Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics

The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of 1,855 open reading frames (ORFs) have been identified that appear to encode polypeptides, 844 (46%) of which have been assigned putative functions based on their similarities to database sequences with assigned functions. A total of 514 (28%) of the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and Archaea-specific databases reveal that 1,013 of the putative gene products (54%) are most similar to polypeptide sequences described previously for other organisms in the domain Archaea. Comparisons with the Methanococcus jannaschii genome data underline the extensive divergence that has occurred between these two methanogens; only 352 (19%) of M. thermoautotrophicum ORFs encode sequences that are >50% identical to M. jannaschii polypeptides, and there is little conservation in the relative locations of orthologous genes. When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more similar to eucaryal sequences. The bacterial domain-like gene products include the majority of those predicted to be involved in cofactor and small molecule biosyntheses, intermediary metabolism, transport, nitrogen fixation, regulatory functions, and interactions with the environment. Most proteins predicted to be involved in DNA metabolism, transcription, and translation are more similar to eucaryal sequences. Gene structure and organization have features that are typical of the Bacteria, including genes that encode polypeptides closely related to eucaryal proteins. There are 24 polypeptides that could form two-component sensor kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK and DnaJ, which are notably absent in M. jannaschii. DNA replication initiation and chromosome packaging in M. thermoautotrophicum are predicted to have eucaryal features, based on the presence of two Cdc6 homologs and three histones; however, the presence of an ftsZ gene indicates a bacterial type of cell division initiation. The DNA polymerases include an X-family repair type and an unusual archaeal B type formed by two separate polypeptides. The DNA-dependent RNA polymerase (RNAP) subunits A', A", B', B" and H are encoded in a typical archaeal RNAP operon, although a second A' subunit-encoding gene is present at a remote location. There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most of these occur in clusters. Three of the tRNA genes have introns, including the tRNAPro (GGG) gene, which contains a second intron at an unprecedented location. There is no selenocysteinyl-tRNA gene nor evidence for classically organized IS elements, prophages, or plasmids. The genome contains one intein and two extended repeats (3.6 and 8.6 kb) that are members of a family with 18 representatives in the M. jannaschii genome.

Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum

The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb megaplasmid that contains the majority of genes responsible for solvent production. Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases closer, phylogenetic proximity. This conservation allows the prediction of many previously undetected operons in both bacteria. However, the C. acetobutylicum genome also contains a significant number of predicted operons that are shared with distantly related bacteria and archaea but not with B. subtilis. Phylogenetic analysis is compatible with the dissemination of such operons by horizontal transfer. The enzymes of the solventogenesis pathway and of the cellulosome of C. acetobutylicum comprise a new set of metabolic capacities not previously represented in the collection of complete genomes. These enzymes show a complex pattern of evolutionary affinities, emphasizing the role of lateral gene exchange in the evolution of the unique metabolic profile of the bacterium. Many of the sporulation genes identified in B. subtilis are missing in C. acetobutylicum, which suggests major differences in the sporulation process. Thus, comparative analysis reveals both significant conservation of the genome organization and pronounced differences in many systems that reflect unique adaptive strategies of the two gram-positive bacteria.

Immunosuppressant PG490 (triptolide) inhibits T-cell interleukin-2 expression at the level of purine-box/nuclear factor of activated T-cells and NF-kappaB transcriptional activation

PG490 (triptolide) is a diterpene triepoxide with potent immunosuppressive and antiinflammatory properties. PG490 inhibits interleukin(IL)-2 expression by normal human peripheral blood lymphocytes stimulated with phorbol 12-myristate 13-acetate (PMA) and antibody to CD3 (IC50 of 10 ng/ml), and with PMA and ionomycin (Iono, IC50 of 40 ng/ml). In Jurkat T-cells, PG490 inhibits PMA/Iono-stimulated IL-2 transcription. PG490 inhibits the induction of DNA binding activity at the purine-box/antigen receptor response element (ARRE)/nuclear factor of activated T-cells (NF-AT) target sequence but not at the NF-kappaB site. PG490 can completely inhibit transcriptional activation at the purine-box/ARRE/NF-AT and NF-kappaB target DNA sequences triggered by all stimuli examined (PMA, PMA/Iono, tumor necrosis factor-alpha). PG490 also inhibits PMA-stimulated activation of a chimeric transcription factor in which the C-terminal TA1 transactivation domain of NF-kappaB p65 is fused to the DNA binding domain of GAL4. In 16HBE human bronchial epithelial cells, IL-8 expression is regulated predominantly by NF-kappaB, and PG490 but not cyclosporin A can completely inhibit expression of IL-8. The mechanism of PG490 inhibition of cytokine gene expression differs from cyclosporin A and involves nuclear inhibition of transcriptional activation of NF-kappaB and the purine-box regulator operating at the ARRE/NF-AT site at a step after specific DNA binding.

