The transcriptional landscape of the mammalian genome

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Siberian Peatlands a Net Carbon Sink and Global Methane Source Since the Early Holocene

Interpolar methane gradient (IPG) data from ice cores suggest the "switching on" of a major Northern Hemisphere methane source in the early Holocene. Extensive data from Russia's West Siberian Lowland show (i) explosive, widespread peatland establishment between 11.5 and 9 thousand years ago, predating comparable development in North America and synchronous with increased atmospheric methane concentrations and IPGs, (ii) larger carbon stocks than previously thought (70.2 Petagrams, up to approximately 26% of all terrestrial carbon accumulated since the Last Glacial Maximum), and (iii) little evidence for catastrophic oxidation, suggesting the region represents a long-term carbon dioxide sink and global methane source since the early Holocene.

Transplantation of fetal retinal pigment epithelium in age-related macular degeneration with subfoveal neovascularization

BACKGROUND

Age-related macular degeneration (ARMD) is caused by abnormal retinal pigment epithelium (RPE) and may be complicated by choroidal neovascularization. The object of treatment would be to replace the diseased RPE with normal human RPE.

METHOD

Five patients with ARMD (preoperative visual acuity 0.08-0.2) underwent removal of subretinal fibrovascular membranes using pars plana vitrectomy techniques. Human fetal RPE (15-17 weeks gestational age) was cultured and transplanted as a monolayer patch into the subretinal space. Transplants were followed by funduscopy and fluorescein angiography. Macular function was assessed using scanning laser ophthalmoscopic (SLO) microperimetry.

RESULTS

Three RPE transplants were placed in the fovea; two were placed parafoveally. All transplants have survived for 3 months. They have grown and increased in size covering part of the epithelial defect caused by removal of the fibrovascular membrane. SLO microperimetry indicated that visual function was present in four of the transplants at 1 month but in only two at 3 months after surgery. Function over the transplants, especially those in the fovea, was compromised by cystoidlike macular edema.

CONCLUSIONS

Human fetal RPE transplants survive well in the macula for as long as 3 months. They are capable of growing to cover epithelial defects caused by removal of subretinal neovascular membranes. The causes for development of macular edema in transplants directly in the fovea warrant further evaluation.

Disappearing Arctic Lakes

Historical archived satellite images were compared with contemporary satellite data to track ongoing changes in more than 10,000 large lakes in rapidly warming Siberia. A widespread decline in lake abundance and area has occurred since 1973, despite slight precipitation increases to the region. The spatial pattern of lake disappearance suggests (i) that thaw and "breaching" of permafrost is driving the observed losses, by enabling rapid lake draining into the subsurface; and (ii) a conceptual model in which high-latitude warming of permafrost triggers an initial but transitory phase of lake and wetland expansion, followed by their widespread disappearance.

The classical progesterone receptor mediates Xenopus oocyte maturation through a nongenomic mechanism

Xenopus laevis oocytes are physiologically arrested at G(2) of meiosis I. Resumption of meiosis, or oocyte maturation, is triggered by progesterone. Progesterone-induced Xenopus oocyte maturation is mediated via an extranuclear receptor and is independent of gene transcription. The identity of this extranuclear oocyte progesterone receptor (PR), however, has remained a longstanding problem. We have isolated the amphibian homologue of human PR from a Xenopus oocyte cDNA library. The cloned Xenopus progesterone receptor (xPR) functioned in heterologous cells as a progesterone-regulated transcription activator. However, endogenous xPR was excluded from the oocyte nucleus and instead appeared to be a cytosolic protein not associated with any membrane structures. Injection of xPR mRNA into Xenopus oocytes accelerated the progesterone-induced oocyte maturation and reduced the required concentrations of progesterone. In enucleated oocytes, xPR accelerated the progesterone-induced mitogen-activated protein kinase activation. These data suggest that xPR is the long sought after Xenopus oocyte receptor responsible for progesterone-induced oocyte maturation.

