Profiling the metatranscriptome of the protistan community in Coptotermes formosanus with emphasis on the lignocellulolytic system.

The symbiotic protists in the hindgut of lower termites are critical for lignocellulose decomposition. Due to the unculturability of these protists, information on lignocellulases and their abundance within the gut is unavailable. The advent of high-throughput sequencing technologies enables an investigation of the gene expression profile in this community without culturing these organisms. Here, we carried out 454 pyrosequencing to profile the metatranscriptome of the protistan community in Coptotermes formosanus. In total, 223,477 reads were obtained by sequencing the enriched protistan mRNA. Phagocytosis and cytoskeletal homeostasis pathways were highly represented in the metatranscriptome. Among the metabolic pathways, starch and sucrose metabolism were dominant. A detailed analysis combining Pfam and KEGG annotation identified 118 glycosyl hydrolases belonging to 18 different glycosyl hydrolase families (GHFs). Subsequently, a novel GHF10 endo-1,4-beta-xylanase was functionally characterized to complement our understanding of the protistan hemicellulases.

Identification of primitive human hematopoietic cells capable of repopulating NOD/SCID mouse bone marrow: implications for gene therapy.

The development of stem-cell gene therapy is hindered by the absence of repopulation assays for primitive human hematopoietic cells. Current methods of gene transfer rely on in vitro colony-forming cell (CFC) and long-term culture-initiating cell (LTC-IC) assays, as well as inference from other mammalian species. We have identified a novel human hematopoietic cell, the SCID-repopulating cell (SRC), a cell more primitive than most LTC-ICs and CFCs. The SRC, exclusively present in the CD4+CD8- fraction, is capable of multilineage repopulation of the bone marrow of nonobese diabetic mice with severe combined immunodeficiency disease (NOD/SCID mice). SRCs were rarely transduced with retroviruses, distinguishing them from most CFCs and LTC-ICs. This observation is consistent with the low level of gene marking seen in human gene therapy trials. An SRC assay may aid in the characterization of hematopoiesis, as well as the improvement of transduction methods.

Quantitative analysis reveals expansion of human hematopoietic repopulating cells after short-term ex vivo culture.

Ex vivo culture of human hematopoietic cells is a crucial component of many therapeutic applications. Although current culture conditions have been optimized using quantitative in vitro progenitor assays, knowledge of the conditions that permit maintenance of primitive human repopulating cells is lacking. We report that primitive human cells capable of repopulating nonobese diabetic (NOD)/severe combined immunodeficiency (SCID) mice (SCID-repopulating cells; SRC) can be maintained and/or modestly increased after culture of CD34+CD38- cord blood cells in serum-free conditions. Quantitative analysis demonstrated a 4- and 10-fold increase in the number of CD34+CD38- cells and colony-forming cells, respectively, as well as a 2- to 4-fold increase in SRC after 4 d of culture. However, after 9 d of culture, all SRC were lost, despite further increases in total cells, CFC content, and CD34+ cells. These studies indicate that caution must be exercised in extending the duration of ex vivo cultures used for transplantation, and demonstrate the importance of the SRC assay in the development of culture conditions that support primitive cells.

Germinal center founder cells display propensity for apoptosis before onset of somatic mutation.

B lymphocytes undergo affinity maturation of their antigen receptors within germinal centers. These anatomical structures develop in secondary lymphoid organs from the clonal expansion of a few antigen-specific founder B cells, whose isolation and characterization are reported here. Human germinal center founder cells express the naive B cell markers surface IgM and IgD as well as the germinal center B cell markers CD10 and CD38. They express low levels of Bcl-2, high levels of Fas, and undergo rapid apoptosis in culture. The smaller nonproliferating sIgM+IgD+CD38+ B cells displayed a lower level of somatic mutation in their immunoglobulin variable region genes compared with the large proliferating ones. Unmutated sIgM+IgD-CD38+ tonsillar B cells may thus represent germinal center founder cells in which the program for apoptotic cell death is triggered before the onset of somatic mutation, allowing the selection of the germline antibody repertoire at an early stage.