Interleukin-17 exacerbates hepatic steatosis and inflammation in non-alcoholic fatty liver disease

Mechanisms associated with the progression of simple steatosis to non-alcoholic fatty liver disease (NAFLD) remain undefined. Regulatory T cells (T(regs)) play a critical role in regulating inflammatory processes in non-alcoholic steatohepatitis (NASH) and because T helper type 17 (Th17) functionally oppose T(reg)-mediated responses, this study focused on characterizing the role of Th17 cells using a NAFLD mouse model. C57BL/6 mice were fed either a normal diet (ND) or high fat (HF) diet for 8 weeks. Mice in the HF group had a significantly higher frequency of liver Th17 cells compared to ND-fed mice. Neutralization of interleukin (IL)-17 in HF mice ameliorated lipopolysaccharide (LPS)-induced liver injury reflected by decreased serum alanine aminotransferase (ALT) levels and reduced inflammatory cell infiltrates in the liver. In vitro, HepG2 cells cultured in the presence of free fatty acids (FFA; oleic acid and palmitic acid) for 24 h and IL-17 developed steatosis via insulin-signalling pathway interference. IL-17 and FFAs synergized to induce IL-6 production by HepG2 cells and murine primary hepatocytes which, in combination with transforming growth factor (TGF-β), expanded Th17 cells. It is likely that a similar process occurs in NASH patients, as there were significant levels of IL-17(+) cell infiltrates in NASH patient livers. The hepatic expression of Th17 cell-related genes [retinoid-related orphan receptor gamma (ROR)γt, IL-17, IL-21 and IL-23] was also increased significantly in NASH patients compared to healthy controls. Th17 cells and IL-17 were associated with hepatic steatosis and proinflammatory response in NAFLD and facilitated the transition from simple steatosis to steatohepatitis. Strategies designed to alter the balance between Th17 cells and T(regs) should be explored as a means of preventing progression to NASH and advanced liver diseases in NAFLD patients.

The human bone marrow response to acute air pollution caused by forest fires

Atmospheric pollution increases cardiopulmonary morbidity and mortality by unexplained mechanisms. Phagocytosis of fine particles (PM(10)) by rabbit alveolar macrophages elevates white blood cells (WBC) by releasing precursors from the bone marrow and this could contribute to the pathogenesis of cardiopulmonary disease. The present study examined the association between acute air pollution caused by biomass burning and peripheral WBC counts in humans. Serial measurements of the WBC count made during the 1997 Southeast Asian Smoke-haze (Sep 29, Oct 27) were compared with a period after the haze cleared (Nov 21, Dec 5) using peripheral blood PMN band cells to monitor marrow release. The results showed that indices of atmospheric pollution were significantly associated with elevated band neutrophil counts expressed as a percentage of total polymorphonuclear leukocytes (PMN), with maximal association on zero and 1 lag day for PM(10) and 3, and 4 lag days for SO(2) (p value < 0.000). We conclude that atmospheric pollution caused by biomass burning is associated with elevated circulating band cell counts in humans because of the increased release of PMN precursors from the marrow. We speculate that this response contributes to the pathogenesis of the cardiorespiratory morbidity associated with acute air pollution.