Transformation of Escherichia coli with large DNA molecules by electroporation

We have examined bacterial electroporation with a specific interest in the transformation of large DNA, i.e. molecules > 100 kb. We have used DNA from bacterial artificial chromosomes (BACs) ranging from 7 to 240 kb, as well as BAC ligation mixes containing a range o different sized molecules. The efficiency of electroporation with large DNA is strongly dependent on the strain of Escherichia coli used; strains which offer comparable efficiencies for 7 kb molecules differ in their uptake of 240 kb DNA by as much as 30-fold. Even with a host strain that transforms relatively well with large DNA, transformation efficiency drops dramatically with increasing size of the DNA. Molecules of 240 kb transform approximately 30-fold less well, on a molar basis, than molecules of 80 kb. Maximum transformation of large DNA occurs with different voltage gradients and with different time constants than are optimal for smaller DNA. This provides the opportunity to increase the yield of transformants which have taken up large DNA relative to the number incorporating smaller molecules. We have demonstrated that conditions may be selected which increase the average size of BAC clones generated by electroporation and compare the overall efficiency of each of the conditions tested.

Transplantation of RPE in age-related macular degeneration: observations in disciform lesions and dry RPE atrophy

A study was carried out to investigate whether human RPE allografts are tolerated or rejected in the subretinal space and to determine the feasibility of RPE transplantation in subjects with age-related macular degeneration (AMD).

METHODS

Patches of human fetal RPE (13-20 weeks of gestational age) were transplanted into the subretinal space of five patients after surgical removal of subfoveal fibrovascular membranes, and to four subjects with dry geographic atrophy. Suspensions of RPE cells were transplanted to four other patients with nonexudative AMD. Results were evaluated with clinical ophthalmological examination, SLO microperimetry and fluorescein angiography over 8-20 months.

RESULTS

In disciform lesions, RPE transplants developed macular edema and fluorescein leakage concomitant with gradual reduction of visual acuity, implying host-graft rejection, over 1-6 months. In geographic atrophy, three of four transplants showed little change in shape and size after 12 months (one transplant was slowly rejected). In non-exudative AMD, RPE suspension transplants showed no evidence of rejection and were associated with the disappearance of drusen; visual acuity remained stable and SLO microperimetry confirmed retinal function over the transplanted area.

CONCLUSION

Human RPE allografts are not invariably rejected in the subretinal space without immunosuppression. The rejection rate is lower in nonexudative than in neovascular AMD. An intact blood-retinal barrier is likely to protect against rejection. It is technically feasible to transplant human RPE into the submacular space without adversely affecting visual function in nonexudative AMD over relatively long periods of time.

Transcriptional regulation of the N-acetylglucosaminyltransferase V gene in human bile duct carcinoma cells (HuCC-T1) is mediated by Ets-1

N-Acetylglucosaminyltransferase V (GnT-V) catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to alpha-6-D-mannoside to produce the beta1-6 linked branching of N-glycan oligosaccharides, which controls the polylactosamine content. The expression of N-acetylglucosaminyltransferase V, which contains 17 exons and spans 155 kilobase pairs, is expressed in a tissue- and cell type-specific manner and is regulated at the level of transcription by multiple promoters (Saito, H., Gu, J., Nishikawa, A., Ihara, Y., Fujii, J., Kohgo, Y., and Taniguchi, N. (1995) Eur. J. Biochem. 233, 18-26). To elucidate the mechanism by which the GnT-V gene is expressed in a cell- and tissue-specific manner, cell-restricted expression was analyzed using the 5'-upstream regions of the human GnT-V gene spanning base pairs -2760 to +23 in a human bile duct carcinoma cell line, HuCC-T1. We characterized two cis-acting elements that are potentially important in HuCC-T1 cell-specific expression. The two elements each contain an Ets-1 binding site, 5'-GGA-3'. Specific binding of Ets-1 to the respective elements was demonstrated by competition analysis as well as by antibody supershift experiments. Cotransfection of an Ets-1 expression plasmid along with a GnT-V promoter-luciferase reporter plasmid revealed the participation of Ets-1 in the regulation of the GnT-V gene transcription. These data indicated that the transcriptional regulation of the GnT-V gene was mediated by transcription factor Ets-1.