Golgi apparatus, GERL, and lysosomes of neurons in rat dorsal root ganglia, studied by thick section and thin section cytochemistry.

New insights into the ultrastructure and phosphatase localizations of Golgi apparatus and GERL, and into the probable origin of lysosomes in the neurons of fetal dorsal root ganglia and the small neurons of adult ganglia have come from studying thick (0.5-1.0 micro) as well as thin (up to 500 A) sections by conventional electron microscopy. Tilting the thick specimens, by a goniometer stage, has helped to increase our understanding of the three-dimensional aspects of the Golgi apparatus and GERL. One Golgi element, situated at the inner aspect of the Golgi stack, displays thiamine pyrophosphatase and nucleoside diphosphatase activities. This element exhibits regular geometric arrays (hexagons) of interconnected tubules without evidence of a flattened portion (saccule or cisterna). In contrast, GERL shows acid phosphatase activity and possesses small cisternal portions and anastomosing tubules. Lysosomes appear to bud from GERL. Osmium deposits, following prolonged osmication, are found in the outer Golgi element. Serial 0.5-micro and thin sections of thiamine pyrophosphatase-incubated material demonstrate that, in the neurons studied, the Golgi apparatus is a continuous network coursing through the cytoplasm. Serial thick sections of acid phosphatase-incubated tissue suggest that GERL is also a continuous structure throughout the cytoplasm. Tubules of smooth endoplasmic reticulum, possibly part of GERL, extend into the polygonal compartments of the inner Golgi element. The possible physiological significance of a polygonal arrangement of a phosphatase-rich Golgi element in proximity to smooth ER is considered. A tentative diagram of the Golgi stack and associated endoplasmic reticulum in these neurons has been drawn.

Reusable, label-free electrochemical aptasensor for sensitive detection of small molecules.

We report a sensitive electrochemical aptasensor for adenosine based on electrochemical impedance spectroscopy measurement, which gives not only a label-free but also a reusable platform to make the detection of small molecules simple and convenient.

Expression and differential intracellular localization of two major forms of human 8-oxoguanine DNA glycosylase encoded by alternatively spliced OGG1 mRNAs.

We identified seven alternatively spliced forms of human 8-oxoguanine DNA glycosylase (OGG1) mRNAs, classified into two types based on their last exons (type 1 with exon 7: 1a and 1b; type 2 with exon 8: 2a to 2e). Types 1a and 2a mRNAs are major in human tissues. Seven mRNAs are expected to encode different polypeptides (OGG1-1a to 2e) that share their N terminus with the common mitochondrial targeting signal, and each possesses a unique C terminus. A 36-kDa polypeptide, corresponding to OGG1-1a recognized only by antibodies against the region containing helix-hairpin-helix-PVD motif, was copurified from the nuclear extract with an activity introducing a nick into DNA containing 8-oxoguanine. A 40-kDa polypeptide corresponding to a processed form of OGG1-2a was detected in their mitochondria using antibodies against its C terminus. Electron microscopic immunocytochemistry and subfractionation of the mitochondria revealed that OGG1-2a locates on the inner membrane of mitochondria. Deletion mutant analyses revealed that the unique C terminus of OGG1-2a and its mitochondrial targeting signal are essential for mitochondrial localization and that nuclear localization of OGG1-1a depends on the NLS at its C terminus.

Regulation of intracellular localization of human MTH1, OGG1, and MYH proteins for repair of oxidative DNA damage.