PG490 (triptolide) cooperates with tumor necrosis factor-alpha to induce apoptosis in tumor cells

Progress in the treatment of solid tumors has been slow and sporadic. The efficacy of conventional chemotherapy in solid tumors is limited because tumors frequently have mutations in the p53 gene. Also, chemotherapy only kills rapidly dividing cells. Members of the tumor necrosis factor (TNF) family, however, induce apoptosis regardless of the p53 phenotype. Unfortunately, the cytotoxicity of TNF-alpha is limited by its activation of NF-kappaB and activation of NF-kappaB is proinflammatory. We have identified a compound called PG490, that is composed of purified triptolide, which induces apoptosis in tumor cells and sensitizes tumor cells to TNF-alpha-induced apoptosis. PG490 potently inhibited TNF-alpha-induced activation of NF-kappaB. PG490 also blocked TNF-alpha-mediated induction of c-IAP2 (hiap-1) and c-IAP1 (hiap-2), members of the inhibitor of apoptosis (IAP) family. Interestingly, PG490 did not block DNA binding of NF-kappaB, but it blocked transactivation of NF-kappaB. Our identification of a compound that blocks TNF-alpha-induced activation of NF-kappaB may enhance the cytotoxicity of TNF-alpha on tumors in vivo and limit its proinflammatory effects.

Repetitive transcranial magnetic stimulation activates specific regions in rat brain

Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive technique to induce electric currents in the brain. Although rTMS is being evaluated as a possible alternative to electroconvulsive therapy for the treatment of refractory depression, little is known about the pattern of activation induced in the brain by rTMS. We have compared immediate early gene expression in rat brain after rTMS and electroconvulsive stimulation, a well-established animal model for electroconvulsive therapy. Our result shows that rTMS applied in conditions effective in animal models of depression induces different patterns of immediate-early gene expression than does electroconvulsive stimulation. In particular, rTMS evokes strong neural responses in the paraventricular nucleus of the thalamus (PVT) and in other regions involved in the regulation of circadian rhythms. The response in PVT is independent of the orientation of the stimulation probe relative to the head. Part of this response is likely because of direct activation, as repetitive magnetic stimulation also activates PVT neurons in brain slices.

A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content

We have developed a new DH mapping population for oilseed rape, named TNDH, using genetically and phenotypically diverse parental lines. We used the population in the construction of a high stringency genetic linkage map, consisting of 277 loci, for use in quantitative genetic analysis. A proportion of the markers had been used previously in the construction of linkage maps for Brassica species, thus permitting the alignment of maps. The map includes 68 newly developed Sequence Tagged Site (STS) markers targeted to the homologues of defined genes of A. thaliana. The use of these markers permits the alignment of our linkage map with the A. thaliana genome sequence. An additional 74 loci (31 newly developed STS markers and 43 loci defined by SSR and RFLP markers that had previously been used in published linkage maps) were added to the map. These markers increased the resolution of alignment of the newly constructed linkage map with existing Brassica linkage maps and the A. thaliana genome sequence. We conducted field trials with the TNDH population at two sites, and over 2 years, and identified reproducible QTL for seed oil content and erucic acid content. The results provide new insights into the genetic control of seed oil and erucic acid content in oilseed rape, and demonstrate the utility of the linkage map and population.

Continuous cytomegalovirus seroconversion in a large group of healthy blood donors

BACKGROUND AND OBJECTIVES

Transmission of cytomegalovirus (CMV) to seronegative, immunocompromised recipients can cause serious and fatal complications. Although the seroprevalence of CMV is high, the risk of primary CMV infection among healthy blood donors has not yet been analysed in a large population.

MATERIALS AND METHODS

We developed an algorithm to determine the rate of CMV seroconversion in an overall cohort of 24,260 subjects who donated 176,474 blood units during an 11-year observation period.

RESULTS

We detected CMV seroconversion in all relevant age groups (18-60 years) with an overall seroconversion rate of 0.55% per year. Both CMV seroconversion and seroprevalence occurred more frequently in female donors (P = 0.02 and P < 0.001, respectively). We identified 30-35-year-old blood donors as the group with the highest rate of CMV seroconversion per year (1.33% vs. 0.46%; P < 0.0001).

CONCLUSIONS

We conclude that the risk of primary CMV infection is a continuous lifelong event and correlates with age and female gender.

