removal capability of 75%, even at a high concentration of RED RBN (500 mg l(-1)) within 12 h using flask culture. The continuous operation was conducted at a hydraulic retention time (HRT) of 5-20 h in which the dye loading rate ranged from 240 to 60 mg dye h(-1). A removal efficiency exceeding 90% was obtained at the HRT higher than 10 h. No recognizable destruction of bead appearance was observed in the 6-month operation. Examination of the mechanism of the decolorization process by cell beads indicated that it proceeded primarily by biological decolorization associated with partial adsorption of the dye onto the entrapped cells and gel matrix. Microscopic observation revealed that the microbial consortium contained in the gel beads was at least made up of three kinds of bacterial species. From the economical viewpoint, alternative cheaper nitrogen sources such as fish meal, soybean meal, pharmamedia and vita yeast powder were examined.     

Novel recombinant human lactoferrin: Differential activation of oxidative stress related gene expression

Lactoferrin, an iron-binding protein found in high concentrations in mammalian exocrine secretions, is an important component of the host defense system. It is also a major protein of the secondary granules of neutrophils from which is released upon activation. Due to its potential clinical utility, recombinant human lactoferrin (rhLF) has been produced in various eukaryotic expression systems; however, none of these are fully compatible with humans. Most of the biopharmaceuticals approved by the FDA for use in humans are produced in mammalian expression systems. The Chinese hamster ovary cells (CHO) have become the system of choice for proteins that require post-translational modifications, such as glycoproteins.     

Overexpression of ATP Sulfurylase in Indian Mustard Leads to Increased Selenate Uptake, Reduction, and Tolerance

In earlier studies, the assimilation of selenate by plants appeared to be limited by its reduction, a step that is thought to be mediated by ATP sulfurylase. Here, the Arabidopsis APS1 gene, encoding a plastidic ATP sulfurylase, was constitutively overexpressed in Indian mustard (Brassica juncea). Compared with that in untransformed plants, the ATP sulfurylase activity was 2- to 2.5-fold higher in shoots and roots of transgenic seedlings, and 1.5- to 2-fold higher in shoots but not roots of selenate-supplied mature ATP-sulfurylase-overexpressing (APS) plants. The APS plants showed increased selenate reduction: x-ray absorption spectroscopy showed that root and shoot tissues of mature APS plants contained mostly organic Se (possibly selenomethionine), whereas wild-type plants accumulated selenate. The APS plants were not able to reduce selenate when shoots were removed immediately before selenate was supplied. In addition, Se accumulation in APS plants was 2- to 3-fold higher in shoots and 1.5-fold higher in roots compared with wild-type plants, and Se tolerance was higher in both seedlings and mature APS plants. These studies show that ATP sulfurylase not only mediates selenate reduction in plants, but is also rate limiting for selenate uptake and assimilation.     

Pretreatment efficiency and structural characterization of rice straw by an integrated process of dilute-acid and steam explosion for bioethanol production

The combined pretreatment of rice straw using dilute-acid and steam explosion followed by enzymatic hydrolysis was investigated and compared with acid-catalyzed steam explosion pretreatment. In addition to measuring the chemical composition, including glucan, xylan and lignin content, changes in rice straw features after pretreatment were investigated in terms of the straw's physical properties. These properties included crystallinity, surface area, mean particle size and scanning electron microscopy imagery. The effect of acid concentration on the acid-catalyzed steam explosion was studied in a range between 1% and 15% acid at 180°C for 2 min. We also investigated the influence of the residence time of the steam explosion in the combined pretreatment and the optimum conditions for the dilute-acid hydrolysis step in order to develop an integrated process for the dilute-acid and steam explosion. The optimum operational conditions for the first dilute-acid hydrolysis step were determined to be 165°C for 2 min with 2% H(2)SO(4) and for the second steam explosion step was to be carried out at 180°C for 20 min; this gave the most favorable combination in terms of an integrated process. We found that rice straw pretreated by the dilute-acid/steam explosions had a higher xylose yield, a lower level of inhibitor in the hydrolysate and a greater degree of enzymatic hydrolysis; this resulted in a 1.5-fold increase in the overall sugar yield when compared to the acid-catalyzed steam explosion.