In mammalian cells, more than one genome has to be maintained throughout the entire life of the cell, one in the nucleus and the other in mitochondria. It seems likely that the genomes in mitochondria are highly exposed to reactive oxygen species (ROS) as a result of their respiratory function. Human MTH1 (hMTH1) protein hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP, 8-oxo-dATP, and 2-hydroxy (OH)-dATP, thus suggesting that these oxidized nucleotides are deleterious for cells. Here, we report that a single-nucleotide polymorphism (SNP) in the human MTH1 gene alters splicing patterns of hMTH1 transcripts, and that a novel hMTH1 polypeptide with an additional mitochondrial targeting signal is produced from the altered hMTH1 mRNAs; thus, intracellular location of hMTH1 is likely to be affected by a SNP. These observations strongly suggest that errors caused by oxidized nucleotides in mitochondria have to be avoided in order to maintain the mitochondrial genome, as well as the nuclear genome, in human cells. Based on these observations, we further characterized expression and intracellular localization of 8-oxoG DNA glycosylase (hOGG1) and 2-OH-A/adenine DNA glycosylase (hMYH) in human cells. These two enzymes initiate base excision repair reactions for oxidized bases in DNA generated by direct oxidation of DNA or by incorporation of oxidized nucleotides. We describe the detection of the authentic hOGG1 and hMYH proteins in mitochondria, as well as nuclei in human cells, and how their intracellular localization is regulated by alternative splicing of each transcript.

3-Methyladenine DNA glycosylase activity in a glial cell line sensitive to the haloethylnitrosoureas in comparison with a resistant cell line.

Extracts of a glial cell line (SF-126) which is sensitive to the cytotoxic effect of the haloethylnitrosoureas and of a cell line (SF-188) which is resistant to these agents have been tested for their ability to release methylated bases from a DNA substrate which has been modified with [3H]dimethyl sulfate. In comparison with the sensitive cell line, extracts from the resistant cell line have 2-3-fold higher enzymatic activity. High performance liquid chromatography profiles of the bases which are released by these extracts show that the activity is specific for 3-methyladenine, suggesting that the resistant cells contain elevated levels of 3-methyladenine DNA glycosylase. Previous studies have shown that these cells also contain elevated levels of O6-alkylguanine-DNA alkyl-transferase, suggesting that both enzyme activities may be involved in the resistance of this cell line to the haloethylnitrosoureas.

Immunocytochemical localization of the base excision repair enzyme uracil DNA glycosylase in quiescent and proliferating normal human cells.

The immunocytochemical localization of the base excision repair enzyme uracil DNA glycosylase was examined as a function of cell proliferation. Two nontransformed normal human fibroblast cell strains were analyzed using an anti-human uracil DNA glycosylase monoclonal antibody. In quiescent cells, basal levels of a nonnuclear immunocytochemically reactive glycosylase protein were detected. No nuclear immunofluorescence was observed. In contrast, in proliferating cells, intense immunofluorescence could be detected exclusively in the nuclear or perinuclear regions. As proliferation diminished, basal levels of the nonnuclear immunocytochemically reactive glycosylase were again observed. The subcellular distribution of the glycosylase was examined in parallel by in vitro biochemical assay. In quiescent cells, glycosylase activity was observed in both the nuclear and membrane fractions. A small amount of enzyme activity could be detected in the soluble cytoplasmic fraction. Immunoblot analysis demonstrated a Mr 37,000 glycosylase protein in each subcellular fraction. During cell proliferation, there was an increase in glycosylase activity in each of the subcellular fractions. These results suggest a correlation between the proliferative state of normal human cells and the preferential nuclear or perinuclear localization of an immunocytochemically reactive glycosylase protein. Further, immunofluorescence of the nuclear enzyme may be dependent on defined conformational states of that nuclear glycosylase in the cell cycle.

O6-Methylguanine-DNA methyltransferase of human lymphoid cells: structural and kinetic properties and absence in repair-deficient cells.

Human lymphoid cell lines contain a DNA repair enzyme which removes the mutagenic alkylation lesion O6-methylguanine from DNA. The enzyme transfers the methyl group to a protein cysteine residue, generating S-methylcysteine, and is inactivated as a consequence of the reaction. Apparently the methylated enzyme represents a dead-end complex. The transfer reaction is very rapid and is completed in less than 1 min at 37 degrees, but methyl group transfer from single-stranded DNA or heavily damaged DNA is less efficient. The active methyltransferase and the methylated protein both have molecular weights of 21,000 to 22,000, as determined by gel filtration. Lymphoid cell lines proficient in repair of O6-methylguanine in vivo, Mex+, contain 10,000 to 25,000 molecules of the methyltransferase per cell. In contrast, repair-deficient cell lines, Mex-, do not contain detectable amounts of the enzyme. The latter point was verified by applying a partial purification procedure for the enzyme to cell-free extracts from two Mex- cell lines.