Remodeling of the gut microbiota and structural shifts in Preeclampsia patients in South China

Preeclampsia (PE) is one of the pregnancy metabolic diseases. Since Gut microbiota play important roles in the hosts' metabolism, it is necessary to investigate the gut microbiota in PE patients, so that some intestinal dysbiosis might be detected as a biomarker for PE early diagnosis or as a target for intervention. One hundred subjects were categorized into four groups: 26 PE patients in late pregnancy, healthy individuals in early, middle, and late pregnancy (26/24/24 women). Gut microbiota were analyzed by sequencing the V4 region of the 16S rDNA gene using Illuminal MiSeq. Data were analyzed by multivariate statistics. Bacteroidetes was the dominant bacterium (47.57-52.35%) in the pregnant women in South China. Tenericutes increased while Verrucomicrobia almost disappeared in late pregnancy. In the PE patients, there was an overall increase in pathogenic bacteria, Clostridium perfringens (p = 0.03) and Bulleidia moorei (p = 0.00) but a reduction in probiotic bacteria Coprococcus catus (p = 0.03). Our research suggests that there is a significant structural shift of the gut microbiota in PE patients, which might be associated with the occurrence and development of the disease. However, further studies are required to understand the underlying mechanisms.

Specificities of anti-sialyl-Tn and anti-Tn monoclonal antibodies generated using novel clustered synthetic glycopeptide epitopes

The fine specificities of MAbs generated using novel synthetic clustered STn and Tn glycopeptides as immunogens were compared with the anti-TAG-72 antibodies B72.3 and CC49. Hapten inhibition experiments demonstrated the specificity of several of the MAbs for STn and Tn expressed on ovine submaxillary mucin and tumor derived MUC-1 mucin. Amongst the STn specific MAbs only the B195.3 MAb shows absolute dependence on the presence of sialic acid and specificity to the simple disaccharide NANAA alpha2-6-GalNAc. Identification of tumor associated carbohydrate epitopes in cluster and monomer configurations are possible using MAbs detecting the defined structure specificities described herein.

Anti-inflammatory effects of triptolide in human bronchial epithelial cells

Triptolide (PG490, 97% pure) is a diterpenoid triepoxide with potent anti-inflammatory and immunosuppressive effects in transformed human bronchial epithelial cells and T cells (Qiu D, Zhao G, Aoki Y, Shi L, Uyei A, Nazarian S, Ng JC-H, and Kao PN. J Biol Chem 274: 13443-13450, 1999). Triptolide, with an IC(50) of approximately 20-50 ng/ml, inhibits normal and transformed human bronchial epithelial cell expression of interleukin (IL)-6 and IL-8 stimulated by phorbol 12-myristate 13-acetate (PMA), tumor necrosis factor-alpha, or IL-1 beta. Nuclear runoff and luciferase reporter gene assays demonstrate that triptolide inhibits IL-8 transcription. Triptolide also inhibits the transcriptional activation, but not the DNA binding, of nuclear factor-kappa B. A cDNA array and clustering algorithm analysis reveals that triptolide inhibits expression of the PMA-induced genes tumor necrosis factor-alpha, IL-8, macrophage inflammatory protein-2 alpha, intercellular adhesion molecule-1, integrin beta(6), vascular endothelial growth factor, granulocyte-macrophage colony-stimulating factor, GATA-3, fra-1, and NF45. Triptolide also inhibits constitutively expressed cell cycle regulators and survival genes cyclins D1, B1, and A1, cdc-25, bcl-x, and c-jun. Thus anti-inflammatory, antiproliferative, and proapoptotic properties of triptolide are associated with inhibition of nuclear factor-kappa B signaling and inhibition of genes known to regulate cell cycle progression and survival.

MR vascular fingerprinting: A new approach to compute cerebral blood volume, mean vessel radius, and oxygenation maps in the human brain

In the present study, we describe a fingerprinting approach to analyze the time evolution of the MR signal and retrieve quantitative information about the microvascular network. We used a Gradient Echo Sampling of the Free Induction Decay and Spin Echo (GESFIDE) sequence and defined a fingerprint as the ratio of signals acquired pre- and post-injection of an iron-based contrast agent. We then simulated the same experiment with an advanced numerical tool that takes a virtual voxel containing blood vessels as input, then computes microscopic magnetic fields and water diffusion effects, and eventually derives the expected MR signal evolution. The parameter inputs of the simulations (cerebral blood volume [CBV], mean vessel radius [R], and blood oxygen saturation [SO2]) were varied to obtain a dictionary of all possible signal evolutions. The best fit between the observed fingerprint and the dictionary was then determined by using least square minimization. This approach was evaluated in 5 normal subjects and the results were compared to those obtained by using more conventional MR methods, steady-state contrast imaging for CBV and R and a global measure of oxygenation obtained from the superior sagittal sinus for SO2. The fingerprinting method enabled the creation of high-resolution parametric maps of the microvascular network showing expected contrast and fine details. Numerical values in gray matter (CBV=3.1±0.7%, R=12.6±2.4μm, SO2=59.5±4.7%) are consistent with literature reports and correlated with conventional MR approaches. SO2 values in white matter (53.0±4.0%) were slightly lower than expected. Numerous improvements can easily be made and the method should be useful to study brain pathologies.