MESPEUS: a database of the geometry of metal sites in proteins

A database with details of the geometry of metal sites in proteins has been set up. The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura & Markley (2006).Nucleic Acids Res.35, D301–D303] and have been determined at 2.5 Å resolution or better. The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn. The stored information includes PDB code, crystal data, resolution of structure determination, refinement program andRfactor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies,Bvalues, coordination numbers, information on coordination shapes, and metal–metal distances. This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole Nδ of histidine] or which delivers details of all the metal sites in a specified protein. The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://eduliss.bch.ed.ac.uk/MESPEUS/. Some applications are briefly described, including a study of the characteristics of Mg sites that bind adenosine triphosphate, the derivation of an average Mg—Ophosphatedistance and some problems that arise when average bond distances with high precision are required.

Impaired thrombin generation in beta 2-glycoprotein I null mice

Autoimmune antibodies to beta(2)-glycoprotein I (beta2GPI) have been proposed to be clinically relevant because of their strong association with thrombosis, miscarriage, and thrombocytopenia. By using a homologous recombination approach, beta2GPI-null mice were generated to begin to understand the physiologic and pathologic role of this prominent plasma protein in mammals. When beta2GPI heterozygotes on a 129/Sv/C57BL/6 mixed genetic background were intercrossed, only 8.9% of the resulting 336 offspring possessed both disrupted alleles. These data suggest that beta2GPI plays a beneficial role in implantation and/or fetal development in at least some mouse strains. Although those beta2GPI-null mice that were born appeared to be relatively normal anatomically and histologically, subsequent analysis revealed that they possessed an impaired in vitro ability to generate thrombin relative to wild type mice. Thus, beta2GPI also appears to play an important role in thrombin-mediated coagulation.

Colonic microbiota can promote rapid local improvement of murine colitis by thioguanine independently of T lymphocytes and host metabolism

OBJECTIVE

Mercaptopurine (MP) and pro-drug azathioprine are 'first-line' oral therapies for maintaining remission in IBD. It is believed that their pharmacodynamic action is due to a slow cumulative decrease in activated lymphocytes homing to inflamed gut. We examined the role of host metabolism, lymphocytes and microbiome for the amelioration of colitis by the related thioguanine (TG).

DESIGN

C57Bl/6 mice with or without specific genes altered to elucidate mechanisms responsible for TG's actions were treated daily with oral or intrarectal TG, MP or water. Disease activity was scored daily. At sacrifice, colonic histology, cytokine message, caecal luminal and mucosal microbiomes were analysed.

RESULTS

Oral and intrarectal TG but not MP rapidly ameliorated spontaneous chronic colitis in Winnie mice (point mutation in Muc2 secretory mucin). TG ameliorated dextran sodium sulfate-induced chronic colitis in wild-type (WT) mice and in mice lacking T and B lymphocytes. Remarkably, colitis improved without immunosuppressive effects in the absence of host hypoxanthine (guanine) phosphoribosyltransferase (Hprt)-mediated conversion of TG to active drug, the thioguanine nucleotides (TGN). Colonic bacteria converted TG and less so MP to TGN, consistent with intestinal bacterial conversion of TG to so reduce inflammation in the mice lacking host Hprt. TG rapidly induced autophagic flux in epithelial, macrophage and WT but not Hprt^-/- fibroblast cell lines and augmented epithelial intracellular bacterial killing.

CONCLUSIONS

Treatment by TG is not necessarily dependent on the adaptive immune system. TG is a more efficacious treatment than MP in Winnie spontaneous colitis. Rapid local bacterial conversion of TG correlated with decreased intestinal inflammation and immune activation.

Regulation of Xenopus oocyte meiosis arrest by G protein betagamma subunits

BACKGROUND

Progesterone induces the resumption of meiosis (maturation) in Xenopus oocytes through a nongenomic mechanism involving inhibition of an oocyte adenylyl cyclase and reduction of intracellular cAMP. However, progesterone action in Xenopus oocytes is not blocked by pertussis toxin, and this finding indicates that the inhibition of the oocyte adenylyl cyclase is not mediated by the alpha subunits of classical G(i)-type G proteins.