Wide distribution of an enzyme that catalyzes the hydrolysis of cyclic ADP-ribose.

Cyclic ADP-ribose (cADPR) is a metabolite of NAD+ that is as effective as inositol trisphosphate in mobilizing intracellular-Ca2+ stores. Its synthesizing enzyme, ADP-ribosyl cyclase, has been shown to be present in mammalian and invertebrate tissues. In this study we identify another widely-distributed enzyme that can hydrolyze cADPR to ADP-ribose. Incubation of cADPR with brain extracts resulted in progressive decrease in its Ca2+ mobilizing activity. The degradation of cADPR was catalyzed by a heat-labile protein factor in the brain extracts. Analysis by HPLC indicated a single degradation product was produced in equal molar quantity and that it has identical elution time as ADP-ribose. Proton NMR confirmed that the product was ADP-ribose. The degradation enzyme had a Michaelis constant of 0.16 mM and a broad pH maximum around neutrality. Centrifugation studies of the total brain extracts showed that the degradation activity was membrane-bound. Survey of tissues from various animals established that both the degradation and the synthesizing enzyme of cADPR were widely distributed from mammals to invertebrates. Since the degradation enzyme hydrolyzes an unique linkage between the adenine group and the terminal ribosyl moiety of cADPR, we propose to call it cyclic ADP-ribose hydrolase.

Direct visualization of a DNA glycosylase searching for damage.

DNA glycosylases preserve the integrity of genetic information by recognizing damaged bases in the genome and catalyzing their excision. It is unknown how DNA glycosylases locate covalently modified bases hidden in the DNA helix amongst vast numbers of normal bases. Here we employ atomic-force microscopy (AFM) with carbon nanotube probes to image search intermediates of human 8-oxoguanine DNA glycosylase (hOGG1) scanning DNA. We show that hOGG1 interrogates DNA at undamaged sites by inducing drastic kinks. The sharp DNA bending angle of these non-lesion-specific search intermediates closely matches that observed in the specific complex of 8-oxoguanine-containing DNA bound to hOGG1. These findings indicate that hOGG1 actively distorts DNA while searching for damaged bases.

Expression and characterisation in E. coli of mutant forms of saporin.

In the present communication, we report on the expression and characterisation in Escherichia coli of mutant derivatives of saporin, a type 1 ribosome-inactivating protein from Saponaria officinalis L. The effects of substitution of Glu 176 with Lys and those of deletion of 19 amino acids at the C-terminal were evaluated both in vivo, testing the influence of expressed proteins on bacterial growth and in vitro measuring their N-glycosidase and supercoiled DNA relaxation activities. Results indicate that both modifications of the wild-type protein abolish its toxicity to bacterial cells and impair its enzymatic activity on polynucleotide substrates, either RNA or DNA.

Trisomy 4 in 'stem cell-like' leukemic cells of a patient with AML.

CD34 positive progenitor cells were analyzed in the bone marrow aspirate from a patient with newly diagnosed AML FAB M4. The patient had trisomy 4 as sole cytogenetic abnormality and a dominant population of CD34 negative leukemic blasts. Karyotyping of the FACS isolated, minor subpopulation of CD34+/CD38-, 'stem cell'-like cells (incidence 0.29%) revealed trisomy 4 in 11/13 metaphases. No metaphases were obtained in the CD34 negative subpopulation. The experiments point to the existence of leukemic stem cells in the CD34+/CD38- compartment in AML patients with trisomy 4.

The hematopoietic stem cell in elderly patients with leukemia.