The risk predictive values of UK-PBC and GLOBE scoring system in Chinese patients with primary biliary cholangitis: the additional effect of anti-gp210

BACKGROUND

Adequate risk stratification is critical for the management of the patients with primary biliary cholangitis (PBC). The UK-PBC and GLOBE scoring systems for prognosis of PBC have been proposed recently, but have not been validated in Asian population.

AIM

To validate the UK-PBC and GLOBE scoring systems in Chinese patients for prognosis of PBC. To clarify the role of anti-gp210 as a biomarker, and to investigate whether anti-gp210 could affect the prognostic values of UK-PBC and GLOBE scoring systems.

METHODS

We retrospectively analysed 276 patients with PBC evaluated between September 2004 and May 2016, including 133 anti-gp210+ and 143 anti-gp210- patients.

RESULTS

The 5-year adverse outcome-free survivals of anti-gp210+ vs. anti-gp210- patients were 70% and 85%, respectively (P = 0.005). Cirrhosis (P = 0.001), albumin level ≤40 g/L (P = 0.011) and platelet count ≤153 × 10⁹ (P < 0.001) had a superimposition effect on anti-gp210 antibody as a risk factor. Furthermore, long-term prognoses were evaluated using the UK-PBC and GLOBE scores. For UK-PBC scoring system, the area under receiver operating characteristic curve (AUROC) was 0.924 for all patients with PBC (n = 223), 0.940 for anti-gp210+ patients (n = 110) and 0.888 for anti-gp210- patients (n = 113). For GLOBE scoring system, the area under receiver operating characteristic curve was 0.901 for all patients with PBC (n = 223), 0.924 for anti-gp210+ patients (n = 110) and 0.848 for anti-gp210- patients (n = 113). UK-PBC score >0.0578 (P < 0.001, HR: 32.736, 95% CI: 11.368-94.267) and GLOBE score <0.850 (P < 0.001, HR: 18.763, 95% CI: 7.968-44.180) were associated with poorer outcomes in the whole cohort.

CONCLUSIONS

The UK-PBC and GLOBE scoring systems were good 5-year prognostic predictors in Chinese patients with PBC, especially in anti-gp210+ patients. As a biomarker, anti-gp210 antibody was associated with a more severe cholestatic manifestation and a worse long-term prognosis. The anti-gp210 antibody could be added to further optimise the UK-PBC and GLOBE scoring systems.

A novel and efficient method for synthetic carbohydrate conjugate vaccine preparation: synthesis of sialyl Tn-KLH conjugate using a 4-(4-N-maleimidomethyl) cyclohexane-1-carboxyl hydrazide (MMCCH) linker arm

STn (NeuAcalpha2 --> 6GalNAc alpha-O-Ser/Thr) is a carbohydrate epitope overexpressed in various human carcinomas. Clinical trials are underway using synthetic STn or STn trimeric glycopeptides [STn, cluster; STn(c)] conjugated with keyhole limpet hemocyanin (KLH) as active specific immunotherapy for these cancers. These vaccines have been prepared by conjugating a crotyl ethyl amide derivative of STn or STn(c) to KLH by direct reductive amination after ozonolysis. In the case of STn(c) the conjugation efficiency and the resulting epitope ratios were low. This may be due to steric hinderance of the short spacer arm. To overcome these difficulties, without resynthesis, the STn(c) glycopeptide was modified by attachment of an MMCCH (4-(4-N-maieimidomethyl) cyclohexane-1-carboxyl hydrazide) spacer arm to the aldehyde derivative, and then conjugated with thiolated KLH. This method gave a higher epitope ratio and yield than the direct method. The STn(c)-MMCCH-KLH conjugate induced high titer antibodies in mice against STn(c). This method may be generally applicable for large synthetic oligosaccharides.