RESULTS

To investigate the possibility that G protein betagamma subunits, rather than alpha subunits, play a key role in regulating oocyte maturation, we have employed two structurally distinct G protein betagamma scavengers (G(t)alpha and betaARK-C(CAAX)) to sequester free Gbetagamma dimers. We demonstrated that the injection of mRNA encoding either of these Gbetagamma scavengers induced oocyte maturation. The Gbetagamma scavengers bound an endogenous, membrane-associated Gbeta subunit, indistinguishable from Xenopus Gbeta1 derived from mRNA injection. The injection of Xenopus Gbeta1 mRNA, together with bovine Ggamma2 mRNA, elevated oocyte cAMP levels and inhibited progesterone-induced oocyte maturation.

CONCLUSION

An endogenous G protein betagamma dimer, likely including Xenopus Gbeta1, is responsible for maintaining oocyte meiosis arrest. Resumption of meiosis is induced by Gbetagamma scavengers in vitro or, naturally, by progesterone via a mechanism that suppresses the release of Gbetagamma.

Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects

Advances in defining the target antigen(s) for the autoantibodies in the APS highlight the inadequacies of the current classification of these autoantibodies into anticardiolipin and LA antibodies. The discovery that beta 2GPI is the target antigen for the autoantibodies detected in solid-phase immunoassays has opened a number of areas of research linking these autoantibodies to atherogenesis and thrombus formation. Although the role of beta 2GPI in the regulation of blood coagulation in unclear, current evidence suggests that anti-beta 2GPI antibodies interfere with its "normal" role and appear to promote a procoagulant tendency. The expansion of research in this area and the diversity of the clinical manifestations of patients with APS have resulted in the inclusion of molecular biologists and pharmaceutical companies joining immunologists, hematologists, rheumatologists, obstetricians, neurologists, vascular surgeons, and protein and lipid biochemists in attempting to understand the pathophysiology of this condition. Although the published literature may result in conflicting results and introduce new controversies, developing standardized laboratory methods and extrapolation of in vitro experimental results to the vivo situation will advance our understanding of the regulation of the immune system and its interaction with normal hemostatic mechanisms. Since the authors' last review in 1991, the study and understanding of the pathophysiology of APS have evolved from lipid biochemistry to molecular techniques that may eventually provide specific therapies for the clinical manifestations of this condition. Although current treatment has improved the morbidity associated with this condition, especially in improving pregnancy outcomes, future therapies, as outlined in this review, may specifically address the biological abnormalities and have fewer side effects. Better diagnostic tools, such as magnetic resonance imaging with perfusion studies, will allow the study of the true incidence and prevalence of vascular flow changes/tissue ischemia and infarction associated with aPL antibodies and help determine treatment and prophylaxis for APS patients. APS is still the only hypercoagulable condition where both arterial and venous beds can be affected independently or in the same individual.

Hypochlorous acid/N-chloramines are naturally produced DNA repair inhibitors

Human mononuclear leukocytes (HML) respond to oxidative DNA damage by activation of ADP ribosylation and initiation of DNA repair synthesis (i.e. unscheduled DNA synthesis, UDS), whereas neutrophils do not. When neutrophils are added to HML cultures in ratios up to 4:1 ADP ribosylation becomes inhibited to approximately 50-60%. The ability of neutrophils to inhibit HML ADP ribosylation was shown to be dependent on H2O2, chloride ions and myeloperoxidase, which in turn are factors known to govern HOCl and N-chloramine production by phagocytic cells. HOCl and a model N-chloramine, chloramine T, were shown to give a dose-dependent inhibition of DNA repair using four independent estimates, namely ADP ribosylation, UDS and the repair of DNA strand breaks estimated by nucleoid sedimentation and alkaline elution profiles. All the DNA repair measurements used on HML were inhibited approximately 70-80% by 100 microM doses of HOCl or chloramine T, which was considered a biologically relevant dose because: (i) viable neutrophils equal in concentration to those found in blood could easily produce 100 microM levels in short-term culture; (ii) 100 microM doses of these agents were not acutely cytotoxic judged by trypan blue stained cells after 30-60 min exposure and under the conditions used for assay, but yet they abolished 86-95% of the growth response of HML to phytohemagglutinin.