Stem cell reserve and the proliferative capacity of pluripotent hematopoietic progenitors as influenced by age are of intrinsic biologic interest and potential therapeutic importance. The latter is especially true in older persons receiving intensive but not marrow-ablative chemotherapy. Studies of stem cell aging using murine models yield conflicting data. Unfortunately, few studies address the effect of aging on human hematopoietic stem cells, largely because there is no true pluripotent stem cell assay. Some work indicates that the proliferative capacity of human hematopoietic stem cells appears to decrease with age but is unclear whether this is of clinical significance. Our preliminary analysis of more than 500 autotransplant candidates by univariate analysis indicates that higher patient age correlates with reduced committed hematopoietic progenitor cell levels but not with delayed engraftment. In the future, the use of combinations of assays that include phenotypic (CD34+thy1+CD38lo) and functional (long-term culture-initiating cell) characteristics may better identify the effects of aging on candidate stem cells. The development of assays that predict delayed hematopoietic recovery after chemotherapy in older adults may help to tailor therapy for specific patients with the hope of reducing morbidity while retaining efficacy.

Efficient long-term maintenance of chronic myeloid leukemic cobblestone area forming cells on a murine stromal cell line.

Stroma-supported long-term cultures (LTC) of chronic myeloid leukemia (CML) progenitor cells have previously revealed differences between normal and malignant stem cells with respect to their maintenance and adhesive properties. Using the cobblestone area forming cell (CAFC) assay and LTC, we have examined the frequencies of stem cell subsets, their ability for long-term progenitor cell production and the relative frequencies of malignant and normal progenitor cells before and after a 5-6 week culture period. Cells were obtained from bone marrow (BM) and peripheral blood (PB) samples of patients in chronic phase CML. CD34-enriched cells were sorted by FACS on the basis of CD34 and CD38 expression and overlaid on confluent stromal layers of murine FBMD-1 cells. The presence of the bcr/abl chimeric gene was detected by fluorescent in situ hybridization (FISH) using differently labelled bcr and abl-specific probes. In the CD34pos/CD38pos subset of CML-PB, representing 64-95% of CD34pos cells, CAFC frequencies at week 1 (wk-1) were much higher than those of CAFC wk-5 (1.10(4)/10(5) cells vs 1.10(3)/10(5)). In contrast, in the CD34pos/CD38neg subset, representing 2-3% of CD34pos cells, the frequency of CAFC wk-1 was only 1.10(2)/10(5) cells, but a high CAFC frequency (10(3)-10(4)/10(5)) was detected after 5 weeks of culture. CAFC frequencies in the CD34pos subset obtained from CML-BM were 10- to 100-fold lower than those from CML-PB, but displayed a similar distribution over CD38pos, CD38dim and CD38neg cells. Analysis of the percentage of Philadelphia chromosome-positive (Ph+) and Ph- cells by FISH on freshly sorted cells revealed that normal cells were not enriched in any CD34pos/CD38 subset. In addition, Ph- as well as Ph+ cells were maintained with similar efficiency throughout 5 week LTC. These results demonstrate that immature normal and malignant stem cells in CML have a comparable distribution on the basis of CD34 and CD38 expression. The ability to maintain immature normal and malignant hemopoietic cells with similar efficiency in LTC provides a model enabling a direct comparison of differential effects of cytokines or drugs on either normal or malignant immature stem cells in CML.

Phenotype and progeny of primitive adherent human hematopoietic progenitors.