A methylnickel intermediate in a bimetallic mechanism of acetyl-coenzyme A synthesis by anaerobic bacteria

Resonance Raman (RR) spectroscopy was used to identify a methylnickel adduct (upsilon Ni-C = 422 wave numbers) of carbon monoxide dehydrogenase (CODH) from Clostridium thermoaceticum. Formed at a nickel/iron-sulfur cluster on CODH called center A, the methylnickel species is the precursor of the methyl group of acetyl-coenzyme A in an anaerobic pathway of carbon monoxide or carbon dioxide fixation. Rapid kinetic and RR studies demonstrated that methylation of nickel occurs by heterolysis of the methyl-cobalt bond (upsilon Co-C = 429 wave numbers) of a methylated corrinoid/iron-sulfur protein. In combination with the earlier finding of an iron-carbonyl adduct at center A, detection of the methylnickel intermediate establishes a bimetallic mechanism for acetyl-coenzyme A synthesis.

Performance and Predictive Value of a User-Independent Platform for CT Perfusion Analysis: Threshold-Derived Automated Systems Outperform Examiner-Driven Approaches in Outcome Prediction of Acute Ischemic Stroke

BACKGROUND AND PURPOSE

Treatment strategies in acute ischemic stroke aim to curtail ischemic progression. Emerging paradigms propose patient subselection using imaging biomarkers derived from CT, CTA, and CT perfusion. We evaluated the performance of a fully-automated computational tool, hypothesizing enhancements compared with qualitative approaches. The correlation between imaging variables and clinical outcomes in a cohort of patients with acute ischemic stroke is reported.

MATERIALS AND METHODS

Sixty-two patients with acute ischemic stroke and MCA or ICA occlusion undergoing multidetector CT, CTA, and CTP were retrospectively evaluated. CTP was processed on a fully operator-independent platform (RApid processing of PerfusIon and Diffusion [RAPID]) computing automated core estimates based on relative cerebral blood flow and relative cerebral blood volume and hypoperfused tissue volumes at varying thresholds of time-to-maximum. Qualitative analysis was assigned by 2 independent reviewers for each variable, including CT-ASPECTS, CBV-ASPECTS, CBF-ASPECTS, CTA collateral score, and CTA clot burden score. Performance as predictors of favorable clinical outcome and final infarct volume was established for each variable.

RESULTS

Both RAPID core estimates, CT-ASPECTS, CBV-ASPECTS, and clot burden score correlated with favorable clinical outcome (P < .05); CBF-ASPECTS and collateral score were not significantly associated with favorable outcome, while hypoperfusion estimates were variably associated, depending on the selected time-to-maximum thresholds. Receiver operating characteristic analysis demonstrated disparities among tested variables, with RAPID core and hypoperfusion estimates outperforming all qualitative approaches (area under the curve, relative CBV = 0.86, relative CBF = 0.81; P < .001).

CONCLUSIONS

Qualitative approaches to acute ischemic stroke imaging are subject to limitations due to their subjective nature and lack of physiologic information. These findings support the benefits of high-speed automated analysis, outperforming conventional methodologies while limiting delays in clinical management.

Collagen fibril surface displays a constellation of sites capable of promoting fibril assembly, stability, and hemostasis

Fibrillar collagens form the structural basis of organs and tissues including the vasculature, bone, and tendon. They are also dynamic, organizational scaffolds that present binding and recognition sites for ligands, cells, and platelets. We interpret recently published X-ray diffraction findings and use atomic force microscopy data to illustrate the significance of new insights into the functional organization of the collagen fibril. These data indicate that collagen's most crucial functional domains localize primarily to the overlap region, comprising a constellation of sites we call the "master control region." Moreover, the collagen's most exposed aspect contains its most stable part-the C-terminal region that controls collagen assembly, cross-linking, and blood clotting. Hidden beneath the fibril surface exists a constellation of "cryptic" sequences poised to promote hemostasis and cell-collagen interactions in tissue injury and regeneration. These findings begin to address several important, and previously unresolved, questions: How functional domains are organized in the fibril, which domains are accessible, and which require proteolysis or structural trauma to become exposed? Here we speculate as to how collagen fibrillar organization impacts molecular processes relating to tissue growth, development, and repair.