Anion effect on the nanostructure of a metal ion binding self-assembling peptide

Effects of copper salts containing different anions (SO(4)(2)(-), Cl(-), and NO(3)(-)) on the self-assembly of a designed peptide EAK16(II)GGH with affinity for Cu(2+) have been investigated. The peptide secondary structure, self-assembled nanostructures, and surface activity were observed to depend strongly on the type of anion. Over a salt concentration range from 0.05 to 10.0 mM, SO(4)(2)(-) induced long fiber formation, whereas Cl(-) and NO(3)(-) caused short fiber formation. The fiber length increased with copper sulfate concentration, but the concentration of copper chloride and copper nitrate did not affect the peptide nanostructures significantly. Analysis by Fourier transform infrared spectroscopy (FTIR) revealed that the addition of the copper salts tended to cause the peptide conformation to change from alpha-helix/random coil to beta-sheet, the extent to which depended on the anion type. This evidence of the anion effect was also supported by surface tension measurements using the axisymmetric drop shape analysis-profile (ADSA-P) technique. An explanation for the effect of anions on the peptide self-assembly was proposed. The divalent anion SO(4)(2)(-) might serve as a bridge by electrostatically interacting with two lysine residues from different peptide molecules, promoting beta-sheet formation. The extensive beta-sheet formation may further promote peptide self-assembly into long fibers. On the other hand, monovalent anions Cl(-) and NO(3)(-) may only electrostatically interact with one charged residue of the peptide; hence, a mixed secondary structure of alpha-helix/random coil and beta-sheet was observed. This observation might explain the predominant formation of short fibers in copper chloride and copper nitrate solutions.

Coronavirus-induced membrane fusion requires the cysteine-rich domain in the spike protein

The spike glycoprotein of mouse hepatitis virus strain A59 mediates the early events leading to infection of cells, including fusion of the viral and cellular membranes. The spike is a type I membrane glycoprotein that possesses a conserved transmembrane anchor and an unusual cysteine-rich (cys) domain that bridges the putative junction of the anchor and the cytoplasmic tail. In this study, we examined the role of these carboxyl-terminal domains in spike-mediated membrane fusion. We show that the cytoplasmic tail is not required for fusion but has the capacity to enhance membrane fusion activity. Chimeric spike protein mutants containing substitutions of the entire transmembrane anchor and cys domain with the herpes simplex virus type 1 glycoprotein D (gD-1) anchor demonstrated that fusion activity requires the presence of the A59 membrane-spanning domain and the portion of the cys domain that lies upstream of the cytoplasmic tail. The cys domain is a required element since its deletion from the wild-type spike protein abrogates fusion activity. However, addition of the cys domain to fusion-defective chimeric proteins was unable to restore fusion activity. Thus, the cys domain is necessary but is not sufficient to complement the gD-1 anchor and allow for membrane fusion. Site-specific mutations of conserved cysteine residues in the cys domain markedly reduce membrane fusion, which further supports the conclusion that this region is crucial for spike function. The results indicate that the carboxyl-terminus of the spike transmembrane anchor contains at least two distinct domains, both of which are necessary for full membrane fusion.

Perceiving affordances for another person's actions

The perception of affordances for the actions of other people (actors) was examined. Observers judged the maximum and preferred sitting heights of tall and short actors. Judgments were scaled in centimeters, as a proportion of the observer's leg length, and as a proportion of each actor's leg length. In Experiment 1 observers viewed live actors standing next to a chair. When judgments were scaled by actor leg length, they reflected the actual ordinal relation between the capabilities of the actors. The perception of affordances from kinematic displays was then evaluated. Observers differentiated tall and short actors, but only when the displays contained direct information about relations between the actors and the chair. It is concluded that observers can perceive affordances for the actions of actors and that kinematic displays can be enough to support such percepts if they preserve actor-environment relations that define affordances.