Hematopoietic progenitor cells can be classified as plastic- and stroma-adherent (P+S+), stroma-adherent (P-S+) and non-adherent (P-S-). Both P+S+ and P-S+ populations are detected in delta (delta) culture systems where they produce non-adherent (P-S-) granulocyte-macrophage colony-forming cells (CFU-GM) and erythroid burst-forming units (BFU-E). Here we demonstrate that the plastic-adherent progenitor cells (P delta cells) comprise 5-10 percent of the CD34+, population in adult human marrow. Moreover, they do not express CD3 or CD22 and 88 percent of them are CD38-, 88 percent are CD33- and 74 percent are HLA-DR-. Production of CFU-GM by purified plastic-adherent CD34+, adherent cells was 60 percent of the number produced by recombined CD34+, and CD34- fractions. We have shown also that the plastic-adherent P+S+ cells are the precursors of the stroma-adherent P-S+ cells (S delta cells), day 21 cobblestone-area forming cells (CAFC) and cells capable of sustained hematopoiesis in a modified long-term bone marrow culture system. These observations support the primitive nature of P delta cells and establish a phenotypic sequence of plastic and stroma adherence through stroma adherence to non-adherence in hematopoietic cell development. To further investigate the relationship between P delta cells, S delta cells and long-term culture-initiating cells (LTCIC), we cultured whole mononuclear cell tractions and plastic-adherent cell-depleted mononuclear cell fractions in long-term culture and in the S delta assay. The results indicated the P delta cells were inhibited in the presence of stromal cells.

Peripheral blood is a source of BCR-ABL-negative pre-progenitors in early chronic phase chronic myeloid leukemia.

Manipulation of autologous bone marrow cells (BM) for transplantation in chronic myeloid leukemia (CML) to enrich for normal cells is a novel approach that may improve survival for patients not suitable for allogeneic transplantation. Limitations of this technique include the reported low frequency of normal stem cells in CML and the difficulties in obtaining sufficient BM for manipulation. To address these problems we compared the apheresis product with the diagnostic bone marrow at diagnosis as a source of primitive BCR/ABL-negative progenitors. We analyzed the CD34+ HLA-DR- and CD34+CD38(-) populations in five CML patients to evaluate the frequency of BCR-ABL-negative progenitors and pre-progenitors in these populations. Progenitor analysis was performed by RT-PCR of individual hemopoietic colonies from a standard CFU-GM assay. Analysis of pre-progenitors involved RT-PCR of secondary colonies derived from a stroma-free pre-CFU assay. Our results show variable levels of BCR-ABL-negative progenitors in the 34+DR- population but very low levels of BCR-ABL-negative progenitors in the 34+38- population in blood. Analysis of pre-progenitors from the 34+DR- fraction of peripheral blood (PB) and BM showed 80-100% and 85-100% of colonies were BCR-ABL negative at days 14 and 28, respectively. Analysis of pre-progenitors from the 34+38- fraction of PB and BM showed 23-100% and 42-100% of colonies were BCR-ABL negative at days 14 and 28, respectively. In summary, pre-progenitors from the 34+DR- and 34+38- populations are predominantly BCR-ABL negative in both marrow and blood at diagnosis. Apheresis product collected at diagnosis is a more abundant sources of BCR-ABL-negative pre-progenitors than BM. Thus, apheresis product could potentially be utilized as a source of BCR-ABL-negative stem cells in CML.

In vitro long-term culture of human primitive hematopoietic cells supported by murine stromal cell line MS-5.

When Lin-CD34+CD38- cells from normal human cord blood were cocultured with MS-5, colony forming cells were maintained for over 8 weeks. Prevention of contact between MS-5 and Lin-CD34+CD38- cells by using a membrane filter was negligible for this activity, indicating that the activity of MS-5 on human primitive hematopoietic cells may be due to soluble factor(s) secreted from MS-5. We tried to purify this activity by a [3H]TdR incorporation assay. The activity was found in 150 kD fraction and was neutralized with anti-mSCF (stem cell factor) antibody. Another 20-30 kD fraction synergized with mSCF to stimulate the growth of Lin-CD34+CD38- cells but failed alone. This fraction supported the growth of the G-CSF (granulocyte-colony stimulating factor)-dependent cell line FD/GR3, FDC-P2 transfected with mG-CSF receptor cDNA. This synergy was canceled in the presence of soluble mG-CSF receptor. Addition of anti-mSCF antibody and soluble mG-CSF receptor to the culture completely abrogated the activity of MS-5-culture supernatant. These results indicate the activity of MS-5 on Lin-CD34+CD38- cells is due to synergistic effect of mSCF and mG-CSF.