Purkinje cell fate in staggerer mutants: agenesis versus cell death

Staggerer (sg/sg) is an autosomal recessive mutation in an orphan nuclear hormone receptor gene, RORalpha, that causes a cell-autonomous, lineage-specific block in the development of the Purkinje cell. Purkinje cell number is reduced by about 75-90% in adult mutants, and many of the surviving cells are small and ectopically positioned. To determine whether Purkinje cell numbers are reduced owing to either agenesis or cell death, cohorts of Purkinje cells were labeled with the birth-date marker bromodeoxyuridine (BrdU) at embryonic day (E) 10.5 or E11.5. The total number of BrdU-labeled profiles was then compared between cerebella from wild-type mice, heterozygous staggerer, and staggerer mutants at E17.5 and postnatal day (P)5. There was no significant difference between sg/sg mutants and +/sg or +/+ controls in the number of BrdU-labeled profiles or in cerebellar volumes in the E17 embryos. By P5, however, cerebellar volume was significantly reduced in the sg/sg mutants compared to controls (p <.005) and the number of BrdU-labeled profiles was reduced by 33% following E11.5 BrdU injections (p <.02). The results suggest that Purkinje cell genesis is not affected by the staggerer mutation and that Purkinje cell loss begins some time after E17. RORalpha is highly expressed in Purkinje cells by E14, so the delay between initial RORalpha expression and sg/sg Purkinje cell loss suggests that the staggerer mutation does not directly cause Purkinje cell death.

Comparison of different methods of total RNA extraction for viral detection in sputum

Examination of sputum specimens can be used for monitoring airway inflammation by means of immunological and molecular techniques. RNA extraction is essential for measurement of cytokine gene expression and for detection of many viral pathogens in sputum. In this study, three RNA extraction methods used commonly (acid guanidinium thiocyanate-phenol-chloroform extraction, Trizol and RNeasy Mini kit) were compared on the sputum of 14 patients who had chronic obstructive pulmonary disease. The effect of dithiothreitol pre-treatment on sputum RNA extraction was also investigated. The yield and purity of total RNA were determined by spectrophotometry. Reverse transcription-polymerase chain reaction (RT-PCR) results of the house keeping gene (glyceraldehyde-3-phosphate dehydrogenase) and RNA sequences specific to common respiratory viruses were compared. The results showed that (1) total RNA extracted with Trizol had highest yield and purity among the three RNA extraction methods; (2) there was no significant difference among the three RNA extraction methods on the house keeping gene and viral detection by RT-PCR; (3) dithiothreitol pre-treatment did not improve either the purity of total RNA, or RT-PCR signal. Moreover, dithiothreitol treatment reduced significantly the yield of total RNA. The results of the study indicate that the Trizol method appears to be superior for total RNA extraction from sputum, and dithiothreitol pre-treatment does not increase the efficiency of RNA extraction and RNA detection in sputum specimens.

The prevalence and odds of depression in patients with vitiligo: a meta-analysis

OBJECTIVE

The objective of this study was to provide a pooled estimate of the prevalence and odds of depression in patients with vitiligo.

METHODS

A systematic literature search of Medline, Embase and Cochrane library databases was conducted. The proportions and mean questionnaire values for depression were pooled according to different evaluation methods. In controlled studies, odds ratio and standardized mean differences compared depression in vitiligo patients with healthy controls.

RESULTS

One thousand nine hundred and sixty-five patients were identified from 20 eligible cohorts to be included in the present meta-analysis review. Sample sizes ranged from 30 to 308 for each analysis. The pooled prevalence of depression across 17 unique populations (n = 1711) was 29% (95% CI 20-39). The prevalence of clinical depression was 8% (95% CI 2%-14%) using Diagnostic and Statistical Manual of Mental Disorders IV or International Classification of Diseases codes-10, and the prevalence of depressive symptoms was 33% (95% CI 23%-44%) using validated screening inventory and rating scales. Patient with vitiligo was 4.96 times more likely to display depression compared with controls. Subgroup analysis showed that the prevalence of depression in Asian and female patients with vitiligo was significantly higher than that in Caucasian and male ones. The pooled prevalence of depressive symptoms was higher (56%, 95% CI 0.5-0.62), and the heterogeneity was lowering cases with Hamilton Depression Rating Scale (HDRS) questionnaire when compared with other questionnaires.