Enhanced DNA repair, immune function and reduced toxicity of C-MED-100, a novel aqueous extract from Uncaria tomentosa

Female W/Fu rats were gavaged daily with a water-soluble extract (C-MED-100) of Uncaria tomentosa supplied commercially by CampaMed at the doses of 0, 5, 10, 20, 40 and 80 mg/kg for 8 consecutive weeks. Phytohemagglutinin (PHA) stimulated lymphocyte proliferation was significantly increased in splenocytes of rats treated at the doses of 40 and 80 mg/kg. White blood cells (WBC) from the C-MED-100 treatment groups of 40 and 80 mg/kg for 8 weeks or 160 mg/kg for 4 weeks were significantly elevated compared with controls (P < 0.05). In a human volunteer study, C-MED-100 was given daily at 5 mg/kg for 6 consecutive weeks to four healthy adult males. No toxicity was observed and again, WBC were significantly elevated (P < 0.05) after supplement. Repair of DNA single strand breaks (SSB) and double strand breaks (DSB) 3 h after 12 Gy whole body irradiation of rats were also significantly improved in C-MED-100 treated animals (P < 0.05). The LD50 and MTD of a single oral dose of C-MED-100 in the rat were observed to be greater than 8 g/kg. Although the rats were treated daily with U. tomentosa extracts at the doses of 10-80 mg/kg for 8 weeks or 160 mg/kg for 4 weeks, no acute or chronic toxicity signs were observed symptomatically. In addition, no body weight, food consumption, organ weight and kidney, liver, spleen, and heart pathological changes were found to be associated with C-MED-100 treatment.

Treatment of chemotherapy-induced leukopenia in a rat model with aqueous extract from Uncaria tomentosa

The Uncaria tomentosa water extracts (C-Med-100) depleted of indole alkaloids (< 0.05%, w/w) have been shown to induce apoptosis and inhibit proliferation in tumor cells in vitro and to enhance DNA repair, mitogenic response and white blood cells in vivo. In this study, the effect of C-Med-100 in the treatment of chemically induced leukopenia was evaluated in a rat model. W/Fu rats were treated first with doxorubicin (DXR) 2 mg/kg x 3 (i.p. injection at 24 hour-intervals) to induce leukopenia. Twenty-four hours after the last DXR treatment, the rats were daily gavaged with C-Med-100 for 16 consecutive days. As a positive control, Neupogen, a granulocyte colony stimulator was also administered by subcutaneous injection at a dose of 5 and 10 microg/ml for 10 consecutive days. The results showed that both C-Med-100 and Neupogen treatment groups recovered significantly sooner (p < 0.05 by Duncan test) than DXR group. However, the recovery by C-Med-100 treatment was a more natural process than Neupogen because all fractions of white blood cells were proportionally increased while Neupogen mainly elevated the neutrophil cells. These results were also confirmed by microscopic examination of the blood smears. The mechanism of the C-Med-100 effect on WBC is not known but other data showing enhanced effects on DNA repair and immune cell proliferative response support a general immune enhancement.

Detection of 'antiphospholipid' antibodies: a single chromogenic assay of thrombin generation sensitively detects lupus anticoagulants, anticardiolipin antibodies, plus antibodies binding beta(2)-glycoprotein I and prothrombin