CONCLUSIONS

This meta-analysis review indicates that the prevalence of depression is high in patients with vitiligo. The HDRS questionnaire may be the most sensitive tool for testing the depressive symptoms among patients with vitiligo.

Estimating the distribution of worm burden and egg excretion of Schistosoma japonicum by risk group in Sichuan Province, China

During autumn 2000 an extensive cross-sectional survey of the prevalence of Schistosomiasis japonicum was conducted among about 4000 villagers within 20 villages in the Anning River Valley located in the southwestern Sichuan Province. Two procedures were used to assess infection status, the Kato-Katz thick smear procedure and a miracidia hatch test. Whereas the Kato-Katz procedure provides information on both prevalence and intensity, the hatch test provides only prevalence data, albeit on a much larger volume of stool. In addition, we performed Kato-Katz smears for 15 consecutive samples on a subset of 15 individuals. The proportion of both hatch-test and Kato-Katz positive individuals in the larger cross-sectional survey was 25%. The goal of the study was to estimate both the egg and worm distributions among risk groups using both the hatch and Kato-Katz tests from the cross-sectional data and the repeated Kato-Katz smears from the longitudinal data sets. As a prelude to parameter estimation, individuals were classified into risk groups by natural village and occupation; the proportion of Kato-Katz positive subjects among the risk groups varied from 10% to 60%. We used the statistical model of de Vlas et al. (1992) and Bayesian techniques to derive both estimates of and inference about the worm and egg distribution parameters. The parameter estimates imply (1) similar eggs per gram stool (e.p.g.) per worm pair compared with earlier estimates, (2) a range of worm burdens among the risk groups and (3) estimates of risk heterogeneity within groups is sensitive to prior information on the within-person variability in egg excretion.

Infection with multiple strains of Borrelia burgdorferi sensu stricto in patients with Lyme disease

OBJECTIVE

To assess human skin biopsy specimens from erythema migrans lesions for the presence of infection with multiple strains of the Lyme disease spirochete, Borrelia burgdorferi.

DESIGN

Skin biopsy specimens were obtained prospectively from patients with erythema migrans. To determine allelic differences and strain identification of B burgdorferi, the biopsy specimens were analyzed by cold single-strand conformation polymorphism of an amplified fragment of the outer surface protein C (ospC) gene. Further single-strand conformation polymorphism patterns of amplified ospC genes from culture isolates were compared with polymerase chain reaction products obtained directly from erythema migrans biopsy specimens.

SETTING

A private dermatology office and a university medical center outpatient department.

PATIENTS

Sixteen patients presenting with erythema migrans.

RESULTS

Two of the 16 patients in this cohort were infected with 2 B burgdorferi sensu stricto strains, as evidenced by 2 ospC alleles in their skin biopsy results.

CONCLUSION

This is the first documented description of the existence of more than a single strain of B burgdorferi sensu stricto in a human specimen.

Nature's carbonylation catalyst: Raman spectroscopic evidence that carbon monoxide binds to iron, not nickel, in CO dehydrogenase

Carbon monoxide dehydrogenase catalyzes the synthesis of acetyl-coenzyme A from coenzyme A, a methyl group, and carbon monoxide. The carbon monoxide binds to a mixed metal center of the enzyme, which contains nickel bridged to an iron-sulfur cluster. Resonance Raman spectroscopy has been used to identify both C-O stretching and metal-CO stretching vibrations of the carbon monoxide adduct of the enzyme. This adduct was shown by isotopic exchange to be on the pathway for acetyl-coenzyme A synthesis. The metal to which carbon monoxide is bound was established to be iron, not nickel, by preparation of enzyme from bacteria grown on iron-54 and nickel-64. The Fe-CO frequency is low, 360 wave numbers, implying a weak bond, probably because of electron donation from sulfide and thiolate ligands of the iron. A bimetallic mechanism is proposed, in which carbon monoxide binds to an iron atom and is subsequently attacked by a methyl group on a nearby nickel atom, forming an acetyl ligand, which is then transferred to coenzyme A.