The diagnosis of the antiphospholipid syndrome (APS) requires both a typical clinical event plus a persistently positive test in an assay for either anticardiolipin (aCL) antibodies or a lupus anticoagulant (LA). Enzyme linked immunosorbent assays (ELISA) specific for autoantibodies against beta(2)-glycoprotein I (beta(2)GPI) or prothrombin are also used, but none of the tests are adequately sensitive or specific. A chromogenic assay was developed that measures the effect of test antibody or plasma samples on in vitro thrombin formation. It is able to detect both LA and beta(2)GPI-dependent aCL antibodies and may have greater specificity for APS than currently available tests. Using this method various monoclonal antibodies (MoAbs) were examined, from mice immunized with beta(2)GPI, mice with a spontaneous animal model of APS, and from three humans with APS. Plasma and affinity purified antibodies from patients with APS and control groups were also examined. Thrombin inhibition was more sensitive to perturbation by MoAbs than a combination of tests for LA (P < 0.05) and at lower antibody concentrations (12.5 microg/ml versus 100 microg/ml). There was a significant correlation between inhibition of thrombin generation and the level of MoAb reactivity to beta(2)GPI (r = 0.90; P < 0.001) but not to CL (r = 0.06; P = 0.76). Plasma and affinity purified antibodies from patients with APS also inhibited thrombin generation, and significantly more so than patients with aPL from causes other than APS. APS patient samples showed thrombin inhibition in the presence of anti-beta(2)GPI or antiprothrombin antibodies. All MoAbs binding beta(2)GPI showed inhibition of thrombin generation, while MoAbs binding domain I of beta(2)GPI had more LA effect.

Structural and functional similarities in the ADP-forming amide bond ligase superfamily: implications for a substrate-induced conformational change in folylpolyglutamate synthetase

Comparison of the three-dimensional structures of folylpolyglutamate synthetase (FPGS) and the bacterial cell wall ligase UDP-N-acetylmuramoyl-l-alanine:d-glutamate ligase (MurD) reveals that these two enzymes have a remarkable structural similarity despite a low level of sequence identity. Both enzymes have a modular, multi-domain structure and catalyse a similar ATP-dependent reaction involving the addition of a glutamate residue to a carboxylate-containing substrate, tetrahydrofolate in the case of FPGS, and UDP-N-acetylmuramoyl-l-alanine in the case of MurD. Site-directed mutations of selected residues in the active site of Lactobacillus casei FPGS (P74A, E143A, E143D, E143Q, K185A, D313A, H316A, G411A and S412A) showed that most of these changes resulted in an almost complete loss of activity. Several of these amino acid residues in FPGS are found in structurally equivalent positions to active-site residues in MurD. Some insights into the function of these residues in FPGS activity are proposed, based on the roles surmised from the structures of two MurD. UDP-N-acetylmuramoyl-l-alanine.ADP complexes and a MurD. UDP-N-acetylmuramoyl-l-alanine-d-glutamate complex. Furthermore, the comparison has led us to propose that conformational changes induced by substrate binding in the reaction mechanism of FPGS result in a movement of the domains towards each other to more closely resemble the orientation of the corresponding domains in MurD. This relative domain movement may be a key feature of this new family of ADP-forming amide bond ligases.

DNA repair enhancement of aqueous extracts of Uncaria tomentosa in a human volunteer study

The Uncaria tomentosa water extracts (C-Med-100) have been shown to enhance DNA repair, mitogenic response and leukocyte recovery after chemotherapy-induced DNA damage in vivo. In this study, the effect of C-Med-100 supplement was evaluated in a human volunteer study. Twelve apparently healthy adults working in the same environment were randomly assigned into 3 groups with age and gender matched. One group was daily supplemented with a 250 mg tablet containing an aqueous extract of Uncaria tomentosa of C-Med-100, and another group with a 350 mg tablet, for 8 consecutive weeks. DNA repair after induction of DNA damage by a standard dose of hydrogen peroxide was measured 3 times before supplement and 3 times after the supplement for the last 3 weeks of the 8 week-supplement period. There were no drug-related toxic responses to C-Med-100 supplement when judged in terms of clinical symptoms, serum clinical chemistry, whole blood analysis and leukocyte differential counts. There was a statistically significant decrease of DNA damage and a concomitant increase of DNA repair in the supplement groups (250 and 350 mg/day) when compared with non-supplemented controls (p < 0.05). There was also an increased tendency of PHA induced lymphocyte proliferation in the treatment groups. Taken together, this trial has confirmed the earlier results obtained in the rat model when estimating DNA repair enhancement by C-Med-100.